Erik van Nimwegen
Affiliation: The Rockefeller University
- Scaling laws in the functional content of genomesErik 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
- Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomicsErik 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...
- PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogenyRahul 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...
- A probabilistic method to detect regulatory modulesSaurabh Sinha
Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 0021, USA
Bioinformatics 19:i292-301. 2003..The discovery of cis-regulatory modules in metazoan genomes is crucial for understanding the connection between genes and organism diversity...
- Transformation fingerprint: induced STAT3-C, v-Src and Ha-Ras cause small initial changes but similar established profiles in mRNAKeren 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...
- Decay rates of human mRNAs: correlation with functional characteristics and sequence attributesEdward Yang
Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10021 6399, USA
Genome Res 13:1863-72. 2003....
- Splice variation in mouse full-length cDNAs identified by mapping to the mouse genomeMihaela 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...
- Finding regulatory elements and regulatory motifs: a general probabilistic frameworkErik 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...
- Detecting regulatory sites using PhyloGibbsRahul 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...
- Universal patterns of purifying selection at noncoding positions in bacteriaNacho Molina
Biozentrum, The University of Basel, and Swiss Institute of Bioinformatics, 4056 CH, Basel, Switzerland
Genome Res 18:148-60. 2008....
- Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programsTzu 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...
- Inference of miRNA targets using evolutionary conservation and pathway analysisDimos 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...
- SwissRegulon: a database of genome-wide annotations of regulatory sitesMikhail 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...
- A simple physical model predicts small exon length variationsTzu 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...
- SPA: a probabilistic algorithm for spliced alignmentErik 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...
- Identification of clustered microRNAs using an ab initio prediction methodAlain 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...
- Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian methodLukas Burger
Biozentrum, The University of Basel, and Swiss Institute of Bioinformatics, Basel, Switzerland
Mol Syst Biol 4:165. 2008....
- Epidemiology. Influenza escapes immunity along neutral networksErik van Nimwegen
Division of Bioinformatics, Biozentrum, University of Basel, 4056 Basel, Switzerland
Science 314:1884-6. 2006
- The types and prevalence of alternative splice formsMihaela 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...