Medical Bioinformatics

Publications

2012

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.

  • MD Stobbe, SM Houten, GA Jansen, AHC van Kampen, PD Moerland (2011). Critical assessment of human metabolic pathway databases: a stepping stone for future integration. BMC Systems Biology, 5:165.

  • BM Sondermeijer, A Bakker, A Halliani, MWJ de Ronde, JA Marquart, AJ Tijsen, TA Mulders, M Kok, S Battjes, S Maiwald, S Sivapalaratnam, MD Trip, PD Moerland, JCM. Meijers, EE Creemers, SJ Pinto-Sietsma. Platelets in patients with premature coronary artery disease exhibit upregulation of miRNA340* and miRNA624*. PLoS ONE, 6(10): e25946.

  • SM Bol, T Booiman, EM Bunnik, PD Moerland, K van Dort, JF Strauss 3rd, M Sieberer, H Schuitemaker, NA Kootstra, AB van ’t Wout (2011). Polymorphism in HIV-1 dependency factor PDE8A affects gene expression and HIV-1 replication in primary macrophages. Virology, 420(1): 32-42.

  • D van Manen, O Delaneau, NA Kootstra, BD Boeser-Nunnink, S Limou, J Burger, SM Bol, AH Zwinderman, PD Moerland, R van ’t Slot, J-F Zagury, AB van ‘t Wout, H Schuitemaker (2011). Genome-wide association scan in HIV-1-infected individuals identifying variants influencing disease course. PLoS ONE, 6(7): e22208.

  • HMJ Sontrop, WFJ Verhaegh, MJT Reinders, PD Moerland (2011). An evaluation protocol for subtype-specific breast cancer event prediction. PLoS ONE, 6(7): e21681.

  • S. Shahand, M. Santcroos, Y. Mohammed, V. Korkhov, A. C. M. Luyf, A. van Kampen, S. Olabarriaga, "Front-ends to Biomedical Data Analysis on Grids", proceedings of the HealthGrid 2011 (in press), 2011. PDF

  • Ritz K, van Schaik BD, Jakobs ME, Aronica E, Tijssen MA, van Kampen AH, Baas F (2011) Looking ultra deep: Short identical sequences and transcriptional slippage. Genomics 2011 May 23. Epub ahead of print pubmed

  • SM Bol, PD Moerland, S Limou, Y van Remmerden, C Coulonges, D van Manen, JT Herbeck, J Fellay, M Sieberer, JG Sietzema, R van ’t Slot, J Martinson, J-F Zagury, H Schuitemaker, AB van ’t Wout (2011). Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages. PLoS ONE, 6(2): e17190.

  • MG Noordhuis, RSN Fehrmann, GBA Wisman, ER Nijhuis, JJ van Zanden, PD Moerland, E Ver Loren van Themaat, HH Volders, M Kok, KA ten Hoor, H Hollema, EGE de Vries, GH de Bock, AGJ van der Zee, E Schuuring (2011). Involvement of the TGF-β and β-catenin pathways in pelvic lymph node metastasis in early stage cervical cancer. Clinical Cancer Research, 17(6): 1317-30.

  • Piet JR, Huis In 't Veld RA, van Schaik BD, van Kampen AH, 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 BD, 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.

  • Hakvoort TB, Moerland PD, Frijters R, Sokolovic A, Labruyere WT, Vermeulen JL, Ver Loren van Themaat E, Breit TM, Wittink FR, van Kampen AH, Verhoeven AJ, Lamers WH, Sokolovic M. (2011) Interorgan coordination of the murine adaptive response to fasting. Journal of Biological Chemistry. 2011 Mar 10. (Note: Moerland=co first author)

2010

  • Ritz K, van Schaik BD, Jakobs ME, van Kampen AH, Aronica E, Tijssen MA, Baas F. (2010) SGCE isoform characterization and expression in human brain: implications for myoclonus-dystonia pathogenesis. Eur J Hum Genet, 19(4):438-44.

  • Luyf AC, van Schaik BD, de Vries M, Baas F, van Kampen AH, Olabarriaga SD. Initial steps towards a production platform for DNA sequence analysis on the grid. BMC Bioinformatics. 11(1), 598. (Note: Luyf AC, van Schaik BD =first authors)

  • KML Hertoghs, PD Moerland, A van Stijn, EBM Remmerswaal, SL Yong, PJEJ van de Berg, SM van Ham, IJM ten Berge and RAW van Lier (2010). Molecular profiling of cytomegalovirus-induced human CD8+ T cell differentiation. Journal of Clinical Investigation, 120(11):4077-90. (Note: Moerland=co first author)

  • TCTM van der Pouw Kraan, SH Schirmer, JO Fledderus, PD Moerland, JM Baggen, TA Leyen, AM van der Laan, JJ Piek, N van Royen, AJG Horrevoets (2010). The transcriptome of circulating CD34 cells reveals loss of the naïve signature in coronary artery disease patients, consistent with a retinoic acid-induced program. BMC Genomics 11(1):388. (PubMed)

  • M.W.A. Caan, H.G. Khedoe, D.H.J. Poot, A.J. den Dekker, S.D. Olabarriaga, C.A. Grimbergen, L.J. van Vliet, F.M. Vos. (2010) Estimation of diffusion properties in crossing fiber bundles, IEEE Transactions on Medical Imaging 2010 Jun 17. [Epub ahead of print] (PubMed)

  • F. Gwadry-Sridhar, S.D. Olabarriaga, A. van Kampen, Michael Bauer, Tony Solomonides. (2010) Hitting the ground running: Healthgrid deployment and adoption. Proceedings of HealthGrid 2010 .Stud Health Technol Inform. 2010;159:40-51. (PubMed)

  • Yassene Mohammed, Ulrich Sax, Frank Dickmann, Joerg Lippert, Juri Solodenko, Gabriele Von Voigt, Matthew Smith, Otto Rienhoffo (2010) Transferring the Grid Technology to the Biomedical Community. Proceedings of HealthGrid 2010 . Stud Health Technol Inform. 2010;159:28-39. (PubMed)

  • M.W.A. Caan, F.M. Vos, L.J. van Vliet, A.H.C. van Kampen, S.D. Olabarriaga. (2010) Gridifying a Diffusion Tensor Imaging Analysis Pipeline. Proceedings of the 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing (CCGrid 2010) Melbourne, VIC, Australia, May 17-May 20. IEEE Computer Society. pp.733-738, 2010. (Abstract)

  • 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. Epub ahead of print (PubMed)

  • AJ Tijsen, EE Creemers, PD Moerland, LJ de Windt, AC van der Wal, WE Kok, YM Pinto. MiR423-5p as a circulating biomarker for heart failure. Circulation Research, 106: 1035-9. (PubMed)

  • S. D. Olabarriaga and J. Montagnat (2010) Special section: Medical imaging on grids. Future Generation Computer Systems 26 (4), 678-680.

  • S.D. Olabarriaga, T. Glatard, P. de Boer (2010) A Virtual Laboratory for Medical Image Analysis, IEEE Transactions on Information Technology In Biomedicine (TITB) 2010 Apr 5. [Epub ahead of print](PubMed)

  • T. Glatard, R. S. Soleman, D. J. Veltman, A. Nederveen, and Silvia Olabarriaga (2010). Large scale functional MRI study on a production grid. Future Generation Computer Systems vol. 26, no. 4, pp. 685-692.

  • van Batenburg MF, Li H, Polman JA, Lachize S, Datson NA, Bussemaker HJ, Meijer OC. (2010) Paired hormone response elements predict caveolin-1 as a glucocorticoid target gene. PLoS One. 5(1), e8839. (PubMed)

2009

  • HMJ Sontrop, PD Moerland, R van den Ham, MJ Reinders, WFJ Verhaegh (2009). A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability. BMC Bioinformatics, 10:389. (PubMed)

  • Roos M, Marshall MS, Gibson AP, Schuemie M, Meij E, Katrenko S, van Hage WR, Krommydas K, Adriaans PW (2009) Structuring and extracting knowledge for the support of hypothesis generation in molecular biology. BMC Bioinformatics 2009, 10(Suppl 10):S9 (PubMed)

  • Nora Bijl, Milka Sokolovic, Carlos Vrins, Mirjam Langeveld, Perry D. Moerland, Nike Claessen, Roelof Ottenhoff, Cindy van Roomen, Peter Dubbelhuis, Rolf Boot, Jan Aten, Bert Groen, Johannes M.F.G. Aerts, Marco van Eijk (2009). Modulation of glycosphingolipid metabolism significantly improves hepatic insulin sensitivity and reverses hepatic steatosis in mice. Hepatology, 50(5):1431-41. (PubMed)

  • Miinalainen IJ, Schmitz W, Huotari A, Autio KJ, Soininen R, Ver Loren van Themaat E, Baes M, Herzig KH, Conzelmann E, Hiltunen JK (2009). Mitochondrial 2,4-dienoyl-CoA reductase deficiency in mice results in severe hypoglycemia with stress intolerance and unimpaired ketogenesis. PLoS Genetics, 5(7):e1000453.

  • Sluimer JD, van der Flier WM, Karas GB, van Schijndel R, Barnes J, Boyes RG, Cover KS, Olabarriaga SD, Fox NC, Scheltens P, Vrenken H, Barkhof F (2009) Accelerating regional atrophy rates in the progression from normal aging to Alzheimer's disease. Eur Radiol, [Epub ahead of print].

  • Wegdam W*, Moerland PD*, Buist MR, Ver Loren van Themaat E, Bleijlevens B, Hoefsloot HC, de Koster CG, Aerts JM (2009) Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets. Proteome Science, 14;7:19. *Contributed equally

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

  • Stephan H. Schirmer, Niels van Royen, Perry D. Moerland, Joost O. Fledderus, José P. Henriques, René J. van der Schaaf, Marije M. Vis, Jan Baan Jr., Karel T. Koch, Anton J.G. Horrevoets, Jan J. Piek (2009). Local cytokine concentrations and oxygen pressure are related to maturation of the collateral circulation in humans. Journal of the American College of Cardiology, 53(23):2141-2147 .

  • Stephan H. Schirmer, Joost O. Fledderus, Anja M. van der Laan, Tineke C.T.M. van der Pouw-Kraan, Perry D. Moerland, Oscar L. Volger, Josefien M. Baggen, Michael Böhm, Jan J. Piek, Anton J.G. Horrevoets, Niels van Royen (2009). Suppression of inflammatory signaling in monocytes from patients with coronary artery disease. Journal of Molecular and Cellular Cardiology, 46(2):177-85.
  • BC van Munster, MJ van Breemen, PD Moerland, D Speijer, SE de Rooij, CJG Pfrommer, M Levi, MW Hollmann, JM Aerts, AH Zwinderman, JC Korevaar. Proteomic Profiling of Plasma and Serum of Elderly Patients with Postoperative Delirium. Journal of Neuropsychiatry and Clinical Neuroscience. Accepted.

  • S. Olabarriaga, T. Glatard, A. Hoheisel, A. Nederveen, D. Krefting. (2009) Crossing HealthGrid Borders: Early Results in Medical Imaging. Proceedings of Healthgrid. Studies in Health Technology and Informatics. 147:62-71

  • Herman Sontrop, René van den Ham, Perry Moerland, Marcel Reinders and Wim Verhaegh. (2009) A sensitivity analysis of microarray feature selection and classification under measurement noise. Genomic Signal Processing and Statistics, GENSIPS 2009. IEEE International Workshop, p. 1– 4.

2008

  • T. Glatard, K. Boulebiar and S. D. Olabarriaga. (2008) Workflow integration in VL-e medical, in Proceedings of the 21st IEEE International Symposium on Computer-Based Medical Systems (CBMS'08), Jyväskylä, Finland, 17-19 June 2008.

  • S.D. Olabarriaga, T. Glatard, K. Boulebiar, and P. de Boer (2008) From 'low-hanging' to 'user-ready': initial steps into a healthgrid, Healthgrid, Chicago, June 2008. p. 70-79 (best paper award).

  • R.S. Soleman, T. Glatard, D.J. Veltman, A. Nederveen, S. Olabarriaga (2008). Large scale fMRI parameter study on a production grid. Proceedings of the MICCAI Workshop on Medical imaging on grids: achievements and perspectives (MICCAI-Grid), New-York, 6 September 2008, p.65-74.

  • T. Glatard, S. Olabarriaga (2008). From gridified scripts to workflows: the FSL Feat case. Proceedings of the MICCAI Workshop on Medical imaging on grids: achievements and perspectives (MICCAI-Grid), New-York, 6 September 2008. p. 33-42.

  • T. Glatard, S. Olabarriaga (2008). "User friendly management of workflow results: from provenance information to grid logical file names". Proceedings of the 4th IEEE International Conference on e-Science (eScience'08), Indianapolis, 7-12 December 2008

  • G. van Noordende, S.D. Olabarriaga, M. Koot, C. de Laat (2008) A Trusted Data Storage Infrastructure for Grid-Based Medical Applications. International Journal of Grid and High Performance Computing (IJGHPC) accepted

  • M. M. L. de Win, G. Jager, J. Booij, L. Reneman, T. Schilt, C. Lavini, S. D. Olabarriaga, G. J. den Heeten and W. van den Brink (2008) Sustained effects of ecstasy on the human brain: a prospective neuroimaging study in novel users. Brain, 131(11):2936-45 .

  • M. M. L. de Win, G. Jager, J. Booij, L. Reneman, T. Schilt, C. Lavini, S. D. Olabarriaga, N. F. Ramsey, G. J. den Heeten and W. van den Brink (2008) Neurotoxic effects of ecstasy on the thalamus. British Journal of Psychiatry, 193(4), 289-96.

  • Sokolovic M, Sokolovic A, Wehkamp D, Ver Loren van Themaat E, de Waart DR, Gilhuijs-Pederson LA, Nikolsky Y, van Kampen AH, Hakvoort TB, Lamers WH (2008). The transcriptomic signature of fasting murine liver. BMC Genomics, 9:528.

  • 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. (2008) Analysis of gene expression identifies differentially expressed genes and pathways associated with lymphatic dissemination in patients with adenocarcinoma of the esophagus. Annals of Surgical Oncology, 15(12):3459-3470.* Contributed equally

  • Schaaf GJ, van Ruissen F, van Kampen A, Kool M, Ruijter JM. (2008) Statistical comparison of two or more SAGE libraries: one tag at a time. Methods Mol Biol. 387, 151-68.

  • Buimer M, Keijser R, Jebbink JM, Wehkamp D, van Kampen AH, Boer K, van der Post JA, Ris-Stalpers C. (2008) Seven placental transcripts characterize HELLP-syndrome. Placenta, 29(5):444-53.

  • S. van der Laan, RA Sarabdjitsingh, MF van Batenburg, SB Lachize, H Li, TF Dijkmans, E Vreugdenhil, ER de Kloet and OC Meijer (2008) Chromatin immunoprecipitation (ChIP) scanning identifies glucocorticoid receptor binding regions in the proximal of a ubiquitously expressed glucocorticoid target gene in brain. Journal of Neurochemistry, 106(6):2515-2523.
  • Marcia A Inda, Marinus F van Batenburg, Marco Roos, Adam SZ Belloum, Dmitry Vasunin, Adianto Wibisono, Antoine HC van Kampen and Timo M Breit (2008) SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences. BMC Research Notes 2008, 1:63.
  • Willemsen AM, Jansen GA, Komen JC, van Hooff S, Waterham HR, Brites PM, Wanders RJ, van Kampen AH (2008) Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways. Bioinformatics, 24(16):i21-7.
  • Stephan H. Schirmer, Joost O. Fledderus, Pieter T.G. Bot, Perry D. Moerland, Jan Baan Jr. , Jose P. Henriques, Renee J. van der Schaaf, Marije M. Vis, Anton J.G. Horrevoets, Jan J. Piek, Niels van Royen (2008). Interferon-beta signaling Is enhanced in patients with insufficient coronary collateral artery development and inhibits arteriogenesis in mice. Circulation Research;102(10):1286-94 [PubMed]

  • Petra Biewenga, Marrije R. Buist, Perry D. Moerland, Emiel Ver Loren van Themaat, Antoine H.C. van Kampen, Fiebo J. ten Kate, Frank Baas (2008) Gene expression in early stage cervical cancer (2008). Gynaecologic Oncology; 108(3):520-6 [PubMed]

  • Judith E. van de Mortel, Henk Schat, Perry D. Moerland, Emiel Ver Loren van Themaat, Hetty Blankestijn, Liana Tsiatsiani, and Mark G. M. Aarts (2008) Expression differences for genes involved in lignin-, glutathione-, sulfate- and nitrate metabolism in response to cadmium in Arabidposis thaliana and the related Zn/Cd hyperaccumulator Thlaspi caerulescens (2008). Plant, Cell & Environment; 31:301-324 [PubMed]
  • Zuzana Zelinkova, Astrid J. van Beelen, Floor de Kort, Perry D. Moerland, P.E. Ver Loren van Themaat, Anje A.te Velde, Sander J. Van Deventer, Esther C. de Jong, Daniel W. Hommes (2008) Muramyl dipeptide-induced differential gene expression in NOD2 mutant and wild type Crohn`s disease patients-derived dendritic cells. Inflamm. Bowel. Dis. 14(2):186-94 [Pubmed]

2007

  • Stephen O. Nyangoma, Antoine A. H. C. van Kampen, Theo H. Reijmers, Natalia I. Govorukhina, Ate G. J. van der Zee, Lucinda J. Billingham, Rainer Bischoff, and Ritsert C. Jansen (2007) Multiple Testing Issues in Discriminating Compound-Related Peaks and Chromatograms from High Frequency Noise, Spikes and Solvent-Based Noise in LC – MS Data Sets. Statistical Applications in Genetics and Molecular Biology, 6(1), art 23.

  • Sokolovic M, Wehkamp D, Sokolovic A, Vermeulen J, Gilhuijs-Pederson LA, van Haaften RI, Nikolsky Y, Evelo CT, van Kampen AH, Hakvoort TB, Lamers WH (2007) Fasting induces a biphasic adaptive metabolic response in murine small intestine. BMC Genomics, 8(1), 361

  • Volger OL, Fledderus JO, Kisters N, Fontijn RD, Moerland PD, Kuiper J, van Berkel TJ, Bijnens AP, Daemen MJ, Pannekoek H, Horrevoets AJ (2007) Distinctive expression of chemokines and transforming growth factor-beta signaling in human arterial endothelium during atherosclerosis. Am J Pathol. 2007 Jul; 171(1): 326-37. [Pubmed]
  • Soufan AT, Van den Berg G, Moerland PD, Massink MM, Van den Hoff MJ, Moorman AF, Ruijter JM (2007) Three-dimensional measurement and visualization of morphogenesis applied to cardiac embryology. Journal of Microscopy, 225 (Pt 3), 268-73. [Pubmed]

2006

  • Halasz G, van Batenburg MF, Perusse J, Hua S, Lu XJ, White KP, Bussemaker HJ. (2006) Detecting transcriptionally active regions using genomic tiling arrays. Genome Biology, 7(7), R59.

  • Vos JB, Datson NA, van Kampen AHC, AC Luyf, Verhoosel RM, Zeeuwen PLMJ, Olthuis D, Rabe KF, Schalkwijk J, Hiemstra PS (2006) A molecular signature of epitheial inflammation: a comparative gene expression analysis of cultured bronchial epithelial cels and keratinocytes. BMC Genomics, 7(1), 9. [Pubmed]
  • Zelinkova Z, Derijks LJ, Stokkers PC, Vogels EW, van Kampen AH, Curvers WL, Cohn D, van Deventer SJ, Hommes DW. (2006) Inosine triphosphate pyrophosphatase and thiopurine s-methyltransferase genotypes relationship to azathioprine-induced myelosuppression. Clinical Gastroenterology and Hepatology, 4(1), 44-9. [Pubmed]
  • MWJ van Passel, A Bart, ACM Luyf, AHC van Kampen, A van der Ende (2006) Compositional discordance between prokaryotic plasmids and host chromosomes. BMC Genomics, 7(1), 26. [Pubmed]
  • MWJ van Passel, A Bart, ACM Luyf, AHC van Kampen, A van der Ende (2006) Identification of acquired DNA in Neisseria Lactamica. FEMS Microbiology Letters, 262, 77-84. [Pubmed]
  • Jansen GA, Wanders RJ (2006) Alpha Oxidation. Biochim Biophys Acta, 1763(12),1403-12. [Pubmed]
  • van de Mortel JE, Almar Villanueva L, Schat H, Kwekkeboom J, Coughlan S, Moerland PD, Ver Loren van Themaat E, Koornneef M, Aarts MG. (2006) Large expression differences in genes for iron and zinc homeostasis, stress response and lignin biosynthesis distinguish Arabidopsis thaliana and the related metal hyperaccumulator Thlaspi caerulescens. Plant Physiol. 142, 1127-1147. [Pubmed]
  • MW van Passel, EE Kuramae, AC Luyf, A Bart, T Boekhout (2006) The reach of the genome signature in prokaryotes. BMC Evol Biol. 6(1), 84. [Pubmed]

2005

  • Schaaf, GJ, Ruijter JM, van Ruissen F, Zwijnenburg DA, Waaijer R, van Kampen AHC, Valentijn L, Benit-Deekman J, Baas F, Kool M (2005) Full transcriptome analysis of rhabdomyosarcoma, normal and fetal skeletal muscle: statistical comparison of multiple SAGE libraries. FASEB J, 19(3), 404-406. [Pubmed]
  • MWJ. van Passel, A Bart, ACM, Luyf, AHC van Kampen, A van der Ende (2005) Delta-Rho-Web: an application for the detection of anomylous DNA. Bioinformatics, 21(13), 3053. [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. (2005) Consequence of functional Nod2 and Tlr4 mutations on gene transcription in Crohn's disease patients. Journal of Molecular Medicine, 83(8), 601-9. [Pubmed]
  • MWJ van Passel, A Bart, HH Thygesen, ACM Luyf, AHC van Kampen, A van der Ende (2005) An acquisition account of genomic islands based on genome signature comparisons. BMC genomics. 6(1), 163. [Pubmed]

2004

  • MWJ van Passel, A Bart, RJA Waaijer, ACM Luyf, AHC van Kampen, A van der Ende (2004) An in vitro strategy for the selective isolation of anomylous DNA from prokaryotic genomics. Nucleic Acids Research, 32(14), e114. [Pubmed]

2003

  • de Jonge RR, Vreijling JP, Meintjes A, Kwa MS, van Kampen AHC, van Schaik IN, Baas F. (2003) Transcriptional profile of the human peripheral nervous system by serial analysis of gene expression. Genomics, 82(20), 97-108. [Pubmed]
  • 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

  • Luyf ACM, de Gast J, van Kampen AHC (2002) Visualizing metabolic activity on a genome-wide scale Bioinformatics,18(6), 813-818. [Pubmed]
  • Ruijter JM, van Kampen AHC and Baas F (2002) Statistical evaluation of Serial Analysis of Gene Expression (SAGE) libraries: consequences for experimental design. Physiological Genomics, 11(2), 37-44. [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, Voûte 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]
  • Pauws E, van Kampen AHC, van de Graaf SAR, de Vijlder JJM, Ris-Stalpers C (2001) Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis, Nucleic Acids Research, 29(8), 1690-1694. [Pubmed]
  • Moreno JC, Pauws E, van Kampen AHC, Jedlickova M, de Vijlder JJM, Ris-Stalpers C(2001) Cloning of tissue-specific genes using serial analysis of gene expression and a novel computational substraction method, Genomics,75,70-76. [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]
Topic revision: r23 - 09 Oct 2012, ShayanShahand
 

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