• Principal Investigator
  • Male

Prof. dr. A.H.C. van Kampen

Position: Professor
Main activities: Research, Teaching
Specialisation: Medical Bioinformatics
foto A.H.C. van Kampen is one of the AMC Principal Investigators
Focus of research:
  • Bioinformatics methods for analysis of omics data
  • Use and integration of public biological database
  • Systems Medicine / Systems Genomics
AMC themes: Infection & Immunity, Public Health & Epidemiology
Departments: Clinical Epidemiology, Biostatistics and Bioinformatics
Doorenspleet ME , Westera L, Peters CP, Hakvoort TBM, Esveldt RE, Vogels E, van Kampen AHC, Baas F, Buskens C, Bemelman WA, D'Haens G, Ponsioen CY, te Velde AA, de Vries N, van den Brink GR, Profoundly Expanded T-cell Clones in the Inflamed and Uninflamed Intestine of Patients With Crohn's Disease. J CROHNS COLITIS 2017;11 (7):831-839 [PubMed]
Gao AW, Chatzispyrou IA, Kamble R, Liu YJ, Herzog K, Smith RL, van Lenthe H, Vervaart MAT, van Cruchten A, Luyf AC, van Kampen A, Pras-Raves ML, Vaz FM, Houtkooper RH, A sensitive mass spectrometry platform identifies metabolic changes of life history traits in C-elegans. SCI REP-UK 2017;7 (1):2408 [PubMed]
Herzog K, Pras-Raves ML, Ferdinandusse S, Vervaart MAT, Luyf ACM, van Kampen AHC, Wanders RJA, Waterham HR, Vaz FM, Functional characterisation of peroxisomal β-oxidation disorders in fibroblasts using lipidomics. J INHERIT METAB DIS 2017;ahead of print [PubMed]
Klaassen I, de Vries EW, Vogels IMC, van Kampen AHC, Bosscha MI, Steel DHW, van Noorden CJF, Lesnik-Oberstein SY, Schlingemann RO, Identification of proteins associated with clinical and pathological features of proliferative diabetic retinopathy in vitreous and fibrovascular membranes. PLOS ONE 2017;12 (11):e0187304 [PubMed]
Reshetova P. Use of prior knowledge in biological systems modelling. S.l.: s.n.; 2017. 129p. [UvA Dissertations Online] Proefschrift Universiteit van Amsterdam, onderzoek bij Faculty of Science (FNWI), -. (Promotor(s): van Kampen AHC, Smilde AK; copromotor(s): Westerhuis JA)
Reshetova P, van Schaik BDC, Klarenbeek PL, Doorenspleet ME, Esveldt REE, Tak PP, Guikema JEJ, de Vries N, van Kampen AHC, Computational Model Reveals Limited Correlation between Germinal Center B-Cell Subclone Abundancy and Affinity: Implications for Repertoire Sequencing. FRONT IMMUNOL 2017;8:221 [PubMed]
Smith RL, Tan JME, Jonker MJ, Jongejan A, Buissink T, Veldhuijzen S, van Kampen AHC, Brul S, van der Spek H, Beyond the polymerase-γ theory: Production of ROS as a mode of NRTI-induced mitochondrial toxicity. PLOS ONE 2017;12 (11):e0187424 [PubMed]
Tak PP, Doorenspleet ME, de Hair MJH, Klarenbeek PL, van Beers-Tas MH, van Kampen AHC, van Schaardenburg D, Gerlag DM, Baas F, de Vries N, Dominant B cell receptor clones in peripheral blood predict onset of arthritis in individuals at risk for rheumatoid arthritis. ANN RHEUM DIS 2017;76 (11):1924-1930 [PubMed]
van Groningen T , Koster J, Valentijn LJ, Zwijnenburg DA, Akogul N , Hasselt NE, Broekmans M, Haneveld F, Nowakowska NE, Bras J, van Noesel CJM, Jongejan A, van Kampen AH, Koster L, Baas F, van Dijk-Kerkhoven L, Huizer-Smit M, Lecca MC, Chan A, Lakeman A, Molenaar P, Volckmann R, Westerhout EM, Hamdi M, van Sluis PG, Ebus ME, Molenaar JJ, Tytgat GA, Westerman BA, van Nes J, Versteeg R, Neuroblastoma is composed of two super-enhancer-associated differentiation states. NAT GENET 2017;49 (8):1261-1266 [PubMed]
Weijer R, Clavier S, Zaal EA, Pijls MME, van Kooten RT, Vermaas K, Leen R, Jongejan A, Moerland PD, van Kampen AHC, van Kuilenburg ABP, Berkers CR, Lemeer S, Heger M, Multi-OMIC profiling of survival and metabolic signaling networks in cells subjected to photodynamic therapy. CELL MOL LIFE SCI 2017;74 (6):1133-1151 [PubMed]
Zhao J, Hakvoort TBM, Jongejan A, Ruijter JM, van Kampen AHC, Lamers WH, Unexpected regulation of miRNA abundance during adaptation of early-somite mouse embryos to diabetic pregnancy. BIOCHEM BIOPH RES CO 2017;482 (4):1013-1018 [PubMed]
Harwig A, Jongejan A, van Kampen AHC, Berkhout B, Das AT, Tat-dependent production of an HIV-1 TAR-encoded miRNA-like small RNA. NUCLEIC ACIDS RES 2016;44 (9):4340-4353 [PubMed]
Herzog K, Pras-Raves ML, Vervaart MAT, Luyf ACM, van Kampen AHC, Wanders RJA, Waterham HR, Vaz FM, Lipidomic analysis of fibroblasts from Zellweger spectrum disorder patients identifies disease-specific phospholipid ratios. J LIPID RES 2016;57 (8):1447-1454 [PubMed]
Lu YW, Galbraith L, Herndon JD, Lu YL, Pras-Raves M, Vervaart M, van Kampen A, Luyf A, Koehler CM, McCaffery JM, Gottlieb E, Vaz FM, Claypool SM, Defining functional classes of Barth syndrome mutation in humans. HUM MOL GENET 2016;25 (9):1754-1770 [PubMed]
Nandal UK, van Kampen AHC, Moerland PD, compendiumdb: an R package for retrieval and storage of functional genomics data. BIOINFORMATICS 2016;32 (18):2856-2857 [PubMed]
Potze L, Di Franco S, Grandela C, Pras-Raves ML, Picavet DI, van Veen HA, van Lenthe H, Mullauer FB, van der Wel NN, Luyf A, van Kampen AHC, Kemp S, Everts V, Kessler JH, Vaz FM, Medema JP, Betulinic acid induces a novel cell death pathway that depends on cardiolipin modification. ONCOGENE 2016;35 (4):427-437 [PubMed]
Raemy E, Montessuit S, Pierredon S, van Kampen AH, Vaz FM, Martinou JC, Cardiolipin or MTCH2 can serve as tBID receptors during apoptosis. CELL DEATH DIFFER 2016;23 (7):1165-1174 [PubMed]
Slot LM, Hoogeboom R, Smit LA, Wormhoudt TAM, Biemond BJ, Oud MECM, Schilder-Tol EJM, Mulder AB, Jongejan A, van Kampen AHC, Kluin PM, Guikema JEJ, Bende RJ, van Noesel CJM, B-Lymphoblastic Lymphomas Evolving from Follicular Lymphomas Co-Express Surrogate Light Chains and Mutated Gamma Heavy Chains. AM J PATHOL 2016;186 (12):3273-3284 [PubMed]
te Velde AA, Bezema T, van Kampen AHC, Kraneveld AD, 't Hart BA, van Middendorp H, Hack EC, van Montfrans JM, Belzer C, Jans-Beken L, Pieters RH, Knipping K, Huber M, Boots AMH, Garssen J, Radstake TR, Evers AWM, Prakken BJ, Joosten I, Embracing Complexity beyond Systems Medicine: A New Approach to Chronic Immune Disorders. FRONT IMMUNOL 2016;7:587 [PubMed]
van Kampen AHC, Moerland PD, Taking Bioinformatics to Systems Medicine. METHODS MOL BIOL 2016;1386:17-41 [PubMed]
Zhao J, Hakvoort TBM, Willemsen AM, Jongejan A, Sokolovic M, Bradley EJ, de Boer VCJ, Baas F, van Kampen AHC, Lamers WH, Effect of Hyperglycemia on Gene Expression during Early Organogenesis in Mice. PLOS ONE 2016;11 (7):e0158035 [PubMed]
Canuti M, van Beveren NJM, Jazaeri Farsani SM, de Vries M, Deijs M, Jebbink MF, Zaaijer HL, van Schaik BDC, van Kampen AHC, van der Kuyl AC, de Haan L, Storosum JG, van der Hoek L, Viral metagenomics in drug-naïve, first-onset schizophrenia patients with prominent negative symptoms. PSYCHIAT RES 2015;229 (3):678-684 [PubMed]
Harwig A, Herrera-Carrillo E, Jongejan A, van Kampen AH, Berkhout B, Deep Sequence Analysis of AgoshRNA Processing Reveals 3' A Addition and Trimming. MOL THER-NUCL ACIDS 2015;4:e247 [PubMed]
Klarenbeek PL, Doorenspleet ME, Esveldt REE, van Schaik BDC, Lardy N, van Kampen AHC, Tak PP, Plenge RM, Baas F, de Bakker PIW, de Vries N, Somatic Variation of T-Cell Receptor Genes Strongly Associate with HLA Class Restriction. PLOS ONE 2015;10 (10):e0140815 [PubMed]
Liu YP, Karg M, Harwig A, Herrera-Carrillo E, Jongejan A, van Kampen A, Berkhout B, Mechanistic insights on the Dicer-independent AGO2-mediated processing of AgoshRNAs. RNA BIOL 2015;12 (1):92-100 [PubMed]
Nandal UK, Vlietstra WJ, Byrman C, Jeeninga RE, Ringrose JH, van Kampen AHC, Speijer D, Moerland PD, Candidate prioritization for low-abundant differentially expressed proteins in 2D-DIGE datasets. BMC BIOINFORMATICS 2015;16 (1):25 [PubMed]
Remmerswaal EBM, Klarenbeek PL, Alves NL, Doorenspleet ME, van Schaik BDC, Esveldt REE, Idu MM, van Leeuwen EMM, van der Bom-Baylon N, van Kampen AHC, Koch SD, Pircher H, Bemelman FJ, ten Brinke A, Baas F, ten Berge IJM, van Lier RAW, de Vries N, Clonal evolution of CD8+ T cell responses against latent viruses: relationship among phenotype, localization, and function. J VIROL 2015;89 (1):568-580 [PubMed]
Reshetova P, Smilde AK, Westerhuis JA, van Kampen AHC, Using Petri nets for experimental design in a multi-organ elimination pathway. COMPUT BIOL MED 2015;63:19-27 [PubMed]
Shahand S. Science gateways for biomedical big data analysis. S.l.: s.n.; 2015. 178p. ISBN 978-94-6182-606-0 [UvA Dissertations Online] Proefschrift Universiteit van Amsterdam. (Promotor(s): van Kampen AHC; copromotor(s): Olabarriaga SD)
Shahand S, Benabdelkader A, Jaghoori MM, al Mourabit M, Huguet J, Caan MWA, van Kampen AHC, Olabarriaga SD, A data-centric neuroscience gateway: design, implementation, and experiences. CONCURR COMP-PRACT E 2015;27 (2):489-506
Shahand S, van Kampen AHC, Olabarriaga SD. Science Gateway Canvas: A business reference model for Science Gateways in: Jha S, Katz DS, Weissman J, editors. SCREAM '15 Proceedings of the 1st Workshop on The Science of Cyberinfrastructure: Research, Experience, Applications and Models. New York: ACM; 2015., p. 45-52
Vaz FM, Pras-Raves M, Bootsma AH, van Kampen AHC, Principles and practice of lipidomics. J INHERIT METAB DIS 2015;38 (1):41-52 [PubMed]
Weijer R, Broekgaarden M, van Golen RF, Bulle E, Nieuwenhuis E, Jongejan A, Moerland PD, van Kampen AHC, van Gulik TM, Heger M, Low-power photodynamic therapy induces survival signaling in perihilar cholangiocarcinoma cells. BMC CANCER 2015;15 (1):1014 [PubMed]
Willemsen AM, Hendrickx DM, Hoefsloot HCJ, Hendriks MMWB, Wahl SA, Teusink B, Smilde AK, van Kampen AHC, MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis. MOL BIOSYST 2015;11 (1):137-145 [PubMed]
Backer RA, Helbig C, Gentek R, Kent A, Laidlaw BJ, Dominguez CX, de Souza YS, van Trierum SE, van Beek R, Rimmelzwaan GF, ten Brinke A, Willemsen AM, van Kampen AHC, Kaech SM, Blander JM, van Gisbergen K, Amsen D, A central role for Notch in effector CD8(+) T cell differentiation. NAT IMMUNOL 2014;15 (12):1143-1151 [PubMed]
Cobos Jiménez V, Bradley EJ, Willemsen AM, van Kampen AHC, Baas F, Kootstra NA, Next-generation sequencing of microRNAs uncovers expression signatures in polarized macrophages. PHYSIOL GENOMICS 2014;46 (3):91-103 [PubMed]
Cobos Jiménez V, Willemsen AM, Bradley EJ, Baas F, van Kampen AHC, Kootstra NA, Next-generation sequencing of microRNAs in primary human polarized macrophages. GENOM DATA 2014;2:181-183 [PubMed]
Cordeddu V, Redeker B, Stellacci E, Jongejan A, Fragale A, Bradley TEJ, Anselmi M, Ciolfi A, Cecchetti S, Muto V, Bernardini L, Azage M, Carvalho DR, Espay AJ, Male A, Molin AM, Posmyk R, Battisti C, Casertano A, Melis D, van Kampen A, Baas F, Mannens MM, Bocchinfuso G, Stella L, Tartaglia M, Hennekam RC, Mutations in ZBTB20 cause Primrose syndrome. NAT GENET 2014;46 (8):815-817 [PubMed]
Doorenspleet ME , Klarenbeek PL, de Hair MJH, van Schaik BDC, Esveldt REE, van Kampen AHC, Gerlag DM, Musters A, Baas F, Tak PP, de Vries N, Rheumatoid arthritis synovial tissue harbours dominant B-cell and plasma-cell clones associated with autoreactivity. ANN RHEUM DIS 2014;73 (4):756-762 [PubMed]
Houten SM, Denis S, te Brinke H, Jongejan A, van Kampen AHC, Bradley EJ, Baas F, Hennekam RCM, Millington DS, Young SP, Frazier DM, Gucsavas-Calikoglu M, Wanders RJA, Mitochondrial NADP(H) deficiency due to a mutation in NADK2 causes dienoyl-CoA reductase deficiency with hyperlysinemia. HUM MOL GENET 2014;23 (18):5009-5016 [PubMed]
Piet JR, Geldhoff M, van Schaik BDC, Brouwer MC, Valls Seron M , Jakobs ME, Schipper K, Pannekoek Y, Zwinderman AH, van der Poll T, van Kampen AHC, Baas F, van der Ende A, van de Beek D, Streptococcus pneumoniae arginine synthesis genes promote growth and virulence in pneumococcal meningitis. J INFECT DIS 2014;209 (11):1781-1791 [PubMed]
Reshetova P, Smilde AK, van Kampen AHC, Westerhuis JA, Use of prior knowledge for the analysis of high-throughput transcriptomics and metabolomics data. BMC SYST BIOL 2014;8 (Suppl. 2):S2 [PubMed]
Shahand S, Jaghoori MM, Benabdelkader A, Font-Calvo JL, Huguet J, Caan MWA, van Kampen AHC, Olabarriaga SD. Computational Neuroscience. Gateway: A science Gateway Based on the WS-PGRADE/gUSE in: Kacsuk P, editor. Science Gateways for Distributed Computing Infrastructures. Budapest: Springer; 2014., p. 139-149
Stobbe MD, Jansen GA, Moerland PD, van Kampen AHC, Knowledge representation in metabolic pathway databases. BRIEF BIOINFORM 2014;15 (3):455-470 [PubMed]
van Schaik B, Klarenbeek P, Doorenspleet M, van Kampen A, Moody DB, de Vries N, van Rhijn I, Discovery of invariant T cells by next-generation sequencing of the human TCR α-chain repertoire. J IMMUNOL 2014;193 (10):5338-5344 [PubMed]
Madougou S, Shahand S, Santcroos M, Schaik B van, Benabdelkader A, Kampen A , Olabarriaga S, Characterizing workflow-based activity on a production e-infrastructure using provenance data. FUTURE GENER COMP SY 2013;29 (8):1931-1942
Olabarriaga SD, Jaghoori MM, Korkhov V, van Schaik B, van Kampen A. Understanding workflows for distributed computing: nitty-gritty details in: Montagnat J, Taylor I, editors. WORKS '13 : Proceedings of the 8th Workshop on Workflows in Support of Large-Scale Science. New York: ACM; 2013., p. 68-76
Shahand S, Benabdelkader A, Huguet J, Jaghouri M , Santcroos M, al Mourabit M, Groot PFC, Caan MWA, van Kampen AHC, Olabarriaga SD. A Data-Centric Science Gateway for Computational Neuroscience in: Kiss T, editors. IWSG 2013 : International Workshop on Science Gateways : Proceedings of the 5th International Workshop on Science Gateways : Zurich, Switzerland, 3-5 June, 2013. Clermont‐Ferrand: CEUR-WS.org; 2013., p. 12
Stobbe MD, Swertz MA, Thiele I, Rengaw T, van Kampen AHC, Moerland PD, Consensus and conflict cards for metabolic pathway databases. BMC SYST BIOL 2013;7 (1):50 [PubMed]
Caan MWA, Shahand S, Vos FM, van Kampen AHC, Olabarriaga SD, Evolution of grid-based services for Diffusion Tensor Image analysis. FUTURE GENER COMP SY 2012;28 (8):1194-1204
de Vries M, Oude Munnink BB, Deijs M, Canuti M, Koekkoek SM, Molenkamp R, Bakker M, Jurriaans S, van Schaik BDC, Luyf AC, Olabarriaga SD, van Kampen AHC, van der Hoek L, Performance of VIDISCA-454 in Feces-Suspensions and Serum. VIRUSES-BASEL 2012;4 (8):1328-1334 [PubMed]
Klarenbeek PL, de Hair MJH, Doorenspleet ME , van Schaik BDC, Esveldt REE, van de Sande MGH, Cantaert T, Gerlag DM, Baeten D, van Kampen AHC, Baas F, Tak PP, de Vries N, Inflamed target tissue provides a specific niche for highly expanded T-cell clones in early human autoimmune disease. ANN RHEUM DIS 2012;71 (6):1088-1093 [PubMed]
Klarenbeek PL, Remmerswaal EBM, ten Berge IJM, Doorenspleet ME , van Schaik BDC, Esveldt REE, Koch SD, ten Brinke A, van Kampen AHC, Bemelman FJ, Tak PP, Baas F, de Vries N, van Lier RAW, Deep sequencing of antiviral T-cell responses to HCMV and EBV in humans reveals a stable repertoire that is maintained for many years. PLOS PATHOG 2012;8 (9):e1002889 [PubMed]
Madougou S, Santcroos M, Benabdelkader A, van Schaik BDC, Shahand S, Korkhov V, van Kampen AHC, Olabarriaga SD, Provenance for distributed biomedical workflow execution. STUD HEALTH TECHNOL INFORM 2012;175:91-100 [PubMed]
Marquering H, Engelberts J, Groot P, Majoie C, Beenen L , van Kampen A, Olabarriaga SD. Optimization and Parallelization of the Matched Masked Bone Elimination Method for CTA in: Montagnat J, editor. Proceedings of the DCICTIA-MICCAI 2012 Workshop : Data- and Compute-Intensive Clinical and Translational Imaging Applications. S.l.: s.n.; 2012., p. 31-40
Mouw E, van't Noordende G, van Kampen AHC, Louter B, Santcroos M, Olabarriaga SD, Legal constraints on genetic data processing in European grids. STUD HEALTH TECHNOL INFORM 2012;175:49-58 [PubMed]
Schopman NCT, van Montfort T, Willemsen M, Knoepfel SA, Pollakis G, van Kampen A, Sanders RW, Haasnoot J, Berkhout B, Selective packaging of cellular miRNAs in HIV-1 particles. VIRUS RES 2012;169 (2):438-447 [PubMed]
Schopman NCT, Willemsen M, Liu YP, Bradley T, van Kampen A, Baas F, Berkhout B, Haasnoot J, Deep sequencing of virus-infected cells reveals HIV-encoded small RNAs. NUCLEIC ACIDS RES 2012;40 (1):414-427 [PubMed]
Shahand S, Caan MWA, van Kampen AHC, Olabarriaga SD, Integrated support for neuroscience research: from study design to publication. STUD HEALTH TECHNOL INFORM 2012;175:195-204 [PubMed]
Shahand S, Santcroos M, van Kampen AHC, Olabarriaga SD, A Grid-Enabled Gateway for Biomedical Data Analysis. J GRID COMPUT 2012;10 (4):725-742
Stobbe MD. The road to knowledge: from biology to databases and back again. s.l.: s.n.; 2012. 168p. [UvA Dissertations Online] Proefschrift Universiteit van Amsterdam. (Promotor(s): van Kampen AHC; copromotor(s): Moerland PD)
Stobbe MD, Houten SM, van Kampen AHC, Wanders RJA, Moerland PD, Improving the description of metabolic networks: the TCA cycle as example. FASEB J 2012;26 (9):3625-3636 [PubMed]
van Houdt JKJ, Nowakowska BA, Sousa SB, van Schaik BDC, Seuntjens E, Avonce N, Sifrim A, Abdul-Rahman OA, van den Boogaard MJH, Bottani A, Castori M, Cormier-Daire V, Deardorff MA, Filges I, Fryer A, Fryns JP, Gana S, Garavelli L, Gillessen-Kaesbach G, Hall BD, Horn D, Huylebroeck D, Klapecki J, Krajewska-Walasek M, Kuechler A, Lines MA, Maas S, Macdermot KD, McKee S, Magee A, de Man SA, Moreau Y, Morice-Picard F, Obersztyn E, Pilch J, Rosser E, Shannon N, Stolte-Dijkstra I, van Dijck P, Vilain C, Vogels A, Wakeling E, Wieczorek D, Wilson L, Zuffardi O, van Kampen AHC, Devriendt K, Hennekam R, Vermeesch JR, Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome. NAT GENET 2012;44 (4):445-U261 [PubMed]
van Schaik BDC, Santcroos M, Korkhov V, Jongejan A, Willemsen M, van Kampen AHC, Olabarriaga SD. Challenges in DNA sequence analysis on a production grid in: Anonymous A, editor. EGI Community Forum 2012 / EMI Second Technical Conference. S.l.: s.n.; 2012., p. 1-19
Benabdelkader A, Santcroos M, Madougou S, van Kampen AHC, Olabarriaga SD. A Provenance Approach to Trace Scientific Experiments on a Grid Infrastructure in: Kranzlmüller D, et al -, editors. eScienceW 2011 : The Seventh IEEE International Conference on e-Science Workshops : Stockholm, Sweden 5–8 December 2011. Los Alamitos: IEEE; 2011., p. 134-141
Hakvoort TBM, Moerland PD, Frijters R, Sokolovic A, Labruyere WT, Vermeulen JLM, Ver Loren van Themaat E, Breit TM, Wittink FRA, van Kampen AHC, Verhoeven AJ, Lamers WH, Sokolovic M, Interorgan Coordination of the Murine Adaptive Response to Fasting. J BIOL CHEM 2011;286 (18):16332-16343 [PubMed]
Huis In 't Veld RAG, Willemsen AM, van Kampen AHC, Bradley EJ, Baas F, Pannekoek Y, van der Ende A, Deep sequencing whole transcriptome exploration of the σE regulon in Neisseria meningitidis. PLOS ONE 2011;6 (12):e29002 [PubMed]
Mohammed Y, Shahand S, Korkhov V, Luyf ACM, van Schaik BDC, Caan MWA, van Kampen AHC, Palmblad M, Olabarriaga SD. Data Decomposition in Biomedical e-Science Applications in: Kranzlmüller D, et al -, editors. eScienceW 2011 : The Seventh IEEE International Conference on e-Science Workshops : Stockholm, Sweden 5–8 December 2011. Los Alamitos: IEEE; 2011., p. 158-165
Peeters A, Fraisl P, van den Berg S, Ver Loren van Themaat E, van Kampen A, Rider MH, Takemori H, van Dijk KW, van Veldhoven PP, Carmeliet P, Baes M, Carbohydrate metabolism is perturbed in peroxisome-deficient hepatocytes due to mitochondrial dysfunction, AMP-activated protein kinase (AMPK) activation, and peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) suppression. J BIOL CHEM 2011;286 (49):42162-42179 [PubMed]
Piet JR, Huis in 't Veld RAG, van Schaik BDC, van Kampen AHC, Baas F, van de Beek D, Pannekoek Y, van der Ende A, Genome sequence of Neisseria meningitidis serogroup B strain H44/76. J BACTERIOL 2011;193 (9):2371-2372 [PubMed]
Ritz K, van Schaik BDC, Jakobs ME, Aronica E, Tijssen MA, van Kampen AHC, Baas F, Looking ultra deep: short identical sequences and transcriptional slippage. GENOMICS 2011;98 (2):90-95 [PubMed]
Ritz K, van Schaik BD, Jakobs ME, van Kampen AH, Aronica E, Tijssen MA, Baas F, SGCE isoform characterization and expression in human brain: implications for myoclonus-dystonia pathogenesis?. EUR J HUM GENET 2011;19 (4):438-444 [PubMed]
Stobbe MD, Houten SM, Jansen GA, van Kampen AHC, Moerland PD, Critical assessment of human metabolic pathway databases: a stepping stone for future integration. BMC SYST BIOL 2011;5 (1):165 [PubMed]
Caan MWA, Vos FM, van Kampen AHC, Olabarriaga SD, van Vliet LJ. Gridifying a Diffusion Tensor Imaging Analysis Pipeline in: Parashar M, Buyyar R, editors. CCGrid 2010 : 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing : 17-20 May, Melbourne, Australia. Los Alamitos: IEEE Computer Society; 2010., p. 733-738
Gwadry-Sridhar F, Olabarriaga SD, van Kampen A, Bauer M, Solomonides T, Hitting the ground running: Healthgrid deployment and adoption. STUD HEALTH TECHNOL INFORM 2010;159:40-51 [PubMed]
Klarenbeek PL, Tak PP, van Schaik BDC, Zwinderman AH, Jakobs ME, Zhang Z, van Kampen AHC, van Lier RAW, Baas F, de Vries N, Human T-cell memory consists mainly of unexpanded clones. IMMUNOL LETT 2010;133 (1):42-48 [PubMed]
Luyf ACM, van Schaik BDC, de Vries M, Baas F, van Kampen AHC, Olabarriaga SD, Initial steps towards a production platform for DNA sequence analysis on the grid. BMC BIOINFORMATICS 2010;11 (1):598 [PubMed]
van Hooff SR, Koster J, Hulsen T, van Schaik BDC, Roos M, van Batenburg MF, Versteeg R, van Kampen AHC, The Construction of Genome-Based Transcriptional Units. OMICS 2009;13 (2):105-114 [PubMed]
Biewenga P, Buist MR, Moerland PD, van Thernaat EVL, van Kampen AHC, ten Kate FJW, Baas F, Gene expression in early stage cervical cancer. GYNECOL ONCOL 2008;108 (3):520-526 [PubMed]
Buimer M, Keijser R, Jebbink JM, Wehkamp D, van Kampen AHC, Boer K, van der Post JAM, Ris-Stalpers C, Seven placental transcripts characterize HELLP-syndrome. PLACENTA 2008;29 (5):444-453 [PubMed]
Inda MA, van Batenburg MF, Roos M, Belloum AS, Vasunin D, Wibisono A, van Kampen AHC, Breit TM, SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences. BMC RES NOTES 2008;1 (1):63 [PubMed]
Lagarde SM, Ver Loren van Themaat PE, Moerland PD, Gilhuijs-Pederson LA, ten Kate FJW, Reitsma PH, van Kampen AHC, Zwinderman AH, Baas F, van Lanschot JJB, Analysis of Gene Expression Identifies Differentially Expressed Genes and Pathways Associated with Lymphatic Dissemination in Patients with Adenocarcinoma of the Esophagus. ANN SURG ONCOL 2008;15 (12):3459-3470 [PubMed]
Martens K, Ver Loren van Themaat E, van Batenburg MF, Heinäniemi M, Huyghe S, van Hummelen P, Carlberg C, van Veldhoven PP, van Kampen A, Baes M, Coordinate induction of PPAR alpha and SREBP2 in multifunctional protein 2 deficient mice. BBA-MOL CELL BIOL L 2008;1781 (11-12):694-702 [PubMed]
Schaaf GJ, van Ruissen F, van Kampen A, Kool M, Ruijter JM, Statistical comparison of two or more SAGE libraries: one tag at a time. METHODS MOL BIOL 2008;387:151-168 [PubMed]
Sokolović M, Sokolović A, Wehkamp D, Ver Loren van Themaat E, de Waart DR, Gilhuijs-Pederson LA, Nikolsky Y, van Kampen AHC, Hakvoort TBM, Lamers WH, The transcriptomic signature of fasting murine liver. BMC GENOMICS 2008;9 (1):528 [PubMed]
Willemsen AM, Jansen GA, Komen JC, van Hooff S, Waterham HR, Brites PMT, Wanders RJA, van Kampen AHC, Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways. BIOINFORMATICS 2008;24 (16):i21-i27 [PubMed]
Nyangoma SO, van Kampen AAHC, Reijmers TH, Govorukhina NI, van der Zee AGJ, Billingham LJ, Bischoff R, Jansen RC, Multiple testing issues in discriminating compound-related peaks and chromatograms from high frequency noise, spikes and solvent-based noise in LC-MS data sets. STAT APPL GENET MOL 2007;6:23
Schaaf GJ, van Ruissen F, van Kampen A, Kool M, Ruijter JM, Statistical Comparison of Two or More SAGE Libraries: One Tag at the Time. METHODS MOL BIOL 2007;397:151-168
Sokolović M, Wehkamp D, Sokolović A, Vermeulen J, Gilhuijs-Pederson LA, van Haaften RIM, Nikolsky Y, Evelo CTA, van Kampen AHC, Hakvoort TBM, Lamers WH, Fasting induces a biphasic adaptive metabolic response in murine small intestine. BMC GENOMICS 2007;8 (1):361 [PubMed]
van Passel MWJ, Bart A, Luyf ACM, van Kampen AHC, van der Ende A, Compositional discordance between prokaryotic plasmids and host chromosomes. BMC GENOMICS 2006;7:26 [PubMed]
van Passel MWJ, Bart A, Luyf ACM, van Kampen AHC, van der Ende A, Identification of acquired DNA in Neisseria lactamica. FEMS MICROBIOL LETT 2006;262 (1):77-84 [PubMed]
Vos JB, Datson NA, van Kampen AH, Luyf AC, Verhoosel RM, Zeeuwen PL, Olthuis D, Rabe KF, Schalkwijk J, Hiemstra PS, A molecular signature of epithelial host defense: comparative gene expression analysis of cultured bronchial epithelial cells and keratinocytes. BMC GENOMICS 2006;7:9 [PubMed]
Zelinkova Z, Derijks LJJ, Stokkers PCF, Vogels EWM, van Kampen AHC, Curvers WL, Cohn D, van Deventer SJH, Hommes DW, Inosine triphosphate pyrophosphatase and thiopurine s-methyltransferase genotypes relationship to azathioprine-induced myelosuppression. CLIN GASTROENTEROL H 2006;4 (1):44-49 [PubMed]
Braat H, Stokkers P, Hommes T, Cohn D, Vogels E, Pronk I, Spek A, van Kampen A, van Deventer S, Peppelenbosch M, Hommes D, Consequence of functional Nod2 and Tlr4 mutations on gene transcription in Crohn's disease patients. J MOL MED-JMM 2005;83 (8):601-609 [PubMed]
Schaaf GJ, Ruijter JM, van Ruissen F, Zwijnenburg DA, Waaijer R, Valentijn LJ, Benit-Deekman J, van Kampen AHC, Baas F, Kool M, Full transcriptome analysis of rhabdomyosarcoma, normal, and fetal skeletal muscle: statistical comparison of multiple SAGE libraries. FASEB J 2005;19 (3):404-406 [PubMed]
van Kampen AHC, Horrevoets AJG. The role of bioinformatics in genomic medicine in: Pasterkamp G, de Kleijn DPV, editors. Cardiovascular research. New technologies, methods, and applications. Newe York: Springer Science+Business Media Inc; 2005., p. 103-121
van Passel MWJ, Bart A, Thygesen HH, Luyf ACM, van Kampen AHC, van der Ende A, An acquisition account of genomic islands based on genome signature comparisons. BMC GENOMICS 2005;6:163 [PubMed]
van Passel MWJ, Luyf ACM, van Kampen AHC, Bart A, van der Ende A, Deltarho-web, an online tool to assess composition similarity of individual nucleic acid sequences. BIOINFORMATICS 2005;21 (13):3053-3055 [PubMed]
van Passel MWJ, Bart A, Waaijer RJA, Luyf ACM, van Kampen AHC, van der Ende A, An in vitro strategy for the selective isolation of anomalous DNA from prokaryotic genomes. NUCLEIC ACIDS RES 2004;32 (14):e114 [PubMed]
de Jonge RR, Vreijling JP, Meintjes A, Kwa MSG, van Kampen AHC, van Schaik IN, Baas F, Transcriptional profile of the human peripheral nervous system by serial analysis of gene expression. GENOMICS 2003;82 (2):97-108 [PubMed]
van Kampen AHC, Ruijter JM, van Schaik BDC, Caron HN, Versteeg R. Gene expression informatics and analysis in: Barnes MR, Gray IC, editors. Bioinformatics for geneticists. Chichester: John Wiley & Sons; 2003., p. 319-344
Versteeg R, van Schaik BDC, van Batenburg MF, Roos M, Monajemi R, Caron H, Bussemaker HJ, van Kampen AHC, The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. GENOME RES 2003;13 (9):1998-2004 [PubMed]
Luyf ACM, de Gast J, van Kampen AHC, Visualizing metabolic activity on a genome-wide scale. BIOINFORMATICS 2002;18 (6):813-818 [PubMed]
Ruijter JM, van Kampen AHC, Baas F, Statistical evaluation of SAGE libraries: consequences for experimental design. PHYSIOL GENOMICS 2002;11 (2):37-44 [PubMed]
Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voûte PA, Heisterkamp S, van Kampen A, Versteeg R, The human transcriptome map: clustering of highly expressed genes in chromosomal domains. SCIENCE 2001;291 (5507):1289-1292 [PubMed]
Moreno JC, Pauws E, van Kampen AH, Jedlicková M, de Vijlder JJ, Ris-Stalpers C, Cloning of tissue-specific genes using serial analysis of gene expression and a novel computational substraction approach. GENOMICS 2001;75 (1-3):70-76 [PubMed]
Pauws E, van Kampen AH, van de Graaf SA, de Vijlder JJ, Ris-Stalpers C, Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis. NUCLEIC ACIDS RES 2001;29 (8):1690-1694 [PubMed]
Spieker N, van Sluis P, Beitsma M, Boon K, van Schaik BD, van Kampen AH, Caron H, Versteeg R, The MEIS1 oncogene is highly expressed in neuroblastoma and amplified in cell line IMR32. GENOMICS 2001;71 (2):214-221 [PubMed]
van Kampen AH, van Schaik BD, Pauws E, Michiels EM, Ruijter JM, Caron HN, Versteeg R, Heisterkamp SH, Leunissen JA, Baas F, van der Mee M, USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression. BIOINFORMATICS 2000;16 (10):899-905 [PubMed]
van Kampen AH, Buydens LM, Reinvestigation of a genetic-based classifier system: the effectiveness of recombination. COMPUT CHEM 1997;21 (3):153-160 [PubMed]
van Kampen AHC, Beckers MLM, Buydens LMC, A comparative study of the DG-OMEGA (DG Omega), DGII, and GAT method for the structure elucidation of a methylene-acetal linked thymine dinucleotide. COMPUT CHEM 1997;21 (5):281-297
van Kampen AHC, Buydens LMC, The Ineffectiveness of Recombination in a Genetic Algorithm for the Structure Elucidation of a Heptapeptide in Torsion Angle Space. A Comparison to Simulated Annealing. CHEMOMETR INTELL LAB 1997;36:141-152
van Kampen AHC, Ramadan Z, Mulholland M, Hibbert DB, Buydens LMC, Learning Classification Rules from an Ion Chromatography Database Using a Genetic Algorithm Based Classifier System. ANAL CHIM ACTA 1997;344:1-15
van Kampen AH, Buydens LM, Lucasius CB, Blommers MJ, Optimisation of metric matrix embedding by genetic algorithms. J BIOMOL NMR 1996;7 (3):214-224 [PubMed]
van Kampen AHC, Buydens LMC. The Effectiveness of Recombination in the Genetic Algorithm Methodology. A Comparison to Simulated Annealing in: Alander JT, editor. Proceedings of the Second Nordic Workshop on Genetic Algorithms and Their Applications (2NWGA). Finland: University of Vaasa; 1996., p. 115-130
van Kampen AHC, Strom CS, Buydens LMC, Lethalization, Penalty and Repair Functions for Constraint Handling in the Genetic Algorithm Methodology. CHEMOMETR INTELL LAB 1996;34 (1):55-68
van Kampen AHC. Genetic Algorithms and Structure Analysis of Biomolecules by Nmr in Chemometrics in: Buydens LMC, Melssen WJM, editors. Exploring and Exploiting Chemical Information : Libris Amicorum on the occasion of the retirement of Gerrit Kateman as professor of analytical chemistry at the Catholic University of Nijmegen. Nijmegen: Katholieke Universiteit Nijmegen; 1994., p. 145-157
Key publications

van Houdt JKJ, Nowakowska BA, Sousa SB, van Schaik BDC, Seuntjens E, Avonce N, Sifrim A, Abdul-Rahman OA, van den Boogaard MJH, Bottani A, Castori M, Cormier-Daire V, Deardorff MA, Filges I, Fryer A, Fryns JP, Gana S, Garavelli L, Gillessen-Kaesbach G, Hall BD, Horn D, Huylebroeck D, Klapecki J, Krajewska-Walasek M, Kuechler A, Lines MA, Maas S, Macdermot KD, McKee S, Magee A, de Man SA, Moreau Y, Morice-Picard F, Obersztyn E, Pilch J, Rosser E, Shannon N, Stolte-Dijkstra I, van Dijck P, Vilain C, Vogels A, Wakeling E, Wieczorek D, Wilson L, Zuffardi O, van Kampen AHC, Devriendt K, Hennekam R, Vermeesch JR, Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome. NAT GENET 2012;44 (4):445-U261 [PubMed]
Doorenspleet ME , Klarenbeek PL, de Hair MJH, van Schaik BDC, Esveldt REE, van Kampen AHC, Gerlag DM, Musters A, Baas F, Tak PP, de Vries N, Rheumatoid arthritis synovial tissue harbours dominant B-cell and plasma-cell clones associated with autoreactivity. ANN RHEUM DIS 2014;73 (4):756-762 [PubMed]
Willemsen AM, Hendrickx DM, Hoefsloot HCJ, Hendriks MMWB, Wahl SA, Teusink B, Smilde AK, van Kampen AHC, MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis. MOL BIOSYST 2015;11 (1):137-145 [PubMed]
Stobbe MD, Jansen GA, Moerland PD, van Kampen AHC, Knowledge representation in metabolic pathway databases. BRIEF BIOINFORM 2014;15 (3):455-470 [PubMed]
Reshetova P, van Schaik BDC, Klarenbeek PL, Doorenspleet ME, Esveldt REE, Tak PP, Guikema JEJ, de Vries N, van Kampen AHC, Computational Model Reveals Limited Correlation between Germinal Center B-Cell Subclone Abundancy and Affinity: Implications for Repertoire Sequencing. FRONT IMMUNOL 2017;8:221 [PubMed]


All Publications

Curriculum Vitae

Professor Antoine van Kampen obtained his PhD in chemometrics at the University of Nijmegen (1997) for the thesis 'Complex optimization problems in chemistry'. For this work he received the Clemens Rothaan price (1997) for ‘excellent scientific research in the domain of computer applications’ from the Royal Netherlands Chemistry Society (KNCV). After a short position as postdoctoral researcher at the same university he move to the Academic Medical Center (AMC) of the University of Amsterdam. Here he initiated the Bioinformatics Laboratory, which he is still heading.

Van Kampen was scientific director of the Netherlands Bioinformatics Center (NBIC) from 2006 - 2010. Here he was responsible for budgets (>50 MEuro) and the initiation, stimulation, and coordination of bioinformatics programmes in research, support, e-bioscience infrastructure, and education.

Van Kampen has a broad interest in bioinformatics research, support and education. Part of this time and group is devoted to AMC bioinformatics support. In addition, he dedicates significant amount of time to education of biomedical, bioinformatics, systems biology, and informatics students, and to the further training of postdoctoral researchers.

Research programmes

Medical Bioinformatics

The Bioinformatics Laboratory is engaged in different types of research and support projects. The main research efforts comprise (a) Bioinformatics, (b) Systems Genomics, and (c) Systems Medicine  


 

Faculty
Prof. dr. A.H.C. van Kampen (Faculty of Science, University of Amsterdam)
Dr. F.M. van der Kloet
Dr. ir. P.D. Moerland
B.D.C. van Schaik

Postdocs
Dr. A. Jongejan
Dr. M. Pras-Raves

PhD Students
U.K. Nandal MSc
R. Sales Barros MSc
E. Tejero
A. Nigam MSc (UvA - Faculty of Science)
M. Soleimani MSc

Others
P.F. de Geest MSc
A.C.M. Luyf

Other research related activities
  • Other, Netherlands Bioinformatics Centre
  • Contribution to training of professionals, NBIC PhD school
  • Membership of advisory board / Consultant, Other
Current research funding
  • AMC