K. Kazemzadeh, L. Pelosi, C. Chenal, S.-C. Chobert et al.. Diversification of ubiquinone biosynthesis via gene duplications, transfers, losses, and parallel evolution, Molecular Biology and Evolution, October 2023

N. Varoquaux, W. S. Noble, J.-P. Vert. Inference of 3D genome architecture by modeling overdispersion of Hi-C data, Bioinformatics, January 2023

L. Etourneau, N. Varoquaux, T. Burger. Unveiling the Links Between Peptide Identification and Differential Analysis FDR Controls by Means of a Practical Introduction to Knockoff Filters, 2023

A. Paxton, N. Varoquaux, C. Holdgraf, R. S. Geiger. Community, Time, and (Con)text: A Dynamical Systems Analysis of Online Communication and Community Health among Open‐Source Software Communities, Cognitive Science, May 2022

C. Gao, P.-E. Courty, N. Varoquaux, B. Cole et al.. Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression, January 2022

N. Varoquaux, V. S. Lioy, F. Boccard, I. Junier. Computational Tools for the Multiscale Analysis of Hi-C Data in Bacterial Chromosomes, 2022

L. Xu, Z. Dong, D. Chiniquy, G. Pierroz et al.. Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics, Nature Communications, December 2021

V. S. Lioy, J.-N. Lorenzi, S. Najah, T. Poinsignon et al.. Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation, Nature Communications, December 2021

T. Scavuzzo-Duggan, N. Varoquaux, M. Madera, J. P. Vogel et al.. Cell Wall Compositions of Sorghum bicolor Leaves and Roots Remain Relatively Constant Under Drought Conditions, Frontiers in Plant Science, November 2021

N. Varoquaux, E. Purdom. A pipeline to analyse time-course gene expression data, F1000Research, December 2020

I. Junier, N. Varoquaux. circHiC: circular visualization of Hi-C data and integration of genomic data, August 2020

N. Varoquaux, B. Cole, C. Gao, G. Pierroz et al.. Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses, Proceedings of the National Academy of Sciences, December 2019

N. Varoquaux, N. Servant. iced: fast and memory efficient normalization of contact maps, Journal of Open Source Software, 4 2019

A. G. Cauer, G. Yardimci, J.-P. Vert, N. Varoquaux et al.. Inferring Diploid 3D Chromatin Structures from Hi-C Data, 2019

N. Servant, N. Varoquaux, E. Heard, E. Barillot et al.. Effective normalization for copy number variation in Hi-C cancer data, BMC bioinformatics, Aug 2018

N. Varoquaux. Unfolding the Genome: the case study of \em P. falciparum, The International Journal of Biostatistics, May 2018

R. S. Geiger, N. Varoquaux, C. Holdgraf, C. Cabasse-Mazel. The types, roles, and practices of documentation in Data Analytics Open Source Software Libraries: A Collaborative Ethnography of Documentation Work, The Journal of Computer-Supported Cooperative Work, 2018

E. M. Bunnik, K. B. Cook, N. Varoquaux, G. Batugedara et al.. Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages, Nat. Comm., 2018

R. Giordano, R. Liu, N. Varoquaux, M. I. Jordan et al.. Measuring Cluster Stability for Bayesian non-Parametrics Using the Linear Bootstrap, NIPS workshop: Advances in Approximate Bayesian Inference, 2017

N. Varoquaux, I. Liachko, F. Ay, J. N. Burton et al.. Accurate identification of centromere locations in yeast genomes using Hi-C, NAR, 2015

N. Servant, N. Varoquaux, B. R. Lajoie, E. Viara et al.. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing, Genome Biol., 2015

F. Ay, T. H. Vu, M. J. Zeitz, N. Varoquaux et al.. Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C, BMC Genomics, 2015

F. Ay, E. M. Bunnik, N. Varoquaux, J.-P. Vert et al.. Multiple dimensions of epigenetic gene regulation in the malaria parasite \em Plasmodium \em falciparum, Bioessays, 2015

J. C. Costello, L. M. Heiser, E. Georgii, M. Gonen et al.. A community effort to assess and improve drug sensitivity prediction algorithms, Nat. Biotechnol., Dec 2014

N. Varoquaux, F. Ay, W. S. Noble, J.-P. Vert. A statistical approach for inferring the 3D structure of the genome, Bioinformatics, 2014

F. Ay, E. M. Bunnik, N. Varoquaux, S. M. Bol et al.. Three-dimensional modeling of the \em P. \em falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression, Genome Research, 2014

M. Magnin, G. Moreau, N. Varoquaux, B. Vialle et al.. MarkUs: An Open-Source Web Application to Annotate Student Papers On-Line, ASME 2012 11th Biennial Conference on Engineering Systems Design and Analysis, 2012