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Erik van Nimwegen - Publications

Affiliations: 
Biozentrum University of Basel, Basel, Basel-Stadt, Switzerland 
Area:
computational biology, genomics, systems biology, transcription regulation, genome evolution
Website:
https://www.biozentrum.unibas.ch/research/researchgroups/overview/unit/nimwegen/research-group-erik-van-nimwegen/
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33 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Katsantoni M, van Nimwegen E, Zavolan M. Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs. Genome Biology. 24: 77. PMID 37069586 DOI: 10.1186/s13059-023-02913-0  0.384
2022 Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N, Wragg J, D'Orazio FM, Relic D, Pachkov M, Díaz N, ... ... van Nimwegen E, et al. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nature Genetics. PMID 35789323 DOI: 10.1038/s41588-022-01089-w  0.396
2021 Sakoparnig T, Field C, van Nimwegen E. Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species. Elife. 10. PMID 33416498 DOI: 10.7554/eLife.65366  0.327
2019 Berger SM, Pachkov M, Arnold P, Omidi S, Kelley N, Salatino S, van Nimwegen E. Crunch: Integrated processing and modeling of ChIP-seq data in terms of regulatory motifs. Genome Research. PMID 31138617 DOI: 10.1101/gr.239319.118  0.407
2018 Gruber AJ, Schmidt R, Ghosh S, Martin G, Gruber AR, van Nimwegen E, Zavolan M. Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC. Genome Biology. 19: 44. PMID 29592812 DOI: 10.1186/s13059-018-1415-3  0.309
2017 Omidi S, Zavolan M, Pachkov M, Breda J, Berger S, van Nimwegen E. Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. Plos Computational Biology. 13: e1005176. PMID 28753602 DOI: 10.1371/journal.pcbi.1005176  0.349
2016 Salatino S, Kupr B, Baresic M, Omidi S, van Nimwegen E, Handschin C. The Genomic Context and Corecruitment of SP1 Affect ERRα Coactivation by PGC-1α in Muscle Cells. Molecular Endocrinology (Baltimore, Md.). 30: 809-25. PMID 27182621 DOI: 10.1210/me.2016-1036  0.306
2014 Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, ... ... van Nimwegen E, et al. A promoter-level mammalian expression atlas. Nature. 507: 462-70. PMID 24670764 DOI: 10.1038/Nature13182  0.324
2014 Bertels F, Silander OK, Pachkov M, Rainey PB, van Nimwegen E. Automated reconstruction of whole-genome phylogenies from short-sequence reads. Molecular Biology and Evolution. 31: 1077-88. PMID 24600054 DOI: 10.1093/Molbev/Msu088  0.37
2014 Balwierz PJ, Pachkov M, Arnold P, Gruber AJ, Zavolan M, van Nimwegen E. ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs. Genome Research. 24: 869-84. PMID 24515121 DOI: 10.1101/gr.169508.113  0.368
2013 Ozonov EA, van Nimwegen E. Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers. Plos Computational Biology. 9: e1003181. PMID 23990766 DOI: 10.1371/journal.pcbi.1003181  0.331
2013 Pachkov M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E. SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Research. 41: D214-20. PMID 23180783 DOI: 10.1093/nar/gks1145  0.556
2013 Arnold P, Schöler A, Pachkov M, Balwierz PJ, Jørgensen H, Stadler MB, van Nimwegen E, Schübeler D. Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome Research. 23: 60-73. PMID 22964890 DOI: 10.1101/gr.142661.112  0.308
2012 Arnold P, Erb I, Pachkov M, Molina N, Van Nimwegen E. MotEvo: Integrated bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences Bioinformatics. 28: 487-494. PMID 22334039 DOI: 10.1093/Bioinformatics/Btr695  0.615
2011 Erb I, van Nimwegen E. Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters. Plos One. 6: e24279. PMID 21931670 DOI: 10.1371/journal.pone.0024279  0.376
2011 Kawaji H, Severin J, Lizio M, Forrest AR, van Nimwegen E, Rehli M, Schroder K, Irvine K, Suzuki H, Carninci P, Hayashizaki Y, Daub CO. Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Research. 39: D856-60. PMID 21075797 DOI: 10.1093/Nar/Gkq1112  0.409
2010 Chen K, van Nimwegen E, Rajewsky N, Siegal ML. Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae. Genome Biology and Evolution. 2: 697-707. PMID 20829281 DOI: 10.1093/gbe/evq054  0.37
2009 Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biology. 10: R79. PMID 19624849 DOI: 10.1186/Gb-2009-10-7-R79  0.374
2009 Molina N, van Nimwegen E. Scaling laws in functional genome content across prokaryotic clades and lifestyles Trends in Genetics. 25: 243-247. PMID 19457568 DOI: 10.1016/J.Tig.2009.04.004  0.618
2009 Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics. 41: 553-62. PMID 19377474 DOI: 10.1038/Ng.375  0.309
2009 Taddei A, Van Houwe G, Nagai S, Erb I, van Nimwegen E, Gasser SM. The functional importance of telomere clustering: global changes in gene expression result from SIR factor dispersion. Genome Research. 19: 611-25. PMID 19179643 DOI: 10.1101/gr.083881.108  0.31
2008 Molina N, van Nimwegen E. The evolution of domain-content in bacterial genomes Biology Direct. 3. PMID 19077245 DOI: 10.1186/1745-6150-3-51  0.628
2008 Schlecht U, Erb I, Demougin P, Robine N, Borde V, van Nimwegen E, Nicolas A, Primig M. Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast. Molecular Biology of the Cell. 19: 2193-207. PMID 18305101 DOI: 10.1091/Mbc.E07-12-1242  0.36
2008 Burger L, van Nimwegen E. Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Molecular Systems Biology. 4: 165. PMID 18277381 DOI: 10.1038/msb4100203  0.318
2008 Molina N, Van Nimwegen E. Universal patterns of purifying selection at noncoding positions in bacteria Genome Research. 18: 148-160. PMID 18032729 DOI: 10.1101/Gr.6759507  0.652
2007 Siddharthan R, van Nimwegen E. Detecting regulatory sites using PhyloGibbs. Methods in Molecular Biology (Clifton, N.J.). 395: 381-402. PMID 17993687  0.305
2007 Pachkov M, Erb I, Molina N, van Nimwegen E. SwissRegulon: A database of genome-wide annotations of regulatory sites Nucleic Acids Research. 35. PMID 17130146 DOI: 10.1093/Nar/Gkl857  0.649
2006 Chern TM, van Nimwegen E, Kai C, Kawai J, Carninci P, Hayashizaki Y, Zavolan M. A simple physical model predicts small exon length variations. Plos Genetics. 2: e45. PMID 16683028 DOI: 10.1371/Journal.Pgen.0020045  0.311
2006 van Nimwegen E, Paul N, Sheridan R, Zavolan M. SPA: a probabilistic algorithm for spliced alignment. Plos Genetics. 2: e24. PMID 16683023 DOI: 10.1371/journal.pgen.0020024  0.415
2005 Siddharthan R, Siggia ED, van Nimwegen E. PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. Plos Computational Biology. 1: e67. PMID 16477324 DOI: 10.1371/Journal.Pcbi.0010067  0.381
2003 van Nimwegen E. Scaling laws in the functional content of genomes. Trends in Genetics : Tig. 19: 479-84. PMID 12957540 DOI: 10.1016/S0168-9525(03)00203-8  0.449
2002 Zavolan M, Van Nimwegen E, Gaasterland T. Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome Genome Research. 12: 1377-1385. PMID 12213775 DOI: 10.1101/gr.191702  0.34
2002 van Nimwegen E, Zavolan M, Rajewsky N, Siggia ED. Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics. Proceedings of the National Academy of Sciences of the United States of America. 99: 7323-8. PMID 12032281 DOI: 10.1073/Pnas.112690399  0.333
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