Prof. PhD B. Berkhout publications

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Publications Prof. PhD B. Berkhout

Position
Full Professor
Main activities
Research
Specialisation
Virology
Focus of research
  • Mechanism of HIV-1 gene expression and latency
  • Structure and function of the HIV-1 RNA genome
  • Virus evolution and drug-resistance
  • Novel vaccine strategies
  • RNA interference as antiviral therapy
  • Patient-related virus studies

2020

  • Darcis Gilles, Kootstra Neeltje A., Hooibrink Berend, van Montfort Thijs, Maurer Irma, Groen Kevin, Jurriaans Suzanne, Bakker Margreet, van Lint Carine, Berkhout Ben, Pasternak Alexander O. CD32+CD4+ T Cells Are Highly Enriched for HIV DNA and Can Support Transcriptional Latency Cell reports 2020;30 (7):2284-2296.e3 [PubMed]
  • Hentzschel Franziska, Mitesser Vera, Fraschka Sabine Anne-Kristin, Krzikalla Daria, Carrillo Elena Herrera, Berkhout Ben, Bártfai Richárd, Mueller Ann-Kristin, Grimm Dirk Gene knockdown in malaria parasites via non-canonical RNAi Nucleic acids research 2020;48 (1):e2 [PubMed]

2019

  • Gao Zongliang, Herrera-Carrillo Elena, Berkhout Ben A Single H1 Promoter Can Drive Both Guide RNA and Endonuclease Expression in the CRISPR-Cas9 System Molecular therapy. Nucleic acids 2019;14:32-40 [PubMed]
  • Benkirane Monsef, Berkhout Ben, Borrow Persephone, Fassati Ariberto, Fujii Masahiro, Garcia-Martinez J. Victor, Margolis D., Nijhuis Monique, Parent Leslie, Strebel Klaus, Venter François, Kirchhoff Frank, Lever Andrew, Ross Susan, Mak Johnson A trip down memory lane with Retrovirology Retrovirology 2019;16 (1):22 [PubMed]
  • Gao Zongliang, Berkhout Ben, Herrera-Carrillo Elena Boosting AgoshRNA activity by optimized 5’-terminal nucleotide selection RNA biology 2019;16 (7):890-898 [PubMed]
  • van Montfort Thijs, van der Sluis Renée, Darcis Gilles, Beaty Doyle, Groen Kevin, Pasternak Alexander O., Pollakis Georgios, Vink Monique, Westerhout Ellen M., Hamdi Mohamed, Bakker Margreet, van der Putten Boas, Jurriaans Suzanne, Prins Jan H., Jeeninga Rienk, Thomas Adri A.M., Speijer Dave, Berkhout Ben Dendritic cells potently purge latent HIV-1 beyond TCR-stimulation, activating the PI3K-Akt-mTOR pathway EBioMedicine 2019;42:97-108 [PubMed]
  • Liang Chen, Berkhout Ben Editorial overview: Engineering cellular resistance towards the HIV cure Current opinion in virology 2019;38:iii-v [PubMed]
  • Das Atze T., Binda Caroline S., Berkhout Ben Elimination of infectious HIV DNA by CRISPR–Cas9 Current opinion in virology 2019;38:81-88 [PubMed]
  • Eggink Dirk, Bontjer Ilja, de Taeye Steven W., Langedijk Johannes P. M., Berkhout Ben, Sanders Rogier W. HIV-1 anchor inhibitors and membrane fusion inhibitors target distinct but overlapping steps in virus entry Journal of biological chemistry 2019;294 (15):5736-5746 [PubMed]
  • Hotter Dominik, Bosso Matteo, Jønsson Kasper L., Krapp Christian, Stürzel Christina M., Das Atze, Littwitz-Salomon Elisabeth, Berkhout Ben, Russ Alina, Wittmann Sabine, Gramberg Thomas, Zheng Yue, Martins Laura J., Planelles Vicente, Jakobsen Martin R., Hahn Beatrice H., Dittmer Ulf, Sauter Daniel, Kirchhoff Frank IFI16 Targets the Transcription Factor Sp1 to Suppress HIV-1 Transcription and Latency Reactivation Cell host & microbe 2019;25 (6):858-872.e13 [PubMed]
  • Herrera-Carrillo Elena, Gao Zongliang, Berkhout Ben Influence of a 3′ Terminal Ribozyme on AgoshRNA Biogenesis and Activity Molecular therapy. Nucleic acids 2019;16:452-462 [PubMed]
  • Tomonaga Keizo, Suzuki Nobuhiro, Berkhout Ben “Integration of viral sequences into eukaryotic host genomes: legacy of ancient infections” Virus research 2019;262:1 [PubMed]
  • Turrini Filippo, Saliu Fabio, Forlani Greta, Das Atze T., van Lint Carine, Accolla Roberto S., Berkhout Ben, Poli Guido, Vicenzi Elisa Interferon-inducible TRIM22 contributes to maintenance of HIV-1 proviral latency in T cell lines Virus research 2019;269 [PubMed]
  • Das Atze T., Pasternak Alexander O., Berkhout Ben On the generation of the MSD class of defective HIV proviruses Retrovirology 2019;16 (1) [PubMed]
  • Gao Zongliang Optimized expression of small therapeutic RNAs 2019. 179p. ISBN 9789463753203. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Herrera Carrillo E.)
  • Steba Gaby S., Koekkoek Sylvie M., Tanck Michael W. T., Vanhommerig Joost W., van der Meer Jan T. M., Kwa David, Brinkman Kees, Prins Maria, Berkhout Ben, Pollakis Georgios, Molenkamp Richard, Schinkel Janke, Paxton William A. SNP rs688 within the low-density lipoprotein receptor (LDL-R) gene associates with HCV susceptibility Liver international 2019;39 (3):463-469 [PubMed]
  • Darcis Gilles, Binda Caroline S., Klaver Bep, Herrera-Carrillo Elena, Berkhout Ben, Das Atze T. The impact of HIV-1 genetic diversity on CRISPR-Cas9 antiviral activity and viral escape Viruses 2019;11 (3) [PubMed]
  • Darcis Gilles, Berkhout Ben, Pasternak Alexander O. The quest for cellular markers of HIV reservoirs: Any color you like Frontiers in immunology 2019;10 [PubMed]

2018

  • Jin Dong-Yan, Berkhout Ben CRISPR-Cas Antiviral Strategies Virus research 2018;244:285 [PubMed]
  • Wang Gang, Zhao Na, Berkhout Ben, Das Atze T. CRISPR-Cas based antiviral strategies against HIV-1 Virus research 2018;244:321-332 [PubMed]
  • Wang Gang CRISPR-Cas based strategies against HIV-1 2018. 135p. ISBN 9789462998162. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Das A. T.)
  • Steba Gaby S., Koekkoek Sylvie M., Vanhommerig Joost W., Brinkman Kees, Kwa David, van der Meer Jan T. M., Prins Maria, Berkhout Ben, Tanck Michael, Paxton William A., Molenkamp Richard, Schinkel Janke DC-SIGN Polymorphisms Associate with Risk of Hepatitis C Virus Infection Among Men who Have Sex with Men but not Among Injecting Drug Users Journal of infectious diseases 2018;217 (3):353-357 [PubMed]
  • Gao Zongliang, Herrera-Carrillo Elena, Berkhout Ben Delineation of the Exact Transcription Termination Signal for Type 3 Polymerase III Molecular therapy. Nucleic acids 2018;10:36-44 [PubMed]
  • Wymant Chris, Blanquart François, Golubchik Tanya, Gall Astrid, Bakker Margreet, Bezemer Daniela, Croucher Nicholas J, Hall Matthew, Hillebregt Mariska, Ong Swee Hoe, Ratmann Oliver, Albert Jan, Bannert Norbert, Fellay Jacques, Fransen Katrien, Gourlay Annabelle, Grabowski M Kate, Gunsenheimer-Bartmeyer Barbara, Günthard Huldrych F, Kivelä Pia, Kouyos Roger, Laeyendecker Oliver, Liitsola Kirsi, Meyer Laurence, Porter Kholoud, Ristola Matti, van Sighem Ard, Berkhout Ben, Cornelissen Marion, Kellam Paul, Reiss Peter, Fraser Christophe Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver Virus evolution 2018;4 (1):vey007 [PubMed]
  • van Hemert Formijn, Jebbink Maarten, van der Ark Andries, Scholer Frits, Berkhout Ben Euclidean distance analysis enables nucleotide skew analysis in viral genomes Computational and Mathematical Methods in Medicine 2018;2018 [PubMed]
  • Das Atze T., Berkhout Ben How polypurine tract changes in the HIV-1 RNA genome can cause resistance against the integrase inhibitor dolutegravir mBio 2018;9 (2) [PubMed]
  • Darcis Gilles, Berkhout Ben Human Immunodeficiency Virus Resistance to Dolutegravir: Are We Looking in the Wrong Place? Journal of infectious diseases 2018;218 (12):2020 [PubMed]
  • Gao Zongliang, Herrera-Carrillo Elena, Berkhout Ben Improvement of the CRISPR-Cpf1 system with ribozyme-processed crRNA RNA biology 2018;15 (12):1458-1497 [PubMed]
  • Smolders E. J., Smit C., de Kanter C. T. M. M., Dofferhoff A. S. M., Arends J. E., Brinkman K., Rijnders B., van der Valk M., Reiss P., Burger D. M., Prins J. M., Kuijpers T. W., Scherpbier H. J., van der Meer J. T. M., Wit F. W. M. N., Godfried M. H., van der Poll T., Nellen F. J. B., Geerlings S. E., van Vugt M., Pajkrt D., Wiersinga W. J., Goorhuis A., Hovius J. W., Bijsterveld M. A. H., van Eden J., van Hes A. M. H., Mutschelknauss M., Nobel H. E., Pijnappel F. J. J., Weijsenfeld A. M., Jurriaans S., Back N. K. T., Zaaijer H. L., Berkhout B., Cornelissen M. T. E., Schinkel C. J., Thomas X. V., van den Berge M., Stegeman A., Baas S., Hage de Looff L., Wintermans B., Veenemans J., Pronk M. J. H., Ammerlaan H. S. M., de Munnik E. S., Langebeek N., van Wijk M., Vandenbroucke-Grauls C. M. J. E. Management of drug interactions with direct-acting antivirals in Dutch HIV/hepatitis C virus-coinfected patients: adequate but not perfect HIV medicine 2018;19 (3):216-226 [PubMed]
  • Sarracino Ambra, Gharu Lavina, Kula Anna, Pasternak Alexander O., Avettand-Fenoel Veronique, Rouzioux Christine, Bardina Maryana, de Wit Stéphane, Benkirane Monsef, Berkhout Ben, van Lint Carine, Marcello Alessandro Posttranscriptional Regulation of HIV-1 Gene Expression during Replication and Reactivation from Latency by Nuclear Matrix Protein MATR3 mBio 2018;9 (6) [PubMed]
  • Berkhout Ben RNAi-mediated antiviral immunity in mammals Current opinion in virology 2018;32:9-14 [PubMed]
  • Gao Zongliang, Herrera-Carrillo Elena, Berkhout Ben RNA Polymerase II Activity of Type 3 Pol III Promoters Molecular therapy. Nucleic acids 2018;12:135-145 [PubMed]
  • van der Velden Yme U., Villaudy Julien, Siteur-van Rijnstra Esther, van der Linden Cynthia A., Frankin Esmay, Weijer Kees, Schermer Edith, Vink Monique A., Berkhout Ben, Sanders Rogier W., van Gils Marit J. Short Communication: Protective Efficacy of Broadly Neutralizing Antibody PGDM1400 Against HIV-1 Challenge in Humanized Mice AIDS research and human retroviruses 2018;34 (9):790-793 [PubMed]
  • van Zoest Rosan A., Underwood Jonathan, de Francesco Davide, Sabin Caroline A., Cole James H., Wit Ferdinand W., Caan Matthan W. A., Kootstra Neeltje A., Fuchs Dietmar, Zetterberg Henrik, Majoie Charles B. L. M., Portegies Peter, Winston Alan, Sharp David J., Gisslén Magnus, Reiss Peter, Winston A., Prins M., Schim van der Loeff M. F., Schouten J., Schmand B., Geurtsen G. J., Sharp D. J., Villaudy J., Berkhout B., Gisslén M., Pasternak A., Sabin C. A., Guaraldi G., Bürkle A., Libert C., Franceschi C., Kalsbeek A., Fliers E., Hoeijmakers J., Pothof J., van der Valk M., Bisschop P. H., Zaheri S., Burger D., Cole J. H., Zikkenheiner W., Janssen F. R., Underwood J., Kooij K. W., Doyle N., Verbraak F., Demirkaya N., Weijer K., Boeser-Nunnink B. Structural Brain Abnormalities in Successfully Treated HIV Infection: Associations With Disease and Cerebrospinal Fluid Biomarkers Journal of infectious diseases 2018;217 (1):69-81 [PubMed]
  • Torrents de la Peña Alba Structure-based stabilization of HIV-1 trimer vaccines 2018. ISBN 9789462999626. [UvA Dissertations Online] University of Amsterdam. (Supervisors: Berkhout B., Sanders R. W.)
  • Darcis Gilles, Das Atze T., Berkhout Ben Tackling HIV persistence: pharmacological versus CRISPR-based shock strategies Viruses 2018;10 (4) [PubMed]
  • van der Kuyl Antoinette C., Vink Monique, Zorgdrager Fokla, Bakker Margreet, Wymant Chris, Hall Matthew, Gall Astrid, Blanquart François, Berkhout Ben, Fraser Christophe, Cornelissen Marion The evolution of subtype B HIV-1 tat in the Netherlands during 1985–2012 Virus research 2018;250:51-64 [PubMed]
  • Mueller Nancy, Pasternak Alexander O., Klaver Bep, Cornelissen Marion, Berkhout Ben, Das Atze T. The HIV-1 tat protein enhances splicing at the major splice donor site Journal of virology 2018;92 (14) [PubMed]
  • Thiel Volker, Berkhout Ben Virus Research starts publishing the new “Virus Research Consortia Series” Virus research 2018;257:119 [PubMed]
  • Pasternak Alexander O., Berkhout Ben What do we measure when we measure cell-associated HIV RNA Retrovirology 2018;15 (1):13 [PubMed]
  • Cornelissen Marion, Gall Astrid, van der Kuyl Antoinette, Wymant Chris, Blanquart François, Fraser Christophe, Berkhout Ben Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes Methods in molecular biology (Clifton, N.J.) 2018;1746:55-61 [PubMed]

2017

  • Berkhout Ben A Fourth Generation Lentiviral Vector: Simplifying Genomic Gymnastics Molecular therapy 2017;25 (8):1741-1743 [PubMed]
  • Harwig Alex, Kruize Zita, Yang Zhenhuang, Restle Tobias, Berkhout Ben Analysis of AgoshRNA maturation and loading into Ago2 PLoS ONE 2017;12 (8):e0183269 [PubMed]
  • Wang Wenshi, Wang Yijin, Debing Yannick, Zhou Xinying, Yin Yuebang, Xu Lei, Herrera Carrillo Elena, Brandsma Johannes H., Poot Raymond A., Berkhout Ben, Neyts Johan, Peppelenbosch Maikel P., Pan Qiuwei Biological or pharmacological activation of protein kinase C alpha constrains hepatitis E virus replication Antiviral research 2017;140:1-12 [PubMed]
  • Zhao Na, Wang Gang, Das Atze T., Berkhout Ben Combinatorial CRISPR-Cas9 and RNA Interference Attack on HIV-1 DNA and RNA Can Lead to Cross-Resistance Antimicrobial agents and chemotherapy 2017;61 (12):e01486-17 [PubMed]
  • Blanquart François, Wymant Chris, Cornelissen Marion, Gall Astrid, Bakker Margreet, Bezemer Daniela, Hall Matthew, Hillebregt Mariska, Ong Swee Hoe, Albert Jan, Bannert Norbert, Fellay Jacques, Fransen Katrien, Gourlay Annabelle J., Grabowski M. Kate, Gunsenheimer-Bartmeyer Barbara, Günthard Huldrych F., Kivelä Pia, Kouyos Roger, Laeyendecker Oliver, Liitsola Kirsi, Meyer Laurence, Porter Kholoud, Ristola Matti, van Sighem Ard, Vanham Guido, Berkhout Ben, Kellam Paul, Reiss Peter, Fraser Christophe Correction: Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe PLoS biology 2017;15 (7):e1002608 [PubMed]
  • van Montfort T., Speijer D., Berkhout B. Dendritic cells as natural latency reversing agent: A wake-up call for HIV-1 Virulence 2017;8 (8):1494-1497 [PubMed]
  • Herrera-Carrillo Elena, Berkhout Ben Dicer-independent processing of small RNA duplexes: mechanistic insights and applications Nucleic acids research 2017;45 (18):10369-10379 [PubMed]
  • Beerenwinkel Niko, Berkhout Ben, Domingo Esteban Foreword Virus research 2017;239:VII
  • Cornelissen Marion, Gall Astrid, Vink Monique, Zorgdrager Fokla, Binter Špela, Edwards Stephanie, Jurriaans Suzanne, Bakker Margreet, Ong Swee Hoe, Gras Luuk, van Sighem Ard, Bezemer Daniela, de Wolf Frank, Reiss Peter, Kellam Paul, Berkhout Ben, Fraser Christophe, van der Kuyl Antoinette C. From clinical sample to complete genome: Comparing methods for the extraction of HIV-1 RNA for high-throughput deep sequencing Virus research 2017;239:10-16 [PubMed]
  • Booiman Thijs, Wit Ferdinand W., Maurer Irma, de Francesco Davide, Sabin Caroline A., Harskamp Agnes M., Prins Maria, Garagnani Paolo, Pirazzini Chiara, Franceschi Claudio, Fuchs Dietmar, Gisslén Magnus, Winston Alan, Reiss Peter, Kootstra Neeltje A., Schouten J., Kooij K. W., van Zoest R. A., Elsenga B. C., Janssen F. R., Heidenrijk M., Zikkenheiner W., van der Valk M., Booiman T., Harskamp-Holwerda A. M., Boeser-Nunnink B., Maurer I., Mangas Ruiz M. M., Girigorie A. F., Villaudy J., Frankin E., Pasternak A., Berkhout B., van der Kuyl T., Portegies P., Schmand B. A., Geurtsen G. J., ter Stege J. A., Klein Twennaar M., Majoie C. B. L. M., Caan M. W. A., Su T., Weijer K., Bisschop P. H. L. T., Kalsbeek A., Wezel M., Visser I., Ruhé H. G., Franceschi C., Garagnani P. High Cellular Monocyte Activation in People Living With Human Immunodeficiency Virus on Combination Antiretroviral Therapy and Lifestyle-Matched Controls Is Associated With Greater Inflammation in Cerebrospinal Fluid Open forum infectious diseases 2017;4 (3):ofx108 [PubMed]
  • Klaver Bep, van der Velden Yme, van Hemert Formijn, van der Kuyl Antoinette C., Berkhout Ben HIV-1 tolerates changes in A-count in a small segment of the pol gene Retrovirology 2017;14 (1):43 [PubMed]
  • Bartelsman M., Joore I. K., van Bergen J. E., Hogewoning A. A., Zuure F. R., van Veen M. G., Deug F., Heidenrijk M., Prins J. M., Prins M. [= Maria], Smit P. J., van der Valk M., Reiss P., de Bree G. J., Hoornenborg E., Davidovich U., Geerlings S. E., Oomen A., van sighem A., Zuilhof W., Achterbergh R. C. A., van Agtmael M., Ananworanich J., van de Beek D., van den Berk G. E. L., Berkhout B., Berretty B., Bezemer D., Blok W. L., Bomers M., Boucher C. A. B., Brokking W., Burger D., Brinkman K., de Bruin M., Geijtenbeek T. B. H., Godfried M. H., Goorhuis A., van der Helm J. J., Hovius J. W., Kootstra N. A., van der Meer J. T., Nellen F. J., Pasternak A. O., van der Poll T., van Rooijen M. S., de Vries H. J., van Vugt M., Wiersinga W. J., Wit F. W. HIV testing week 2015: lowering barriers for HIV testing among high-risk groups in Amsterdam BMC infectious diseases 2017;17 (1):529 [PubMed]
  • Herrera-Carrillo Elena, Liu Ying Poi, Berkhout Ben Improving miRNA Delivery by Optimizing miRNA Expression Cassettes in Diverse Virus Vectors Human gene therapy methods 2017;28 (4):177-190 [PubMed]
  • Cole James H., Underwood Jonathan, Caan Matthan W. A., de Francesco Davide, van Zoest Rosan A., Leech Robert, Wit Ferdinand W. N. M., Portegies Peter, Geurtsen Gert J., Schmand Ben A., Schim van der Loeff Maarten F., Franceschi Claudio, Sabin Caroline A., Majoie Charles B. L. M., Winston Alan, Reiss Peter, Sharp David J., Schouten J., Kooij K. W., Elsenga B. C., Janssen F. R., Heidenrijk M., Schrijver J. H. N., Zikkenheiner W., van der Valk M., Henderiks A., Kootstra N. A., Harskamp-Holwerda A. M., Maurer I., Ruiz M. M. Mangas, Booiman T., Girigorie A. F., Villaudy J., Frankin E., Pasternak A., Berkhout B., van der Kuyl T., Stege J. A. ter, Twennaar M. Klein, Su T., Siteur-van Rijnstra E., Weijer K., Bisschop P. H. L. T., Kalsbeek A., Wezel M., Visser I., Ruhé H. G., Tembo L., Stott M., Prins M. [= Maria] Increased brain-predicted aging in treated HIV disease Neurology 2017;88 (14):1349-1357 [PubMed]
  • Herrera-Carrillo Elena, Harwig Alex, Berkhout Ben Influence of the loop size and nucleotide composition on AgoshRNA biogenesis and activity RNA biology 2017;14 (11):1559-1569 [PubMed]
  • Gao Zongliang, Harwig Alex, Berkhout Ben, Herrera-Carrillo Elena Mutation of nucleotides around the +1 position of type 3 polymerase III promoters: The effect on transcriptional activity and start site usage Transcription 2017;8 (5):275-287 [PubMed]
  • Herrera-Carrillo Elena, Berkhout Ben Novel AgoshRNA molecules for silencing of the CCR5 co-receptor for HIV-1 infection PLoS ONE 2017;12 (5):e0177935 [PubMed]
  • Benkirane Monsef, Berkhout Ben, Borrow Persephone, Fassati Ariberto, Fujii Masahiro, Garcia J. Victor, Gorry Paul, Lever Andrew, Mak Johnson, Nijhuis Monique, Strebel Klaus, Venter Francois, Weiss Robin Professor Mark Wainberg Retrovirology 2017;14 (1):30 [PubMed]
  • Herrera-Carrillo E., Harwig A., Berkhout B. Silencing of HIV-1 by AgoshRNA molecules Gene therapy 2017;24 (8):453-461 [PubMed]
  • de Taeye Steven W. Stabilization of HIV-1 envelope glycoprotein trimers to induce neutralizing antibodies 2017. 288p. ISBN 9789462995413. [UvA Dissertations Online] University of Amsterdam. (Supervisors: Berkhout B., Sanders R. W.)
  • Harwig Alex, Landick Robert, Berkhout Ben The Battle of RNA Synthesis: Virus versus Host Viruses 2017;9 (10):309 [PubMed]
  • Amadori Céline, Ubeles van der Velden Yme, Bonnard Damien, Orlov Igor, van Bel Nikki, Le Rouzic Erwann, Miralles Laia, Brias Julie, Chevreuil Francis, Spehner Daniele, Chasset Sophie, Ledoussal Benoit, Mayr Luzia, Moreau François, García Felipe, Gatell José, Zamborlini Alessia, Emiliani Stéphane, Ruff Marc, Klaholz Bruno P., Moog Christiane, Berkhout Ben, Plana Montserrat, Benarous Richard The HIV-1 integrase-LEDGF allosteric inhibitor MUT-A: resistance profile, impairment of virus maturation and infectivity but without influence on RNA packaging or virus immunoreactivity Retrovirology 2017;14 (1):50 [PubMed]
  • Herrera-Carrillo Elena, Gao Zong-Liang, Harwig Alex, Heemskerk Matthias T., Berkhout Ben The influence of the 5΄-terminal nucleotide on AgoshRNA activity and biogenesis: importance of the polymerase III transcription initiation site Nucleic acids research 2017;45 (7):4036-4050 [PubMed]
  • Blanquart François, Wymant Chris, Cornelissen Marion, Gall Astrid, Bakker Margreet, Bezemer Daniela, Hall Matthew, Hillebregt Mariska, Ong Swee Hoe, Albert Jan, Bannert Norbert, Fellay Jacques, Fransen Katrien, Gourlay Annabelle J., Grabowski M. Kate, Gunsenheimer-Bartmeyer Barbara, Günthard Huldrych F., Kivelä Pia, Kouyos Roger, Laeyendecker Oliver, Liitsola Kirsi, Meyer Laurence, Porter Kholoud, Ristola Matti, van Sighem Ard, Vanham Guido, Berkhout Ben, Kellam Paul, Reiss Peter, Fraser Christophe Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe PLoS biology 2017;15 (6):e2001855 [PubMed]

2016

  • Wang Gang, Zhao Na, Berkhout Ben, Das Atze T. A Combinatorial CRISPR-Cas9 Attack on HIV-1 DNA Extinguishes All Infectious Provirus in Infected T Cell Cultures Cell reports 2016;17 (11):2819-2826 [PubMed]
  • Derking Ronald Antigenic structure of the HIV-1 envelope glycoprotein trimer 2016. 221p. ISBN 9789462994263. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Sanders R. W.)
  • Mueller Nancy, Das Atze T., Berkhout Ben A Phylogenetic Survey on the Structure of the HIV-1 Leader RNA Domain That Encodes the Splice Donor Signal Viruses 2016;8 (7):200 [PubMed]
  • Chtarto Abdelwahed, Humbert-Claude Marie, Bockstael Olivier, Das Atze T., Boutry Sébastien, Breger Ludivine S., Klaver Bep, Melas Catherine, Barroso-Chinea Pedro, Gonzalez-Hernandez Tomas, Muller Robert N., DeWitte Olivier, Levivier Marc, Lundberg Cecilia, Berkhout Ben, Tenenbaum Liliane A regulatable AAV vector mediating GDNF biological effects at clinically-approved sub-antimicrobial doxycycline doses Molecular therapy. Methods & clinical development 2016;5:16027 [PubMed]
  • Herrera-Carrillo Elena, Berkhout Ben Attacking HIV-1 RNA versus DNA by sequence-specific approaches: RNAi versus CRISPR-Cas Biochemical Society transactions 2016;44 (5):1355-1365 [PubMed]
  • Das Atze T., Berkhout Ben Conditionally replicating HIV and SIV variants Virus research 2016;216:66-75 [PubMed]
  • van der Velden Yme U., Kleibeuker Wendy, Harwig Alex, Klaver Bep, Siteur-Van Rijnstra Esther, Frankin Esmay, Berkhout Ben, Das Atze T. Construction of Nef-positive doxycycline-dependent HIV-1 variants using bicistronic expression elements Virology 2016;488:96-107 [PubMed]
  • Liang Chen, Wainberg Mark A., Das Atze T., Berkhout Ben CRISPR/Cas9: a double-edged sword when used to combat HIV infection Retrovirology 2016;13 (1):37 [PubMed]
  • Wang Gang, Zhao Na, Berkhout Ben, Das Atze T. CRISPR-Cas9 Can Inhibit HIV-1 Replication but NHEJ Repair Facilitates Virus Escape Molecular therapy 2016;24 (3):522-526 [PubMed]
  • Mocroft Amanda, Lundgren Jens D., Ross Michael, Fux Christoph A., Reiss Peter, Moranne Olivier, Morlat Philippe, Monforte Antonella d'Arminio, Kirk Ole, Ryom Lene, Steering D., Powderly B., Shortman N., Moecklinghoff C., Reilly G., Franquet X., Ryom L., Hatleberg C. I., Sabin C. A., Kamara D., Smith C., Phillips A., Mocroft A., Bojesen A., Grevsen A. L., Prins J. M., Kuijpers T. W., Scherpbier H. J., van der Meer J. T. M., Wit F. W. M. N., Godfried M. H., van der Poll T., Nellen F. J. B., Geerlings S. E., van Vugt M., Pajkrt D., Bos J. C., Wiersinga W. J., van der Valk M., Goorhuis A., Hovius J. W., Jurriaans S., Back N. K. T., Zaaijer H. L., Berkhout B., Cornelissen M. T. E., Schinkel C. J., Stelma F. F., Langebeek N., Vandenbroucke-Grauls C. M. J. E. Cumulative and current exposure to potentially nephrotoxic antiretrovirals and development of chronic kidney disease in HIV-positive individuals with a normal baseline estimated glomerular filtration rate: a prospective international cohort study Lancet HIV 2016;3 (1):e23-e32 [PubMed]
  • Op de Coul Eline L. M., van Sighem Ard, Brinkman Kees, van Benthem Birgit H., van der Ende Marchina E., Geerlings Suzanne, Reiss Peter, Prins J. M., Kuijpers T. W., Scherpbier H. J., van der Meer J. T. M., Wit F. W. M. N., Godfried M. H., van der Poll T., Nellen F. J. B., van Vugt M., Pajkrt D., Bos J. C., Wiersinga W. J., van der Valk M., Goorhuis A., Hovius J. W., van Eden J., Henderiks A., van Hes A. M. H., Mutschelknauss M., Nobel H. E., Pijnappel F. J. J., Westerman A. M., Jurriaans S., Back N. K. T., Zaaijer H. L., Berkhout B., Cornelissen M. T. E., Schinkel C. J., Thomas X. V., van den Berge M., Stegeman A., Baas S., Hage de Looff L., Versteeg D., Pronk M. J. H., Ammerlaan H. S. M., Korsten-Vorstermans E. M. H. M., de Munnik E. S., Jansz A. R., Tjhie J., Stelma F. F., Langebeek N., Vandenbroucke-Grauls C. M. J. E. Factors associated with presenting late or with advanced HIV disease in the Netherlands, 1996-2014: results from a national observational cohort BMJ open 2016;6 (1):e009688 [PubMed]
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Robin, Higaki Katsumi, Hilfiker Sabine, Hill Bradford G., Hill Joseph A., Hill William D., Hino Keisuke, Hofius Daniel, Hofman Paul, Höglinger Günter U., Höhfeld Jörg, Holz Marina K., Hong Yonggeun, Hood David A., Hoozemans Jeroen Jm, Hoppe Thorsten, Hsu Chin, Hsu Chin-Yuan, Hsu Li-Chung, Hu Dong, Hu Guochang, Hu Hong-Ming, Hu Hongbo, Hu Ming Chang, Hu Yu-Chen, Hu Zhuo-Wei, Hua Fang, Hua Ya, Huang Canhua, Huang Huey-Lan, Huang Kuo-How, Huang Kuo-Yang, Huang Shile, Huang Shiqian, Huang Wei-Pang, Huang Yi-Ran, Huang Yong, Huang Yunfei, Huber Tobias B., Huebbe Patricia, Huh Won-Ki, Hulmi Juha J., Hur Gang Min, Hurley James H., Husak Zvenyslava, Hussain Sabah Na, Hussain Salik, Hwang Jung Jin, Hwang Seungmin, Hwang Thomas Is, Ichihara Atsuhiro, Imai Yuzuru, Imbriano Carol, Inomata Megumi, Into Takeshi, Iovane Valentina, Iovanna Juan L., Iozzo Renato V., Ip Nancy Y., Irazoqui Javier E., Iribarren Pablo, Isaka Yoshitaka, Isakovic Aleksandra J., Ischiropoulos Harry, Isenberg Jeffrey S., Ishaq Mohammad, Ishida Hiroyuki, Ishii Isao, Ishmael Jane E., Isidoro Ciro, Isobe Ken-ichi, Isono Erika, Issazadeh-Navikas Shohreh, Itahana Koji, Itakura Eisuke, Ivanov Andrei I., Iyer Anand Krishnan V., Izquierdo José M., Izumi Yotaro, Izzo Valentina, Jäättelä Marja, Jaber Nadia, Jackson Daniel John, Jackson William T., Jacob Tony George, Jacques Thomas S., Jagannath Chinnaswamy, Jain Ashish, Jana Nihar Ranjan, Jang Byoung Kuk, Jani Alkesh, Janji Bassam, Jannig Paulo Roberto, Jansson Patric J., Jean Steve, Jendrach Marina, Jeon Ju-Hong, Jessen Niels, Jeung Eui-Bae, Jia Kailiang, Jia Lijun, Jiang Hong, Jiang Hongchi, Jiang Liwen, Jiang Teng, Jiang Xiaoyan, Jiang Xuejun, Jiang Ying, Jiang Yongjun, Jiménez Alberto, Jin Cheng, Jin Hongchuan, Jin Lei, Jin Meiyan, Jin Shengkan, Jinwal Umesh Kumar, Jo Eun-Kyeong, Johansen Terje, Johnson Daniel E., Johnson Gail Vw, Johnson James D., Jonasch Eric, Jones Chris, Joosten Leo Ab, Jordan Joaquin, Joseph Anna-Maria, Joseph Bertrand, Joubert Annie M., Ju Dianwen, Ju Jingfang, Juan Hsueh-Fen, Juenemann Katrin, Juhász Gábor, Jung Hye Seung, Jung Jae U., Jung Yong-Keun, Jungbluth Heinz, Justice Matthew J., Jutten Barry, Kaakoush Nadeem O., Kaarniranta Kai, Kaasik Allen, Kabuta Tomohiro, Kaeffer Bertrand, Kågedal Katarina, Kahana Alon, Kajimura Shingo, Kakhlon Or, Kalia Manjula, Kalvakolanu Dhan V., Kamada Yoshiaki, Kambas Konstantinos, Kaminskyy Vitaliy O., Kampinga Harm H., Kandouz Mustapha, Kang Chanhee, Kang Rui, Kang Tae-Cheon, Kanki Tomotake, Kanneganti Thirumala-Devi, Kanno Haruo, Kanthasamy Anumantha G., Kantorow Marc, Kaparakis-Liaskos Maria, Kapuy Orsolya, Karantza Vassiliki, Karim Md Razaul, Karmakar Parimal, Kaser Arthur, Kaushik Susmita, Kawula Thomas, Kaynar A. 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R., Lane Jon D., Lanzi Cinzia, Lapaquette Pierre, Lapierre Louis R., Laporte Jocelyn, Laukkarinen Johanna, Laurie Gordon W., Lavandero Sergio, Lavie Lena, LaVoie Matthew J., Law Betty Yuen Kwan, Law Helen Ka-Wai, Law Kelsey B., Layfield Robert, Lazo Pedro A., Le Cam Laurent, Le Roch Karine G., Le Stunff Hervé, Leardkamolkarn Vijittra, Lecuit Marc, Lee Byung-Hoon, Lee Che-Hsin, Lee Erinna F., Lee Gyun Min, Lee He-Jin, Lee Hsinyu, Lee Jae Keun, Lee Jongdae, Lee Ju-Hyun, Lee Jun Hee, Lee Michael, Lee Myung-Shik, Lee Patty J., Lee Sam W., Lee Seung-Jae, Lee Shiow-Ju, Lee Stella Y., Lee Sug Hyung, Lee Sung Sik, Lee Sung-Joon, Lee Sunhee, Lee Ying-Ray, Lee Yong J., Lee Young H., Leeuwenburgh Christiaan, Lefort Sylvain, Legouis Renaud, Lei Jinzhi, Lei Qun-Ying, Leib David A., Leibowitz Gil, Lekli Istvan, Lemaire Stéphane D., Lemasters John J., Lemberg Marius K., Lemoine Antoinette, Leng Shuilong, Lenz Guido, Lenzi Paola, Lerman Lilach O., Lettieri Barbato Daniele, Leu Julia I.-Ju, Leung Hing Y., Levine Beth, Lewis Patrick A., Lezoualc'h Frank, Li Chi, Li Faqiang, Li Feng-Jun, Li Jun, Li Ke, Li Lian, Li Min, Li Qiang, Li Rui, Li Sheng, Li Wei, Li Xiaotao, Li Yumin, Lian Jiqin, Liang Chengyu, Liang Qiangrong, Liao Yulin, Liberal Joana, Liberski Pawel P., Lie Pearl, Lieberman Andrew P., Lim Hyunjung Jade, Lim Kah-Leong, Lim Kyu, Lima Raquel T., Lin Chang-Shen, Lin Chiou-Feng, Lin Fang, Lin Fangming, Lin Fu-Cheng, Lin Kui, Lin Kwang-Huei, Lin Pei-Hui, Lin Tianwei, Lin Wan-Wan, Lin Yee-Shin, Lin Yong, Linden Rafael, Lindholm Dan, Lindqvist Lisa M., Lingor Paul, Linkermann Andreas, Liotta Lance A., Lipinski Marta M., Lira Vitor A., Lisanti Michael P., Liton Paloma B., Liu Bo, Liu Chong, Liu Chun-Feng, Liu Fei, Liu Hung-Jen, Liu Jianxun, Liu Jing-Jing, Liu Jing-Lan, Liu Ke, Liu Leyuan, Liu Liang, Liu Quentin, Liu Rong-Yu, Liu Shiming, Liu Shuwen, Liu Wei, Liu Xian-De, Liu Xiangguo, Liu Xiao-Hong, Liu Xinfeng, Liu Xu, Liu Xueqin, Liu Yang, Liu Yule, Liu Zexian, Liu Zhe, Liuzzi Juan P., Lizard Gérard, Ljujic Mila, Lodhi Irfan J., Logue Susan E., Lokeshwar Bal L., Long Yun Chau, Lonial Sagar, Loos Benjamin, López-Otín Carlos, López-Vicario Cristina, Lorente Mar, Lorenzi Philip L., Lõrincz Péter, Los Marek, Lotze Michael T., Lovat Penny E., Lu Binfeng, Lu Bo, Lu Jiahong, Lu Qing, Lu She-Min, Lu Shuyan, Lu Yingying, Luciano Frédéric, Luckhart Shirley, Lucocq John Milton, Ludovico Paula, Lugea Aurelia, Lukacs Nicholas W., Lum Julian J., Lund Anders H., Luo Honglin, Luo Jia, Luo Shouqing, Luparello Claudio, Lyons Timothy, Ma Jianjie, Ma Yi, Ma Yong, Ma Zhenyi, Machado Juliano, Machado-Santelli Glaucia M., Macian Fernando, MacIntosh Gustavo C., MacKeigan Jeffrey P., Macleod Kay F., MacMicking John D., MacMillan-Crow Lee Ann, Madeo Frank, Madesh Muniswamy, Madrigal-Matute Julio, Maeda Akiko, Maeda Tatsuya, Maegawa Gustavo, Maellaro Emilia, Maes Hannelore, Magariños Marta, Maiese Kenneth, Maiti Tapas K., Maiuri Luigi, Maiuri Maria Chiara, Maki Carl G., Malli Roland, Malorni Walter, Maloyan Alina, Mami-Chouaib Fathia, Man Na, Mancias Joseph D., Mandelkow Eva-Maria, Mandell Michael A., Manfredi Angelo A., Manié Serge N., Manzoni Claudia, Mao Kai, Mao Zixu, Mao Zong-Wan, Marambaud Philippe, Marconi Anna Maria, Marelja Zvonimir, Marfe Gabriella, Margeta Marta, Margittai Eva, Mari Muriel, Mariani Francesca V., Marin Concepcio, Marinelli Sara, Mariño Guillermo, Markovic Ivanka, Marquez Rebecca, Martelli Alberto M., Martens Sascha, Martin Katie R., Martin Seamus J., Martin Shaun, Martin-Acebes Miguel A., Martín-Sanz Paloma, Martinand-Mari Camille, Martinet Wim, Martinez Jennifer, Martinez-Lopez Nuria, Martinez-Outschoorn Ubaldo, Martínez-Velázquez Moisés, Martinez-Vicente Marta, Martins Waleska Kerllen, Mashima Hirosato, Mastrianni James A., Matarese Giuseppe, Matarrese Paola, Mateo Roberto, Matoba Satoaki, Matsumoto Naomichi, Matsushita Takehiko, Matsuura Akira, Matsuzawa Takeshi, Mattson Mark P., Matus Soledad, Maugeri Norma, Mauvezin Caroline, Mayer Andreas, Maysinger Dusica, Mazzolini Guillermo D., McBrayer Mary Kate, McCall Kimberly, McCormick Craig, McInerney Gerald M., McIver Skye C., McKenna Sharon, McMahon John J., McNeish Iain A., Mechta-Grigoriou Fatima, Medema Jan Paul, Medina Diego L., Megyeri Klara, Mehrpour Maryam, Mehta Jawahar L., Mei Yide, Meier Ute-Christiane, Meijer Alfred J., Meléndez Alicia, Melino Gerry, Melino Sonia, de Melo Edesio Jose Tenorio, Mena Maria A., Meneghini Marc D., Menendez Javier A., Menezes Regina, Meng Liesu, Meng Ling-Hua, Meng Songshu, Menghini Rossella, Menko A. 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Javier, Ollinger Karin, Olsson Stefan, Orban Daniel P., Ordonez Paulina, Orhon Idil, Orosz Laszlo, O'Rourke Eyleen J., Orozco Helena, Ortega Angel L., Ortona Elena, Osellame Laura D., Oshima Junko, Oshima Shigeru, Osiewacz Heinz D., Otomo Takanobu, Otsu Kinya, Ou Jing-hsiung James, Outeiro Tiago F., Ouyang Dong-Yun, Ouyang Hongjiao, Overholtzer Michael, Ozbun Michelle A., Ozdinler P. 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Ashutosh, Rasmussen Blake B., Rasse Tobias M., Ratovitski Edward A., Rautou Pierre-Emmanuel, Ray Swapan K., Razani Babak, Reed Bruce H., Reggiori Fulvio, Rehm Markus, Reichert Andreas S., Rein Theo, Reiner David J., Reits Eric, Ren Jun, Ren Xingcong, Renna Maurizio, Reusch Jane Eb, Revuelta Jose L., Reyes Leticia, Rezaie Alireza R., Richards Robert I., Richardson Des R., Richetta Clémence, Riehle Michael A., Rihn Bertrand H., Rikihisa Yasuko, Riley Brigit E., Rimbach Gerald, Rippo Maria Rita, Ritis Konstantinos, Rizzi Federica, Rizzo Elizete, Roach Peter J., Robbins Jeffrey, Roberge Michel, Roca Gabriela, Roccheri Maria Carmela, Rocha Sonia, Rodrigues Cecilia Mp, Rodríguez Clara I., de Cordoba Santiago Rodriguez, Rodriguez-Muela Natalia, Roelofs Jeroen, Rogov Vladimir V., Rohn Troy T., Rohrer Bärbel, Romanelli Davide, Romani Luigina, Romano Patricia Silvia, Roncero M. Isabel G., Rosa Jose Luis, Rosello Alicia, Rosen Kirill V., Rosenstiel Philip, Rost-Roszkowska Magdalena, Roth Kevin A., Roué Gael, Rouis Mustapha, Rouschop Kasper M., Ruan Daniel T., Ruano Diego, Rubinsztein David C., Rucker Edmund B., Rudich Assaf, Rudolf Emil, Rudolf Ruediger, Ruegg Markus A., Ruiz-Roldan Carmen, Ruparelia Avnika Ashok, Rusmini Paola, Russ David W., Russo Gian Luigi, Russo Giuseppe, Russo Rossella, Rusten Tor Erik, Ryabovol Victoria, Ryan Kevin M., Ryter Stefan W., Sabatini David M., Sacher Michael, Sachse Carsten, Sack Michael N., Sadoshima Junichi, Saftig Paul, Sagi-Eisenberg Ronit, Sahni Sumit, Saikumar Pothana, Saito Tsunenori, Saitoh Tatsuya, Sakakura Koichi, Sakoh-Nakatogawa Machiko, Sakuraba Yasuhito, Salazar-Roa María, Salomoni Paolo, Saluja Ashok K., Salvaterra Paul M., Salvioli Rosa, Samali Afshin, Sanchez Anthony Mj, Sánchez-Alcázar José A., Sanchez-Prieto Ricardo, Sandri Marco, Sanjuan Miguel A., Santaguida Stefano, Santambrogio Laura, Santoni Giorgio, Dos Santos Claudia Nunes, Saran Shweta, Sardiello Marco, Sargent Graeme, Sarkar Pallabi, Sarkar Sovan, Sarrias Maria Rosa, Sarwal Minnie M., Sasakawa Chihiro, Sasaki Motoko, Sass Miklos, Sato Ken, Sato Miyuki, Satriano Joseph, Savaraj Niramol, Saveljeva Svetlana, Schaefer Liliana, Schaible Ulrich E., Scharl Michael, Schatzl Hermann M., Schekman Randy, Scheper Wiep, Schiavi Alfonso, Schipper Hyman M., Schmeisser Hana, Schmidt Jens, Schmitz Ingo, Schneider Bianca E., Schneider E. 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James, Shen Chiung-Chyi, Shen Han-Ming, Shen Sanbing, Shen Weili, Sheng Rui, Sheng Xianyong, Sheng Zu-Hang, Shepherd Trevor G., Shi Junyan, Shi Qiang, Shi Qinghua, Shi Yuguang, Shibutani Shusaku, Shibuya Kenichi, Shidoji Yoshihiro, Shieh Jeng-Jer, Shih Chwen-Ming, Shimada Yohta, Shimizu Shigeomi, Shin Dong Wook, Shinohara Mari L., Shintani Michiko, Shintani Takahiro, Shioi Tetsuo, Shirabe Ken, Shiri-Sverdlov Ronit, Shirihai Orian, Shore Gordon C., Shu Chih-Wen, Shukla Deepak, Sibirny Andriy A., Sica Valentina, Sigurdson Christina J., Sigurdsson Einar M., Sijwali Puran Singh, Sikorska Beata, Silveira Wilian A., Silvente-Poirot Sandrine, Silverman Gary A., Simak Jan, Simmet Thomas, Simon Anna Katharina, Simon Hans-Uwe, Simone Cristiano, Simons Matias, Simonsen Anne, Singh Rajat, Singh Shivendra V., Singh Shrawan K., Sinha Debasish, Sinha Sangita, Sinicrope Frank A., Sirko Agnieszka, Sirohi Kapil, Sishi Balindiwe Jn, Sittler Annie, Siu Parco M., Sivridis Efthimios, Skwarska Anna, Slack Ruth, Slaninová Iva, Slavov Nikolai, Smaili Soraya S., Smalley Keiran Sm, Smith Duncan R., Soenen Stefaan J., Soleimanpour Scott A., Solhaug Anita, Somasundaram Kumaravel, Son Jin H., Sonawane Avinash, Song Chunjuan, Song Fuyong, Song Hyun Kyu, Song Ju-Xian, Song Wei, Soo Kai Y., Sood Anil K., Soong Tuck Wah, Soontornniyomkij Virawudh, Sorice Maurizio, Sotgia Federica, Soto-Pantoja David R., Sotthibundhu Areechun, Sousa Maria João, Spaink Herman P., Span Paul N., Spang Anne, Sparks Janet D., Speck Peter G., Spector Stephen A., Spies Claudia D., Springer Wolfdieter, Clair Daret St, Stacchiotti Alessandra, Staels Bart, Stang Michael T., Starczynowski Daniel T., Starokadomskyy Petro, Steegborn Clemens, Steele John W., Stefanis Leonidas, Steffan Joan, Stellrecht Christine M., Stenmark Harald, Stepkowski Tomasz M., Stern Stęphan T., Stevens Craig, Stockwell Brent R., Stoka Veronika, Storchova Zuzana, Stork Björn, Stratoulias Vassilis, Stravopodis Dimitrios J., Strnad Pavel, Strohecker Anne Marie, Ström Anna-Lena, Stromhaug Per, Stulik Jiri, Su Yu-Xiong, Su Zhaoliang, Subauste Carlos S., Subramaniam Srinivasa, Sue Carolyn M., Suh Sang Won, Sui Xinbing, Sukseree Supawadee, Sulzer David, Sun Fang-Lin, Sun Jiaren, Sun Jun, Sun Shi-Yong, Sun Yang, Sun Yi, Sun Yingjie, Sundaramoorthy Vinod, Sung Joseph, Suzuki Hidekazu, Suzuki Kuninori, Suzuki Naoki, Suzuki Tadashi, Suzuki Yuichiro J., Swanson Michele S., Swanton Charles, Swärd Karl, Swarup Ghanshyam, Sweeney Sean T., Sylvester Paul W., Szatmari Zsuzsanna, Szegezdi Eva, Szlosarek Peter W., Taegtmeyer Heinrich, Tafani Marco, Taillebourg Emmanuel, Tait Stephen Wg, Takacs-Vellai Krisztina, Takahashi Yoshinori, Takáts Szabolcs, Takemura Genzou, Takigawa Nagio, Talbot Nicholas J., Tamagno Elena, Tamburini Jerome, Tan Cai-Ping, Tan Lan, Tan Mei Lan, Tan Ming, Tan Yee-Joo, Tanaka Keiji, Tanaka Masaki, Tang Daolin, Tang Dingzhong, Tang Guomei, Tanida Isei, Tanji Kunikazu, Tannous Bakhos A., Tapia Jose A., Tasset-Cuevas Inmaculada, Tatar Marc, Tavassoly Iman, Tavernarakis Nektarios, Taylor Allen, Taylor Graham S., Taylor Gregory A., Taylor J. Paul, Taylor Mark J., Tchetina Elena V., tee Andrew R., Teixeira-Clerc Fatima, Telang Sucheta, Tencomnao Tewin, Teng Ba-Bie, Teng Ru-Jeng, Terro Faraj, Tettamanti Gianluca, Theiss Arianne L., Theron Anne E., Thomas Kelly Jean, Thomé Marcos P., Thomes Paul G., Thorburn Andrew, Thorner Jeremy, Thum Thomas, Thumm Michael, Thurston Teresa Lm, Tian Ling, Till Andreas, Ting Jenny Pan-Yun, Titorenko Vladimir I., Toker Lilach, Toldo Stefano, Tooze Sharon A., Topisirovic Ivan, Torgersen Maria Lyngaas, Torosantucci Liliana, Torriglia Alicia, Torrisi Maria Rosaria, Tournier Cathy, Towns Roberto, Trajkovic Vladimir, Travassos Leonardo H., Triola Gemma, Tripathi Durga Nand, Trisciuoglio Daniela, Troncoso Rodrigo, Trougakos Ioannis P., Truttmann Anita C., Tsai Kuen-Jer, Tschan Mario P., Tseng Yi-Hsin, Tsukuba Takayuki, Tsung Allan, Tsvetkov Andrey S., Tu Shuiping, Tuan Hsing-Yu, Tucci Marco, Tumbarello David A., Turk Boris, Turk Vito, Turner Robin Fb, Tveita Anders A., Tyagi Suresh C., Ubukata Makoto, Uchiyama Yasuo, Udelnow Andrej, Ueno Takashi, Umekawa Midori, Umemiya-Shirafuji Rika, Underwood Benjamin R., Ungermann Christian, Ureshino Rodrigo P., Ushioda Ryo, Uversky Vladimir N., Uzcátegui Néstor L., Vaccari Thomas, Vaccaro Maria I., Váchová Libuše, Vakifahmetoglu-Norberg Helin, Valdor Rut, Valente Enza Maria, Vallette Francois, Valverde Angela M., van den Berghe Greet, van den Bosch Ludo, van den Brink Gijs R., van der Goot F. Gisou, van der Klei Ida J., van der Laan Luc Jw, van Doorn Wouter G., van Egmond Marjolein, van Golen Kenneth L., van Kaer Luc, van Lookeren Campagne Menno, Vandenabeele Peter, Vandenberghe Wim, Vanhorebeek Ilse, Varela-Nieto Isabel, Vasconcelos M. Helena, Vasko Radovan, Vavvas Demetrios G., Vega-Naredo Ignacio, Velasco Guillermo, Velentzas Athanassios D., Velentzas Panagiotis D., Vellai Tibor, Vellenga Edo, Vendelbo Mikkel Holm, Venkatachalam Kartik, Ventura Natascia, Ventura Salvador, Veras Patrícia St, Verdier Mireille, Vertessy Beata G., Viale Andrea, Vidal Michel, Vieira Helena L. A., Vierstra Richard D., Vigneswaran Nadarajah, Vij Neeraj, Vila Miquel, Villar Margarita, Villar Victor H., Villarroya Joan, Vindis Cécile, Viola Giampietro, Viscomi Maria Teresa, Vitale Giovanni, Vogl Dan T., Voitsekhovskaja Olga V., von Haefen Clarissa, von Schwarzenberg Karin, Voth Daniel E., Vouret-Craviari Valérie, Vuori Kristina, Vyas Jatin M., Waeber Christian, Walker Cheryl Lyn, Walker Mark J., Walter Jochen, Wan Lei, Wan Xiangbo, Wang Bo, Wang Caihong, Wang Chao-Yung, Wang Chengshu, Wang Chenran, Wang Chuangui, Wang Dong, Wang Fen, Wang Fuxin, Wang Guanghui, Wang Hai-Jie, Wang Haichao, Wang Hong-Gang, Wang Hongmin, Wang Horng-Dar, Wang Jing, Wang Junjun, Wang Mei, Wang Mei-Qing, Wang Pei-Yu, Wang Peng, Wang Richard C., Wang Shuo, Wang Ting-Fang, Wang Xian, Wang Xiao-Jia, Wang Xiao-Wei, Wang Xin, Wang Xuejun, Wang Yan, Wang Yanming, Wang Ying, Wang Ying-Jan, Wang Yipeng, Wang Yu, Wang Yu Tian, Wang Yuqing, Wang Zhi-Nong, Wappner Pablo, Ward Carl, Ward Diane McVey, Warnes Gary, Watada Hirotaka, Watanabe Yoshihisa, Watase Kei, Weaver Timothy E., Weekes Colin D., Wei Jiwu, Weide Thomas, Weihl Conrad C., Weindl Günther, Weis Simone Nardin, Wen Longping, Wen Xin, Wen Yunfei, Westermann Benedikt, Weyand Cornelia M., White Anthony R., White Eileen, Whitton J. Lindsay, Whitworth Alexander J., Wiels Joëlle, Wild Franziska, Wildenberg Manon E., Wileman Tom, Wilkinson Deepti Srinivas, Wilkinson Simon, Willbold Dieter, Williams Chris, Williams Katherine, Williamson Peter R., Winklhofer Konstanze F., Witkin Steven S., Wohlgemuth Stephanie E., Wollert Thomas, Wolvetang Ernst J., Wong Esther, Wong G. William, Wong Richard W., Wong Vincent Kam Wai, Woodcock Elizabeth A., Wright Karen L., Wu Chunlai, Wu Defeng, Wu Gen Sheng, Wu Jian, Wu Junfang, Wu Mian, Wu Min, Wu Shengzhou, Wu William Kk, Wu Yaohua, Wu Zhenlong, Xavier Cristina Pr, Xavier Ramnik J., Xia Gui-Xian, Xia Tian, Xia Weiliang, Xia Yong, Xiao Hengyi, Xiao Jian, Xiao Shi, Xiao Wuhan, Xie Chuan-Ming, Xie Zhiping, Xie Zhonglin, Xilouri Maria, Xiong Yuyan, Xu Chuanshan, Xu Congfeng, Xu Feng, Xu Haoxing, Xu Hongwei, Xu Jian, Xu Jianzhen, Xu Jinxian, Xu Liang, Xu Xiaolei, Xu Yangqing, Xu Ye, Xu Zhi-Xiang, Xu Ziheng, Xue Yu, Yamada Takahiro, Yamamoto Ai, Yamanaka Koji, Yamashina Shunhei, Yamashiro Shigeko, Yan Bing, Yan Bo, Yan Xianghua, Yan Zhen, Yanagi Yasuo, Yang Dun-Sheng, Yang Jin-Ming, Yang Liu, Yang Minghua, Yang Pei-Ming, Yang Peixin, Yang Qian, Yang Wannian, Yang Wei Yuan, Yang Xuesong, Yang Yi, Yang Ying, Yang Zhifen, Yang Zhihong, Yao Meng-Chao, Yao Pamela J., Yao Xiaofeng, Yao Zhenyu, Yao Zhiyuan, Yasui Linda S., Ye Mingxiang, Yedvobnick Barry, Yeganeh Behzad, Yeh Elizabeth S., Yeyati Patricia L., Yi Fan, Yi Long, Yin Xiao-Ming, Yip Calvin K., Yoo Yeong-Min, Yoo Young Hyun, Yoon Seung-Yong, Yoshida Ken-Ichi, Yoshimori Tamotsu, Young Ken H., Yu Huixin, Yu Jane J., Yu Jin-Tai, Yu Jun, Yu Li, Yu W. Haung, Yu Xiao-Fang, Yu Zhengping, Yuan Junying, Yuan Zhi-Min, Yue Beatrice Yjt, Yue Jianbo, Yue Zhenyu, Zacks David N., Zacksenhaus Eldad, Zaffaroni Nadia, Zaglia Tania, Zakeri Zahra, Zecchini Vincent, Zeng Jinsheng, Zeng Min, Zeng Qi, Zervos Antonis S., Zhang Donna D., Zhang Fan, Zhang Guo, Zhang Guo-Chang, Zhang Hao, Zhang Hong, Zhang Hongbing, Zhang Jian, Zhang Jiangwei, Zhang Jianhua, Zhang Jing-Pu, Zhang Li, Zhang Lin, Zhang Long, Zhang Ming-Yong, Zhang Xiangnan, Zhang Xu Dong, Zhang Yan, Zhang Yang, Zhang Yanjin, Zhang Yingmei, Zhang Yunjiao, Zhao Mei, Zhao Wei-Li, Zhao Xiaonan, Zhao Yan G., Zhao Ying, Zhao Yongchao, Zhao Yu-Xia, Zhao Zhendong, Zhao Zhizhuang J., Zheng Dexian, Zheng Xi-Long, Zheng Xiaoxiang, Zhivotovsky Boris, Zhong Qing, Zhou Guang-Zhou, Zhou Guofei, Zhou Huiping, Zhou Shu-Feng, Zhou Xu-Jie, Zhu Hongxin, Zhu Hua, Zhu Wei-Guo, Zhu Wenhua, Zhu Xiao-Feng, Zhu Yuhua, Zhuang Shi-Mei, Zhuang Xiaohong, Ziparo Elio, Zois Christos E., Zoladek Teresa, Zong Wei-Xing, Zorzano Antonio, Zughaier Susu M. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) Autophagy 2016;12 (1):1-222 [PubMed]
  • Sliepen Kwinten HIV-1 envelope trimer fusion proteins and their applications 2016. 183p. ISBN 9789462993594. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Sanders R. W.)
  • Eggink Dirk, de Taeye Steven W., Bontjer Ilja, Klasse Per Johan, Langedijk Johannes P. M., Berkhout Ben, Sanders Rogier W. HIV-1 Escape from a Peptidic Anchor Inhibitor through Stabilization of the Envelope Glycoprotein Spike Journal of virology 2016;90 (23):10587-10599 [PubMed]
  • Pasternak Alexander O., Berkhout Ben HIV Reservoir: Finding the Right Needles in a Needlestack Cell host & microbe 2016;20 (3):280-282 [PubMed]
  • van Hemert Formijn, van der Kuyl Antoinette C., Berkhout Ben Impact of the biased nucleotide composition of viral RNA genomes on RNA structure and codon usage Journal of general virology 2016;97 (10):2608-2619 [PubMed]
  • Pasternak Alexander O., DeMaster Laura K., Kootstra Neeltje A., Reiss Peter, O'Doherty Una, Berkhout Ben Minor Contribution of Chimeric Host-HIV Readthrough Transcripts to the Level of HIV Cell-Associated gag RNA Journal of virology 2016;90 (2):1148-1151 [PubMed]
  • van Hemert Formijn, Berkhout Ben Nucleotide composition of the Zika virus RNA genome and its codon usage Virology journal 2016;13 (1):95 [PubMed]
  • Mouser Emily E. I. M. Parasitic helminths and HIV-1 infection: the effect of immunomodulatory antigens 2016. 152p. ISBN 9789461825797. [UvA Dissertations Online] University of Amsterdam. (Supervisors: Berkhout B., Paxton W. A.; Co-supervisors: de Jong E. C., Pollakis G.)
  • Müller Nancy Regulation of HIV-1 splicing 2016. 155p. ISBN 9789461826121. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Das A. T.)
  • Berry Neil, Manoussaka Maria, Ham Claire, Ferguson Deborah, Tudor Hannah, Mattiuzzo Giada, Klaver Bep, Page Mark, Stebbings Richard, Das Atze T., Berkhout Ben, Almond Neil, Cranage Martin P. Role of Occult and Post-acute Phase Replication in Protective Immunity Induced with a Novel Live Attenuated SIV Vaccine PLoS pathogens 2016;12 (12):e1006083 [PubMed]
  • Das Atze T., Zhou Xue, Metz Stefan W., Vink Monique A., Berkhout Ben Selecting the optimal Tet-On system for doxycycline-inducible gene expression in transiently transfected and stably transduced mammalian cells Biotechnology journal 2016;11 (1):71-79 [PubMed]
  • Harwig Alex, Jongejan Aldo, van Kampen Antoine H. C., Berkhout Ben, Das Atze T. Tat-dependent production of an HIV-1 TAR-encoded miRNA-like small RNA Nucleic acids research 2016;44 (9):4340-4353 [PubMed]
  • Das Atze T., Tenenbaum Liliane, Berkhout Ben Tet-On Systems For Doxycycline-inducible Gene Expression Current gene therapy 2016;16 (3):156-167 [PubMed]
  • Cornelissen Marion, Zorgdrager Fokla, Bruisten Sylvia M., Bakker Margreet, Berkhout Ben, van der Kuyl Antoinette C. Widespread hepatitis B virus genotype G (HBV-G) infection during the early years of the HIV epidemic in the Netherlands among men who have sex with men BMC infectious diseases 2016;16 (1):268 [PubMed]

2015

  • Berkhout Ben, van der Velden Yme U. ABX464: a good drug candidate instead of a magic bullet Retrovirology 2015;12 (1):64 [PubMed]
  • Pollakis Georgios, Baan Elly, van Werkhoven Maaike B., Berkhout Ben, Bakker Margreet, Jurriaans Suzanne, Paxton William A. Association between gp120 envelope V1V2 and V4V5 variable loop profiles in a defined HIV-1 transmission cluster AIDS (London, England) 2015;29 (10):1161-1171 [PubMed]
  • Herrera-Carrillo Elena, Berkhout Ben Bone Marrow Gene Therapy for HIV/AIDS Viruses 2015;7 (7):3910-3936 [PubMed]
  • Harwig Alex, Herrera-Carrillo Elena, Jongejan Aldo, van Kampen Antonius Hubertus, Berkhout Ben Deep Sequence Analysis of AgoshRNA Processing Reveals 3' A Addition and Trimming Molecular therapy. Nucleic acids 2015;4:e247 [PubMed]
  • van der Sluis Renée M., van Capel Toni M. M., Speijer Dave, Sanders Rogier W., Berkhout Ben, de Jong Esther C., Jeeninga Rienk E., van Montfort Thijs Dendritic cell type-specific HIV-1 activation in effector T cells: implications for latent HIV-1 reservoir establishment AIDS (London, England) 2015;29 (9):1003-1014 [PubMed]
  • Mocroft Amanda, Lundgren Jens D., Ross Michael, Law Matthew, Reiss Peter, Kirk Ole, Smith Colette, Wentworth Deborah, Neuhaus Jacqueline, Fux Christoph A., Moranne Olivier, Morlat Phillipe, Johnson Margaret A., Ryom Lene, Lundgren J. D., Powderly B., Shortman N., Moecklinghoff C., Reilly G., Franquet X., Sabin C. A., Prins J. M., Kuijpers T. W., Scherpbier H. J., van der Meer J. T. M., Wit F. W. M. N., Godfried M. H., van der Poll T., Nellen F. J. B., Geerlings S. E., van Vugt M., Pajkrt D., Bos J. C., Wiersinga W. J., van der Valk M., Goorhuis A., Hovius J. W., Jurriaans S., Back N. K. T., Zaaijer H. L., Berkhout B., Cornelissen M. T. E., Schinkel C. J., Stelma F. F., Langebeek N., Vandenbroucke-Grauls C. M. J. E., Grijsen M., Lange J., van der Horst C., Frank M. Development and validation of a risk score for chronic kidney disease in HIV infection using prospective cohort data from the D:A:D study PLoS medicine 2015;12 (3):e1001809 [PubMed]
  • Schoffelen Annelot F., Smit Colette, van Lelyveld Steven F. L., Vogt Liffert, Bauer Martijn P., Reiss Peter, Hoepelman Andy I. M., Barth Roos E., Prins J. M., Kuijpsers T. W., Scherpbier H. J., van der Meer J. T. M., Wit F. W. M. N., Godfried M. H., van der Poll T., Nellen F. J. B., Lange J. M. A., Geerlings S. E., van Vugt M., Pajkrt D., Bos J. C., Wiersinga W. J., van der Valk M., Goorhuis A., Hovius J. W., van Eden J., Henderiks A., van Hes A. M. H., Mutschelknauss M., Nobel H. E., Pijnappel F. J. J., Westerman A. M., Jurriaans S., Back N. K. T., Zaaijer H. L., Berkhout B., Cornelissen M. T. E., Schinkel C. J., Thomas X. V., van den Berge M., Stegeman A., Baas S., Sabbe L., Goudswaard J., Pronk M. J. H., Ammerlaan H. S. M., Stelma F. F., Langebeek N., Vandenbroucke-Grauls C. M. J. E., Gras L. A. J. Diminished impact of ethnicity as a risk factor for chronic kidney disease in the current HIV treatment era Journal of infectious diseases 2015;212 (2):264-274 [PubMed]
  • Bezemer Daniela, Cori Anne, Ratmann Oliver, van Sighem Ard, Hermanides Hillegonda S., Dutilh Bas E., Gras Luuk, Rodrigues Faria Nuno, van den Hengel Rob, Duits Ashley J., Reiss Peter, de Wolf Frank, Fraser Christophe, Prins J. M., Kuijpers T. W., Scherpbier H. J., van der Meer J. T. M., Wit F. W. M. N., Godfried M. H., van der Poll T., Nellen F. J. B., Geerlings S. E., van Vugt M., Pajkrt D., Bos J. C., Wiersinga W. J., van der Valk M., Goorhuis A., Hovius J. W., van Eden J., Henderiks A., van Hes A. M. H., Mutschelknauss M., Nobel H. E., Pijnappel F. J. J., Westerman A. M., Jurriaans S., Back N. K. T., Zaaijer H. L., Berkhout B., Cornelissen M. T. E., Schinkel C. J., Thomas X. V., van den Berge M., Stegeman A., Baas S., de Looff L. Hage, Stelma F. F., Langebeek N., Vandenbroucke-Grauls C. M. J. E. Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis PLoS medicine 2015;12 (11):e1001898; discussion e1001898 [PubMed]
  • Berkhout Ben, Ertl Hildegund C. J., Weinberg Marc S. Gene Therapy for HIV and Chronic Infections Preface Advances in experimental medicine and biology 2015;848:v-vii [PubMed]
  • Herrera-Carrillo Elena, Berkhout Ben Gene Therapy Strategies to Block HIV-1 Replication by RNA Interference Advances in experimental medicine and biology 2015;848:71-95 [PubMed]
  • Pasternak Alexander O., de Bruin Marijn, Bakker Margreet, Berkhout Ben, Prins Jan M. High Current CD4+ T Cell Count Predicts Suboptimal Adherence to Antiretroviral Therapy PLoS ONE 2015;10 (10):e0140791 [PubMed]
  • Harwig Alex HIV-1 in the RNA world: Transcription regulation, miRNAs and antiviral RNAs 2015. 186p. ISBN 9789461825377. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Das A. T.)
  • Harwig Alex, Das Atze T., Berkhout Ben HIV-1 RNAs: sense and antisense, large mRNAs and small siRNAs and miRNAs Current opinion in HIV and AIDS 2015;10 (2):103-109 [PubMed]
  • Mueller Nancy, Berkhout Ben, Das Atze T. HIV-1 splicing is controlled by local RNA structure and binding of splicing regulatory proteins at the major 5' splice site Journal of general virology 2015;96 (Part 7):1906-1917 [PubMed]
  • Harwig Alex, Berkhout Ben Hiv-1-transcriptie: recente verrassingen HIV Bulletin 2015;3:7-9
  • Turrini Filippo, Marelli Sara, Kajaste-Rudnitski Anna, Lusic Marina, van Lint Carine, Das Atze T., Harwig Alex, Berkhout Ben, Vicenzi Elisa HIV-1 transcriptional silencing caused by TRIM22 inhibition of Sp1 binding to the viral promoter Retrovirology 2015;12 (1):104 [PubMed]
  • Roy Upal, Berkhout Ben HIV infection and adipose tissue resident stem cells: their involvement in pathology and treatmentin: M. A. Hayat, editors. Stem Cells and Cancer Stem Cells, Therapeutic applications in disease and injury, Volume 13. Dordrecht: Springer Netherlands; 2015. p. 21-34, ISBN 9789401772327
  • Mueller Nancy, Klaver Bep, Berkhout Ben, Das Atze T. Human immunodeficiency virus type 1 splicing at the major splice donor site is controlled by highly conserved RNA sequence and structural elements Journal of general virology 2015;96 (11):3389-3395 [PubMed]
  • de Taeye Steven W., Ozorowski Gabriel, Torrents de la Peña Alba, Guttman Miklos, Julien Jean-Philippe, van den Kerkhof Tom L. G. M., Burger Judith A., Pritchard Laura K., Pugach Pavel, Yasmeen Anila, Crampton Jordan, Hu Joyce, Bontjer Ilja, Torres Jonathan L., Arendt Heather, DeStefano Joanne, Koff Wayne C., Schuitemaker Hanneke, Eggink Dirk, Berkhout Ben, Dean Hansi, Labranche Celia, Crotty Shane, Crispin Max, Montefiori David C., Klasse P. J., Lee Kelly K., Moore John P., Wilson Ian A., Ward Andrew B., Sanders Rogier W. Immunogenicity of Stabilized HIV-1 Envelope Trimers with Reduced Exposure of Non-neutralizing Epitopes Cell 2015;163 (7):1702-1715 [PubMed]
  • van Hemert Formijn J., Zaaijer Hans L., Berkhout Ben In silico prediction of ebolavirus RNA polymerase inhibition by specific combinations of approved nucleotide analogues Journal of clinical virology 2015;73:89-94 [PubMed]
  • Berkhout Ben, Bukrinsky Michael Jan van der Noordaa (1934-2015); A Virologist Pur Sang Viruses 2015;7 (9):5016-5017 [PubMed]
  • Liu Ying Poi, Karg Margarete, Harwig Alex, Herrera-Carrillo Elena, Jongejan Aldo, van Kampen Antoine, Berkhout Ben Mechanistic insights on the Dicer-independent AGO2-mediated processing of AgoshRNAs RNA biology 2015;12 (1):92-100 [PubMed]
  • Berkhout Ben, van Hemert Formijn On the biased nucleotide composition of the human coronavirus RNA genome Virus research 2015;202:41-47 [PubMed]
  • Berkhout Ben, Das Atze T. On the primer binding site mutation that appears and disappears during HIV and SIV replication Retrovirology 2015;12:75 [PubMed]
  • Herrera-Carrillo Elena, Berkhout Ben Potential mechanisms for cell-based gene therapy to treat HIV/AIDS Expert opinion on therapeutic targets 2015;19 (2):245-263 [PubMed]
  • van Montfort Thijs, Thomas Adri A. M., Krawczyk Przemek M., Berkhout Ben, Sanders Rogier W., Paxton William A. Reactivation of Neutralized HIV-1 by Dendritic Cells Is Dependent on the Epitope Bound by the Antibody Journal of immunology (Baltimore, Md. 2015;195 (8):3759-3768 [PubMed]
  • Mirabelli Carmen, Surdo Matteo, van Hemert Formijn, Lian Zhichao, Salpini Romina, Cento Valeria, Cortese Maria Francesca, Aragri Marianna, Pollicita Michela, Alteri Claudia, Bertoli Ada, Berkhout Ben, Micheli Valeria, Gubertini Guido, Santoro Maria Mercedes, Romano Sara, Visca Michela, Bernassola Martina, Longo Roberta, de Sanctis Giuseppe Maria, Trimoulet Pascal, Fleury Hervè, Marino Nicoletta, Mazzotta Francesco, Cappiello Giuseppina, Spanò Alberto, Sarrecchia Cesare, Zhang Jing Maria, Andreoni Massimo, Angelico Mario, Verheyen Jens, Perno Carlo Federico, Svicher Valentina Specific mutations in the C-terminus domain of HBV surface antigen significantly correlate with low level of serum HBV-DNA in patients with chronic HBV infection Journal of infection 2015;70 (3):288-298 [PubMed]
  • van Bel Nikki Structure and sequence motifs in the HIV-1 RNA genome 2015. 177p. ISBN 9789461825360. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Das A. T.)
  • van Bel Nikki, Ghabri Anouar, Das Atze T., Berkhout Ben The HIV-1 leader RNA is exquisitely sensitive to structural changes Virology 2015;483:236-252 [PubMed]
  • Herrera-Carrillo E., Berkhout B. The impact of HIV-1 genetic diversity on the efficacy of a combinatorial RNAi-based gene therapy Gene therapy 2015;22 (6):485-495 [PubMed]
  • Herrera-Carrillo Elena, Harwig Alex, Berkhout Ben Toward optimization of AgoshRNA molecules that use a non-canonical RNAi pathway: variations in the top and bottom base pairs RNA biology 2015;12 (4):447-456 [PubMed]
  • Liu Ying Poi, Karg Margarete, Herrera-Carrillo Elena, Berkhout Ben Towards Antiviral shRNAs Based on the AgoshRNA Design PLoS ONE 2015;10 (6):e0128618 [PubMed]
  • Berkhout Ben With a Little Help from my Enteric Microbial Friends Frontiers in Medicine 2015;2:30 [PubMed]

2014

  • van Bel Nikki, Das Atze T., Cornelissen Marion, Abbink Truus E. M., Berkhout Ben A short sequence motif in the 5' leader of the HIV-1 genome modulates extended RNA dimer formation and virus replication Journal of biological chemistry 2014;289 (51):35061-35074 [PubMed]
  • Kiselinova Maja, Pasternak Alexander O., de Spiegelaere Ward, Vogelaers Dirk, Berkhout Ben, Vandekerckhove Linos Comparison of droplet digital PCR and seminested real-time PCR for quantification of cell-associated HIV-1 RNA PLoS ONE 2014;9 (1):e85999 [PubMed]
  • van Hemert Formijn J., Berkhout Ben, Zaaijer Hans L. Differential binding of tenofovir and adefovir to reverse transcriptase of hepatitis B virus PLoS ONE 2014;9 (9):e106324 [PubMed]
  • Liu Ying Poi, Berkhout Ben Gene Silencing Methods Using Vector-Encoded siRNAs or miRNAsin: Roland K. Hartmann, Albrecht Bindereif, Astrid Schön, Eric Westhof, editors. Handbook of RNA Biochemistry (2nd rev. and enl. ed.). S.l.: Wiley-VCH; 2014. p. 1221-1242, ISBN 9783527327645; 9783527647064
  • Liu Ying Poi, Berkhout Ben HIV-1-based lentiviral vectors Methods in molecular biology (Clifton, N.J.) 2014;1087:273-284 [PubMed]
  • Isik Gözde HIV-1 envelope glycoproteins with costimulatory domains for vaccine applications 2014. 229p. ISBN 9789053358986. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Sanders R. W.)
  • Mueller Nancy, van Bel Nikki, Berkhout Ben, Das Atze T. HIV-1 splicing at the major splice donor site is restricted by RNA structure Virology 2014;468-470:609-620 [PubMed]
  • van der Sluis Renée M., Derking Ronald, Breidel Seyguerney, Speijer Dave, Berkhout Ben, Jeeninga Rienk E. Interplay between viral Tat protein and c-Jun transcription factor in controlling LTR promoter activity in different human immunodeficiency virus type I subtypes Journal of general virology 2014;95 (4):968-979 [PubMed]
  • van Bel Nikki, Das Atze T., Berkhout Ben In Vivo SELEX of Single-Stranded Domains in the HIV-1 Leader RNA Journal of virology 2014;88 (4):1870-1880 [PubMed]
  • Berkhout Ben, Bodem Jochen, Erlwein Otto, Herchenröder Ottmar, Khan Arifa S., Lever Andrew Ml, Lindemann Dirk, Linial Maxine L., Löchelt Martin, McClure Myra O., Scheller Carsten, Weiss Robin A. Obituary: Axel Rethwilm (1959-2014) Retrovirology 2014;11 (1):85 [PubMed]
  • van Hemert Formijn, van der Kuyl Antoinette C., Berkhout Ben On the nucleotide composition and structure of retroviral RNA genomes Virus research 2014;193:16-23 [PubMed]
  • Herrera-Carrillo Elena, Harwig Alex, Liu Ying Poi, Berkhout Ben Probing the shRNA characteristics that hinder Dicer recognition and consequently allow Ago-mediated processing and AgoshRNA activity RNA (New York, N.Y.) 2014;20 (9):1410-1418 [PubMed]
  • Jazaeri Farsani Seyed Mohammad Respiratory viruses and novel methods for virus discovery 2014. 133p. ISBN 9789461824943. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: van der Hoek C. M.)
  • Harwig Alex, Das Atze T., Berkhout Ben Retroviral microRNAs Current opinion in virology 2014;7:47-54 [PubMed]
  • Berkhout Ben, Mouland Andrew J., Musier-Forsyth Karin SPECIAL ISSUE: Retroviral Nucleocapsid Protein and Assembly Foreword Virus research 2014;193:1 [PubMed]
  • de Vree Paula J. P., de Wit Elzo, Yilmaz Mehmet, van de Heijning Monique, Klous Petra, Verstegen Marjon J. A. M., Wan Yi, Teunissen Hans, Krijger Peter H. L., Geeven Geert, Eijk Paul P., Sie Daoud, Ylstra Bauke, Hulsman Lorette O. M., van Dooren Marieke F., van Zutven Laura J. C. M., van den Ouweland Ans, Verbeek Sjef, van Dijk Ko Willems, Cornelissen Marion, Das Atze T., Berkhout Ben, Sikkema-Raddatz Birgit, van den Berg Eva, van der Vlies Pieter, Weening Desiree, den Dunnen Johan T., Matusiak Magdalena, Lamkanfi Mohamed, Ligtenberg Marjolijn J. L., ter Brugge Petra, Jonkers Jos, Foekens John A., Martens John W., van der Luijt Rob, van Amstel Hans Kristian Ploos, van Min Max, Splinter Erik, de Laat Wouter Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping Nature biotechnology 2014;32 (10):1019-1025 [PubMed]
  • van Bel Nikki, van der Velden Yme, Bonnard Damien, Le Rouzic Erwann, Das Atze T., Benarous Richard, Berkhout Ben The allosteric HIV-1 integrase inhibitor BI-D affects virion maturation but does not influence packaging of a functional RNA genome PLoS ONE 2014;9 (7):e103552 [PubMed]
  • Herrera-Carrillo Elena, Liu Ying Poi, Berkhout Ben The impact of unprotected T cells in RNAi-based gene therapy for HIV-AIDS Molecular therapy 2014;22 (3):596-606 [PubMed]
  • Herrera-Carrillo Elena, Paxton William A., Berkhout Ben The search for a T cell line for testing novel antiviral strategies against HIV-1 isolates of diverse receptor tropism and subtype origin Journal of virological methods 2014;203:88-96 [PubMed]
  • Berkhout Ben, Liu Ying Poi Towards improved shRNA and miRNA reagents as inhibitors of HIV-1 replication Future microbiology 2014;9 (4):561-571 [PubMed]

2013

  • Duverger Alexandra, Wolschendorf Frank, Zhang Mingce, Wagner Fredric, Hatcher Brandon, Jones Jennifer, Cron Randall Q., van der Sluis Renee M., Jeeninga Rienk E., Berkhout Ben, Kutsch Olaf An AP-1 binding site in the enhancer/core element of the HIV-1 promoter controls the ability of HIV-1 to establish latent infection Journal of virology 2013;87 (4):2264-2277 [PubMed]
  • van der Velden Gisela J., Vink Monique A., Klaver Bep, Das Atze T., Berkhout Ben An AUG codon upstream of rev and env open reading frames ensures optimal translation of the simian immunodeficiency virus Env protein Virology 2013;436 (1):191-200 [PubMed]
  • Cento Valeria, van Hemert Formijn, Neumann-Fraune Maria, Mirabelli Carmen, Di Maio Velia-Chiara, Salpini Romina, Bertoli Ada, Micheli Valeria, Gubertini Guido, Romano Sara, Visca Michela, de Sanctis Giuseppe-Maria, Berkhout Ben, Marino Nicoletta, Mazzotta Francesco, Cappiello Giuseppina, Spanò Alberto, Sarrecchia Cesare, Ceccherini-Silberstein Francesca, Andreoni Massimo, Angelico Mario, Verheyen Jens, Perno Carlo Federico, Svicher Valentina Anti-HBV treatment induces novel reverse transcriptase mutations with reflective effect on HBV S antigen Journal of infection 2013;67 (4):303-312 [PubMed]
  • Boutimah Fatima, Eekels Julia J. M., Liu Ying Poi, Berkhout Ben Antiviral strategies combining antiretroviral drugs with RNAi-mediated attack on HIV-1 and cellular co-factors Antiviral research 2013;98 (1):121-129 [PubMed]
  • Oude Munnink Bas B., Jazaeri Farsani Seyed Mohammad, Deijs Martin, Jonkers Jiri, Verhoeven Joost T. P., Ieven Margareta, Goossens Herman, de Jong Menno D., Berkhout Ben, Loens Katherine, Kellam Paul, Bakker Margreet, Canuti Marta, Cotten Matthew, van der Hoek Lia Autologous antibody capture to enrich immunogenic viruses for viral discovery PLoS ONE 2013;8 (11):e78454 [PubMed]
  • Pasternak Alexander O., Lukashov Vladimir V., Berkhout Ben Cell-associated HIV RNA: a dynamic biomarker of viral persistence Retrovirology 2013;10 (1):41 [PubMed]
  • Bontjer Ilja, Melchers Mark, Tong Tommy, van Montfort Thijs, Eggink Dirk, Montefiori David, Olson William C., Moore John P., Binley James M., Berkhout Ben, Sanders Rogier W. Comparative Immunogenicity of Evolved V1V2-Deleted HIV-1 Envelope Glycoprotein Trimers PLoS ONE 2013;8 (6):e67484 [PubMed]
  • Manoussaka Maria S., Berry Neil, Ferguson Deborah, Stebbings Richard, Robinson Mark, Ham Claire, Page Mark, Li Bo, Das Atze T., Berkhout Ben, Almond Neil, Cranage Martin P. Conditionally-live attenuated SIV upregulates global T effector memory cell frequency under replication permissive conditions Retrovirology 2013;10 (1):59 [PubMed]
  • van der Sluis Renée M., van Montfort Thijs, Pollakis Georgios, Sanders Rogier W., Speijer Dave, Berkhout Ben, Jeeninga Rienk E. Dendritic cell-induced activation of latent HIV-1 provirus in actively proliferating primary T lymphocytes PLoS pathogens 2013;9 (3):e1003259-(15 p.) [PubMed]
  • Liu Ying Poi, Berkhout Ben Design of lentivirally expressed siRNAs Methods in molecular biology (Clifton, N.J.) 2013;942:233-257 [PubMed]
  • Liu Ying Poi, Schopman Nick C. T., Berkhout Ben Dicer-independent processing of short hairpin RNAs Nucleic acids research 2013;41 (6):3723-3733 [PubMed]
  • van der Sluis Renée M., Jeeninga Rienk E., Berkhout Ben Establishment and molecular mechanisms of HIV-1 latency in T cells Current opinion in virology 2013;3 (6):700-706 [PubMed]
  • Gras Luuk, Geskus Ronald B., Jurriaans Suzanne, Bakker Margreet, van Sighem Ard, Bezemer Daniela, Fraser Christophe, Prins Jan M., Berkhout Ben, de Wolf Frank, Kuijpers T. W., Scherpbier H. J., Boer K., van der Meer J. T. M., Wit F. W. M. N., Godfried M. H., Reiss P., van der Poll T., Nellen F. J. B., Lange J. M. A., Geerlings S. E., van Vugt M., Vrouenraets S. M. E., Pajkrt D., Bos J. C., van der Valk M., Schreij G., Lowe S., Oude Lashof A., Pronk M. J. H., Bravenboer B., van der Ende M. E., de Vries-Sluijs T. E. M. S., Schurink C. A. M., van der Feltz M., Nouwen J. L., Gelinck L. B. S., Verbon A., Rijnders B. J. A., van de Ven-de Ruiter E. D., Slobbe L., Kauffmann R. H., Schippers E. F., Groeneveld P. H. P., Alleman M. A., Bouwhuis J. W., ten Kate R. W., Soetekouw R., Kroon F. P., van den Broek P. J. Has the rate of CD4 cell count decline before initiation of antiretroviral therapy changed over the course of the Dutch HIV epidemic among MSM? PLoS ONE 2013;8 (5):e64437 [PubMed]
  • van der Kuyl Antoinette C., Zorgdrager Fokla, Hogema Boris, Bakker Margreet, Jurriaans Suzanne, Back Nicole K. T., Berkhout Ben, Zaaijer Hans L., Cornelissen Marion High prevalence of hepatitis B virus dual infection with genotypes A and G in HIV-1 infected men in Amsterdam, the Netherlands, during 2000-2011 BMC infectious diseases 2013;13 (1):540 [PubMed]
  • Baan Elly HIV-1 Genotypes and phenotypes associated with mother to child transmission 2013. 140p. ISBN 9789461918871. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisors: Paxton W. A., Pollakis G.)
  • van der Sluis Renée M. HIV-1 latency in proliferating T cells 2013. 209p. ISBN 9789461917553. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Jeeninga R. E.)
  • Berkhout Ben HIV, leukemia, and new horizons in molecular therapy Journal of the Formosan Medical Association = Taiwan yi zhi 2013;112 (8):441-444 [PubMed]
  • Baan Elly, van der Sluis Renée M., Bakker Margreet E., Bekker Vincent, Pajkrt Dasja, Jurriaans Suzanne, Kuijpers Taco W., Berkhout Ben, Wolthers Katja C., Paxton William A., Pollakis Georgios Human immunodeficiency virus type 1 gp120 envelope characteristics associated with disease progression differ in family members infected with genetically similar viruses Journal of general virology 2013;94 (1):20-29 [PubMed]
  • Beemon Karen, Berkhout Ben In memoriam Kuan-Teh Jeang (1958-2013): retrovirologist par excellence and founding editor of Retrovirology Journal of virology 2013;87 (12):6539-6540 [PubMed]
  • van der Velden Gisela J. In vitro and in vivo testing of conditionally replicating SIV and HIV-1 strains to study viral gene expression 2013. 160p. ISBN 9789462032699. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Das A. T.)
  • Berkhout Ben Kuan-Teh Jeang Obituary Cell host & microbe 2013;13 (3):263-264
  • Berkhout Ben, Lever Andrew, Wainberg Mark, Fassati Ariberto, Borrow Persephone, Fujii Masahiro Monsef Benkirane awarded 2013 Ming K. Jeang Foundation Retrovirology Prize: landmark HIV-1 research honoured Retrovirology 2013;10 (1):38 [PubMed]
  • Berkhout Ben, Benkirane Monsef, Lever Andrew, Wainberg Mark, Fassati Ariberto, Borrow Persephone, Fujii Masahiro, Sriskantharajah Srimathy, Cockerill Matthew Obituary: Kuan-Teh Jeang Retrovirology 2013;10 (1):28 [PubMed]
  • Knoepfel Stefanie A., Berkhout Ben On the role of four small hairpins in the HIV-1 RNA genome RNA biology 2013;10 (4):540-552 [PubMed]
  • Centlivre Mireille, Legrand Nicolas, Klamer Sofieke, Liu Ying Poi, Eije Karin Jasmijn von, Bohne Martino, Rijnstra Esther Siteur-van, Weijer Kees, Blom Bianca, Voermans Carlijn, Spits Hergen, Berkhout Ben Preclinical In Vivo Evaluation of the Safety of a Multi-shRNA-based Gene Therapy Against HIV-1 Molecular therapy. Nucleic acids 2013;2:e120 [PubMed]
  • van der Sluis Renée M., van Montfort Thijs, Centlivre Mireille, Schopman Nick C. T., Cornelissen Marion, Sanders Rogier W., Berkhout Ben, Jeeninga Rienk E., Paxton William A., Pollakis Georgios Quantitation of HIV-1 DNA with a sensitive TaqMan assay that has broad subtype specificity Journal of virological methods 2013;187 (1):94-102 [PubMed]
  • Berkhout Ben, Coombs Kevin M. Quantitative omics and its application to study virus-host interactions-a new frontier Frontiers in microbiology 2013;4:31 [PubMed]
  • Berkhout Ben, Jeang Kuan-Teh Retrovirus replication strategies Current opinion in virology 2013;3 (6):601-603 [PubMed]
  • Berkhout B., Eekels J. J. M. RNAi as antiviral therapy: the HIV-1 casein: Kenneth Alan Howard, editors. RNA Interference from Biology to Therapeutics. New York: Springer; 2013. p. 221-242, ISBN 9781461447443
  • van Hemert Formijn J., van der Kuyl Antoinette C., Berkhout Ben The A-nucleotide preference of HIV-1 in the context of its structured RNA genome RNA biology 2013;10 (2):211-215 [PubMed]
  • van der Kuyl Antoinette C., Bakker Margreet, Jurriaans Suzanne, Back Nicole K. T., Pasternak Alexander O., Cornelissen Marion, Berkhout Ben Translational HIV-1 research: from routine diagnostics to new virology insights in Amsterdam, the Netherlands during 1983-2013 Retrovirology 2013;10 (1):93 [PubMed]
  • Lukashov Vladimir V., Jurriaans Suzanne, Bakker Margreet, Berkhout Ben Transmission of risk-group specific HIV-1 strains among Dutch drug users for more than 20 years and their replacement by nonspecific strains after switching to low-harm drug practices JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES 2013;62 (2):234-238 [PubMed]
  • de Vries Michel Virus discovery and human parechoviruses 2013. 137p. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: van der Hoek C. M.)

2012

  • Eekels J. J. M., Pasternak A. O., Schut A. M., Geerts D., Jeeninga R. E., Berkhout B. A competitive cell growth assay for the detection of subtle effects of gene transduction on cell proliferation Gene therapy 2012;19 (11):1058-1064 [PubMed]
  • Legrand Nicolas, van der Velden Gisela J., Fang Raphaël Ho Tsong, Douaisi Marc, Weijer Kees, Das Atze T., Blom Bianca, Uittenbogaart Christel H., Berkhout Ben, Centlivre Mireille A doxycycline-dependent human immunodeficiency virus type 1 replicates in vivo without inducing CD4(+) T-cell depletion Journal of general virology 2012;93 (9):2017-2027 [PubMed]
  • Schopman Nick C. T., Willemsen Marcel, Liu Ying Poi, Bradley Ted, van Kampen Antoine, Baas Frank, Berkhout Ben, Haasnoot Joost Deep sequencing of virus-infected cells reveals HIV-encoded small RNAs Nucleic acids research 2012;40 (1):414-427 [PubMed]
  • Knoepfel Stefanie A., Abad Amaya, Abad Xabi, Fortes Puri, Berkhout Ben Design of modified U1i molecules against HIV-1 RNA Antiviral research 2012;94 (3):208-216 [PubMed]
  • Schopman Nick C. T., Braun Anja, Berkhout Ben Directed HIV-1 evolution of protease inhibitor resistance by second-generation short hairpin RNAs Antimicrobial agents and chemotherapy 2012;56 (1):479-486 [PubMed]
  • Schenk Geert J., Haasnoot P. C. Joost, Centlivre Mireille, Legrand Nicolas, Rip Jaap, de Boer Albertus G., Berkhout Ben Efficient CRM197-mediated drug targeting to monocytes Journal of controlled release 2012;158 (1):139-147 [PubMed]
  • Mirambeau Gilles, Darlix Jean-Luc, Summers Michael, Berkhout Ben Foreword to the virus research special issue on "retroviral RNA, protein co-factors and chaperones" Virus research 2012;169 (2):322-323 [PubMed]
  • Berkhout Ben, Sanders Rogier W. Gene therapy as a vaccine for HIV-1 Expert opinion on biological therapy 2012;12 (10):1315-1321 [PubMed]
  • May Margaret T., Hogg Robert S., Justice Amy C., Shepherd Bryan E., Costagliola Dominique, Ledergerber Bruno, Thiébaut Rodolphe, Gill M. John, Kirk Ole, van Sighem Ard, Saag Michael S., Navarro Gemma, Sobrino-Vegas Paz, Lampe Fiona, Ingle Suzanne, Guest Jodie L., Crane Heidi M., D'Arminio Monforte Antonella, Vehreschild Jörg J., Sterne Jonathan A. C., Gras L. A., van Sighem A. I., Smit C., de Wolf F., Prins J. M., Bos J. C., Eeftinck-Schattenkerk J. K. M., Geerlings S. E., Godfried M. H., Lange J. M. A., van der Meer J. T. M., Nellen F. J. B., Olszyna D. P., van der Poll T., Reiss P., Sankatsing S. U. C., van der Valk M., Vermeulen J. N., Vrouenraets S. M. E., van Vugt M., Wit F. W. M. N., Kuijpers T. W., Pajkrt D., Scherpbier H. J., Hoornenborg E., Back N. K. T., Zaaijer H. L., Berkhout B., Jurriaans S., van Kan H. J. M. Heterogeneity in outcomes of treated HIV-positive patients in Europe and North America: relation with patient and cohort characteristics International journal of epidemiology 2012;41 (6):1807-1820 [PubMed]
  • Berkhout Ben, Das Atze T. HIV-1 Escape From RNAi Antivirals: Yet Another Houdini Action? Molecular therapy. Nucleic acids 2012;1 (6):e26 [PubMed]
  • Eekels Julia J. M., Sagnier Sophie, Geerts Dirk, Jeeninga Rienk E., Biard-Piechaczyk Martine, Berkhout Ben Inhibition of HIV-1 replication with stable RNAi-mediated knockdown of autophagy factors Virology journal 2012;9 (1):69 [PubMed]
  • Steenvoorden Marjan M. C., Cornelissen Marion, van Leeuwen Elisabeth, Schuurman Nancy M., Egberink Herman F., Berkhout Ben, van der Veen Fulco, Repping Sjoerd Integration of immunodeficiency virus in oocytes via intracytoplasmic injection: possible but extremely unlikely Fertility and sterility 2012;98 (1):173-177 [PubMed]
  • Schopman Nick C. T. Interplay between the RNA interference machinery and HIV-1Amsterdam: Off Page; 2012. 165p. ISBN 9789461820747. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.)
  • Berkhout Ben, Eggink Dirk, Sanders Rogier W. Is there a future for antiviral fusion inhibitors? Current opinion in virology 2012;2 (1):50-59 [PubMed]
  • Wagschal Alexandre, Rousset Emilie, Basavarajaiah Poornima, Contreras Xavier, Harwig Alex, Laurent-Chabalier Sabine, Nakamura Mirai, Chen Xin, Zhang Ke, Meziane Oussama, Boyer Frédéric, Parrinello Hugues, Berkhout Ben, Terzian Christophe, Benkirane Monsef, Kiernan Rosemary Microprocessor, Setx, Xrn2, and Rrp6 Co-operate to Induce Premature Termination of Transcription by RNAPII Cell 2012;150 (6):1147-1157 [PubMed]
  • Pasternak Alexander O., de Bruin Marijn, Jurriaans Suzanne, Bakker Margreet, Berkhout Ben, Prins Jan M., Lukashov Vladimir V. Modest Nonadherence to Antiretroviral Therapy Promotes Residual HIV-1 Replication in the Absence of Virological Rebound in Plasma Journal of infectious diseases 2012;206 (9):1443-1452 [PubMed]
  • Das Atze T., Vrolijk Martine M., Harwig Alex, Berkhout Ben Opening of the TAR hairpin in the HIV-1 genome causes aberrant RNA dimerization and packaging Retrovirology 2012;9 (1):59 [PubMed]
  • Berkhout Ben Predicting and preventing viral escape from therapy Future Virology 2012;7 (5):483-487
  • Kramer Gertjan, Moerland Perry D., Jeeninga Rienk E., Vlietstra Wytze J., Ringrose Jeffrey H., Byrman Carsten, Berkhout Ben, Speijer Dave Proteomic analysis of HIV-T cell interaction: an update Frontiers in microbiology 2012;3:240-(6 p.) [PubMed]
  • Knoepfel Stefanie A., Centlivre Mireille, Liu Ying Poi, Boutimah Fatima, Berkhout Ben Selection of RNAi-based inhibitors for anti-HIV gene therapy World journal of virology 2012;1 (3):79-90
  • Schopman Nick C. T., van Montfort Thijs, Willemsen Marcel, Knoepfel Stefanie A., Pollakis Georgios, van Kampen Antoine, Sanders Rogier W., Haasnoot Joost, Berkhout Ben Selective packaging of cellular miRNAs in HIV-1 particles Virus research 2012;169 (2):438-447 [PubMed]
  • Low Justin T., Knoepfel Stefanie A., Watts Joseph M., ter Brake Olivier, Berkhout Ben, Weeks Kevin M. SHAPE-directed Discovery of Potent shRNA Inhibitors of HIV-1 Molecular therapy 2012;20 (4):820-828 [PubMed]
  • Melchers Mark, Bontjer Ilja, Tong Tommy, Chung Nancy P. Y., Klasse Per Johan, Eggink Dirk, Montefiori David C., Gentile Maurizio, Cerutti Andrea, Olson William C., Berkhout Ben, Binley James M., Moore John P., Sanders Rogier W. Targeting HIV-1 Envelope Glycoprotein Trimers to B Cells by Using APRIL Improves Antibody Responses Journal of virology 2012;86 (5):2488-2500 [PubMed]
  • van der Velden Gisela J., Vink Monique A., Berkhout Ben, Das Atze T. Tat has a dual role in simian immunodeficiency virus transcription Journal of general virology 2012;93 (10):2279-2289 [PubMed]
  • van der Kuyl Antoinette C., Berkhout Ben The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus Retrovirology 2012;9 (1):92 [PubMed]
  • Deeks Steven G., Autran Brigitte, Berkhout Ben, Benkirane Monsef, Cairns Scott, Chomont Nicolas, Chun Tae-Wook, Churchill Melissa, Di Mascio Michele, Katlama Christine, Lafeuillade Alain, Landay Alan, Lederman Michael, Lewin Sharon R., Maldarelli Frank, Margolis David, Markowitz Martin, Martinez-Picado Javier, Mullins James I., Mellors John, Moreno Santiago, O'Doherty Una, Palmer Sarah, Penicaud Marie-Capucine, Peterlin Matija, Poli Guido, Routy Jean-Pierre, Rouzioux Christine, Silvestri Guido, Stevenson Mario, Telenti Amalio, van Lint Carine, Verdin Eric, Woolfrey Ann, Zaia John, Barré-Sinoussi Françoise Towards an HIV cure: a global scientific strategy Nature reviews. Immunology 2012;12 (8):607-614 [PubMed]
  • van der Velden Gisela J., Klaver Bep, Das Atze T., Berkhout Ben Upstream AUG Codons in the Simian Immunodeficiency Virus SIVmac239 Genome Regulate Rev and Env Protein Translation Journal of virology 2012;86 (22):12362-12371 [PubMed]

2011

  • van Montfort Thijs, Melchers Mark, Isik Gözde, Menis Sergey, Huang Po-Ssu, Matthews Katie, Michael Elizabeth, Berkhout Ben, Schief William R., Moore John P., Sanders Rogier W. A chimeric HIV-1 envelope glycoprotein trimer with an embedded granulocyte-macrophage colony-stimulating factor (GM-CSF) domain induces enhanced antibody and T cell responses Journal of biological chemistry 2011;286 (25):22250-22261 [PubMed]
  • Centlivre Mireille, Legrand Nicolas, Steingrover Radjin, van der Sluis Renee, Grijsen Marlous L., Bakker Margreet, Jurriaans Suzanne, Berkhout Ben, Paxton William A., Prins Jan M., Pollakis Georgios Altered dynamics and differential infection profiles of lymphoid and myeloid cell subsets during acute and chronic HIV-1 infection Journal of leukocyte biology 2011;89 (5):785-795 [PubMed]
  • von Eije K. J., Berkhout B. Antiviral RNAi, how to silence virusesin: E. de Clercq, editors. Antiviral Drug Strategies. Weinheim: Wiley-VCH Verlag; 2011. p. 329-349, ISBN 9783527326969
  • Melchers Mark, Matthews Katie, de Vries Robert P., Eggink Dirk, van Montfort Thijs, Bontjer Ilja, van de Sandt Carolien, David Kathryn, Berkhout Ben, Moore John P., Sanders Rogier W. A stabilized HIV-1 envelope glycoprotein trimer fused to CD40 ligand targets and activates dendritic cells Retrovirology 2011;8 (1):48 [PubMed]
  • Dijkman Ronald Characterization of novel human respiratory viruses 2011. 210p. ISBN 9789053354469. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: van der Hoek C. M.)
  • Pan Qiuwei, de Ruiter Petra E., Von Eije Karin J., Smits Ron, Kwekkeboom Jaap, Tilanus Hugo W., Berkhout Ben, Janssen Harry L. A., van der Laan Luc J. W. Disturbance of the microRNA pathway by commonly used lentiviral shRNA libraries limits the application for screening host factors involved in hepatitis C virus infection FEBS letters 2011;585 (7):1025-1030 [PubMed]
  • Berkhout Ben Evolution of Live-Attenuated HIV Vaccines BIOPHARM INTERNATIONAL 2011;24 (1):S4-S8
  • Berkhout Ben HIV-1 as RNA evolution machine RNA biology 2011;8 (2):225-229 [PubMed]
  • van Montfort Thijs, Eggink Dirk, Boot Maikel, Tuen Michael, Hioe Catarina E., Berkhout Ben, Sanders Rogier W. HIV-1 N-glycan composition governs a balance between dendritic cell-mediated viral transmission and antigen presentation Journal of immunology (Baltimore, Md. 2011;187 (9):4676-4685 [PubMed]
  • Berkhout Ben HIV/AIDS: the possibilities of an RNAi-based gene therapyin: A. H. Bandivdekar, C. P. Puri, editors. Fundamental and Translational Research on HIV/AIDS: Global Perspectives. Mumbai: National Institute for Research in Reproductive Health; 2011. p. 1-19, ISBN 9788191054026
  • van der Sluis Renée M., Pollakis Georgios, van Gerven Marja L., Berkhout Ben, Jeeninga Rienk E. Latency profiles of full length HIV-1 molecular clone variants with a subtype specific promoter Retrovirology 2011;8 (1):73 [PubMed]
  • Eekels Julia J. M., Geerts Dirk, Jeeninga Rienk E., Berkhout Ben Long-term inhibition of HIV-1 replication with RNA interference against cellular co-factors Antiviral research 2011;89 (1):43-53 [PubMed]
  • Schellens Ingrid M. M., Navis Marjon, van Deutekom Hanneke W. M., Boeser-Nunnink Brigitte, Berkhout Ben, Kootstra Neeltje, Miedema Frank, Keşmir Can, Schuitemaker Hanneke, van Baarle Debbie, Borghans José A. M. Loss of HIV-1-derived cytotoxic T lymphocyte epitopes restricted by protective HLA-B alleles during the HIV-1 epidemic AIDS (London, England) 2011;25 (14):1691-1700 [PubMed]
  • Berkhout Ben, Jeang Kuan-Teh MicroRNAs in viral gene regulation Biochimica et Biophysica Acta-Gene Regulatory Mechanisms 2011;1809 (11-12):587-587 [PubMed]
  • Liu Ying Poi, Berkhout Ben miRNA cassettes in viral vectors: problems and solutions Biochimica et Biophysica Acta-Gene Regulatory Mechanisms 2011;1809 (11-12):732-745 [PubMed]
  • Berkhout Ben, Sanders Rogier W. Molecular strategies to design an escape-proof antiviral therapy Antiviral research 2011;92 (1):7-14 [PubMed]
  • Berkhout Ben, Eggink Dirk New pathogenic viruses and novel antiviral drugs Expert review of anti-infective therapy 2011;9 (2):161-163 [PubMed]
  • van der Kuyl Antoinette Cornelia, Cornelissen Marion, Berkhout Ben Of Mice and Men: On the Origin of XMRV Frontiers in microbiology 2011;1:147 [PubMed]
  • van Hemert Formijn J., van de Klundert Maarten A. A., Lukashov Vladimir V., Kootstra Neeltje A., Berkhout Ben, Zaaijer Hans L. Protein X of hepatitis B virus: origin and structure similarity with the central domain of DNA glycosylase PLoS ONE 2011;6 (8):e23392 [PubMed]
  • Eggink Dirk, Bontjer Ilja, Langedijk Johannes P. M., Berkhout Ben, Sanders Rogier W. Resistance of Human Immunodeficiency Virus Type 1 to a Third-Generation Fusion Inhibitor Requires Multiple Mutations in gp41 and Is Accompanied by a Dramatic Loss of gp41 Function Journal of virology 2011;85 (20):10785-10797 [PubMed]
  • Berkhout Ben, Arts Kelly, Abbink Truus E. M. Ribosomal scanning on the 5'-untranslated region of the human immunodeficiency virus RNA genome Nucleic acids research 2011;39 (12):5232-5244 [PubMed]
  • Haasnoot Joost, Berkhout Ben RNAi and Cellular miRNAs in Infections by Mammalian Viruses Methods in molecular biology (Clifton, N.J.) 2011;721:23-41 [PubMed]
  • Liu Ying Poi, Westerink Jan-Tinus, ter Brake Olivier, Berkhout Ben RNAi-Inducing Lentiviral Vectors for Anti-HIV-1 Gene Therapy Methods in molecular biology (Clifton, N.J.) 2011;721:293-311 [PubMed]
  • White K. Andrew, Enjuanes Luis, Berkhout Ben RNA virus replication, transcription and recombination RNA biology 2011;8 (2):182-183 [PubMed]
  • Didierlaurent L., Racine P. J., Houzet L., Chamontin C., Berkhout B., Mougel M. Role of HIV-1 RNA and protein determinants for the selective packaging of spliced and unspliced viral RNA and host U6 and 7SL RNA in virus particles Nucleic acids research 2011;39 (20):8915-8927 [PubMed]
  • Eekels Julia J. M. Silencing of HIV-1 co-factors 2011. 156p. ISBN 9789053354674. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.)
  • Das Atze T., Harwig Alex, Berkhout Ben The HIV-1 Tat protein has a versatile role in activating viral transcription Journal of virology 2011;85 (18):9506-9516 [PubMed]
  • Eekels Julia J. M., Berkhout Ben Toward a durable treatment of HIV-1 infection usingin: Dirk Grimm, editors. Cellular RNA interference mechanisms. London: Academic Press; 2011. p. 141-163, ISBN 9780124157958
  • Eekels Julia J. M., Berkhout Ben Toward a durable treatment of HIV-1 infection using RNA interference Progress in molecular biology and translational science 2011;102:141-163 [PubMed]
  • van der Kuyl Antoinette C., Jurriaans Suzanne, Back Nicole K. T., Sprenger Herman G., van der Werf Tjip S., Zorgdrager Fokla, Berkhout Ben, Cornelissen Marion Unusual Cluster of HIV Type 1 Dual Infections in Groningen, The Netherlands AIDS research and human retroviruses 2011;27 (4):429-433 [PubMed]
  • van der Kuyl Antoinette C., Berkhout Ben XMRV: not a mousy virus Journal of the Formosan Medical Association = Taiwan yi zhi 2011;110 (5):273-274 [PubMed]

2010

  • Schopman Nick C. T., Heynen Stephan, Haasnoot Joost, Berkhout Ben A miRNA-tRNA mix-up tRNA origin of proposed miRNA RNA biology 2010;7 (5):573-576 [PubMed]
  • van der Kuyl Antoinette C., Kozaczynska Karolina, Arien Kevin K., Gali Youssef, Balazs Victoria R., Dekker Stefan J., Zorgdrager Fokla, Vanham Guido, Berkhout Ben, Cornelissen Marion Analysis of infectious virus clones from two HIV-1 superinfection cases suggests that the primary strains have lower fitness Retrovirology 2010;7 (1):60 [PubMed]
  • Schopman Nick C. T., ter Brake Olivier, Berkhout Ben Anticipating and blocking HIV-1 escape by second generation antiviral shRNAs Retrovirology 2010;7 (1):52 [PubMed]
  • Centlivre M., Zhou X., Pouw S. M., Weijer K., Kleibeuker W., Das A. T., Blom B., Seppen J., Berkhout B., Legrand N. Autoregulatory lentiviral vectors allow multiple cycles of doxycycline-inducible gene expression in human hematopoietic cells in vivo Gene therapy 2010;17 (1):14-25 [PubMed]
  • van der Hoek Lia, Ihorst Gabriele, Sure Klaus, Vabret Astrid, Dijkman Ronald, de Vries Michel, Forster Johannes, Berkhout Ben, Uberla Klaus Burden of disease due to human coronavirus NL63 infections and periodicity of infection Journal of clinical virology 2010;48 (2):104-108 [PubMed]
  • Stax Martijn J. Characterization of DC-sign binding glycoproteins and the role in HIV-1 infection 2010. 116p. ISBN 9789789903719. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Paxton W. A.)
  • Eggink Dirk, Melchers Mark, Wuhrer Manfred, van Montfort Thijs, dey Antu K., Naaijkens Benno A., David Kathryn B., Le Douce Valentin, Deelder Andre M., Kang Kenneth, Olson William C., Berkhout Ben, Hokke Cornelis H., Moore John P., Sanders Rogier W. Corrigendum to: Lack of complex N-glycans on HIV-1 envelope glycoproteins preserves protein conformation and entry function (vol 401, pg 236, 2010) Virology 2010;406 (1):162-163
  • Ayele Workenesh, Mekonnen Yared, Messele Tsehaynesh, Mengistu Yohannes, Tsegaye Aster, Bakker Margreet, Berkhout Ben, Dorigo-Zetsma Wendelien, Wolday Dawit, Goudsmit Jaap, Coutinho Roel, de Baar Michel, Paxton William A., Pollakis Georgios Differences in HIV Type 1 RNA Plasma Load Profile of Closely Related Cocirculating Ethiopian Subtype C Strains: C and C ' AIDS research and human retroviruses 2010;26 (7):805-813 [PubMed]
  • Berkhout Ben Hepatitis C virus therapy: blocking the little microRNA helper of the virus Journal of the Formosan Medical Association = Taiwan yi zhi 2010;109 (3):173-176 [PubMed]
  • Das Atze T., Berkhout Ben HIV-1 evolution: frustrating therapies, but disclosing molecular mechanisms Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2010;365 (1548):1965-1973 [PubMed]
  • Haasnoot Joost, Berkhout Ben HIV-1 Interactions with Small RNA Induced Silencing Mechanismsin: Andrew M. L. Lever, Kuan-Teh Jeang, Ben Berkhout, editors. Recent Advances in Human Retroviruses: Principles of Replication and Pathogenesis. Singapore: World Scientific Publishing Co. Pte. Ltd.; 2010. p. 471-489, ISBN 9789814295307
  • Berkhout Ben HIV-based lentiviral vectors for anti-HIV gene therapy Future Virology 2010;5 (4):367-369
  • Berkhout Ben Hiv-onderzoek na 25 jaarin: A. Schadé, Annette D. Boenink, S. A. Danner, editors. Handboek Hiv en psychische klachten. Utrecht: De Tijdstroom; 2010. p. 45-53, ISBN 9789058981738
  • Melchers Mark Improving HIV-1 enveloppe glycoprotein vaccines 2010. 205p. ISBN 9789490371517. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Sanders R. W.)
  • Heeregrave Edwin J. Influence of CD4+ cell types on HIV-1 infection 2010. 169p. ISBN 9789490371333. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Paxton W. A.)
  • Eggink Dirk, Berkhout Ben, Sanders Rogier W. Inhibition of HIV-1 by Fusion Inhibitors Current pharmaceutical design 2010;16 (33):3716-3728 [PubMed]
  • Eggink Dirk, Melchers Mark, Wuhrer Manfred, van Montfort Thijs, dey Antu K., Naaijkens Benno A., David Kathryn B., Le Douce Valentin, Deelder André M., Kang Kenneth, Olson William C., Berkhout Ben, Hokke Cornelis H., Moore John P., Sanders Rogier W. Lack of complex N-glycans on HIV-1 envelope glycoproteins preserves protein conformation and entry function Virology 2010;401 (2):236-247 [PubMed]
  • Cornelissen Marion, Zorgdrager Fokla, Blom Petra, Jurriaans Suzanne, Repping Sjoerd, van Leeuwen Elisabeth, Bakker Margreet, Berkhout Ben, van der Kuyl Antoinette C. Lack of Detection of XMRV in Seminal Plasma from HIV-1 Infected Men in The Netherlands PLoS ONE 2010;5 (8):e12040 [PubMed]
  • ter Brake Olivier, Westerink Jan-Tinus, Berkhout Ben Lentiviral Vector Engineering for Anti-HIV RNAi Gene Therapy Methods in molecular biology (Clifton, N.J.) 2010;614:201-213 [PubMed]
  • Berkhout Ben Natuurlijke resistentie tegen het humaan immunodeficiëntie virus (HIV) Folia pharmaceutica 2010;97 (4):22-23
  • Schopman Nick C. T., Liu Ying Poi, Konstantinova Pavlina, ter Brake Olivier, Berkhout Ben Optimization of shRNA inhibitors by variation of the terminal loop sequence Antiviral research 2010;86 (2):204-211 [PubMed]
  • Das Atze T., Jeeninga Rienk E., Berkhout Ben Possible applications for replicating HIV 1 vectors HIV therapy 2010;4 (3):361-369 [PubMed]
  • Lever Andrew M. L., Jeang Kuan-Teh, Berkhout Ben Recent Advances in Human Retroviruses: Principles of Replication and PathogenesisSingapore: World Scientific Publishing Co. Pte. Ltd.; 2010. ISBN 9789814295307
  • Eggink W. D. Resistance to HIV-1 fusion inhibitors 2010. 225p. ISBN 9789490371289. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Sanders R. W.)
  • Berkhout Ben, ter Brake Olivier RNAi Gene Therapy to Control HIV-1 Infectionin: Miguel Angel Martínez, editors. RNA Interference and Viruses: Current Innovations and Future Trends. Norfolk: Caister Academic Press; 2010. p. 127-142, ISBN 9781904455561
  • Von Eije Karin J., Berkhout Ben RNAi treatment of HIV-1 infectionin: V. A. Erdmann, Jan Barciszewski, editors. RNA Technologies and Their Applications. Berlin: Springer-Verlag; 2010. p. 191-208, ISBN 9783642121678
  • Sanders Rogier W., Berkhout Ben Sealing the Envelope - The HIV-1 Envelope Glycoproteins as Targets for Therapeutics and Vaccines Current pharmaceutical design 2010;16 (33):3699-3700 [PubMed]
  • Bontjer Ilja, Melchers Mark, Eggink Dirk, David Kathryn, Moore John P., Berkhout Ben, Sanders Rogier W. Stabilized HIV-1 envelope glycoprotein trimers lacking the V1V2 domain, obtained by virus evolution Journal of biological chemistry 2010;285 (47):36456-36470 [PubMed]
  • Pasternak Alexander O., Jurriaans Suzanne, Bakker Margreet, Berkhout Ben, Lukashov Vladimir V. Steady increase in cellular HIV-1 load during the asymptomatic phase of untreated infection despite stable plasma viremia AIDS (London, England) 2010;24 (11):1641-1649 [PubMed]
  • Vrolijk Martine M. Structure and function of the repeat region in the HIV-1 RNA genome 2010. 111p. ISBN 9789090250151. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Das A. T.)
  • Liu Ying Poi, Vink Monique A., Westerink Jan-Tinus, Ramirez de Arellano Eva, Konstantinova Pavlina, ter Brake Olivier, Berkhout Ben Titers of lentiviral vectors encoding shRNAs and miRNAs are reduced by different mechanisms that require distinct repair strategies RNA (New York, N.Y.) 2010;16 (7):1328-1339 [PubMed]
  • Bezemer Daniela, van Sighem Ard, Lukashov Vladimir V., van der Hoek Lia, Back Nicole, Schuurman Rob, Boucher Charles A. B., Claas Eric C. J., Boerlijst Maarten C., Coutinho Roel A., de Wolf Frank, Prins J. M., Bos J. C., Eeftinck-Schattenkerk J. K. M., Geerlings S. E., Godfried M. H., Lange J. M. A., van der Meer J. T. M., Nellen F. J. B., Olszyna D. P., van der Poll T., Reiss P., Sankatsing S. U. C., Steingrover R., van der Valk M., Vermeulen J. N., Vrouenraets S. M. E., van Vugt M., Schrei G., van der Geest S., Oude Lashof A., Lowe S., Verbon A., Bravenboer B., Pronk M. J. H., Kuijpers T. W., Pajkrt D., Scherpbier H. J., van der Ende M. E., Bax H., van der Feltz M., Gelinck L. B. S., de Melo Mendoca, Nouwen J. L., Rijnders B. J. A., de Ruiter E. D., Zaaijer H. L., Berkhout B., Jurriaans S., van Kan H. J. M. Transmission networks of HIV-1 among men having sex with men in the Netherlands AIDS (London, England) 2010;24 (2):271-282 [PubMed]
  • Haasnoot Joost, Berkhout Ben Virus-encoded Suppressors of RNA Silencing and the Role of Cellular miRNAs in Mammalian Antiviral Immune Responsesin: Miguel Angel Martínez, editors. RNA Interference and Viruses: Current Innovations and Future Trends. Norfolk: Caister Academic Press; 2010. p. 67-88, ISBN 9781904455561

2009

  • Berkhout Ben A new Houdini act: multiple routes for HIV-1 escape from RNAi-mediated inhibition Future microbiology 2009;4 (2):151-154 [PubMed]
  • Kleibeuker Wendy, Zhou Xue, Centlivre Mireille, Legrand Nicolas, Page Mark, Almond Neil, Berkhout Ben, Das Atze T. A Sensitive Cell-Based Assay to Measure the Doxycycline Concentration in Biological Samples Human gene therapy 2009;20 (5):524-530 [PubMed]
  • Pasternak Alexander O., Jurriaans Suzanne, Bakker Margreet, Prins Jan M., Berkhout Ben, Lukashov Vladimir V. Cellular Levels of HIV Unspliced RNA from Patients on Combination Antiretroviral Therapy with Undetectable Plasma Viremia Predict the Therapy Outcome PLoS ONE 2009;4 (12):e8490 [PubMed]
  • Liu Ying Poi Combinatorial RNAi against HIV-1 2009. 179p. ISBN 9789490371043. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.)
  • Liu Ying Poi, von Eije Karin Jasmijn, Schopman Nick Ct, Westerink Jan-Tinus, Brake Olivier Ter, Haasnoot Joost, Berkhout Ben Combinatorial RNAi Against HIV-1 Using Extended Short Hairpin RNAs Molecular therapy 2009;17 (10):1712-1723 [PubMed]
  • Vrolijk Martine M., Harwig Alex, Berkhout Ben, Das Atze T. Destabilization of the TAR hairpin leads to extension of the polyA hairpin and inhibition of HIV-1 polyadenylation Retrovirology 2009;6 (1):13 [PubMed]
  • Eggink Dirk, Langedijk Johannes P. M., Bonvin Alexandre M. J. J., Deng Yiqun, Lu Min, Berkhout Ben, Sanders Rogier W. Detailed mechanistic insights into HIV-1 sensitivity to three generations of fusion inhibitors Journal of biological chemistry 2009;284 (39):26941-26950 [PubMed]
  • de Vries Walter, Haasnoot Joost, Fouchier Ron, de Haan Peter, Berkhout Ben Differential RNA silencing suppression activity of NS1 proteins from different influenza A virus strains Journal of general virology 2009;90 (Part 8):1916-1922 [PubMed]
  • ter Brake O., Legrand N., von Eije K. J., Centlivre M., Spits H., Weijer K., Blom B., Berkhout B. Evaluation of safety and efficacy of RNAi against HIV-1 in the human immune system (Rag-2(-/-)gammac(-/-)) mouse model Gene therapy 2009;16 (1):148-153 [PubMed]
  • Kozaczynska Karolina HIV-1 superinfection 2009. 148p. ISBN 9789490371036. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisors: Cornelissen M. T. E., van der Kuyl A. C.)
  • Berkhout Ben, Paxton William A. HIV vaccine: it may take two to tango, but no party time yet Retrovirology 2009;6 (1):88 [PubMed]
  • van Montfort Thijs Interaction of HIV-1 with dendritic cells; implications for pathogenesis 2009. 176p. ISBN 9789490371012. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.; Co-supervisor: Paxton W. A.)
  • Liu Ying Poi, Berkhout Ben Lentiviral Delivery of RNAi Effectors Against HIV-1 Current topics in medicinal chemistry 2009;9 (12):1130-1143 [PubMed]
  • Haasnoot Joost, Berkhout Ben Nucleic acids-based therapeutics in the battle against pathogenic viruses Handbook of experimental pharmacology 2009;189 (189):243-263 [PubMed]
  • Haché Guylaine, Abbink Truus E. M., Berkhout Ben, Harris Reuben S. Optimal translation initiation enables Vif-deficient human immunodeficiency virus type 1 to escape restriction by APOBEC3G Journal of virology 2009;83 (11):5956-5960 [PubMed]
  • Bontjer Ilja, Land Aafke, Eggink Dirk, Verkade Erwin, Tuin Kiki, Baldwin Chris, Pollakis Georgios, Paxton William A., Braakman Ineke, Berkhout Ben, Sanders Rogier W. Optimization of human immunodeficiency virus type 1 envelope glycoproteins with V1/V2 deleted, using virus evolution Journal of virology 2009;83 (1):368-383 [PubMed]
  • Ayele Workenesh, Assefa Tsehai, Lulseged Sileshi, Tegbaru Belete, Berhanu Hiwot, Tamene Wegene, Ahmedin Zenit, Tensai Birzaf W., Tafesse Mengistu, Goudsmit Jaap, Berkhout Ben, Paxton William A., Debaar Michel P., Messele Tsehaynesh, Pollakis Georgios RNA Detection and Subtype C Assessment of HIV-1 in Infants with Diarrhea in Ethiopia open AIDS journal 2009;3:19-23 [PubMed]
  • Von Eije Karin J. RNAi gene ttherapy for HIV-1, from bench to bedsite 2009. 180p. ISBN 9789490371067. [UvA Dissertations Online] University of Amsterdam. (Supervisors: Berkhout B., Rossi J. J.)
  • Liu Ying Poi, Gruber Jens, Haasnoot Joost, Konstantinova Pavlina, Berkhout Ben RNAi-mediated inhibition of HIV-1 by targeting partially complementary viral sequences Nucleic acids research 2009;37 (18):6194-6204 [PubMed]
  • Von Eije Karin J., Berkhout Ben RNA-interference-based gene therapy approaches to HIV type-1 treatment: tackling the hurdles from bench to bedside Antiviral chemistry & chemotherapy 2009;19 (6):221-233 [PubMed]
  • Von Eije Karin J., ter Brake Olivier, Berkhout Ben Stringent testing identifies highly potent and escape-proof anti-HIV short hairpin RNAs journal of gene medicine 2009;11 (6):459-467 [PubMed]
  • Jeeninga Rienk E., de Jong Menno D., Berkhout Ben The New Influenza A (H1N1) Pandemic Journal of the Formosan Medical Association = Taiwan yi zhi 2009;108 (7):523-525 [PubMed]
  • Schnettler Esther, de Vries Walter, Hemmes Hans, Haasnoot Joost, Kormelink Richard, Goldbach Rob, Berkhout Ben The NS3 protein of rice hoja blanca virus complements the RNAi suppressor function of HIV-1 Tat EMBO reports 2009;10 (3):258-263 [PubMed]
  • Berkhout Ben Toward a Durable Anti-HIV Gene Therapy Based on RNA Interference Annals of the New York Academy of Sciences 2009;1175:3-14 [PubMed]
  • Berkhout Ben, ter Brake Olivier Towards a durable RNAi gene therapy for HIV-AIDS Expert opinion on biological therapy 2009;9 (2):161-170 [PubMed]
  • Borderia Antonia V., Berkhout Ben Towards a genetic AIDS vaccine Retrovirology 2009;6 (1):93 [PubMed]
  • Berkhout Ben, ter Brake Olivier Towards an RNAi-based Gene Therapy BIOforum Europe 2009;9:7-9
  • Mocroft Amanda, Sterne Jonathan A. C., Egger Matthias, May Margaret, Grabar Sophie, Furrer Hansjakob, Sabin Caroline, Fatkenheuer Gerd, Justice Amy, Reiss Peter, D'Arminio Monforte Antonella, Gill John, Hogg Robert, Bonnet Fabrice, Kitahata Mari, Staszewski Schlomo, Casabona Jordi, Harris Ross, Saag Michael, Chêne Geneviève, Costagliola Dominique, Dabis François, de Wolf Frank, Ledergerber Bruno, Phillips Andrew, Weller Ian, Sterne Jonathan, Abgrall S., Barin F., Bentata M., Billaud E., Boué F., Gras L. A., Prins J. M., Godfried M. H., Lange J. M. A., van der Meer J. T. M., Nellen F. J. B., van der Poll T., Vermeulen J. N., van Vugt M., Wit F. W. M. N., Kuijpers T. W., Pajkrt D., Scherpbier H. J., Back N. K. T., Berkhout B., Jurriaans S., Zaaijer H. L., van Kan H. J. M. Variable impact on mortality of AIDS-defining events diagnosed during combination antiretroviral therapy: not all AIDS-defining conditions are created equal Clinical infectious diseases 2009;48 (8):1138-1151 [PubMed]
  • Gras Luuk, Jurriaans Suzanne, Bakker Margreet, van Sighem Ard, Bezemer Daniela, Fraser Christophe, Lange Joep, Prins Jan M., Berkhout Ben, de Wolf Frank, Bos J. C., Eeftinck-Schattenkerk J. K. M., Geerlings S. E., Godfried M. H., van der Meer J. T. M., Nellen F. J. B., Olszyna D. P., van der Poll T., Reiss P., Sankatsing S. U. C., Steingrover R., van der Valk M., Vermeulen J. N., Vrouenraets S. M. E., van Vugt M., Wit F. W. M. N., Schreij G., van der Geest S. Viral load levels measured at set-point have risen over the last decade of the HIV epidemic in the Netherlands PLoS ONE 2009;4 (10):e7365 [PubMed]
  • de Vries Walter G. Viral suppressors of RNA interference 2009. 160p. ISBN 9789085702726. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.)
  • Berkhout Ben, Das Atze T. Virus Evolution as a Tool to Study HIV-1 Biology Methods in molecular biology (Clifton, N.J.) 2009;485:436-451 [PubMed]

2008

  • Lever Andrew M. L., Berkhout Ben 2008 Nobel prize in Medicine for discoverers of HIV Retrovirology 2008;5 (1):91 [PubMed]
  • Berkhout Ben, Gorelick Robert, Summers Michael F., Mély Yves, Darlix Jean-Luc 6th international symposium on retroviral nucleocapsid Retrovirology 2008;5:21 [PubMed]
  • Berkhout Ben A balancing act: viruses and miRNAs Journal of the Formosan Medical Association = Taiwan yi zhi 2008;107 (1):1-3 [PubMed]
  • Berkhout Ben An Eye-opener for RNAi Therapeutics Journal of the Formosan Medical Association = Taiwan yi zhi 2008;107 (10):749-750 [PubMed]
  • Wu Ping-Sheng, Chang Luan-Yin, Berkhout B., van der Hoek L., Lu Chun-Yi, Kao Chuan-Liang, Lee Ping-Ing, Shao Pei-Lan, Lee Chin-Yun, Huang Fu-Yuan, Huang Li-Min Clinical manifestations of human coronavirus NL63 infection in children in Taiwan European journal of pediatrics 2008;167 (1):75-80 [PubMed]
  • Liu Ying Poi, Berkhout Ben Combinatorial RNAi strategies against HIV-1 and other escape-prone viruses International journal of biosciences and technology 2008;1 (2):1-10
  • Bonneau Kyle R., Ng Sharon, Foster Hillary, Choi Kelly B., Berkhout Ben, Rabson Arnold, Mackewicz Carl E., Levy Jay A. Derivation of infectious HIV-1 molecular clones with LTR mutations: sensitivity to the CD8+ cell noncytotoxic anti-HIV response Virology 2008;373 (1):30-38 [PubMed]
  • Vrolijk Martine M., Ooms Marcel, Harwig Alex, Das Atze T., Berkhout Ben Destabilization of the TAR hairpin affects the structure and function of the HIV-1 leader RNA Nucleic acids research 2008;36 (13):4352-4363 [PubMed]
  • Pyrc Krzysztof, Jebbink Maarten F., Berkhout Ben, van der Hoek Lia Detection of New Viruses by VIDISCA : Virus Discovery Based on cDNA-Amplified Fragment Length Polymorphism Methods in molecular biology (Clifton, N.J.) 2008;454:1-17 [PubMed]
  • ter Brake Olivier, Berkhout Ben Development of an RNAi-based gene therapy agains HIV-1in: Jens Kurreck, editors. Therapeutic Oligonucleotides. Stuttgart: RSCPublishing; 2008. p. 296-311, ISBN 9780854041169
  • Mugavero Michael J., May Margaret, Harris Ross, Saag Michael S., Costagliola Dominique, Egger Matthias, Phillips Andrew, Günthard Huldrych F., Dabis Francois, Hogg Robert, de Wolf Frank, Fatkenheuer Gerd, Gill M. John, Justice Amy, D'Arminio Monforte Antonella, Lampe Fiona, Miró Jose M., Staszewski Schlomo, Sterne Jonathan A. C., Casabona Jordi, Geneviè Chêne, Dabis François, del Amo Julia, Fätkenheuer Gerd, Gill John, Guest Jodie, Kitahata Mari, Ledergerber Bruno, Mocroft Amanda, Reiss Peter, Saag Michael, Sterne Jonathan, Gras L. A., Prins J. M., Godfried M. H., Lange J. M. A., van der Meer J. T. M., Nellen F. J. B., van der Poll T., Vermeulen J. N., van Vugt M., Wit F. W. M. N., Kuijpers T. W., Pajkrt D., Scherpbier H. J., Back N. K. T., Berkhout B., Jurriaans S., Zaaijer H. L., van Kan H. J. M. Does short-term virologic failure translate to clinical events in antiretroviral-naïve patients initiating antiretroviral therapy in clinical practice? AIDS (London, England) 2008;22 (18):2481-2492 [PubMed]
  • ter Brake Olivier, Haasnoot Joost, Kurreck Jens, Berkhout Ben ESF-EMBO symposium: antiviral applications of RNA interference Retrovirology 2008;5 (1):81 [PubMed]
  • Sanders Rogier W., Hsu Shang-Te D., van Anken Eelco, Liscaljet I. Marije, Dankers Martijn, Bontjer Ilja, Land Aafke, Braakman Ineke, Bonvin Alexandre M. J. J., Berkhout Ben Evolution rescues folding of human immunodeficiency virus-1 envelope glycoprotein GP120 lacking a conserved disulfide bond Molecular biology of the cell 2008;19 (11):4707-4716 [PubMed]
  • Centlivre Mireille, Klaver Bep, Berkhout Ben, Das Atze T. Functional analysis of the complex trans-activating response element RNA structure in simian immunodeficiency virus Journal of virology 2008;82 (18):9171-9178 [PubMed]
  • Pasternak Alexander O., Adema Karen W., Bakker Margreet, Jurriaans Suzanne, Berkhout Ben, Cornelissen Marion, Lukashov Vladimir V. Highly sensitive methods based on seminested real-time reverse transcription-PCR for quantitation of human immunodeficiency virus type 1 unspliced and multiply spliced RNA and proviral DNA Journal of clinical microbiology 2008;46 (7):2206-2211 [PubMed]
  • Jeeninga Rienk E., Westerhout Ellen M., van Gerven Marja L., Berkhout Ben HIV-1 latency in actively dividing human T cell lines Retrovirology 2008;5 (1):37 [PubMed]
  • Abbink Truus E. M., Berkhout Ben HIV-1 reverse transcription initiation: a potential target for novel antivirals? Virus research 2008;134 (1-2):4-18 [PubMed]
  • von Eije Karin Jasmijn, ter Brake Olivier, Berkhout Ben Human immunodeficiency virus type 1 escape is restricted when conserved genome sequences are targeted by RNA interference Journal of virology 2008;82 (6):2895-2903 [PubMed]
  • de Vries Michel, Pyrc Krzysztof, Berkhout Ron, Vermeulen-Oost Wilma, Dijkman Ronald, Jebbink Maarten F., Bruisten Sylvia, Berkhout Ben, van der Hoek Lia Human parechovirus type 1, 3, 4, 5, and 6 detection in picornavirus cultures Journal of clinical microbiology 2008;46 (2):759-762 [PubMed]
  • de Vries W., Haasnoot J., van der velden Joan A., van Montfort T., Zorgdrager F., Paxton W., Cornelissen M., van Kuppeveld F., de Haan P., Berkhout B. Increased virus replication in mammalian cells by blocking intracellular innate defense responses Gene therapy 2008;15 (7):545-552 [PubMed]
  • Berkhout Ben Infectious Diseases of the Nervous System: Pathogenesis and Worldwide Impact IDrugs 2008;11 (11):791-794 [PubMed]
  • Liu Ying Poi, Haasnoot Joost, ter Brake Olivier, Berkhout Ben, Konstantinova Pavlina Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron Nucleic acids research 2008;36 (9):2811-2824 [PubMed]
  • Mathewson Alison C., Bishop Alexandra, Yao Yongxiu, Kemp Fred, Ren Junyuan, Chen Hongying, Xu Xiaodong, Berkhout Ben, van der Hoek Lia, Jones Ian M. Interaction of severe acute respiratory syndrome-coronavirus and NL63 coronavirus spike proteins with angiotensin converting enzyme-2 Journal of general virology 2008;89 (Part 11):2741-2745 [PubMed]
  • ter Brake Olivier, 't Hooft Karen, Liu Ying Poi, Centlivre Mireille, von Eije Karin Jasmijn, Berkhout Ben Lentiviral vector design for multiple shRNA expression and durable HIV-1 inhibition Molecular therapy 2008;16 (3):557-564 [PubMed]
  • Baldwin Chris, Berkhout Ben Mechanistic studies of a T20-dependent human immunodeficiency virus type 1 variant Journal of virology 2008;82 (15):7735-7740 [PubMed]
  • van Hemert Formijn J., Zaaijer Hans L., Berkhout Ben, Lukashov Vladimir V. Mosaic amino acid conservation in 3D-structures of surface protein and polymerase of hepatitis B virus Virology 2008;370 (2):362-372 [PubMed]
  • van Hemert Formijn J., Zaaijer Hans L., Berkhout Ben, Lukashov Vladimir V. Occult hepatitis B infection: an evolutionary scenario Virology journal 2008;5 (1):146 [PubMed]
  • van Anken Eelco, Sanders Rogier W., Liscaljet I. Marije, Land Aafke, Bontjer Ilja, Tillemans Sonja, Nabatov Alexey A., Paxton William A., Berkhout Ben, Braakman Ineke Only five of 10 strictly conserved disulfide bonds are essential for folding and eight for function of the HIV-1 envelope glycoprotein Molecular biology of the cell 2008;19 (10):4298-4309 [PubMed]
  • Das Atze T., Klaver Bep, Centlivre Mireille, Harwig Alex, Ooms Marcel, Page Mark, Almond Neil, Yuan Fang, Piatak Mike, Lifson Jeffrey D., Berkhout Ben Optimization of the doxycycline-dependent simian immunodeficiency virus through in vitro evolution Retrovirology 2008;5 (1):44 [PubMed]
  • ter Brake Olivier, Von Eije Karin J., Berkhout Ben Probing the sequence space available for HIV-1 evolution AIDS (London, England) 2008;22 (14):1875-1877 [PubMed]
  • Ringrose Jeffrey H., Jeeninga Rienk E., Berkhout Ben, Speijer Dave Proteomic studies reveal coordinated changes in T-cell expression patterns upon infection with human immunodeficiency virus type 1 Journal of virology 2008;82 (9):4320-4330 [PubMed]
  • Koff W. C., Parks C. L., Berkhout B., Ackland J., Noble S., Gust I. D. Replicating viral vectors as HIV vaccines: Summary report from IAVI Sponsored Satellite Symposium, International AIDS Society Conference, July 22, 2007 Biologicals 2008;36 (5):277-286 [PubMed]
  • Menéndez-Arias Luis, Berkhout Ben Retroviral reverse transcription - Preface Virus research 2008;134 (1-2):1-3 [PubMed]
  • Smit Colette, van den Berg Charlotte, Geskus Ronald, Berkhout Ben, Coutinho Roel, Prins Maria Risk of hepatitis-related mortality increased among hepatitis C virus/HIV-coinfected drug users compared with drug users infected only with hepatitis C virus: a 20-year prospective study JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES 2008;47 (2):221-225 [PubMed]
  • de Vries Walter, Berkhout Ben RNAi suppressors encoded by pathogenic human viruses international journal of biochemistry & cell biology 2008;40 (10):2007-2012 [PubMed]
  • Abbink Truus E. M., Berkhout Ben RNA structure modulates splicing efficiency at the human immunodeficiency virus type 1 major splice donor Journal of virology 2008;82 (6):3090-3098 [PubMed]
  • Eggink Dirk, Baldwin Christopher E., Deng Yiqun, Langedijk Johannes P. M., Lu Min, Sanders Rogier W., Berkhout Ben Selection of T1249-resistant human immunodeficiency virus type 1 variants Journal of virology 2008;82 (13):6678-6688 [PubMed]
  • Sanders Rogier W., van Anken Eelco, Nabatov Alexei A., Liscaljet I. Marije, Bontjer Ilja, Eggink Dirk, Melchers Mark, Busser Els, Dankers Martijn M., Groot Fedde, Braakman Ineke, Berkhout Ben, Paxton William A. The carbohydrate at asparagine 386 on HIV-1 gp120 is not essential for protein folding and function but is involved in immune evasion Retrovirology 2008;5:10 [PubMed]

2007

  • van Opijnen Tim, de Ronde Anthony, Boerlijst Maarten C., Berkhout Ben Adaptation of HIV-1 depends on the host-cell environment PLoS ONE 2007;2 (3):e271 [PubMed]
  • Pyrc K., Berkhout B., van der Hoek L. Antiviral strategies against human coronaviruses Infectious disorders drug targets 2007;7 (1):59-66 [PubMed]
  • Westerhout Ellen M., Berkhout Ben A systematic analysis of the effect of target RNA structure on RNA interference Nucleic acids research 2007;35 (13):4322-4330 [PubMed]
  • van der Hoek Lia, Pollakis Georgios, Lukashov Vladimir V., Jebbink Maarten F., Jeeninga Rienk E., Bakker Margreet, Dukers Nicole, Jurriaans Suzanne, Paxton William A., Back Nicole K. T., Berkhout Ben Characterization of an HIV-1 group M variant that is distinct from the known subtypes AIDS research and human retroviruses 2007;23 (3):466-470 [PubMed]
  • Ooms Marcel, Abbink Truus E. M., Pham Chi, Berkhout Ben Circularization of the HIV-1 RNA genome Nucleic acids research 2007;35 (15):5253-5261 [PubMed]
  • Das Atze T., Klaver Bep, Harwig Alex, Vink Monique, Ooms Marcel, Centlivre Mireille, Berkhout Ben Construction of a doxycycline-dependent simian immunodeficiency virus reveals a nontranscriptional function of tat in viral replication Journal of virology 2007;81 (20):11159-11169 [PubMed]
  • Liu Ying Poi, Haasnoot Joost, Berkhout Ben Design of extended short hairpin RNAs for HIV-1 inhibition Nucleic acids research 2007;35 (17):5683-5693 [PubMed]
  • ter Brake Olivier Development of an RNAi based gene therapy against HIV-1 2007. 116p. ISBN 9789090216973. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout Ben)
  • van Hemert Formijn J., Lukashov Vladimir V., Berkhout Ben Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function Virology journal 2007;4:25 [PubMed]
  • Jakobsen Martin R., Haasnoot Joost, Wengel Jesper, Berkhout Ben, Kjems Jorgen Efficient inhibition of HIV-1 expression by LNA modified antisense oligonucleotides and DNAzymes targeted to functionally selected binding sites Retrovirology 2007;4:29 [PubMed]
  • Crotti Andrea, Chiara Giulia D., Ghezzi Silvia, Lupo Rossella, Jeeninga Rienk E., Liboi Elio, Lievens Patricia M.-J., Vicenzi Elisa, Bovolenta Chiara, Berkhout Ben, Poli Guido Heterogeneity of signal transducer and activator of transcription binding sites in the long-terminal repeats of distinct HIV-1 subtypes open virology journal 2007;1:26-32 [PubMed]
  • Baldwin Chris, Berkhout Ben HIV-1 drug-resistance and drug-dependence Retrovirology 2007;4 (1):78 [PubMed]
  • Abbink Truus E. M., Berkhout Ben HIV-1 reverse transcription: close encounters between the viral genome and a cellular tRNA Advances in pharmacology (San Diego, Calif.) 2007;55:99-135 [PubMed]
  • van Hemert Formijn J., Berkhout Ben, Lukashov Vladimir V. Host-related nucleotide composition and codon usage as driving forces in the recent evolution of the Astroviridae Virology 2007;361 (2):447-454 [PubMed]
  • Pyrc Krzysztof, Berkhout Ben, van der Hoek Lia Identification of new human coronaviruses Expert review of anti-infective therapy 2007;5 (2):245-253 [PubMed]
  • Zhou Xue, Symons Jori, Hoppes Rieuwert, Krueger Christel, Berens Christian, Hillen Wolfgang, Berkhout Ben, Das Atze T. Improved single-chain transactivators of the Tet-On gene expression system BMC biotechnology 2007;7:6 [PubMed]
  • Naarding Marloes A. Inhibition of mother to child transmission of HIV-1 during breastfeeding 2007. 162p. ISBN 9789078675020. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout Ben; Co-supervisor: Paxton William A.)
  • Centlivre Mireille, Sala Monica, Wain-Hobson Simon, Berkhout Ben In HIV-1 pathogenesis the die is cast during primary infection AIDS (London, England) 2007;21 (1):1-11 [PubMed]
  • ter Brake Olivier, Berkhout Ben Lentiviral vectors that carry anti-HIV shRNAs: problems and solutions journal of gene medicine 2007;9 (9):743-750 [PubMed]
  • van den Berg Charlotte H. S. B., Smit Colette, Bakker Margreet, Geskus Ronald B., Berkhout Ben, Jurriaans Suzanne, Coutinho Roel A., Wolthers Katja C., Prins Maria Major decline of hepatitis C virus incidence rate over two decades in a cohort of drug users European journal of epidemiology 2007;22 (3):183-193 [PubMed]
  • Zhou Xue Optimization of the conditional-live HIV-1 vaccine strain 2007. 113p. ISBN 9789090214689. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout Ben; Co-supervisor: Das Atze T.)
  • Ooms M. P. W. Regulatory RNA structures in the HIV-1 genome 2007. 135p. ISBN 9789085701743. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout Ben)
  • Berkhout Ben, Jeang Kuan-Teh RISCy business: MicroRNAs, pathogenesis, and viruses Journal of biological chemistry 2007;282 (37):26641-26645 [PubMed]
  • Smit Colette, Pfrommer Christiaan, Mindel Adrian, Taylor Janette, Spaargaren Joke, Berkhout Ben, Coutinho Roel, Dukers Nicole H. T. M. Rise in seroprevalence of herpes simplex virus type 1 among highly sexual active homosexual men and an increasing association between herpes simplex virus type 2 and HIV over time (1984-2003) European journal of epidemiology 2007;22 (12):937-944 [PubMed]
  • Haasnoot Joost, Westerhout Ellen M., Berkhout Ben RNA interference against viruses: strike and counterstrike Nature biotechnology 2007;25 (12):1435-1443 [PubMed]
  • van der Kuyl Antoinette C., van den Burg Remco, Zorgdrager Fokla, Groot Fedde, Berkhout Ben, Cornelissen Marion Sialoadhesin (CD169) expression in CD14+ cells is upregulated early after HIV-1 infection and increases during disease progression PLoS ONE 2007;2 (2):e257 [PubMed]
  • Westerhout Ellen M. Silencing of HIV-1 with RNAi 2007. 120p. ISBN 9789085701880. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout Ben)
  • Gali Youssef, Berkhout Ben, Vanham Guido, Bakker Margreet, Back Nicole K. T., Arien Kevin K. Survey of the temporal changes in HIV-1 replicative fitness in the Amsterdam Cohort Virology 2007;364 (1):140-146 [PubMed]
  • Ooms Marcel, Cupac Daniel, Abbink Truus E. M., Huthoff Hendrik, Berkhout Ben The availability of the primer activation signal (PAS) affects the efficiency of HIV-1 reverse transcription initiation Nucleic acids research 2007;35 (5):1649-1659 [PubMed]
  • Haasnoot Joost, de Vries Walter, Geutjes Ernst-Jan, Prins Marcel, de Haan Peter, Berkhout Ben The Ebola virus VP35 protein is a suppressor of RNA silencing PLoS pathogens 2007;3 (6):e86 [PubMed]
  • Geskus Ronald B., Prins Maria, Hubert Jean-Baptiste, Miedema Frank, Berkhout Ben, Rouzioux Christine, Delfraissy Jean-Francois, Meyer Laurence The HIV RNA setpoint theory revisited Retrovirology 2007;4:65 [PubMed]
  • Pyrc Krzysztof, Berkhout Ben, van der Hoek Lia The novel human coronaviruses NL63 and HKU1 Journal of virology 2007;81 (7):3051-3057 [PubMed]
  • Das Atze T., Harwig Alex, Vrolijk Martine M., Berkhout Ben The TAR hairpin of human immunodeficiency virus type 1 can be deleted when not required for Tat-mediated activation of transcription Journal of virology 2007;81 (14):7742-7748 [PubMed]
  • Berkhout Ben Third European Congress of Virology. 1-5 September 2007, Nuremberg, Germany IDrugs 2007;10 (11):772-774 [PubMed]
  • van Wilpe Sandra, Jurriaans S., Stroobants An, Berkhout B., Sturk A. Toepassing van een HIV-sneltest in de praktijk Nederlands tijdschrift voor klinische chemie en laboratoriumgeneeskunde 2007;32:232-236
  • Konstantinova Pavlina, ter Brake Olivier, Haasnoot Joost, de Haan Peter, Berkhout Ben Trans-inhibition of HIV-1 by a long hairpin RNA expressed within the viral genome Retrovirology 2007;4:15 [PubMed]
  • Pyrc Krysztof Virus discovery and human coronavirus NL63 2007. 278p. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout Ben; Co-supervisor: van der Hoek Lia)

2006

  • Westerhout Ellen M., Vink Monique, Haasnoot P. C. Joost, Das Atze T., Berkhout Ben A conditionally replicating HIV-based vector that stably expresses an antiviral shRNA against HIV-1 replication Molecular therapy 2006;14 (2):268-275 [PubMed]
  • Lützelberger Martin, Reinert Line S., Das Atze T., Berkhout Ben, Kjems Jørgen A novel splice donor site in the gag-pol gene is required for HIV-1 RNA stability Journal of biological chemistry 2006;281 (27):18644-18651 [PubMed]
  • Ahuja Sunil K., Aiuti Fernando, Berkhout Ben, Biberfeld Peter, Burton Dennis R., Colizzi Vittorio, Deeks Steven G., Desrosiers Ronald C., Dierich Manfred P., Doms Robert W., Emerman Michael, Gallo Robert C., Girard Marc, Greene Warner C., Hoxie James A., Hunter Eric, Klein George, Korber Bette, Kuritzkes Daniel R., Lederman Michael M., Malim Michael H., Marx Preston A., McCune Joseph M., McMichael Andrew, Miller Christopher, Miller Veronica, Montagnier Luc, Montefiori David C., Moore John P., Nixon Douglas F., Overbaugh Julie, Pauza C. David, Richman Douglas D., Saag Michael S., Sattentau Quentin, Schooley Robert T., Shattock Robin, Shaw George M., Stevenson Mario, Trkola Alexandra, Wainberg Mark A., Weiss Robin A., Wolinsky Steven, Zack Jerome A. A plea for justice for jailed medical workers Science 2006;314 (5801):924-925 [PubMed]
  • Hofmann Heike, Marzi Andrea, Gramberg Thomas, Geier Martina, Pyrc Krzysztof, van der Hoek Lia, Berkhout Ben, Pöhlmann Stefan Attachment factor and receptor engagement of SARS coronavirus and human coronavirus NL63 Advances in experimental medicine and biology 2006;581:219-227 [PubMed]
  • Hofman H., Marzi A., Gramberg T., Geier M., Pyrc K., van der Hoek L., Berkhout B., Pöhlmann S. Attachment factor and receptor engagement of SARS coronavirus and human coronavirus NL63in: S. Perlman, K. V. Holmes, editors. The Nidoviruses: toward control of SARS and other nidovirus diseases. S.l.: Springer; 2006. p. 219-227, ISBN 9780387262024
  • Jeeninga Rienk E., Jan Barbara, van den Berg Henk, Berkhout Ben Construction of doxycyline-dependent mini-HIV-1 variants for the development of a virotherapy against leukemias Retrovirology 2006;3 (sept 27):64 [PubMed]
  • Zheng Qi, Deng Yiqun, Liu Jie, van der Hoek Lia, Berkhout Ben, Lu Min Core structure of S2 from the human coronavirus NL63 spike glycoprotein Biochemistry 2006;45 (51):15205-15215 [PubMed]
  • van der Hoek C. M., Pyrc K., Berkhout B. Coronavirus NL63, de Hollandse nieuwe Tijdschrift voor infectieziekten 2006;1 (3):108-ev
  • Groot Fedde Dendritic cell-mediated HIV-1 transmission 2006. 171p. ISBN 9789085591924. [UvA Dissertations Online] University of Amsterdam. (Supervisors: Berkhout B., Kapsenberg M. L.; Co-supervisor: de Jong E. C.)
  • Groot Fedde, Kuijpers Taco W., Berkhout Ben, de Jong Esther C. Dendritic cell-mediated HIV-1 transmission to T cells of LAD-1 patients is impaired due to the defect in LFA-1 Retrovirology 2006;3:75 [PubMed]
  • Groot Fedde, van Capel Toni M. M., Schuitemaker Joost, Berkhout Ben, de Jong Esther C. Differential susceptibility of naïve, central memory and effector memory T cells to dendritic cell-mediated HIV-1 transmission Retrovirology 2006;3:52 [PubMed]
  • van Opijnen Tim, Boerlijst Maarten C., Berkhout Ben Effects of random mutations in the human immunodeficiency virus type 1 transcriptional promoter on viral fitness in different host cell environments Journal of virology 2006;80 (13):6678-6685 [PubMed]
  • Ruijter Jan M., Thygesen Helene H., Schoneveld Onard J. L. M., Das Atze T., Berkhout Ben, Lamers Wouter H. Factor correction as a tool to eliminate between-session variation in replicate experiments: application to molecular biology and retrovirology Retrovirology 2006;3 (jan 6):2 [PubMed]
  • Lemckert Angelique A. C., Grimbergen Jos, Smits Shirley, Hartkoorn Eric, Holterman Lennart, Berkhout Ben, Barouch Dan H., Vogels Ronald, Quax Paul, Goudsmit Jaap, Havenga Menzo J. E. Generation of a novel replication-incompetent adenoviral vector derived from human adenovirus type 49: manufacture on PER.C6 cells, tropism and immunogenicity Journal of general virology 2006;87 (10):2891-2899 [PubMed]
  • Konstantinova Pavlina, de Haan Peter, Das Atze T., Berkhout Ben Hairpin-induced tRNA-mediated (HITME) recombination in HIV-1 Nucleic acids research 2006;34 (8):2206-2218 [PubMed]
  • Groot Fedde, Sanders Rogier W., ter Brake Olivier, Nazmi Kamran, Veerman Enno C. I., Bolscher Jan G. M., Berkhout Ben Histatin 5-derived peptide with improved fungicidal properties enhances human immunodeficiency virus type 1 replication by promoting viral entry Journal of virology 2006;80 (18):9236-9243 [PubMed]
  • Smith M. K., Tusell S., Travanty E. A., Berkhout B., van der Hoek L., Holmes K. V. Human angiotensin-converting enzyme 2 (ACE2) is a receptor for human respiratory coronavirus NL63in: S. Perlman, K. V. Holmes, editors. The Nidoviruses: toward control of SARS and other nidovirus diseases. S.l.: Springer; 2006. p. 285-288, ISBN 9780387262024
  • Dijkman Ronald, Jebbink Maarten F., Wilbrink Berry, Pyrc Krzysztof, Zaaijer Hans L., Minor Philip D., Franklin Sally, Berkhout Ben, Thiel Volker, van der Hoek Lia Human coronavirus 229E encodes a single ORF4 protein between the spike and the envelope genes Virology journal 2006;3:106 [PubMed]
  • van der Hoek Lia, Pyrc Krzysztof, Berkhout Ben Human coronavirus NL63, a new respiratory virus FEMS microbiology reviews 2006;30 (5):760-773 [PubMed]
  • van der Hoek Lia, Sure Klaus, Ihorst Gabriele, Stang Alexander, Pyrc Krzysztof, Jebbink Maarten F., Petersen Gudula, Forster Johannes, Berkhout Ben, Uberla Klaus Human coronavirus NL63 infection is associated with croup Advances in experimental medicine and biology 2006;581:485-491 [PubMed]
  • van der Hoek L., Sure K., Ihorst G., Stang A., Pyrc K., Jebbink M. F., Petersen G., Forster J., Berkhout B., Überla K. Human coronavirus NL63 infection is associated with groupin: S. Perlman, K. V. Holmes, editors. The Nidoviruses: toward control of SARS and other nidovirus diseases. S.l.: Springer; 2006. p. 485-491, ISBN 9780387262024
  • Benschop K. S. M., Schinkel J., Minnaar R. P., Pajkrt D., Spanjerberg L., Kraakman H. C., Berkhout B., Zaaijer H. L., Beld M. G. H. M., Wolthers K. C. Human parechovirus infections in Dutch children and the association between serotype and disease severity Clinical infectious diseases 2006;42 (2):204-210 [PubMed]
  • Berkhout Ben, Back Nicole Kt, de Ronde Anthony, Jurriaans Suzanne, Bakker Margreet, Parkin Neil T., van der Hoek Lia Identification of alternative amino acid substitutions in drug-resistant variants of the HIV-1 reverse transcriptase AIDS (London, England) 2006;20 (11):1515-1520 [PubMed]
  • Ophorst O. J. A. E., Radosević K., Havenga M. J. E., Pau M. G., Holterman L., Berkhout B., Goudsmit J., Tsuji M. Immunogenicity and protection of a recombinant human adenovirus serotype 35-based malaria vaccine against Plasmodium yoelii in mice Infection and immunity 2006;74 (1):313-320 [PubMed]
  • Pyrc Krzysztof, Bosch Berend Jan, Berkhout Ben, Jebbink Maarten F., Dijkman Ronald, Rottier Peter, van der Hoek Lia Inhibition of human coronavirus NL63 infection at early stages of the replication cycle Antimicrobial agents and chemotherapy 2006;50 (6):2000-2008 [PubMed]
  • Konstantinova P., de Vries W., Haasnoot J., ter Brake O., de Haan P., Berkhout B. Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA Gene therapy 2006;13 (19):1403-1413 [PubMed]
  • Eberhardy Scott R., Goncalves Joao, Coelho Sofia, Segal David J., Berkhout Ben, Barbas Carlos F. Inhibition of human immunodeficiency virus type 1 replication with artificial transcription factors targeting the highly conserved primer-binding site Journal of virology 2006;80 (6):2873-2883 [PubMed]
  • Pöhlmann Stefan, Gramberg Thomas, Wegele Anja, Pyrc Krzysztof, van der Hoek Lia, Berkhout Ben, Hofmann Heike Interaction between the spike protein of human coronavirus NL63 and its cellular receptor ACE2 Advances in experimental medicine and biology 2006;581:281-284 [PubMed]
  • Pöhlmann S., Gramberg T., Wegele A., Pyrc K., van der Hoek L., Berkhout B., Hofman H. Interaction between the spike protein of human coronavirus NL63 and its cellular receptor ACE2in: S. Perlman, K. V. Holmes, editors. The Nidoviruses: toward control of SARS and other nidovirus diseases. S.l.: Springer; 2006. p. 281-284, ISBN 9780387262024
  • Chang Luan-Yin, Chiang Bor-Luen, Kao Chuan-Liang, Wu Mei-Hwan, Chen Pei-Jer, Berkhout Ben, Yang Hui-Ching, Huang Li-Min Lack of association between infection with a novel human coronavirus (HCoV), HCoV-NH, and Kawasaki disease in Taiwan Journal of infectious diseases 2006;193 (2):283-286 [PubMed]
  • Zhou Xue, Vink Monique, Berkhout Ben, Das Atze T. Modification of the Tet-On regulatory system prevents the conditional-live HIV-1 variant from losing doxycycline-control Retrovirology 2006;3:82 [PubMed]
  • Pyrc Krzysztof, Dijkman Ronald, Deng Lea, Jebbink Maarten F., Ross Howard A., Berkhout Ben, van der Hoek Lia Mosaic structure of human coronavirus NL63, one thousand years of evolution Journal of molecular biology 2006;364 (5):964-973 [PubMed]
  • Piotrowski Y., van der Hoek L., Pyrc K., Berkhout B., Moll R., Hilgenfeld R. Nonstructural proteins of human coronavirus NL63in: S. Perlman, K. V. Holmes, editors. The Nidoviruses: toward control of SARS and other nidovirus diseases. S.l.: Springer; 2006. p. 97-100, ISBN 9780387262024
  • Piotrowski Yvonne, van der Hoek Lia, Pyrc Krzysztof, Berkhout Ben, Moll Ralf, Hilgenfeld Rolf Nonstructural proteins of human coronavirus NL63 Advances in experimental medicine and biology 2006;581:97-100 [PubMed]
  • Groot Fedde, van Capel Toni M. M., Kapsenberg Martien L., Berkhout Ben, de Jong Esther C. Opposing roles of blood myeloid and plasmacytoid dendritic cells in HIV-1 infection of T cells: transmission facilitation versus replication inhibition Blood 2006;108 (6):1957-1964 [PubMed]
  • Zhou X., Vink M., Klaver B., Berkhout B., Das A. T. Optimization of the Tet-On system for regulated gene expression through viral evolution Gene therapy 2006;13 (19):1382-1390 [PubMed]
  • Rizzi Chiara, Crippa Massimo P., Jeeninga Rienk E., Berkhout Ben, Blasi Francesco, Poli Guido, Alfano Massimo Pertussis toxin B-oligomer suppresses IL-6 induced HIV-1 and chemokine expression in chronically infected U1 cells via inhibition of activator protein 1 Journal of immunology (Baltimore, Md. 2006;176 (2):999-1006 [PubMed]
  • Haasnoot J., Berkhout B. RNA interference: its use as antiviral therapy Handbook of experimental pharmacology 2006;173 (173):117-150 [PubMed]
  • Baldwin Chris E., Berkhout Ben Second site escape of a T20-dependent HIV-1 variant by a single amino acid change in the CD4 binding region of the envelope glycoprotein Retrovirology 2006;3:84 [PubMed]
  • ter Brake Olivier, Konstantinova Pavlina, Ceylan Mustafa, Berkhout Ben Silencing of HIV-1 with RNA interference: a multiple shRNA approach Molecular therapy 2006;14 (6):883-892 [PubMed]
  • Zhou Xue, Vink Monique, Klaver Bep, Verhoef Koen, Marzio Giuseppe, Das Atze T., Berkhout Ben The genetic stability of a conditional live HIV-1 variant can be improved by mutations in the Tet-On regulatory system that restrain evolution Journal of biological chemistry 2006;281 (25):17084-17091 [PubMed]
  • Berkhout Ben, Haasnoot Joost The interplay between virus infection and the cellular RNA interference machinery FEBS letters 2006;580 (12):2896-2902 [PubMed]
  • Westerhout Ellen M., ter Brake Olivier, Berkhout Ben The virion-associated incoming HIV-1 RNA genome is not targeted by RNA interference Retrovirology 2006;3:57 [PubMed]
  • van Opijnen T. Virus and environment. How HIV-1 replication and evolution are driven by the host-cell environment 2006. 142p. ISBN 9789073838864. [UvA Dissertations Online] University of Amsterdam. (Supervisors: Berkhout B., Sabelis M. W.; Co-supervisor: Boerlijst M. C.)

2005

  • Berkhout Ben, de Ronde Anthony, van der Hoek Lia Aggressive HIV-1? Retrovirology 2005;2 (1):13 [PubMed]
  • Das Atze T., Vink Monique, Berkhout Ben Alternative tRNA priming of human immunodeficiency virus type 1 reverse transcription explains sequence variation in the primer-binding site that has been attributed to APOBEC3G activity Journal of virology 2005;79 (5):3179-3181 [PubMed]
  • ter Brake Olivier, Berkhout Ben A novel approach for inhibition of HIV-1 by RNA interference: counteracting viral escape with a second generation of siRNAs Journal of RNAi and gene silencing 2005;1 (2):56-65 [PubMed]
  • Moës Elien, Vijgen Leen, Keyaerts Els, Zlateva Kalina, Li Sandra, Maes Piet, Pyrc Krzysztof, Berkhout Ben, van der Hoek Lia, van Ranst Marc A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium BMC infectious diseases 2005;5 (1):6 [PubMed]
  • Geskus Ronald B., Meyer Laurence, Hubert Jean-Baptiste, Schuitemaker Hanneke, Berkhout Ben, Rouzioux Christine, Theodorou Ioannis D., Delfraissy Jean-François, Prins Maria, Coutinho Roel A. Causal pathways of the effects of age and the CCR5-Delta32, CCR2-64I, and SDF-1 3'A alleles on AIDS development JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES 2005;39 (3):321-326 [PubMed]
  • Markusic David, Oude-Elferink Ronald, Das Atze T., Berkhout Ben, Seppen Jurgen Comparison of single regulated lentiviral vectors with rtTA expression driven by an autoregulatory loop or a constitutive promoter Nucleic acids research 2005;33 (6):e63 [PubMed]
  • Jeeninga Rienk E., Jan Barbara, van der Linden Birgit, van den Berg Henk, Berkhout Ben Construction of a minimal HIV-1 variant that selectively replicates in leukemic derived T-cell lines: Towards a new virotherapy approach Cancer research 2005;65 (8):3347-3355 [PubMed]
  • van der Hoek Lia, Sure Klaus, Ihorst Gabriele, Stang Alexander, Pyrc Krzysztof, Jebbink Maarten F., Petersen Gudula, Forster Johannes, Berkhout Ben, Uberla Klaus Croup is associated with the novel coronavirus NL63 PLoS medicine 2005;2 (8):764 e240-770 [PubMed]
  • Adal Melaku, Ayele Workenesh, Wolday Dawit, Dagne Kifle, Messele Tsehaynesh, Tilahun Tesfaye, Berkhout Ben, Mayaan Shlomo, Pollakis Georgios, Dorigo-Zetsma Wendelien Evidence of genetic variability of human immunodeficiency virus type 1 in plasma and cervicovaginal lavage in Ethiopian women seeking care for sexually transmitted infections AIDS research and human retroviruses 2005;21 (7):649-653 [PubMed]
  • Kivelä Pia S., Krol Anneke, Salminen Mika O., Geskus Ronald B., Suni Jukka I., Anttila Veli-Jukka, Liitsola Kirsi, Zetterberg Veera, Miedema Frank, Berkhout Ben, Coutinho Roel A., Ristola Matti A. High plasma HIV load in the CRF01-AE outbreak among injecting drug users in Finland Scandinavian journal of infectious diseases 2005;37 (4):276-283 [PubMed]
  • Westerhout Ellen M., Ooms Marcel, Vink Monique, Das Atze T., Berkhout Ben HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome Nucleic acids research 2005;33 (2):796-804 [PubMed]
  • Hofmann Heike, Pyrc Krzysztof, van der Hoek Lia, Geier Martina, Berkhout Ben, Pöhlmann Stefan Human coronavirus NL63 employs the severe acute respiratory syndrome coronavirus receptor for cellular entry Proceedings of the National Academy of Sciences of the United States of America 2005;102 (22):7988-7993 [PubMed]
  • Das Atze T., Baldwin Chris E., Vink Monique, Berkhout Ben Improving the safety of a conditional-live human immunodeficiency virus type 1 vaccine by controlling both gene expression and cell entry Journal of virology 2005;79 (6):3855-3858 [PubMed]
  • Girardi Enrico, Sabin Caroline A., D'Arminio Monforte Antonella, Hogg Bob, Phillips Andrew N., Gill M. John, Dabis Francois, Reiss Peter, Kirk Ole, Bernasconi Enos, Grabar Sophie, Justice Amy, Staszewski Schlomo, Fätkenheuer Gerd, Sterne Jonathan A. C., Prins J. M., Bos J. C., Eeftinck Schattenkerk J. K. M., Geerlings S. E., Godfried M. H., Lange J. M. A., van Leth F. C., Lowe S. H., van der Meer J. T. M., Nellen F. J. B., Pogány K., van der Poll T., Ruys T. A., Sankatsing S., Steingrover R., van Twillert G., van der Valk M., van Vonderen M. G. A., Vrouenraets S. M. E., van Vugt M., Wit F. W. M. N., Kuijpers T. W., Pajkrt D., Scherpbier H. J., Veenstra J., Danner S. A., van Agtmael M. A., Claessen F. A. P., Perenboom R. M., Rijkeboer A., van Vonderen M., Back N. K. T., Bakker M. E. G., Berkhout B., Jurriaans S. Incidence of Tuberculosis among HIV-infected patients receiving highly active antiretroviral therapy in Europe and North America Clinical infectious diseases 2005;41 (12):1772-1782 [PubMed]
  • van der Hoek Lia, Back Nicole, Jebbink Maarten F., de Ronde Anthony, Bakker Margreet, Jurriaans Suzanne, Reiss Peter, Parkin Neil, Berkhout Ben Increased multinucleoside drug resistance and decreased replicative capacity of a human immunodeficiency virus type 1 variant with an 8-amino-acid insert in the reverse transcriptase Journal of virology 2005;79 (6):3536-3543 [PubMed]
  • Berkhout Ben It's the virus, stupid--part 2 Retrovirology 2005;2 (1):78 [PubMed]
  • Groot Fedde, Geijtenbeek Teunis B. H., Sanders Rogier W., Baldwin Christopher E., Sanchez-Hernandez Marta, Floris René, van Kooyk Yvette, de Jong Esther C., Berkhout Ben Lactoferrin prevents dendritic cell-mediated human immunodeficiency virus type 1 transmission by blocking the DC-SIGN--gp120 interaction Journal of virology 2005;79 (5):3009-3015 [PubMed]
  • Naarding Marloes A., Ludwig Irene S., Groot Fedde, Berkhout Ben, Geijtenbeek Teunis B. H., Pollakis Georgios, Paxton William A. Lewis X component in human milk binds DC-SIGN and inhibits HIV-1 transfer to CD4(+) T lymphocytes Journal of clinical investigation 2005;115 (11):3256-3264 [PubMed]
  • Pyrc K., Berkhout B., van der Hoek L. Molecular characterization of human coronavirus NL63in: Recent Res Devel Infection & Immunity. Kerala. India: Transworld Research Network; 2005., ISBN 9788178951829
  • Fernández Ariel, Tawfik Dan S., Berkhout Ben, Sanders Rogier, Kloczkowski Andrzej, Sen Taner, Jernigan Bob Protein promiscuity: drug resistance and native functions--HIV-1 case Journal of biomolecular structure & dynamics 2005;22 (6):615-624 [PubMed]
  • van der Hoek Lia, Berkhout Ben Questions concerning the new haven coronavirus Journal of infectious diseases 2005;192 (2):350-351 [PubMed]
  • Nethe Micha, Berkhout Ben, van der Kuyl Antoinette C. Retroviral superinfection resistance Retrovirology 2005;2 (52):52 [PubMed]
  • Berkhout Ben RNAi Europe 2005 IDrugs 2005;8 (12):978-981 [PubMed]
  • Andersson M. Gunnar, Haasnoot P. C. Joost, Xu Ning, Berenjian Saideh, Berkhout Ben, Akusjärvi Göran Suppression of RNA interference by adenovirus virus-associated RNA Journal of virology 2005;79 (15):9556-9565 [PubMed]
  • Abbink Truus E. M., Ooms Marcel, Haasnoot P. C. Joost, Berkhout Ben The HIV-1 leader RNA conformational switch regulates RNA dimerization but does not regulate mRNA translation Biochemistry 2005;44 (25):9058-9066 [PubMed]
  • van Opijnen Tim, Berkhout Ben The host environment drives HIV-1 fitness Reviews in medical virology 2005;15 (4):219-233 [PubMed]
  • van der Kuyl Antoinette C., Kozaczynska Karolina, van den Burg Remco, Zorgdrager Fokla, Back Nicole, Jurriaans Suzanne, Berkhout Ben, Reiss Peter, Cornelissen Marion Triple HIV-1 infection New England journal of medicine 2005;352 (24):2557-2559 [PubMed]

2004

  • Das Atze T., Verhoef Koen, Berkhout Ben A conditionally replicating virus as a novel approach toward an HIV vaccine Methods in enzymology 2004;388:359-379 [PubMed]
  • Kostense Stefan, Koudstaal Wouter, Sprangers Mieke, Weverling Gerrit Jan, Penders Germaine, Helmus Niels, Vogels Ronald, Bakker Margreet, Berkhout Ben, Havenga Menzo, Goudsmit Jaap Adenovirus types 5 and 35 seroprevalence in AIDS risk groups supports type 35 as a vaccine vector AIDS (London, England) 2004;18 (8):1213-1216 [PubMed]
  • Huthoff Hendrik, Das Atze T., Vink Monique, Klaver Bep, Zorgdrager Fokla, Cornelissen Marion, Berkhout Ben A human immunodeficiency virus type 1-infected individual with low viral load harbors a virus variant that exhibits an in vitro RNA dimerization defect Journal of virology 2004;78 (9):4907-4913 [PubMed]
  • Berkhout Ben, de Ronde Anthony APOBEC3G versus reverse transcriptase in the generation of HIV-1 drug-resistance mutations AIDS (London, England) 2004;18 (13):1861-1863 [PubMed]
  • Ooms Marcel, Huthoff Hendrik, Russell Rodney, Liang Chen, Berkhout Ben A riboswitch regulates RNA dimerization and packaging in human immunodeficiency virus type 1 virions Journal of virology 2004;78 (19):10814-10819 [PubMed]
  • Bezemer Daniela, Jurriaans Suzanne, Prins Maria, van der Hoek Lia, Prins Jan M., de Wolf Frank, Berkhout Ben, Coutinho Roel, Back Nicole K. T. Declining trend in transmission of drug-resistant HIV-1 in Amsterdam AIDS (London, England) 2004;18 (11):1571-1577 [PubMed]
  • Kiselyeva Yana, Ito Yoshinori, Lima Rosangela G., Grivel Jean-Charles, Das Atze T., Berkhout Ben, Margolis Leonid B. Depletion of CD4 T lymphocytes in human lymphoid tissue infected ex vivo with doxycycline-dependent HIV-1 Virology 2004;328 (1):1-6 [PubMed]
  • Baldwin Chris E., Sanders Rogier W., Deng Yiqun, Jurriaans Suzanne, Lange Joep M., Lu Min, Berkhout Ben Emergence of a drug-dependent human immunodeficiency virus type 1 variant during therapy with the T20 fusion inhibitor Journal of virology 2004;78 (22):12428-12437 [PubMed]
  • Huthoff Hendrik, Girard Frederic, Wijmenga Sybren S., Berkhout Ben Evidence for a base triple in the free HIV-1 TAR RNA RNA (New York, N.Y.) 2004;10 (3):412-423 [PubMed]
  • Sanders Rogier W., Busser Els, Moore John P., Lu Min, Berkhout Ben Evolutionary repair of HIV type 1 gp41 with a kink in the N-terminal helix leads to restoration of the six-helix bundle structure AIDS research and human retroviruses 2004;20 (7):742-749 [PubMed]
  • Sanders Rogier W., Dankers Martijn M., Busser Els, Caffrey Michael, Moore John P., Berkhout Ben Evolution of the HIV-1 envelope glycoproteins with a disulfide bond between gp120 and gp41 Retrovirology 2004;1 (1):3 [PubMed]
  • Abbink Truus E. M., Beerens Nancy, Berkhout Ben Forced selection of a human immunodeficiency virus type 1 variant that uses a non-self tRNA primer for reverse transcription: Involvement of viral RNA sequences and the reverse transcriptase enzyme Journal of virology 2004;78 (19):10706-10714 [PubMed]
  • Pyrc Krzysztof, Jebbink Maarten F., Berkhout Ben, van der Hoek Lia Genome structure and transcriptional regulation of human coronavirus NL63 Virology journal 2004;1 (1):7 [PubMed]
  • Das Atze T., Brummelkamp Thijn R., Westerhout Ellen M., Vink Monique, Madiredjo Mandy, Bernards René, Berkhout Ben Human immunodeficiency virus type 1 escapes from RNA interference-mediated inhibition Journal of virology 2004;78 (5):2601-2605 [PubMed]
  • van Opijnen Tim, Jeeninga Rienk E., Boerlijst Maarten C., Pollakis Georgios P., Zetterberg Veera, Salminen Mika, Berkhout Ben Human immunodeficiency virus type 1 subtypes have a distinct long terminal repeat that determines the replication rate in a host-cell-specific manner Journal of virology 2004;78 (7):3675-3683 [PubMed]
  • van der Hoek Lia, Pyrc Krzysztof, Jebbink Maarten F., Vermeulen-Oost Wilma, Berkhout Ron J. M., Wolthers Katja C., Wertheim-van Dillen Pauline M. E., Kaandorp Jos, Spaargaren Joke, Berkhout Ben Identification of a new human coronavirus Nature medicine 2004;10 (4):368-373 [PubMed]
  • Holterman Lennart, Vogels Ronald, van der Vlugt Remko, Sieuwerts Martijn, Grimbergen Jos, Kaspers Jorn, Geelen Eric, van der Helm Esmeralda, Lemckert Angelique, Gillissen Gert, Verhaagh Sandra, Custers Jerome, Zuijdgeest David, Berkhout Ben, Bakker Margreet, Quax Paul, Goudsmit Jaap, Havenga Menzo Novel replication-incompetent vector derived from adenovirus type 11 (Ad11) for vaccination and gene therapy: Low seroprevalence and non-cross-reactivity with Ad5 Journal of virology 2004;78 (23):13207-13215 [PubMed]
  • Ooms Marcel, Verhoef Koen, Southern Edwin, Huthoff Hendrik, Berkhout Ben Probing alternative foldings of the HIV-1 leader RNA by antisense oligonucleotide scanning arrays Nucleic acids research 2004;32 (2):819-827 [PubMed]
  • Berkhout Ben RNA interference as an antiviral approach: Targeting HIV-1 Current opinion in molecular therapeutics 2004;6 (2):141-145 [PubMed]
  • van der Kuyl Antoinette C., van den Burg Remco, Hoyer Mark J., Gruters Rob A., Osterhaus Albert D. M. E., Berkhout Ben SIVdrl detection in captive mandrills: are mandrills infected with a third strain of simian immunodeficiency virus? Retrovirology 2004;1 (1):36 [PubMed]
  • Lemieux Anne-Marie, Paré Marie-Eve, Audet Brigitte, Legault Eric, Lefort Sylvain, Boucher Nancy, Landry Sébastien, van Opijnen Tim, Berkhout Ben, Naghavi Mojgan H., Tremblay Michel J., Barbeau Benoit T-cell activation leads to poor activation of the HIV-1 clade E long terminal repeat and weak association of nuclear factor-kappaB and NFAT with its enhancer region Journal of biological chemistry 2004;279 (51):52949-52960 [PubMed]
  • Berkhout Ben, Floris René, Recio Isidra, Visser Servaas The antiviral activity of the milk protein lactoferrin against the human immunodeficiency virus type 1 Biometals 2004;17 (3):291-294 [PubMed]
  • Sanders R. W. The HIV-1 envelope glycoproteins: folding, function and vaccine design 2004. 337p. ISBN 9789053566671. [UvA Dissertations Online] University of Amsterdam. (Supervisors: Berkhout B., Moore J. P.)
  • van Opijnen Tim, Kamoschinski Joost, Jeeninga Rienk E., Berkhout Ben The human immunodeficiency virus type 1 promoter contains a CATA box instead of a TATA box for optimal transcription and replication Journal of virology 2004;78 (13):6883-6890 [PubMed]
  • Das Atze T., Zhou Xue, Vink Monique, Klaver Bep, Verhoef Koen, Marzio Giuseppe, Berkhout Ben Viral evolution as a tool to improve the tetracycline-regulated gene expression system Journal of biological chemistry 2004;279 (18):18776-18782 [PubMed]

2003

  • Abbink Truus E. M., Berkhout Ben A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon Journal of biological chemistry 2003;278 (13):11601-11611 [PubMed]
  • Florisa René, Recio Isidra, Berkhout Ben, Visser Servaas Antibacterial and antiviral effects of milk proteins and derivatives thereof Current pharmaceutical design 2003;9 (16):1257-1275 [PubMed]
  • Berkhout B., Floris R., Recio I., Visser S. Antibacterial effects of the milk protein lactoferrin AGRO FOOD INDUSTRY HI-TECH 2003;14 (3):32-33
  • Floris R., Berkhout B., Visser S. Antiviral effects of milk proteins NVVL 2003;2:28-35
  • Berkhout B., Floris R., Recio I., Visser S. Antiviral effects of the milk protein lactoferrin AGRO FOOD INDUSTRY HI-TECH 2003;14 (2):43-46
  • Pereira Cândida F., Paridaen Judith T. M. L., Rutten Karla, Huigen Marleen C. D. G., van de Bovenkamp Marja, Middel Jeena, Beerens Nancy, Berkhout Ben, Schuurman Rob, Marnett Lawrence J., Verhoef Jan, Nottet Hans S. L. M. Aspirin-like molecules that inhibit human immunodeficiency virus 1 replication Antiviral research 2003;58 (3):253-263 [PubMed]
  • Andersen Ebbe Sloth, Jeeninga Rienk E., Damgaard Christian Kroun, Berkhout Ben, Kjems Jørgen Dimerization and template switching in the 5 ' untranslated region between various subtypes of human immunodeficiency virus type 1 Journal of virology 2003;77 (5):3020-3030 [PubMed]
  • Berkhout B. Een mens is nooit alleenAmsterdam: Vossiuspers UvA; 2003. ISBN 9789056292959
  • Huthoff H. Higher order structure of the HIV-1 leader RNA: a case for RNA switches that regulate virus replication 2003. 216p. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Berkhout B.)
  • Baldwin C. E., Sanders R. W., Berkhout B. Inhibiting HIV-1 entry with fusion inhibitors Current medicinal chemistry 2003;10 (17):1633-1642 [PubMed]
  • Haasnoot P. C. Joost, Cupac Daniel, Berkhout Ben Inhibition of virus replication by RNA interference Journal of biomedical science 2003;10 (6 Part 1 Sp. Iss.):607-616 [PubMed]
  • Huthoff Hendrik, Bugala Katarzyna, Barciszewski Jan, Berkhout Ben On the importance of the primer activation signal for initiation of tRNA(lys3)-primed reverse transcription of the HIV-1 RNA genome Nucleic acids research 2003;31 (17):5186-5194 [PubMed]
  • Kulinski Tadeusz, Olejniczak Mikolaj, Huthoff Hendrik, Bielecki Lukasz, Pachulska-Wieczorek Katarzyna, Das Atze T., Berkhout Ben, Adamiak Ryszard W. The apical loop of the HIV-1 TAR RNA hairpin is stabilized by a cross-loop base pair Journal of biological chemistry 2003;278 (40):38892-38901 [PubMed]
  • Brasey Ann, Lopez-Lastra Marcelo, Ohlmann Theophile, Beerens Nancy, Berkhout Ben, Darlix Jean-Luc, Sonenberg Nahum The leader of human immunodeficiency virus type 1 genomic RNA harbors an internal ribosome entry segment that is active during the G(2)/M phase of the cell cycle Journal of virology 2003;77 (7):3939-3949 [PubMed]

2002

  • Berkhout Ben, van Wamel Jeroen L. B., Beljaars Leonie, Meijer Dirk K. F., Visser Servaas, Floris René Characterization of the anti-HIV effects of native lactoferrin and other milk proteins and protein-derived peptides Antiviral research 2002;55 (2):341-355 [PubMed]
  • Berkhout Ben, Grigoriev Andrei, Bakker Margreet, Lukashov Vladimir V. Codon and amino acid usage in retroviral genomes is consistent with virus-specific nucleotide pressure AIDS research and human retroviruses 2002;18 (2):133-141 [PubMed]
  • Das Atze T., Zhou Xue, Vink Monique, Klaver Bep, Berkhout Ben Conditional live virus as a novel approach towards a safe live attenuated HIV vaccine Expert review of vaccines 2002;1 (3):293-301 [PubMed]
  • Berkhout Ben, Verhoef Koen, Marzio Giuseppe, Klaver Bep, Vink Monique, Zhou Xue, Das Atze T. Conditional virus replication as an approach to a safe live attenuated human immunodeficiency virus vaccine Journal of neurovirology 2002;8 (Suppl. 2):134-137 [PubMed]
  • Berkhout Ben, Marzio Giuseppe, Verhoef Koen Control over HIV-1 replication by an antibiotic; a novel vaccination strategy with a drug-dependent virus Virus research 2002;82 (1-2):103-108 [PubMed]
  • Sanders Rogier W., de Jong Esther C., Baldwin Christopher E., Schuitemaker Joost H. N., Kapsenberg Martien L., Berkhout Ben Differential transmission of human immunodeficiency virus type 1 by distinct subsets of effector dendritic cells Journal of virology 2002;76 (15):7812-7821 [PubMed]
  • Marzio Giuseppe, Vink Monique, Verhoef Koen, de Ronde Anthony, Berkhout Ben Efficient human immunodeficiency virus replication requires a fine-tuned level of transcription Journal of virology 2002;76 (6):3084-3088 [PubMed]
  • Berkhout Ben, Ooms Marcel, Beerens Nancy, Huthoff Hendrik, Southern Edwin, Verhoef Koen In vitro evidence that the untranslated leader of the HIV-1 genome is an RNA checkpoint that regulates multiple functions through conformational changes Journal of biological chemistry 2002;277 (22):19967-19975 [PubMed]
  • Huthoff Hendrik, Berkhout Ben Multiple secondary structure rearrangements during HIV-1 RNA dimerization Biochemistry 2002;41 (33):10439-10445 [PubMed]
  • Dirac Annette M. G., Huthoff Hendrik, Kjems Jørgen, Berkhout Ben Regulated HIV-2 RNA dimerization by means of alternative RNA conformations Nucleic acids research 2002;30 (12):2647-2655 [PubMed]
  • Beerens N. Regulation of HIV-1 reverse transcription 2002. 125p. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Goudsmit J.; Co-supervisor: Berkhout B.)
  • Dirac Annette M. G., Huthoff Hendrik, Kjems Jørgen, Berkhout Ben Requirements for RNA heterodimerization of the human immunodeficiency virus type 1 (HIV-1) and HIV-2 genomes Journal of general virology 2002;83 (10):2533-2542 [PubMed]
  • Sanders Rogier W., Vesanen Mika, Schuelke Norbert, Master Aditi, Schiffner Linnea, Kalyanaraman Roopa, Paluch Maciej, Berkhout Ben, Maddon Paul J., Olson William C., Lu Min, Moore John P. Stabilization of the soluble, cleaved, trimeric form of the envelope glycoprotein complex of human immunodeficiency virus type 1 Journal of virology 2002;76 (17):8875-8889 [PubMed]
  • Beerens Nancy, Berkhout Ben Switching the in vitro tRNA usage of HIV-1 by simultaneous adaptation of the PBS and PAS RNA (New York, N.Y.) 2002;8 (3):357-369 [PubMed]
  • Quivy Vincent, Adam Emmanuelle, Collette Yves, Demonte Dominique, Chariot Alain, Vanhulle Caroline, Berkhout Ben, Castellano Rémy, de Launoit Yvan, Burny Arsène, Piette Jacques, Bours Vincent, van Lint Carine Synergistic activation of human immunodeficiency virus type 1 promoter activity by NF-kappaB and inhibitors of deacetylases: potential perspectives for the development of therapeutic strategies Journal of virology 2002;76 (21):11091-11103 [PubMed]
  • Beljaars Leonie, Floris René, Berkhout Ben, Smit Catharina, Meijer Dirk K. F., Molema Grietje The influence of charge clustering on the anti-HIV-1 activity and in vivo distribution of negatively charged albumins Biochemical pharmacology 2002;63 (9):1663-1673 [PubMed]
  • Beerens Nancy, Berkhout Ben The tRNA primer activation signal in the human immunodeficiency virus type 1 genome is important for initiation and processive elongation of reverse transcription Journal of virology 2002;76 (5):2329-2339 [PubMed]

2001

  • Jeeninga R. E., Keulen W., Boucher C., Sanders R. W., Berkhout B. Evolution of AZT resistance in HIV-1: the 41-70 intermediate that is not observed in vivo has a replication defect Virology 2001;283 (2):294-305 [PubMed]
  • Berkhout B., Das A. T., Beerens N. HIV-1 RNA editing, hypermutation, and error-prone reverse transcription Science 2001;292 (5514):7 [PubMed]
  • Beerens N., Groot F., Berkhout B. Initiation of HIV-1 reverse transcription is regulated by a primer activation signal Journal of biological chemistry 2001;276 (33):31247-31256 [PubMed]
  • Marzio G., Verhoef K., Vink M., Berkhout B. In vitro evolution of a highly replicating, doxycycline-dependent HIV for applications in vaccine studies Proceedings of the National Academy of Sciences of the United States of America 2001;98 (11):6342-6347 [PubMed]
  • Huthoff H., Berkhout B. Mutations in the TAR hairpin affect the equilibrium between alternative conformations of the HIV-1 leader RNA Nucleic acids research 2001;29 (12):2594-2600 [PubMed]
  • Verhoef K., Bilodeau P. S., van Wamel J. L., Kjems J., Stoltzfus C. M., Berkhout B. Repair of a Rev-minus human immunodeficiency virus type 1 mutant by activation of a cryptic splice site Journal of virology 2001;75 (7):3495-3500 [PubMed]
  • Verhoef K., Marzio G., Hillen W., Bujard H., Berkhout B. Strict control of human immunodeficiency virus type 1 replication by a genetic switch: Tet for Tat Journal of virology 2001;75 (2):979-987 [PubMed]
  • Berkhout B., Vastenhouw N. L., Klasens B. I., Huthoff H. Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription RNA (New York, N.Y.) 2001;7 (8):1097-1114 [PubMed]
  • Dirac A. M., Huthoff H., Kjems J., Berkhout B. The dimer initiation site hairpin mediates dimerization of the human immunodeficiency virus, type 2 RNA genome Journal of biological chemistry 2001;276 (34):32345-32352 [PubMed]
  • Gómez-Gonzalo M., Carretero M., Rullas J., Lara-Pezzi E., Aramburu J., Berkhout B., Alcamí J., López-Cabrera M. The hepatitis B virus X protein induces HIV-1 replication and transcription in synergy with T-cell activation signals: functional roles of NF-kappaB/NF-AT and SP1-binding sites in the HIV-1 long terminal repeat promoter Journal of biological chemistry 2001;276 (38):35435-35443 [PubMed]
  • Huthoff H., Berkhout B. Two alternating structures of the HIV-1 leader RNA RNA (New York, N.Y.) 2001;7 (1):143-157 [PubMed]

2000

  • A structured RNA motif is involved in correct placement of the tRNA(3)(Lys) primer onto the human immunodeficiency virus genome Journal of virology 2000;74 (5):2227-2238 [PubMed]
  • Functional differences between the long terminal repeat transcriptional promoters of human immunodeficiency virus type 1 subtypes A through G Journal of virology 2000;74 (8):3740-3751 [PubMed]
  • Identification of specific molecular structures of human immunodeficiency virus type 1 Tat relevant for its biological effects on vascular endothelial cells Journal of virology 2000;74 (1):344-353 [PubMed]
  • In vitro studies on tRNA annealing and reverse transcription with mutant HIV-1 RNA templates Journal of biological chemistry 2000;275 (20):15474-15481 [PubMed]
  • Stabilization of the U5-leader stem in the HIV-1 RNA genome affects initiation and elongation of reverse transcription Nucleic acids research 2000;28 (21):4130-4137 [PubMed]
  • Subtype-specific sequence variation of the HIV type 1 long terminal repeat and primer-binding site AIDS research and human retroviruses 2000;16 (5):499-504 [PubMed]
  • The leader of the HIV-1 RNA genome forms a compactly folded tertiary structure RNA (New York, N.Y.) 2000;6 (2):282-295 [PubMed]

1999

  • A hairpin structure in the R region of the human immunodeficiency virus type 1 RNA genome is instrumental in polyadenylation site selection Journal of virology 1999;73 (1):81-91 [PubMed]
  • A second-site mutation that restores replication of a Tat-defective human immunodeficiency virus Journal of virology 1999;73 (4):2781-2789 [PubMed]
  • Biased nucleotide composition of the genome of HERV-K related endogenous retroviruses and its evolutionary implications Journal of molecular evolution 1999;48 (1):102-111 [PubMed]
  • Evolution of the human immunodeficiency virus type 1 long terminal repeat promoter by conversion of an NF-kappaB enhancer element into a GABP binding site Journal of virology 1999;73 (2):1331-1340 [PubMed]
  • Genetic instability of live, attenuated human immunodeficiency virus type 1 vaccine strains Journal of virology 1999;73 (2):1138-1145 [PubMed]
  • HIV-1 evolution under pressure of protease inhibitors: climbing the stairs of viral fitness Journal of biomedical science 1999;6 (5):298-305 [PubMed]
  • HIV-1 evolves into a nonsyncytium-inducing virus upon prolonged culture in vitro Virology 1999;263 (1):55-69 [PubMed]
  • Identification of an active reverse transcriptase enzyme encoded by a human endogenous HERV-K retrovirus Journal of virology 1999;73 (3):2365-2375 [PubMed]
  • Increased polymerase fidelity of lamivudine-resistant HIV-1 variants does not limit their evolutionary potential AIDS (London, England) 1999;13 (11):1343-1349 [PubMed]
  • Proposed alternatives for the use of anti-HIV drugs Drug resistance updates 1999;2 (1):69-70 [PubMed]
  • The ability of the HIV-1 AAUAAA signal to bind polyadenylation factors is controlled by local RNA structure Nucleic acids research 1999;27 (2):446-454 [PubMed]
  • The effect of template RNA structure on elongation by HIV-1 reverse transcriptase BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION 1999;1444 (3):355-370 [PubMed]
  • The fidelity of reverse transcription differs in reactions primed with RNA versus DNA primers Journal of biomedical science 1999;6 (2):121-132 [PubMed]

1998

  • Evolutionary relationships within a subgroup of HERV-K-related human endogenous retroviruses Journal of general virology 1998;79 ( Pt 1):61-70 [PubMed]
  • Identification of novel human endogenous retroviral sequences belonging to the HERV-K family AIDS research and human retroviruses 1998;14 (12):1093-1098 [PubMed]
  • Improved envelope function selected by long-term cultivation of a translation-impaired HIV-1 mutant Virology 1998;244 (2):552-562 [PubMed]
  • Inhibition of polyadenylation by stable RNA secondary structure Nucleic acids research 1998;26 (8):1870-1876 [PubMed]
  • On the role of the second coding exon of the HIV-1 Tat protein in virus replication and MHC class I downregulation AIDS research and human retroviruses 1998;14 (17):1553-1559 [PubMed]
  • Similarity of chemokines charge and the V3 domain of HIV-1 env protein Emerging infectious diseases 1998;4 (2):335-336 [PubMed]
  • The 5' and 3' TAR elements of human immunodeficiency virus exert effects at several points in the virus life cycle Journal of virology 1998;72 (11):9217-9223 [PubMed]
  • The first strand transfer during HIV-1 reverse transcription can occur either intramolecularly or intermolecularly Virology 1998;244 (2):245-251 [PubMed]
  • The mechanism of actinomycin D-mediated inhibition of HIV-1 reverse transcription Nucleic acids research 1998;26 (23):5472-5479 [PubMed]
  • The native structure of the human immunodeficiency virus type 1 RNA genome is required for the first strand transfer of reverse transcription Virology 1998;249 (2):211-218 [PubMed]

1997

  • A conserved hairpin motif in the R-U5 region of the human immunodeficiency virus type 1 RNA genome is essential for replication Journal of virology 1997;71 (3):2346-2356 [PubMed]
  • Determination of the minimal amount of Tat activity required for human immunodeficiency virus type 1 replication Virology 1997;237 (2):228-236 [PubMed]
  • Forced evolution of a regulatory RNA helix in the HIV-1 genome Nucleic acids research 1997;25 (5):940-947 [PubMed]
  • Increased polymerase fidelity of the 3TC-resistant variants of HIV-1 reverse transcriptase Nucleic acids research 1997;25 (16):3212-3217 [PubMed]
  • Initial appearance of the 184Ile variant in lamivudine-treated patients is caused by the mutational bias of human immunodeficiency virus type 1 reverse transcriptase Journal of virology 1997;71 (4):3346-3350 [PubMed]
  • Limiting deoxynucleoside triphosphate concentrations emphasize the processivity defect of lamivudine-resistant variants of human immunodeficiency virus type 1 reverse transcriptase Antimicrobial agents and chemotherapy 1997;41 (11):2484-2491 [PubMed]
  • Optimal Tat-mediated activation of the HIV-1 LTR promoter requires a full-length TAR RNA hairpin Nucleic acids research 1997;25 (3):496-502 [PubMed]
  • Reverse transcriptase fidelity and HIV-1 variation Science 1997;275 (5297):229; author reply 230-229; author reply 231 [PubMed]
  • Sequence variation of the human immunodeficiency virus primer-binding site suggests the use of an alternative tRNA(Lys) molecule in reverse transcription Journal of general virology 1997;78 (4):837-840 [PubMed]
  • Structural and functional analysis of negatively charged milk proteins with anti-HIV activity AIDS research and human retroviruses 1997;13 (13):1101-1107 [PubMed]
  • The primer binding site on the RNA genome of human and simian immunodeficiency viruses is flanked by an upstream hairpin structure Nucleic acids research 1997;25 (20):4013-4017 [PubMed]

1996

  • Accurate scanning of the BssHII endonuclease in search for its DNA cleavage site Journal of biological chemistry 1996;271 (4):1837-1840 [PubMed]
  • HIV-1 reverse transcriptase discriminates against non-self tRNA primers Journal of molecular biology 1996;264 (2):243-254 [PubMed]
  • Identification of a novel splice acceptor in the HIV-1 genome: independent expression of the cytoplasmic tail of the envelope protein Archives of virology 1996;141 (5):839-855 [PubMed]
  • Nucleotide substitution patterns can predict the requirements for drug-resistance of HIV-1 proteins Antiviral research 1996;31 (1-2):45-57 [PubMed]
  • Paracrine activation of the HIV-1 LTR promoter by the viral Tat protein is mechanistically similar to trans-activation within a cell Virology 1996;225 (2):316-327 [PubMed]
  • Reduced replication of 3TC-resistant HIV-1 variants in primary cells due to a processivity defect of the reverse transcriptase enzyme EMBO journal 1996;15 (15):4040-4049 [PubMed]
  • Role of the DIS hairpin in replication of human immunodeficiency virus type 1 Journal of virology 1996;70 (10):6723-6732 [PubMed]
  • Structure and function of the human immunodeficiency virus leader RNA Progress in nucleic acid research and molecular biology 1996;54:1-34 [PubMed]

1995

  • A conserved hairpin structure predicted for the poly(A) signal of human and simian immunodeficiency viruses Virology 1995;207 (1):276-281 [PubMed]
  • Efficient extension of a misaligned tRNA-primer during replication of the HIV-1 retrovirus Nucleic acids research 1995;23 (8):1319-1326 [PubMed]
  • Inhibition of human immunodeficiency virus expression by sense transcripts encoding the retroviral leader RNA Antiviral research 1995;26 (2):101-115 [PubMed]
  • Reduced replication of human immunodeficiency virus type 1 mutants that use reverse transcription primers other than the natural tRNA(3Lys) Journal of virology 1995;69 (5):3090-3097 [PubMed]
  • Requirements for DNA strand transfer during reverse transcription in mutant HIV-1 virions Journal of molecular biology 1995;252 (1):59-69 [PubMed]
  • Revertants and pseudo-revertants of human immunodeficiency virus type 1 viruses mutated in the long terminal repeat promoter region Journal of general virology 1995;76 (4):845-853 [PubMed]
  • Structural requirements for the binding of tRNA Lys3 to reverse transcriptase of the human immunodeficiency virus type 1 Journal of biological chemistry 1995;270 (40):23867-23874 [PubMed]
  • The tendency of lentiviral open reading frames to become A-rich: constraints imposed by viral genome organization and cellular tRNA availability Journal of molecular evolution 1995;41 (2):132-140 [PubMed]
  • Variable expression of class 1 outer membrane protein in Neisseria meningitidis is caused by variation in the spacing between the -10 and -35 regions of the promoter Journal of bacteriology 1995;177 (9):2475-2480 [PubMed]

1994

  • A sensitive promoter assay based on the transcriptional activator Tat of the HIV-1 virus Gene 1994;144 (2):243-247 [PubMed]
  • Comparison of 5' and 3' long terminal repeat promoter function in human immunodeficiency virus Journal of virology 1994;68 (6):3830-3840 [PubMed]
  • Evolution of a disrupted TAR RNA hairpin structure in the HIV-1 virus EMBO journal 1994;13 (11):2650-2659 [PubMed]
  • Human immunodeficiency virus uses tRNA(Lys,3) as primer for reverse transcription in HeLa-CD4+ cells FEBS letters 1994;341 (1):49-53 [PubMed]
  • Intracellular analysis of in vitro modified HIV Tat protein Journal of biological chemistry 1994;269 (11):8366-8375 [PubMed]
  • Premature strand transfer by the HIV-1 reverse transcriptase during strong-stop DNA synthesis Nucleic acids research 1994;22 (2):137-144 [PubMed]
  • The restriction enzyme BanI is inhibited by dcm-methylation of the GGCGCm5C site Nucleic acids research 1994;22 (1):108 [PubMed]
  • The unusual nucleotide content of the HIV RNA genome results in a biased amino acid composition of HIV proteins Nucleic acids research 1994;22 (9):1705-1711 [PubMed]

1993

  • Effects of integration and replication on transcription of the HIV-1 long terminal repeat Journal of biological chemistry 1993;268 (33):24940-24949 [PubMed]
  • Electroporation of the HIV Tat trans-activator protein into cells Analytical biochemistry 1993;210 (1):210-214 [PubMed]
  • In vitro dimerization of HIV-2 leader RNA in the absence of PuGGAPuA motifs FASEB journal 1993;7 (1):181-187 [PubMed]
  • In vivo selection of randomly mutated retroviral genomes Nucleic acids research 1993;21 (22):5020-5024 [PubMed]
  • Secondary structure of the HIV-2 leader RNA comprising the tRNA-primer binding site Nucleic acids research 1993;21 (5):1171-1178 [PubMed]

1992

  • Functional roles for the TATA promoter and enhancers in basal and Tat-induced expression of the human immunodeficiency virus type 1 long terminal repeat Journal of virology 1992;66 (1):139-149 [PubMed]
  • Kinetics of HIV-1 long terminal repeat trans-activation. Use of intragenic ribozyme to assess rate-limiting steps Journal of biological chemistry 1992;267 (25):17891-17899 [PubMed]
  • Natural variants of the HIV-1 long terminal repeat: analysis of promoters with duplicated DNA regulatory motifs Virology 1992;191 (2):968-972 [PubMed]
  • Structural features in TAR RNA of human and simian immunodeficiency viruses: a phylogenetic analysis Nucleic acids research 1992;20 (1):27-31 [PubMed]

1991

  • Characterization of a human TAR RNA-binding protein that activates the HIV-1 LTR Science 1991;251 (5001):1597-1600 [PubMed]
  • Detailed mutational analysis of TAR RNA: critical spacing between the bulge and loop recognition domains Nucleic acids research 1991;19 (22):6169-6176 [PubMed]
  • Requirements for cell surface expression of the human TCR/CD3 complex in non-T cells International immunology 1991;3 (4):359-368 [PubMed]

1990

  • Direct evidence for translational regulation by leader RNA and Tat protein of human immunodeficiency virus type 1 Proceedings of the National Academy of Sciences of the United States of America 1990;87 (19):7492-7496 [PubMed]
  • Down modulation of HIV-1 gene expression using a procaryotic RNA-binding protein Nucleic acids research 1990;18 (23):6903-6907 [PubMed]
  • Efficient trans-activation by the HIV-2 Tat protein requires a duplicated TAR RNA structure Nucleic acids research 1990;18 (7):1839-1846 [PubMed]
  • TAR-independent activation of the HIV-1 LTR: evidence that tat requires specific regions of the promoter Cell 1990;62 (4):757-767 [PubMed]

1989

  • Tat trans-activates the human immunodeficiency virus through a nascent RNA target Cell 1989;59 (2):273-282 [PubMed]
  • trans activation of human immunodeficiency virus type 1 is sequence specific for both the single-stranded bulge and loop of the trans-acting-responsive hairpin: a quantitative analysis Journal of virology 1989;63 (12):5501-5504 [PubMed]

1988

  • Assembly of the human T cell receptor-CD3 complex takes place in the endoplasmic reticulum and involves intermediary complexes between the CD3-gamma.delta.epsilon core and single T cell receptor alpha or beta chains Journal of biological chemistry 1988;263 (6):2953-2961 [PubMed]
  • Complete cDNA sequence coding for the human T cell receptor alpha chain HPB-ALL Nucleic acids research 1988;16 (11):5209 [PubMed]
  • Transfection of genes encoding the T cell receptor-associated CD3 complex into COS cells results in assembly of the macromolecular structure Journal of biological chemistry 1988;263 (17):8528-8536 [PubMed]

1987

  • Determination of the RNA secondary structure that regulates lysis gene expression in bacteriophage MS2 Journal of molecular biology 1987;195 (3):505-516 [PubMed]
  • Lysis gene of bacteriophage MS2 is activated by translation termination at the overlapping coat gene Journal of molecular biology 1987;195 (3):517-524 [PubMed]

1986

  • Formylmethionyl-tRNA binding to 30 S ribosomes programmed with homopolynucleotides and the effect of translational initiation factor 3 BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION 1986;866 (2-3):144-153 [PubMed]

1985

  • Mechanism of translational coupling between coat protein and replicase genes of RNA bacteriophage MS2 Nucleic acids research 1985;13 (19):6955-6967 [PubMed]
  • The amino terminal half of the MS2-coded lysis protein is dispensable for function: implications for our understanding of coding region overlaps EMBO journal 1985;4 (12):3315-3320 [PubMed]
  • Translational interference at overlapping reading frames in prokaryotic messenger RNA Gene 1985;37 (1-3):171-179 [PubMed]

1983

  • Effect of the sequences upstream from the ribosome-binding site on the yield of protein from the cloned gene for phage MS2 coat protein Gene 1983;23 (3):245-254 [PubMed]
  • Opening the closed ribosome-binding site of the lysis cistron of bacteriophage MS2 Nature 1983;305 (5936):741-743 [PubMed]

1980

  • The role of the codon and the initiation factor IF-2 in the selection of N-blocked aminoacyl-tRNA for initiation European Journal of Biochemistry / FEBS 1980;104 (1):19-33 [PubMed]