J
Jacques van Helden
Researcher at Aix-Marseille University
Publications - 121
Citations - 10161
Jacques van Helden is an academic researcher from Aix-Marseille University. The author has contributed to research in topics: Gene & Genome. The author has an hindex of 41, co-authored 119 publications receiving 9306 citations. Previous affiliations of Jacques van Helden include Université libre de Bruxelles & French Institute of Health and Medical Research.
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Journal ArticleDOI
Assessing computational tools for the discovery of transcription factor binding sites.
Martin Tompa,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 T. Workman,Chun Ye,Zhou Zhu +24 more
TL;DR: The purpose of the current assessment is 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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Evaluation of clustering algorithms for protein-protein interaction networks
TL;DR: The analysis of high-throughput data supports the superiority of MCL for the extraction of complexes from interaction networks, and shows that MCL is remarkably robust to graph alterations.
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Regulatory Sequence Analysis Tools
TL;DR: The web resource Regulatory Sequence Analysis Tools (RSAT) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA sequences, which include sequence retrieval, pattern discovery, pattern matches, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities.
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Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
Alexander Stark,Michael F. Lin,Pouya Kheradpour,Jakob Skou Pedersen,Jakob Skou Pedersen,Leopold Parts,Leopold Parts,Joseph W. Carlson,Madeline A. Crosby,Matthew D. Rasmussen,Sushmita Roy,Ameya N. Deoras,J. Graham Ruby,Julius Brennecke,Emily Hodges,Angie S. Hinrichs,Anat Caspi,Benedict Paten,Benedict Paten,Benedict Paten,Seung-Won Park,Mira V. Han,Morgan L. Maeder,Benjamin J. Polansky,Bryanne E. Robson,Stein Aerts,Jacques van Helden,Bassem A. Hassan,Donald G. Gilbert,Deborah Eastman,Michael D. Rice,Michael P. Weir,Matthew W. Hahn,Yongkyu Park,Colin N. Dewey,Lior Pachter,W. James Kent,David Haussler,Eric C. Lai,David P. Bartel,Gregory J. Hannon,Thomas C. Kaufman,Michael B. Eisen,Michael B. Eisen,Andrew G. Clark,Douglas Smith,Susan E. Celniker,William M. Gelbart,Manolis Kellis +48 more
TL;DR: This work uses the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly, and identifies several classes of pre- and post-transcriptional regulatory motifs, and predicts individual motif instances with high confidence.
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Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
TL;DR: The dyad and single-word analyses are efficient for the detection of regulatory patterns in gene clusters from DNA chip experiments and should provide a fast and efficient way to discover new regulatory sites for as yet unknown transcription factors.