Literature DB >> 15637633

Assessing computational tools for the discovery of transcription factor binding sites.

Martin Tompa1, Nan Li, Timothy L Bailey, George M Church, Bart De Moor, Eleazar Eskin, Alexander V Favorov, Martin C Frith, Yutao Fu, W James Kent, Vsevolod J Makeev, Andrei A Mironov, William Stafford Noble, Giulio Pavesi, Graziano Pesole, Mireille Régnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu.   

Abstract

The prediction of regulatory elements is a problem where computational methods offer great hope. Over the past few years, numerous tools have become available for this task. The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools.

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Year:  2005        PMID: 15637633     DOI: 10.1038/nbt1053

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


  431 in total

Review 1.  Phylogenetic footprinting: a boost for microbial regulatory genomics.

Authors:  Pramod Katara; Atul Grover; Vinay Sharma
Journal:  Protoplasma       Date:  2011-11-24       Impact factor: 3.356

2.  A computational pipeline for comparative ChIP-seq analyses.

Authors:  Anaïs F Bardet; Qiye He; Julia Zeitlinger; Alexander Stark
Journal:  Nat Protoc       Date:  2011-12-15       Impact factor: 13.491

3.  The power of detecting enriched patterns: an HMM approach.

Authors:  Zhiyuan Zhai; Shih-Yen Ku; Yihui Luan; Gesine Reinert; Michael S Waterman; Fengzhu Sun
Journal:  J Comput Biol       Date:  2010-04       Impact factor: 1.479

4.  Changes in selective effects over time facilitate turnover of enhancer sequences.

Authors:  Kevin Bullaughey
Journal:  Genetics       Date:  2010-11-23       Impact factor: 4.562

5.  Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data.

Authors:  Roger Pique-Regi; Jacob F Degner; Athma A Pai; Daniel J Gaffney; Yoav Gilad; Jonathan K Pritchard
Journal:  Genome Res       Date:  2010-11-24       Impact factor: 9.043

6.  CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments.

Authors:  Lakshmi Kuttippurathu; Michael Hsing; Yongchao Liu; Bertil Schmidt; Douglas L Maskell; Kyungjoon Lee; Aibin He; William T Pu; Sek Won Kong
Journal:  Bioinformatics       Date:  2010-12-23       Impact factor: 6.937

Review 7.  Experimental strategies for studying transcription factor-DNA binding specificities.

Authors:  Marcel Geertz; Sebastian J Maerkl
Journal:  Brief Funct Genomics       Date:  2010-09-23       Impact factor: 4.241

8.  SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.

Authors:  Siwen Hu-Lieskovan; Srabani Bhaumik; Kavita Dhodapkar; Jean-Charles J B Grivel; Sumati Gupta; Brent A Hanks; Sylvia Janetzki; Thomas O Kleen; Yoshinobu Koguchi; Amanda W Lund; Cristina Maccalli; Yolanda D Mahnke; Ruslan D Novosiadly; Senthamil R Selvan; Tasha Sims; Yingdong Zhao; Holden T Maecker
Journal:  J Immunother Cancer       Date:  2020-12       Impact factor: 13.751

9.  Secondary structure and phylogenetic utility of the ribosomal large subunit (28S) in monogeneans of the genus Thaparocleidus and Bifurcohaptor (Monogenea: Dactylogyridae).

Authors:  Anshu Chaudhary; Hridaya Shanker Singh
Journal:  J Parasit Dis       Date:  2012-07-03

10.  Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics.

Authors:  Jason Gertz; Linda Riles; Peter Turnbaugh; Su-Wen Ho; Barak A Cohen
Journal:  Genome Res       Date:  2005-08       Impact factor: 9.043

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