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Benoit Ballester

34
Documents
Identifiants chercheurs

Présentation

Researcher (Academic) - TAGC (INSERM, Aix Marseille Univ)

Publications

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ChagasDB: 80 years of publicly available data on the molecular host response to Trypanosoma cruzi infection in a single database

Pauline Brochet , Jean-Christophe Mouren , Laurent Hannouche , Fabrice Lopez , Benoit Ballester
Database - The journal of Biological Databases and Curation, 2023, 2023, pp.baad037. ⟨10.1093/database/baad037⟩
Article dans une revue hal-04284853v1
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Characterizing intergenic transcription at RNA polymerase II binding sites in normal and cancer tissues

Pierre de Langen , Fayrouz Hammal , Elise Guéret , Jean-Christophe Mouren , Lionel Spinelli
Cell Genomics, 2023, 3, pp.100411. ⟨10.1016/j.xgen.2023.100411⟩
Article dans une revue hal-04228229v1
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ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments

Fayrouz Hammal , Pierre De langen , Aurélie Bergon , Fabrice Lopez , Benoit Ballester
Nucleic Acids Research, 2022, ⟨10.1093/nar/gkab996⟩
Article dans une revue hal-03433360v1
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A predictable conserved DNA base composition signature defines human core DNA replication origins

Ildem Akerman , Bahar Kasaai , Alina Bazarova , Pau Biak Sang , Isabelle Peiffer
Nature Communications, 2020, ⟨10.1038/s41467-020-18527-0⟩
Article dans une revue hal-02945610v1
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ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments

Jeanne Chèneby , Zacharie Ménétrier , Martin Mestdagh , Thomas Rosnet , Allyssa Douida
Nucleic Acids Research, 2020, ⟨10.1093/nar/gkz945⟩
Article dans une revue hal-02351736v1
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JASPAR 2020: update of the open-access database of transcription factor binding profiles.

Oriol Fornés , Jaime Castro-Mondragon , Aziz Khan , Robin van Der Lee , Xi Zhang
Nucleic Acids Research, 2020, 48 (D1), pp.D87-D92. ⟨10.1093/nar/gkz1001⟩
Article dans une revue hal-02365013v1
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Insights gained from a comprehensive all- against-all transcription factor binding motif benchmarking study

Giovanna Ambrosini , Ilya Vorontsov , Dmitry Penzar , Romain Groux , Oriol Fornés
Genome Biology, 2020, 21 (1), ⟨10.1186/s13059-020-01996-3⟩
Article dans une revue hal-02773294v1
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A map of direct TF–DNA interactions in the human genome

Marius Gheorghe , Geir Kjetil Sandve , Aziz Khan , Jeanne Chèneby , Benoit Ballester
Nucleic Acids Research, 2019, 47 (14), pp.7715-7715. ⟨10.1093/nar/gkz582⟩
Article dans une revue hal-02531478v1
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A map of direct TF–DNA interactions in the human genome

Marius Gheorghe , Geir Kjetil Sandve , Aziz Khan , Jeanne Chèneby , Benoit Ballester
Nucleic Acids Research, 2019, ⟨10.1093/nar/gky1210⟩
Article dans une revue hal-01980383v1
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Involvement of G-quadruplex regions in mammalian replication origin activity

Paulina Prorok , Marie Artufel , Antoine Aze , Philippe Coulombe , Isabelle Peiffer
Nature Communications, 2019, 10 (1), pp.3274. ⟨10.1038/s41467-019-11104-0⟩
Article dans une revue hal-03101805v1
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JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

Aziz Khan , Oriol Fornés , Arnaud Stigliani , Marius Gheorghe , Jaime A. Castro-Mondragon
Nucleic Acids Research, 2018, 46 (D1), pp.D260-D266. ⟨10.1093/nar/gkx1126⟩
Article dans une revue hal-01646126v1
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Erratum. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

Robin Van der lee , Benoit Ballester , François Parcy , Aziz Khan , Oriol Fornés
Nucleic Acids Research, 2018, 46 (D1), pp.D1284-D1284. ⟨10.1093/nar/gkx1188⟩
Article dans une revue hal-01980416v1
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ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

Jeanne Chèneby , Marius Gheorghe , Marie Artufel , Anthony Mathelier , Benoit Ballester
Nucleic Acids Research, 2018, 46 (D1), pp.D267-D275. ⟨10.1093/nar/gkx1092⟩
Article dans une revue hal-01646201v1
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High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

Laurent Vanhille , Aurélien Griffon , Muhammad Ahmad Maqbool , Joaquin Zacarias-Cabeza , Lan T.M. Dao
Nature Communications, 2015, 6, pp.6905. ⟨10.1038/ncomms7905⟩
Article dans une revue hal-01614948v1
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Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

Aurélien Griffon , Quentin Barbier , Jordi Dalino , Jacques van Helden , Salvatore Spicuglia
Nucleic Acids Research, 2015, 43 (e27), ⟨10.1093/nar/gku1280⟩
Article dans une revue hal-01219379v1
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The chromatin environment shapes DNA replication origin organization and defines origin classes

Christelle Cayrou , Benoit Ballester , Isabelle Peiffer , Romain Fenouil , Philippe Coulombe
Genome Research, 2015, 25 (12), pp.1873-1885. ⟨10.1101/gr.192799.115⟩
Article dans une revue hal-03101863v1
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Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

Benoit Ballester , Alejandra Medina-Rivera , Dominic Schmidt , Mar Gonzàlez-Porta , Matthew Carlucci
eLife, 2014, 462, pp.e02626. ⟨10.7554/eLife.02626.031⟩
Article dans une revue hal-01455448v1
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TAF4, a subunit of transcription factor II D, directs promoter occupancy of nuclear receptor HNF4A during post-natal hepatocyte differentiation

Daniil Alpern , Diana Langer , Benoit Ballester , Stephanie Le Gras , Christophe Romier
eLife, 2014, 3, pp.308-312. ⟨10.7554/eLife.03613.001⟩
Article dans une revue hal-01404987v1

A CpG mutational hotspot in a ONECUT binding site accounts for the prevalent variant of hemophilia B Leyden.

Alister P W Funnell , Michael D Wilson , Benoit Ballester , Ka Sin Mak , Jon Burdach
American Journal of Human Genetics, 2013, 92 (3), pp.460--467
Article dans une revue hal-01615153v1

Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages

Dominic Schmidt , Petra C Schwalie , Michael D Wilson , Benoit Ballester , Angela Goncalves
Cell, 2012, 148 (1-2), pp.335--348
Article dans une revue hal-01615154v1

Identification of proteomic signatures of mantle cell lymphoma, small lymphocytic lymphoma, and marginal zone lymphoma biopsies by surface enhanced laser desorption/ionization-time of flight mass spectrometry.

Delphine Rolland , Ali Bouamrani , Rémi Houlgatte , Aurélie Barbarat , Claire Ramus
Leukemia & lymphoma, 2011, 52 (4), pp.648--658
Article dans une revue hal-01615155v1

Ensembl's 10th year.

Nathan Johnson , Andreas Kähäri , Damian Keefe , Stephen Keenan , Rhoda Kinsella
Nucleic Acids Research, 2010, 38 (Database issue), pp.D557--62
Article dans une revue hal-01615158v1

Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding

Dominic Schmidt , Michael D Wilson , Benoit Ballester , Petra C Schwalie , Gordon D Brown
Science (New York, NY), 2010, 328 (5981), pp.1036--1040
Article dans une revue hal-01615156v1
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Consistent annotation of gene expression arrays

Benoit Ballester , Nathan Johnson , Glenn Proctor , Paul Flicek
BMC Genomics, 2010, 11, pp.294
Article dans une revue hal-01615157v1

Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues.

Mark Carlile , Daniel Swan , Kelly Jackson , Keziah Preston-Fayers , Benoit Ballester
Nucleic Acids Research, 2009, 37 (7), pp.2274--2282
Article dans une revue hal-01615161v1
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BioMart―biological queries made easy

Damian Smedley , Syed Haider , Benoit Ballester , Richard Holland , Darin London
BMC Genomics, 2009, 10 (1), pp.22. ⟨10.1186/1471-2164-10-22⟩
Article dans une revue hal-01615162v1

BioMart Central Portal―unified access to biological data.

Syed Haider , Benoit Ballester , Damian Smedley , Junjun Zhang , Peter Rice
Nucleic Acids Research, 2009, 37 (Web Server issue), pp.W23--7
Article dans une revue hal-01615159v1

Ensembl 2009.

T J P Hubbard , B L Aken , S Ayling , Benoit Ballester , K Beal
Nucleic Acids Research, 2009, 37 (Database issue), pp.D690--7
Article dans une revue hal-01615160v1

Ensembl 2008

P. Flicek , B. Aken , K. Beal , Benoit Ballester , M. Caccamo
Nucleic Acids Research, 2007, 36 (Database), pp.D707 - D714. ⟨10.1093/nar/gkm988⟩
Article dans une revue hal-01626053v1

Gene expression profiling identifies molecular subgroups among nodal peripheral T-cell lymphomas

B Ballester , O Ramuz , C Gisselbrecht , G Doucet , L Loi
Oncogene, 2006, 25 (10), pp.1560-1570. ⟨10.1038/sj.onc.1209178⟩
Article dans une revue hal-01612147v1

Ensembl 2007.

T J P Hubbard , B L Aken , K Beal , Benoit Ballester , M Caccamo
Nucleic Acids Research, 2006, 35 (Database issue), pp.D610--7
Article dans une revue hal-01615163v1

Gene profiling reveals specific oncogenic mechanisms and signaling pathways in oncocytic and papillary thyroid carcinoma

O Baris , D Mirebeau-Prunier , F Savagner , P Rodien , B Ballester
Oncogene, 2005, 24 (25), pp.4155-4161. ⟨10.1038/sj.onc.1208578⟩
Article dans une revue hal-01612148v1

The Sgp3 locus on mouse chromosome 13 regulates nephritogenic gp70 autoantigen expression and predisposes to autoimmunity

Catherine Laporte , Benoit Ballester , Charles Mary , Shozo Izui , Luc Reininger
Journal of Immunology, 2003, 171 (7), pp.3872--3877
Article dans une revue hal-01615164v1