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Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C

 Ferhat Ay , Thanh H. Vu , Michael J. Zeitz , Nelle Varoquaux , Jan E. Carette , et al.
BMC Genomics, 2015, 16, pp.121. ⟨10.1186/s12864-015-1236-7⟩
Article dans une revue hal-01152400v1
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circHiC: circular visualization of Hi-C data and integration of genomic data

 Ivan Junier , Nelle Varoquaux
2021
Pré-publication, Document de travail hal-02945275v1
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Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics

 Ling Xu , Zhaobin Dong , Dawn Chiniquy , Grady Pierroz , Siwen Deng , et al.
Nature Communications, 2021, 12 (1), ⟨10.1038/s41467-021-23553-7⟩
Article dans une revue hal-03375808v1

iced: fast and memory efficient normalization of contact maps

 Nelle Varoquaux , Nicolas Servant
Journal of Open Source Software, 2019
Article dans une revue hal-02313876v1
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Computational tools for the multiscale analysis of Hi-C data in bacterial chromosomes

 Nelle Varoquaux , Virginia S Lioy , Frédéric Boccard , Ivan Junier
Hi-C Data Analysis, 2301, Springer US, pp.197-207, 2021, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1390-0_10⟩
Chapitre d'ouvrage hal-03375884v1

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

 Ferhat Ay , Evelien M. Bunnik , Nelle Varoquaux , Sebastiaan M. Bol , Jacques Prudhomme , et al.
Genome Research, 2014, 24, pp.974-988. ⟨10.1101/gr.169417.113⟩
Article dans une revue hal-01101873v1

Proceedings of the 7th European Conference on Python in Science (EuroSciPy 2014)

 Pierre de Buyl , Nelle Varoquaux
2014
Ouvrages hal-01584599v1

Measuring Cluster Stability for Bayesian Nonparametrics Using the Linear Bootstrap

 Ryan Giordano , Runjing Liu , Nelle Varoquaux , Michael I. Jordan , Tamara Broderick
2017
Pré-publication, Document de travail hal-01660484v1
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Unfolding the Genome: The Case Study of P. falciparum

 Nelle Varoquaux
The international journal of biostatistics, 2019, 15 (2), ⟨10.1515/ijb-2017-0061⟩
Article dans une revue hal-03375803v1
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A pipeline to analyse time-course gene expression data

 Nelle Varoquaux , Elizabeth Purdom
F1000Research, 2020, 9, pp.1447. ⟨10.12688/f1000research.27262.1⟩
Article dans une revue hal-03375800v1
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Cell Wall Compositions of Sorghum bicolor Leaves and Roots Remain Relatively Constant Under Drought Conditions

 Tess Scavuzzo-Duggan , Nelle Varoquaux , Mary Madera , John P Vogel , Jeffery Dahlberg , et al.
Frontiers in Plant Science, 2021, 12, ⟨10.3389/fpls.2021.747225⟩
Article dans une revue hal-03428264v1

Inference of genome 3D architecture by modeling overdispersion of Hi-C data

 Nelle Varoquaux , William Noble , Jean-Philippe Vert
2021
Pré-publication, Document de travail hal-03375900v1
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Inferring the 3D architecture of the genome

 Nelle Varoquaux
Bioinformatics [q-bio.QM]. Ecole Nationale Supérieure des Mines de Paris, 2015. English. ⟨NNT : 2015ENMP0059⟩
Thèse tel-01306953v1

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum

 Ferhat Ay , Evelien M. Bunnik , Nelle Varoquaux , Jean-Philippe Vert , William Stafford Noble , et al.
BioEssays, 2015, 37 (2), pp.182-194. ⟨10.1002/bies.201400145⟩
Article dans une revue hal-01246696v1

Diversification of ubiquinone biosynthesis via gene duplications, transfers, losses, and parallel evolution

 Katayoun Kazemzadeh , Ludovic Pelosi , Clothilde Chenal , Sophie-Carole Chobert , Mahmoud Hajj Chehade , et al.
Molecular Biology and Evolution, 2023, 40 (10), pp.msad219. ⟨10.1093/molbev/msad219⟩
Article dans une revue hal-04256893v1
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Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses

 Nelle Varoquaux , Benjamin Cole , Cheng Gao , Grady Pierroz , Christopher Baker , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2019, 116 (52), pp.27124-27132. ⟨10.1073/pnas.1907500116⟩
Article dans une revue hal-02945234v1
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Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression

 Cheng Gao , Pierre-Emmanuel Courty , Nelle Varoquaux , Benjamin Cole , Liliam Montoya , et al.
Molecular Ecology, 2023, 32 (10), pp.2674-2687. ⟨10.1111/mec.16343⟩
Article dans une revue hal-03375810v1

Accurate identification of centromere locations in yeast genomes using Hi-C

 Nelle Varoquaux , Ivan Liachko , Ferhat Ay , Joshua N. Burton , Jay Shendure , et al.
Nucleic Acids Research, 2015, 43 (11), pp.5331-5339. ⟨10.1093/nar/gkv424⟩
Article dans une revue hal-01246687v1

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

 Nicolas Servant , Nelle Varoquaux , R. Lajoie Bryan , Eric Viara , Chong-Jian Chen , et al.
Genome Biology, 2015, 16, pp.259. ⟨10.1186/s13059-015-0831-x⟩
Article dans une revue hal-01246671v1

Effective normalization for copy number variation in Hi-C data

 Nicolas Servant , Nelle Varoquaux , Edith Heard , Jean-Philippe Vert , Emmanuel Barillot
2017
Pré-publication, Document de travail hal-01584621v1

Inference of genome 3D architecture by modeling overdispersion of Hi-C data

 Nelle Varoquaux , William Noble , Jean-Philippe Vert
2022
Pré-publication, Document de travail hal-03510305v1

Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages

 Evelien Bunnik , Kate Cook , Nelle Varoquaux , Gayani Batugedara , Jacques Prudhomme , et al.
Nature Communications, 2018, 9 (1)
Article dans une revue hal-01985437v1
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A community effort to assess and improve drug sensitivity prediction algorithms

 James C Costello , Laura M Heiser , Elisabeth Georgii , Mehmet Gönen , Michael P Menden , et al.
Nature Biotechnology, 2014, 32, pp.1202-1212. ⟨10.1038/nbt.2877⟩
Article dans une revue hal-01101874v1
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Inference of 3D genome architecture by modeling overdispersion of Hi-C data

 Nelle Varoquaux , William Noble , Jean-Philippe Vert
Bioinformatics, 2023, 39 (1), ⟨10.1093/bioinformatics/btac838⟩
Article dans une revue hal-04234569v1

A statistical approach for inferring the three-dimensional structure of the genome

 Nelle Varoquaux , Ferhat Ay , William Stafford Noble , Jean-Philippe Vert
Bioinformatics, 2014, 30 (12), pp.i26-i33. ⟨10.1093/bioinformatics/btu268⟩
Article dans une revue hal-01101869v1
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Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation

 Virginia S Lioy , Jean-Noel Lorenzi , Soumaya Najah , Thibault Poinsignon , Herve Leh , et al.
Nature Communications, 2021, 12, pp.5221. ⟨10.1038/s41467-021-25462-1⟩
Article dans une revue hal-03128776v2
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A statistical approach for inferring the three-dimensional structure of the genome

 Nelle Varoquaux , Ferhat Ay , William Stafford Noble , Jean-Philippe Vert
2014
Pré-publication, Document de travail hal-00937182v1
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Inferring Diploid 3D Chromatin Structures from Hi-C Data

 Ra Gesine Cauer , Gurkan Yardimci , Jean-Philippe Vert , Nelle Varoquaux , William Stafford Noble
19th International Workshop on Algorithms in Bioinformatics (WABI 2019), 2019, ⟨10.4230/LIPIcs.WABI.2019.11⟩
Article dans une revue hal-02444745v1
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The Types, Roles, and Practices of Documentation in Data Analytics Open Source Software Libraries

 R. Stuart Geiger , Nelle Varoquaux , Charlotte Mazel-Cabasse , Chris ​ Holdgraf
Computer Supported Cooperative Work, 2018, 27 (3-6), pp.767-802. ⟨10.1007/s10606-018-9333-1⟩
Article dans une revue hal-02313888v1
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Effective normalization for copy number variation in Hi-C data

 Nicolas Servant , Nelle Varoquaux , Edith Heard , Emmanuel Barillot , Jean-Philippe Vert
BMC Bioinformatics, 2018, 19 (1), pp.313. ⟨10.1186/s12859-018-2256-5⟩
Article dans une revue inserm-02059124v1
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