Erik van Nimwegen

Summary

Affiliation: The Rockefeller University
Country: USA

Publications

  1. ncbi request reprint Scaling laws in the functional content of genomes
    Erik van Nimwegen
    Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 12001, USA
    Trends Genet 19:479-84. 2003
  2. pmc Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics
    Erik van Nimwegen
    Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 99:7323-8. 2002
  3. pmc PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny
    Rahul Siddharthan
    Center for Studies in Physics and Biology, The Rockefeller University, New York, New York, United States of America
    PLoS Comput Biol 1:e67. 2005
  4. ncbi request reprint A probabilistic method to detect regulatory modules
    Saurabh Sinha
    Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 0021, USA
    Bioinformatics 19:i292-301. 2003
  5. ncbi request reprint Transformation fingerprint: induced STAT3-C, v-Src and Ha-Ras cause small initial changes but similar established profiles in mRNA
    Keren Paz
    Laboratory of Molecular Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Oncogene 23:8455-63. 2004
  6. pmc Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes
    Edward Yang
    Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10021 6399, USA
    Genome Res 13:1863-72. 2003
  7. pmc Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome
    Mihaela Zavolan
    Laboratory for Computational Genomics, The Rockefeller University, New York, New York 10021, USA
    Genome Res 12:1377-85. 2002
  8. pmc Finding regulatory elements and regulatory motifs: a general probabilistic framework
    Erik van Nimwegen
    Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Klingelbergstrasse 50 70, Basel, Switzerland
    BMC Bioinformatics 8:S4. 2007
  9. ncbi request reprint Detecting regulatory sites using PhyloGibbs
    Rahul Siddharthan
    Institute of Mathematical Sciences, India
    Methods Mol Biol 395:381-402. 2007
  10. pmc Universal patterns of purifying selection at noncoding positions in bacteria
    Nacho Molina
    Biozentrum, The University of Basel, and Swiss Institute of Bioinformatics, 4056 CH, Basel, Switzerland
    Genome Res 18:148-60. 2008

Collaborators

Detail Information

Publications19

  1. ncbi request reprint Scaling laws in the functional content of genomes
    Erik van Nimwegen
    Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 12001, USA
    Trends Genet 19:479-84. 2003
  2. pmc Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics
    Erik van Nimwegen
    Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 99:7323-8. 2002
    ..We predict 50-100 new regulons as well as many new members of existing regulons, potentially doubling the number of known regulatory sites in E. coli...
  3. pmc PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny
    Rahul Siddharthan
    Center for Studies in Physics and Biology, The Rockefeller University, New York, New York, United States of America
    PLoS Comput Biol 1:e67. 2005
    ..biozentrum.unibas.ch/~nimwegen/cgi-bin/phylogibbs.cgi or http://www.imsc.res.in/~rsidd/phylogibbs. The full set of predicted sites from our tests on yeast are available at http://www.swissregulon.unibas.ch...
  4. ncbi request reprint A probabilistic method to detect regulatory modules
    Saurabh Sinha
    Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 0021, USA
    Bioinformatics 19:i292-301. 2003
    ..The novel features are shown to improve detection of modules, in experiments on synthetic as well as biological data...
  5. ncbi request reprint Transformation fingerprint: induced STAT3-C, v-Src and Ha-Ras cause small initial changes but similar established profiles in mRNA
    Keren Paz
    Laboratory of Molecular Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Oncogene 23:8455-63. 2004
    ..However, with additional time and probably additional cell division, a new epigenetic state is established that is mirrored by a changed transcriptional profile emblematic of transformation by each of three oncogenes...
  6. pmc Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes
    Edward Yang
    Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10021 6399, USA
    Genome Res 13:1863-72. 2003
    ....
  7. pmc Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome
    Mihaela Zavolan
    Laboratory for Computational Genomics, The Rockefeller University, New York, New York 10021, USA
    Genome Res 12:1377-85. 2002
    ..This analysis indicates that an alternative choice of transcription start or polyadenylation signal frequently induces splice variation...
  8. pmc Finding regulatory elements and regulatory motifs: a general probabilistic framework
    Erik van Nimwegen
    Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Klingelbergstrasse 50 70, Basel, Switzerland
    BMC Bioinformatics 8:S4. 2007
    ..The main purpose of the article is to elucidate that all these methods are not a disconnected set of individual algorithmic recipes, but that they are just different facets of a single integrated probabilistic theory...
  9. ncbi request reprint Detecting regulatory sites using PhyloGibbs
    Rahul Siddharthan
    Institute of Mathematical Sciences, India
    Methods Mol Biol 395:381-402. 2007
    ..In this article, we explain how to use PhyloGibbs effectively. We describe the essential command-line options in detail, and discuss other considerations that arise in practical situations...
  10. pmc Universal patterns of purifying selection at noncoding positions in bacteria
    Nacho Molina
    Biozentrum, The University of Basel, and Swiss Institute of Bioinformatics, 4056 CH, Basel, Switzerland
    Genome Res 18:148-60. 2008
    ....
  11. pmc Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs
    Tzu Ming Chern
    Division of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50 70, Basel CH 4056, Switzerland
    DNA Res 15:63-72. 2008
    ..Our analysis thus suggests frequent coupling of transcriptional and splicing programs, and provides a large dataset of exons on which the molecular basis of this coupling can be further studied...
  12. pmc Inference of miRNA targets using evolutionary conservation and pathway analysis
    Dimos Gaidatzis
    Biozentrum, University of Basel, Basel, Switzerland
    BMC Bioinformatics 8:69. 2007
    ..In contrast, functional annotations are available only for a very small fraction of these miRNAs, and even in these cases only partially...
  13. pmc SwissRegulon: a database of genome-wide annotations of regulatory sites
    Mikhail Pachkov
    Biozentrum, The University of Basel, Klingelbergstrasse 50 70, 4056 CH, Basel, Switzerland
    Nucleic Acids Res 35:D127-31. 2007
    ..The database can also be queried for regulons, i.e. sites bound by a common factor...
  14. pmc A simple physical model predicts small exon length variations
    Tzu Ming Chern
    Division of Bioinformatics, Biozentrum, University of Basel, Basel, Switzerland
    PLoS Genet 2:e45. 2006
    ..Small exon length variations occur when there are nearby alternative splice sites that have similar affinity for the splicing machinery...
  15. pmc SPA: a probabilistic algorithm for spliced alignment
    Erik van Nimwegen
    Biozentrum, University of Basel, Basel, Switzerland
    PLoS Genet 2:e24. 2006
    ..The SPA software package is available at http://www.biozentrum.unibas.ch/personal/nimwegen/cgi-bin/spa.cgi...
  16. pmc Identification of clustered microRNAs using an ab initio prediction method
    Alain Sewer
    Biozentrum, Universitat Basel, Basel, Switzerland
    BMC Bioinformatics 6:267. 2005
    ..Bioinformatics approaches have proved to be very useful toward this goal by guiding the experimental investigations...
  17. pmc Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method
    Lukas Burger
    Biozentrum, The University of Basel, and Swiss Institute of Bioinformatics, Basel, Switzerland
    Mol Syst Biol 4:165. 2008
    ....
  18. ncbi request reprint Epidemiology. Influenza escapes immunity along neutral networks
    Erik van Nimwegen
    Division of Bioinformatics, Biozentrum, University of Basel, 4056 Basel, Switzerland
    Science 314:1884-6. 2006
  19. ncbi request reprint The types and prevalence of alternative splice forms
    Mihaela Zavolan
    Division of Bioinformatics, Biozentrum, University of Basel, Klingelberstrasse 50 70, Basel, CH 4056, Switzerland
    Curr Opin Struct Biol 16:362-7. 2006
    ..The result of these investigations is a continuously improving catalogue of alternative splice forms. How the expression of these alternative splice forms is regulated remains one of the major open questions...