Barbera

Barbera D.C. van Schaik

Sequence analysis

I'm broadly interested in DNA research and techniques that aid the analysis, and enjoy teaching these topics to students and other researchers. I have worked on topics ranging from transcriptomics and alternative splicing to virus discovery, comparing bacterial genomes, and searching for variants in whole exome data. Currently I work in the field of immunogenomics.

Projects
  • Immunogenomics
    • Reconstruction of B cell lineages (current)
    • Analysis pipeline for TCR and BCR repertoire sequencing (current)
    • Discovery of invariant T cells
  • e-Science
    • Optimization of sequence alignment on a grid infrastructure
    • Porting the GoNL analysis pipeline to the Dutch life science grid
    • Grid-based BLAST gateway
  • Exome and whole genome sequencing
  • Assembly and comparison of bacterial genomes
    • Pneumococcal meningitis
  • Alternative splicing
    • Identification of alternative exon use
  • Virus discovery
    • VIDISCA-454 sequence analysis
  • Human transcriptome map
    • Discovery of high and low expressed regions of the genome
  • USAGE - Gene expression analysis on SAGE data
    • Addition of statistical methods to the USAGE application

Publications

2017
  • Reshetova P, van Schaik BD, Klarenbeek PL, Doorenspleet ME, Esveldt RE, Tak PP, Guikema JE, de Vries N, van Kampen AH (2017) Computational Model Reveals Limited Correlation between Germinal Center B-Cell Subclone Abundancy and Affinity: Implications for Repertoire Sequencing. Front Immunol., 2017 Mar 6;8:221. (pubmed)

2016
  • Francioli LC, Cretu-Stancu M, Garimella KV, Fromer M, Kloosterman WP, Samocha KE, Neale BM, Daly MJ, Banks E, DePristo MA, de Bakker PI; Genome of the Netherlands consortium (2016) A framework for the detection of de novo mutations in family-based sequencing data. Eur J Hum Genet, 2016 Nov 23. (pubmed)
  • Hehir-Kwa JY, Marschall T, Kloosterman WP, Francioli LC, Baaijens JA, Dijkstra LJ, Abdellaoui A, Koval V, Thung DT, Wardenaar R, Renkens I, Coe BP, Deelen P, de Ligt J, Lameijer EW, van Dijk F, Hormozdiari F, Genome of the Netherlands Consortium, Uitterlinden AG, van Duijn CM, Eichler EE, de Bakker PI, Swertz MA, Wijmenga C, van Ommen GB, Slagboom PE, Boomsma DI, Schönhuth A, Ye K, Guryev V (2016) A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nature Communications, 2016 Oct 6;7:12989. (pubmed)
  • Li M, Rothwell R, Vermaat M, Wachsmuth M, Schröder R, Laros JF, van Oven M, de Bakker PI, Bovenberg JA, van Duijn CM, van Ommen GJ, Slagboom PE, Swertz MA, Wijmenga C; Genome of Netherlands Consortium, Kayser M, Boomsma DI, Zöllner S, de Knijff P, Stoneking M (2016) Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck. Genome Research, 26(4), 417-426. (pubmed)

2015
  • Palamara PF, Francioli LC, Wilton PR, Genovese G, Gusev A, Finucane HK, Sankararaman S, Genome of the Netherlands Consortium, Sunyaev SR, de Bakker PI, Wakeley J, Pe'er I, Price AL (2015) Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates. Am J Hum Genet., 97(6), 775-89. (pubmed)
  • Klarenbeek PL, Doorenspleet ME, Esveldt RE, van Schaik BD, Lardy N, van Kampen AH, Tak PP, Plenge RM, Baas F, de Bakker PI, de Vries N (2015) Somatic Variation of T-Cell Receptor Genes Strongly Associate with HLA Class Restriction. PLoS One, 10(10), e0140815. (pubmed)
  • Canuti M, van Beveren NJ, Jazaeri Farsani SM, de Vries M, Deijs M, Jebbink MF, Zaaijer HL, van Schaik BD, van Kampen AH, van der Kuyl AC, de Haan L, Storosum JG, van der Hoek L (2015) Viral metagenomics in drug-naïve, first-onset schizophrenia patients with prominent negative symptoms. Psychiatry Research, S0165-1781(15)30160-8. (pubmed)
  • van Leeuwen EM, Kanterakis A, Deelen P, Kattenberg MV, Genome of the Netherlands Consortium, Slagboom PE, de Bakker PI, Wijmenga C, Swertz MA, Boomsma DI, van Duijn CM, Karssen LC, Hottenga JJ (2015) Population-specific genotype imputations using minimac or IMPUTE2. Nature Protocols, 10(9), 1285-96. (pubmed)
  • Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I; Genome of the Netherlands Consortium, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Ye K, Guryev V, Arndt PF, Kloosterman WP, de Bakker PI, Sunyaev SR (2015) Genome-wide patterns and properties of de novo mutations in humans. Nature Genetics, 47(7), 822-826. (pubmed)
  • Kloosterman WP, Francioli LC, Hormozdiari F, Marschall T, Hehir-Kwa JY, Abdellaoui A, Lameijer EW, Moed MH, Koval V, Renkens I, van Roosmalen MJ, Arp P, Karssen LC, Coe BP, Handsaker RE, Suchiman ED, Cuppen E, Thung DT, McVey M, Wendl MC, Genome of Netherlands Consortium, Uitterlinden A, van Duijn CM, Swertz MA, Wijmenga C, van Ommen GB, Slagboom PE, Boomsma DI, Schönhuth A, Eichler EE, de Bakker PI, Ye K, Guryev V (2015) Characteristics of de novo structural changes in the human genome. Genome Research, 25(6), 792-801. (pubmed)
  • van Leeuwen EM, Karssen LC, Deelen J, Isaacs A, Medina-Gomez C, Mbarek H, Kanterakis A, Trompet S, Postmus I, Verweij N, van Enckevort DJ, Huffman JE, White CC, Feitosa MF, Bartz TM, Manichaikul A, Joshi PK, Peloso GM, Deelen P, van Dijk F, Willemsen G, de Geus EJ, Milaneschi Y, Penninx BW, Francioli LC, Menelaou A, Pulit SL, Rivadeneira F, Hofman A, Oostra BA, Franco OH, Mateo Leach I, Beekman M, de Craen AJ, Uh HW, Trochet H, Hocking LJ, Porteous DJ, Sattar N, Packard CJ, Buckley BM, Brody JA, Bis JC, Rotter JI, Mychaleckyj JC, Campbell H, Duan Q, Lange LA, Wilson JF, Hayward C, Polasek O, Vitart V, Rudan I, Wright AF, Rich SS, Psaty BM, Borecki IB, Kearney PM, Stott DJ, Adrienne Cupples L; Genome of the Netherlands Consortium, Jukema JW, van der Harst P, Sijbrands EJ, Hottenga JJ, Uitterlinden AG, Swertz MA, van Ommen GJ, de Bakker PI, Eline Slagboom P, Boomsma DI, Wijmenga C, van Duijn CM (2015) Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. Nat Commun. 2015 Mar 9;6:6065. doi: 10.1038/ncomms7065. (pubmed)
  • Remmerswaal EB, Klarenbeek PL, Alves NL, Doorenspleet ME, van Schaik BD, Esveldt RE, Idu MM, van Leeuwen EM, van der Bom-Baylon N, van Kampen AH, Koch SD, Pircher H, Bemelman FJ, Ten Brinke A, Baas F, Ten Berge IJ, van Lier RA, de Vries N (2015) Clonal evolution of CD8+ T cell responses against latent viruses: relationship between phenotype, localization and function. J Virol. 2015. pii: JVI.02003-14. [Epub ahead of print] (pubmed)

2014
  • Van Schaik, B., Klarenbeek, P., Doorenspleet, M., van Kampen, a., Moody, D. B., de Vries, N., & Van Rhijn, I. (2014). Discovery of Invariant T Cells by Next-Generation Sequencing of the Human TCR -Chain Repertoire. The Journal of Immunology. (doi)
  • L. C. Francioli, A. Menelaou, S. L. Pulit, F. van Dijk, P. F. Palamara, C. C. Elbers, P. B. T. Neerincx, K. Ye, V. Guryev, W. P. Kloosterman, P. Deelen, A. Abdellaoui, E. M. van Leeuwen, M. van Oven, M. Vermaat, M. Li, J. F. J. Laros, L. C. Karssen, A. Kanterakis, N. Amin, J. J. Hottenga, E.-W. Lameijer, M. Kattenberg, M. Dijkstra, H. Byelas, J. van Setten, B. D. C. van Schaik, J. Bot, I. J. Nijman, I. Renkens, T. Marschall, A. Sch�nhuth, J. Y. Hehir-Kwa, R. E. Handsaker, P. Polak, M. Sohail, D. Vuzman, F. Hormozdiari, D. van Enckevort, H. Mei, V. Koval, M. H. Moed, K. J. van der Velde, F. Rivadeneira, K. Estrada, C. Medina-Gomez, A. Isaacs, S. a McCarroll, M. Beekman, A. J. M. de Craen, H. E. D. Suchiman, A. Hofman, B. Oostra, A. G. Uitterlinden, G. Willemsen, L. C. Study, M. Platteel, J. H. Veldink, L. H. van den Berg, S. J. Pitts, S. Potluri, P. Sundar, D. R. Cox, S. R. Sunyaev, J. T. Den Dunnen, M. Stoneking, P. de Knijff, M. Kayser, Q. Li, Y. Li, Y. Du, R. Chen, H. Cao, N. Li, S. Cao, J. Wang, J. a Bovenberg, I. Pe�er, P. E. Slagboom, C. M. van Duijn, D. I. Boomsma, G.-J. B. van Ommen, P. I. W. de Bakker, M. a Swertz, and C. Wijmenga (2014) Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat. Genet., Jun. 2014. (pubmed, doi)
  • Patrick Deelen, Androniki Menelaou, Elisabeth M van Leeuwen, Alexandros Kanterakis, Freerk van Dijk, Carolina Medina-Gomez, Laurent C Francioli, Jouke Jan Hottenga, Lennart C Karssen, Karol Estrada, Eskil Kreiner-M�ller, Fernando Rivadeneira, Jessica van Setten, Javier Gutierrez-Achury, Harm-Jan Westra, Lude Franke, David van Enckevort, Martijn Dijkstra, Heorhiy Byelas, Cornelia M van Duijn, Genome of the Netherlands Consortium, Paul I W de Bakker, Cisca Wijmenga and Morris A Swertz (2014) Improved imputation quality of low-frequency and rare variants in European samples using the �Genome of The Netherlands�. Eur. J. Hum. Genet., no. August 2013, pp. 1�6, Jun. 2014. (pubmed, doi)
  • Jurgen R. Piet, Madelijn Geldhoff, Barbera D. C. van Schaik, Matthijs C. Brouwer, Mercedes Valls Seron, Marja E. Jakobs, Kim Schipper, Yvonne Pannekoek, Aeilko H. Zwinderman, Tom van der Poll, Antoine H.C. van Kampen, Frank Baas, Arie van der Ende, Diederik van de Beek (2014) Streptococcus pneumoniae arginine synthesis genes promote growth and virulence in pneumococcal meningitis. J Infect Dis. (pubmed, doi)
  • M E Doorenspleet, P L Klarenbeek, M J H de Hair, B D C van Schaik, R E E Esveldt, A H C van Kampen, D M Gerlag, A Musters, F Baas, P P Tak, N de Vries (2014) Rheumatoid arthritis synovial tissue harbours dominant B-cell and plasma-cell clones associated with autoreactivity. Ann Rheum Dis (pubmed)

2013
  • Silvia D Olabarriaga, Mohammad M Jaghoori, Vladimir Korkhov, Barbera van Schaik, Antoine van Kampen (2013) Understanding workflows for distributed computing: nitty-gritty details. Proceedings of the 8th Workshop on Workflows in Support of Large-Scale Science - WORKS '13, 68-76
  • Mark Santcroos, Barbera van Schaik, Shayan Shahand, Silvia Olabarriaga, Andre Luckow, Shantenu Jha (2013) Exploring Dynamic Enactment of Scientific Workflows Using Pilot-Abstractions. In proceedings CCGRID 2013
  • Souley Madougou, Shayan Shahand, Mark Santcroos, Barbera van Schaik, Ammar Benabdelkader, Antoine van Kampen, S�lvia Olabarriaga (2013) Characterizing workflow-based activity on a production e-infrastructure using provenance data. Future Generation Computer Systems
  • Barbera D. C. van Schaik, Mark Santcroos, Souley Madougou, Aldo Jongejan, Antoine H. C. van Kampen, S�lvia Delgado Olabarriaga (2013) e-Bioscience Solutions and Challenges for Next Generation Sequencing Experiments. IWBBIO 2013: 333-334. (pdf)
  • Adam Kiezun, Sara L Pulit, Laurent C Francioli, Freerk van Dijk, Morris Swertz, Dorret I Boomsma, Cornelia M van Duijn, P Eline Slagboom, G J B van Ommen, Cisca Wijmenga, Genome of the Netherlands Consortium, Paul I W de Bakker, Shamil R Sunyaev (2013) Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency. PLoS Genet 9(2) (pubmed)
  • Felix M Wensveen, Paul L Klarenbeek, Klaas P J M van Gisbergen, Maria F Pascutti, Ingrid A M Derks, Barbera D C van Schaik, Anja Ten Brinke, Niek de Vries, Durdica Cekinovic, Stipan Jonjic, Ren� A W van Lier, Eric Eldering (2013) Pro-Apoptotic Protein Noxa Regulates Memory T Cell Population Size and Protects against Lethal Immunopathology. J Immunol (pubmed)

2012
  • Barbera D C van Schaik, Mark Santcroos, Vladimir Korkhov, Aldo Jongejan, Marcel Willemsen, Antoine H C van Kampen, Silvia D Olabarriaga (2012) Challenges in DNA sequence analysis on a production grid In: PoS (EGICF12-EMITC2)039 1-19 (pdf)
  • P L Klarenbeek, E B M Remmerswaal, I J M Ten Berge, M E Doorenspleet, B D C van Schaik, R E E Esveldt, S D Koch, A Ten Brinke, A H C van Kampen, F J Bemelman, P P Tak, F Baas, N de Vries, R A W van Lier (2012) 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 8: 9 (pubmed)
  • Michel de Vries, Bas B Oude Munnink, Martin Deijs, Marta Canuti, Sylvie M Koekkoek, Richard Molenkamp, Margreet Bakker, Suzanne Jurriaans, Barbera D C van Schaik, Angela C Luyf, Silvia D Olabarriaga, Antoine H C van Kampen, Lia van der Hoek (2012) Performance of VIDISCA-454 in Feces-Suspensions and Serum. Viruses 4: 8. 1328-1334 (pubmed)
  • Souley Madougou, Mark Santcroos, Ammar Benabdelkader, Barbera D C van Schaik, Shayan Shahand, Vladimir Korkhov, Antoine H C van Kampen, S�lvia D Olabarriaga (2012) Provenance for distributed biomedical workflow execution. In: Proceedings of Healthgrid, Stud Health Technol Inform 175: 91-100 (pubmed)
  • Van Houdt JK ‡, Nowakowska BA ‡, Sousa SB ‡, van Schaik BD ‡, Seuntjens E, Avonce N, Sifrim A, Abdul-Rahman OA, van den Boogaard MJ, 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 AH, Devriendt K, Hennekam R †, Vermeesch JR † (2012) Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome. Nature Genetics (pubmed)
  • P L Klarenbeek, M J H de Hair, M E Doorenspleet, B D C van Schaik, R E E Esveldt, M G H van de Sande, T Cantaert, D M Gerlag, D Baeten, A H C van Kampen, F Baas, P P Tak, N de Vries (2012) Inflamed target tissue provides a specific niche for highly expanded T-cell clones in early human autoimmune disease. Ann Rheum Dis Jan (pubmed)

2011
  • Y.�Mohammed, S.�Shahand, V.�Korkhov, A.�Luyf, B.�van Schaik, M.�Caan, A.�van Kampen, M.�Palmblad, and S.�Olabarriaga. Data Decomposition in Biomedical e-Science Applications. In: Proceedings of the 7th IEEE International Conference on e-Science, 2011.
  • Ritz K, van Schaik BDC, Jakobs ME, Aronica E, Tijssen MA, van Kampen AHC, Baas F (2011) Looking ultra deep: Short identical sequences and transcriptional slippage. Genomics, 98(2):90-5 (pubmed)
  • Piet JR, Huis In 't Veld RA, van Schaik BDC, van Kampen AHC, Baas F, van de Beek D, Pannekoek Y, van der Ende A. (2011) Genome Sequence of Neisseria meningitidis serogroup B strain H44/76. Journal of Bacteriology.
  • de Vries M, Deijs M, Canuti M, van Schaik BDC, Faria NR, van de Garde MD, Jachimowski LC, Jebbink MF, Jakobs M, Luyf AC, Coenjaerts FE, Claas EC, Molenkamp R, Koekkoek SM, Lammens C, Leus F, Goossens H, Ieven M, Baas F, van der Hoek L. A sensitive assay for virus discovery in respiratory clinical samples. PLoS One., 24;6(1):e16118.
  • Ritz K, van Schaik BDC, Jakobs ME, van Kampen AHC, Aronica E, Tijssen MA, Baas F. (2011) SGCE isoform characterization and expression in human brain: implications for myoclonus-dystonia pathogenesis. Eur J Hum Genet, 19(4):438-44.

2010
  • Luyf AC ‡, 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. 11(1), 598.
  • PL Klarenbeek, PP Tak, BDC van Schaik, AH Zwinderman, ME Jakobs, Z Zhang, AHC van Kampen, RAW van Lier, F Baas, N de Vries (2010) Human T cell memory consists mainly of unexpanded clones. Immunol Lett, 133(1):42-8 (PubMed)

2009
  • van Hooff SR, Koster J, Hulsen T, van Schaik BDC, Roos M, van Batenburg MF, Versteeg R, van Kampen AHC (2009). The construction of genome-based transcriptional units. OMICS, 13(2):105-14.

2003
  • Versteeg R, van Schaik BDC, van Batenburg MF, Roos M, Monajemi R, Caron HN, Bussemaker HJ, van Kampen AHC (2003) 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 Research, 13, 1998-2004. [Pubmed]

2002
  • Godfried MB, Veenstra M, van Sluis P, Boon K, van Asperen R, Hermus M-C, van Schaik BDC, Vo�te TPA, Schwab M, Versteeg R, Caron HN (2002) The N-myc and c-myc downstream pathways include the chromosome 17q genes nm23-H1 and nm23-H2. Oncogene 21: 13. 2097-2101 (pubmed)

2001
  • Spieker N, van Sluis P, Beitsma M, Boon K, van Schaik BDC, van Kampen AHC, Caron H and Versteeg R (2001) The MEIS1 Oncogene Is Highly Expressed in Neuroblastoma and Amplified in Cell Line IMR32. Genomics 71(2), 214-221. [Pubmed]
  • Caron HN, van Schaik BDC, van der Mee M, van Sluis P, Hermus M-C, van Asperen R, Riggins G, Heisterkamp SH, Baas F, Boon K, Vo�te PA, van Kampen AHC and Versteeg R (2001) The Human Transcriptome Map reveals a clustering of highly expressed genes in chromosomal domains, Science, 291, 1289-1292. [Pubmed]

2000
  • van Kampen AHC, van Schaik BDC, Pauws E, Michiels EMC, Ruijter JM, Caron HN, Versteeg R, Heisterkamp SH, Leunissen JAM, Baas F and van der Mee M (2000) USAGE: a web-based approach for the analysis of SAGE data. Bioinformatics, 16(10), 899-905. [Pubmed]

‡ These authors contributed equally to this work

† These authors jointly directed this work

Profile on networks

Personal stuff

In my spare time I go to concerts and festivals, cook (all cuisines), grow vegetables in my garden, read books (fantasy, popular science/philosophy, Dutch literature) and make things (sewing, electronics, laser cutting, welding, 3d-printing). Occasionally, I write about my hobbies and I maintain a database with Indonesian recipes: http://www.van-schaik.org/

Contact information

Bioinformatics Laboratory
Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB)
Phone: (+31) 20 - 566 68 85
http://www.bioinformaticslaboratory.nl/

Academic Medical Center / University of Amsterdam
PO Box 22660 (J1B.214-1)
1100 DD Amsterdam
The Netherlands

monday-thursday, friday (even weeks)
b.d.vanschaik@amc.uva.nl
Topic revision: r68 - 01 Nov 2017, BarberaVanSchaik
 

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