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ORCIDOscar P. Kuipers
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Journal Articles
- 2022
[j19]Anne de Jong
, Oscar P. Kuipers, Jan Kok:
FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes. Nucleic Acids Res. 50(W1): 330-336 (2022)- 2018
- [j18]Auke J. van Heel, Anne de Jong, Chunxu Song, Jakob H. Viel, Jan Kok, Oscar P. Kuipers:
BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Res. 46(Webserver-Issue): W278-W281 (2018) - 2014
- [j17]Robyn T. Eijlander, Anne de Jong, Antonina O. Krawczyk, Siger Holsappel, Oscar P. Kuipers:
SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis. Nucleic Acids Res. 42(Database-Issue): 685-691 (2014) - 2013
- [j16]Auke J. van Heel, Anne de Jong, Manuel Montalbán-López, Jan Kok, Oscar P. Kuipers:
BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Res. 41(Webserver-Issue): 448-453 (2013) - 2010
- [j15]Michel A. Westenberg, Jos B. T. M. Roerdink, Oscar P. Kuipers, Sacha A. F. T. van Hijum:
SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks. Bioinform. 26(22): 2922-2923 (2010) - [j14]Anne de Jong, Auke J. van Heel, Jan Kok, Oscar P. Kuipers:
BAGEL2: mining for bacteriocins in genomic data. Nucleic Acids Res. 38(Web-Server-Issue): 647-651 (2010) - 2009
- [j13]Rutger W. W. Brouwer, Sacha A. F. T. van Hijum, Oscar P. Kuipers:
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context. Bioinform. 25(1): 139-140 (2009) - [j12]Evert-Jan Blom, Jos B. T. M. Roerdink, Oscar P. Kuipers, Sacha A. F. T. van Hijum:
MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data. Bioinform. 25(4): 550-551 (2009) - 2008
- [j11]Rutger W. W. Brouwer, Oscar P. Kuipers, Sacha A. F. T. van Hijum:
The relative value of operon predictions. Briefings Bioinform. 9(5): 367-375 (2008) - [j10]Evert-Jan Blom, Sacha A. F. T. van Hijum, Klaas J. Hofstede, Remko Silvis, Jos B. T. M. Roerdink, Oscar P. Kuipers:
DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites. BMC Bioinform. 9 (2008) - [j9]Sacha A. F. T. van Hijum, Richard J. S. Baerends, Aldert L. Zomer, Harma A. Karsens, Victoria Martin-Requena, Oswaldo Trelles, Jan Kok, Oscar P. Kuipers:
Supervised Lowess normalization of comparative genome hybridization data - application to lactococcal strain comparisons. BMC Bioinform. 9 (2008) - [j8]Michel A. Westenberg, Sacha A. F. T. van Hijum, Oscar P. Kuipers, Jos B. T. M. Roerdink:
Visualizing Genome Expression and Regulatory Network Dynamics in Genomic and Metabolic Context. Comput. Graph. Forum 27(3): 887-894 (2008) - 2007
- [j7]Evert-Jan Blom, Dinne W. J. Bosman, Sacha A. F. T. van Hijum, Rainer Breitling, Lars Tijsma, Remko Silvis, Jos B. T. M. Roerdink, Oscar P. Kuipers:
FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes. Bioinform. 23(9): 1161-1163 (2007) - [j6]Diederik W. J. Bosman, Evert-Jan Blom, Patrick J. Ogao, Oscar P. Kuipers, Jos B. T. M. Roerdink:
MOVE: A Multi-Level Ontology-Based Visualization and Exploration Framework for Genomic Networks. Silico Biol. 7(1): 35-59 (2007) - 2006
- [j5]Casper J. Albers, Ritsert C. Jansen, Jan Kok, Oscar P. Kuipers, Sacha A. F. T. van Hijum:
SIMAGE: simulation of DNA-microarray gene expression data. BMC Bioinform. 7: 205 (2006) - [j4]Anne de Jong, Sacha A. F. T. van Hijum, Jetta J. E. Bijlsma, Jan Kok, Oscar P. Kuipers:
BAGEL: a web-based bacteriocin genome mining tool. Nucleic Acids Res. 34(Web-Server-Issue): 273-279 (2006) - 2005
- [j3]Sacha A. F. T. van Hijum, Aldert L. Zomer, Oscar P. Kuipers, Jan Kok:
Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res. 33(Web-Server-Issue): 560-566 (2005) - 2004
- [j2]Morris A. Swertz, Engbert O. de Brock, Sacha A. F. T. van Hijum, Anne de Jong, Girbe Buist, Richard J. S. Baerends, Jan Kok, Oscar P. Kuipers, Ritsert C. Jansen:
Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. Bioinform. 20(13): 2075-2083 (2004) - 2003
- [j1]Sacha A. F. T. van Hijum, Anne de Jong, Girbe Buist, Jan Kok, Oscar P. Kuipers:
UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons. Bioinform. 19(12): 1580-1582 (2003)
Parts in Books or Collections
- 2008
- [p1]Michel A. Westenberg, Sacha A. F. T. van Hijum, Andrzej T. Lulko, Oscar P. Kuipers, Jos B. T. M. Roerdink:
Interactive Visualization of Gene Regulatory Networks with Associated Gene Expression Time Series Data. Visualization in Medicine and Life Sciences 2008: 293-311
Coauthor Index
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