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Benoit Ballester

Researcher in Bioinformatics at INSERM
74%
Open access
39
Documents
Current affiliations
  • 182200
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Presentation

My research focuses on analyzing the non-coding regions of the human genome using high-throughput sequencing data, including ChIP-seq, RNA-seq, and more. I am particularly interested in understanding the crucial role these so-called non-coding regions play in gene regulation. Once labeled as "junk DNA," these regions are now recognized for their key and complex functions within our genome. My primary goal is to uncover how these yet un-annotated regulatory elements influence gene expression and genomic dynamics. To achieve this, we have created ReMap, a comprehensive catalogue of regulatory elements. This resource integrates data from thousands of public TF ChIP-seq experiments. Explore ReMap here: http://remap.univ-amu.fr/
Mes recherches se concentrent sur l'analyse des régions non codantes du génome humain à l'aide de données de séquençage à haut débit, telles que ChIP-seq, RNA-seq, et autres. Je m'intéresse particulièrement à comprendre le rôle crucial que ces régions dites non codantes jouent dans la régulation des gènes. Autrefois qualifiées de "ADN poubelle", ces régions sont maintenant reconnues pour leurs fonctions clés et complexes au sein de notre génome. Mon objectif principal est de découvrir comment ces éléments régulateurs encore non annotés influencent l'expression des gènes et la dynamique génomique. Pour ce faire, nous avons créé ReMap, un catalogue complet d'éléments régulateurs. Cette ressource intègre des données provenant de milliers d'expériences publiques de TF ChIP-seq. Explorez ReMap : : http://remap.univ-amu.fr/

Publications

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Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits

Jing Wan , Antoinette van Ouwerkerk , Jean-Christophe Mouren , Carla Heredia , Lydie Pradel
Nucleic Acids Research, 2024, ⟨10.1093/nar/gkae1270⟩
Journal articles hal-04882272v1
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MUFFIN: a suite of tools for the analysis of functional sequencing data

Pierre De langen , Benoit Ballester
NAR Genomics and Bioinformatics, 2024, 6 (2), pp.lqae051. ⟨10.1093/nargab/lqae051⟩
Journal articles hal-04642848v1
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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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles hal-03433360v1
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JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

Jaime A Castro-Mondragon , Rafael Riudavets-Puig , Ieva Rauluseviciute , Roza Berhanu Lemma , Laura Turchi
Nucleic Acids Research, 2022, 50 (D1), pp.D165-D173. ⟨10.1093/nar/gkab1113⟩
Journal articles hal-03463821v1
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Anomaly detection in genomic catalogues using unsupervised multi-view autoencoders

Quentin Ferré , Jeanne Chèneby , Denis Puthier , Cécile Capponi , Benoît Ballester
BMC Bioinformatics, 2021, 22 (1), pp.460. ⟨10.1186/s12859-021-04359-2⟩
Journal articles inserm-03356659v1
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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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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
Journal articles 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
Journal articles 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
Journal articles 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
Journal articles hal-01615158v1
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Consistent annotation of gene expression arrays

Benoit Ballester , Nathan Johnson , Glenn Proctor , Paul Flicek
BMC Genomics, 2010, 11, pp.294
Journal articles hal-01615157v1

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
Journal articles hal-01615156v1
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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⟩
Journal articles hal-01615162v1

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
Journal articles hal-01615161v1

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
Journal articles 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
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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
Journal articles 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⟩
Journal articles 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
Journal articles hal-01615164v1
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Genome-wide Characterization of Exons as Regulatory Elements

Jean-Christophe Mouren , Antoinette van Ouwerkerk , Magali Torres , Frédéric Gallardo , Salvatore Spicuglia
JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques 2024, Jun 2024, Toulouse, France
Conference poster hal-04633459v1