Literature DB >> 18703586

GIMSAN: a Gibbs motif finder with significance analysis.

Patrick Ng1, Uri Keich.   

Abstract

UNLABELLED: We present GIMSAN (GIbbsMarkov with Significance ANalysis): a novel tool for de novo motif finding. GIMSAN combines GibbsMarkov, our variant of the Gibbs Sampler, described here for the first time, with our recently introduced significance analysis. AVAILABILITY: GIMSAN is currently available as a web application and a stand-alone application on Unix and PBS (Portable Batch System) cluster through links from http://www.cs.cornell.edu/~keich.

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Year:  2008        PMID： 18703586     DOI： 10.1093/bioinformatics/btn408

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  20 in total

1.  New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior.

Authors:  Seth A Ament; Charles A Blatti; Cedric Alaux; Marsha M Wheeler; Amy L Toth; Yves Le Conte; Greg J Hunt; Ernesto Guzmán-Novoa; Gloria Degrandi-Hoffman; Jose Luis Uribe-Rubio; Gro V Amdam; Robert E Page; Sandra L Rodriguez-Zas; Gene E Robinson; Saurabh Sinha
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-12       Impact factor: 11.205

2.  coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq data.

Authors:  Mengyuan Xu; Clarice R Weinberg; David M Umbach; Leping Li
Journal:  Bioinformatics       Date:  2011-07-19       Impact factor: 6.937

3.  Improving MEME via a two-tiered significance analysis.

Authors:  Emi Tanaka; Timothy L Bailey; Uri Keich
Journal:  Bioinformatics       Date:  2014-03-24       Impact factor: 6.937

Review 4.  Identification of RNA-protein interaction networks using PAR-CLIP.

Authors:  Manuel Ascano; Markus Hafner; Pavol Cekan; Stefanie Gerstberger; Thomas Tuschl
Journal:  Wiley Interdiscip Rev RNA       Date:  2011-12-27       Impact factor: 9.957

5.  PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites.

Authors:  Charles Danan; Sudhir Manickavel; Markus Hafner
Journal:  Methods Mol Biol       Date:  2016

6.  A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.

Authors:  Ivan Liachko; Anand Bhaskar; Chanmi Lee; Shau Chee Claire Chung; Bik-Kwoon Tye; Uri Keich
Journal:  PLoS Genet       Date:  2010-05-13       Impact factor: 5.917

7.  High-resolution profiling of the LEDGF/p75 chromatin interaction in the ENCODE region.

Authors:  Jan De Rijck; Koen Bartholomeeusen; Hugo Ceulemans; Zeger Debyser; Rik Gijsbers
Journal:  Nucleic Acids Res       Date:  2010-05-19       Impact factor: 16.971

8.  Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition.

Authors:  Markus Hafner; Klaas E A Max; Pradeep Bandaru; Pavel Morozov; Stefanie Gerstberger; Miguel Brown; Henrik Molina; Thomas Tuschl
Journal:  RNA       Date:  2013-03-12       Impact factor: 4.942

9.  Intracellular Action of a Secreted Peptide Required for Fungal Virulence.

Authors:  Christina M Homer; Diana K Summers; Alexi I Goranov; Starlynn C Clarke; Darin L Wiesner; Jolene K Diedrich; James J Moresco; Dena Toffaletti; Rajendra Upadhya; Ippolito Caradonna; Sarah Petnic; Veronica Pessino; Christina A Cuomo; Jennifer K Lodge; John Perfect; John R Yates; Kirsten Nielsen; Charles S Craik; Hiten D Madhani
Journal:  Cell Host Microbe       Date:  2016-05-19       Impact factor: 21.023

10.  Towards a theoretical understanding of false positives in DNA motif finding.

Authors:  Amin Zia; Alan M Moses
Journal:  BMC Bioinformatics       Date:  2012-06-27       Impact factor: 3.169
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