Nelle Varoquaux
Nelle Varoquaux
CNRS, Université Grenoble Alpes
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HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
N Servant, N Varoquaux, BR Lajoie, E Viara, CJ Chen, JP Vert, E Heard, ...
Genome Biology 16 (1), 1-11, 2015
A community effort to assess and improve drug sensitivity prediction algorithms
JC Costello, LM Heiser, E Georgii, M Gönen, MP Menden, NJ Wang, ...
Nature biotechnology 32 (12), 1202, 2014
A statistical approach for inferring the 3D structure of the genome
N Varoquaux, F Ay, WS Noble, JP Vert
Bioinformatics 30 (12), i26-i33, 2014
Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression
F Ay, EM Bunnik, N Varoquaux, SM Bol, J Prudhomme, JP Vert, WS Noble, ...
Genome research 24 (6), 974-988, 2014
Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses
N Varoquaux, B Cole, C Gao, G Pierroz, CR Baker, D Patel, M Madera, ...
Proceedings of the National Academy of Sciences 116 (52), 27124-27132, 2019
Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics
L Xu, Z Dong, D Chiniquy, G Pierroz, S Deng, C Gao, S Diamond, ...
Nature communications 12 (1), 3209, 2021
Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages
EM Bunnik, KB Cook, N Varoquaux, G Batugedara, J Prudhomme, L Shi, ...
Nature Communications, 2018
Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum
F Ay, EM Bunnik, N Varoquaux, JP Vert, WS Noble, KG Le Roch
Bioessays 36 (2014), 0000-0000, 2014
Accurate identification of centromere locations in yeast genomes using Hi-C
N Varoquaux, I Liachko, F Ay, JN Burton, J Shendure, MJ Dunham, ...
Nucleic acids research 43 (11), 5331-5339, 2015
Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C
F Ay, TH Vu, MJ Zeitz, N Varoquaux, JE Carette, JP Vert, AR Hoffman, ...
BMC genomics 16 (1), 121, 2015
Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation
VS Lioy, JN Lorenzi, S Najah, T Poinsignon, H Leh, C Saulnier, B Aigle, ...
Nature communications 12 (1), 5221, 2021
Effective normalization for copy number variation in Hi-C data
N Servant, N Varoquaux, E Heard, JP Vert, E Barillot
The Types, Roles, and Practices of Documentation in Data Analytics Open Source Software Libraries
RS Geiger, N Varoquaux, C Mazel-Cabasse, C Holdgraf
Computer Supported Cooperative Work (CSCW) 27 (3-6), 767-802, 2018
Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression
C Gao, PE Courty, N Varoquaux, B Cole, L Montoya, L Xu, E Purdom, ...
Molecular ecology, 2022
Inferring diploid 3D chromatin structures from Hi-C data
AG Cauer, G Yardimci, JP Vert, N Varoquaux, WS Noble
19th International Workshop on Algorithms in Bioinformatics (WABI 2019), 2019
Inference of genome 3D architecture by modeling overdispersion of Hi-C data
N Varoquaux, WS Noble, JP Vert
Bioinformatics, 2023
Unveiling the links between peptide identification and differential analysis FDR controls by means of a practical introduction to knockoff filters
L Etourneau, N Varoquaux, T Burger
Statistical Analysis of Proteomic Data, 1-24, 2023
Cell Wall Compositions of Sorghum bicolor Leaves and Roots Remain Relatively Constant Under Drought Conditions
T Scavuzzo-Duggan, N Varoquaux, M Madera, JP Vogel, J Dahlberg, ...
Frontiers in plant science 12, 747225, 2021
A pipeline to analyse time-course gene expression data
N Varoquaux, E Purdom
F1000Research 9, 1447, 2020
Diversification of ubiquinone biosynthesis via gene duplications, transfers, losses, and parallel evolution
K Kazemzadeh, L Pelosi, C Chenal, SC Chobert, M Hajj Chehade, ...
Molecular Biology and Evolution, msad219, 2023
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