Nelle Varoquaux

I am post-doctorate researcher in Elizabeth Purdom's lab, at UC Berkeley. We're interested in molecular biology probems and intend to help solving them using machine learning, a marriage between applied mathematics and computer science.

After working on inferring the 3D structure of the genome from Hi-C data during my PhD under the supervision of Jean-Philippe Vert, I am currently involed in a project attempting to find the epigenetic factors involved in the Sorghum's resistance to drough.


"HiC-Pro: an optimized and flexible pipeline for Hi-C data processing" *N. Servant, N. Varoquaux, B.R. Lajoie, E. Viara, C.J. Chen, J.-P. Vert, E. Heard, J. Dekker, E. Barillot, Genome Biology 2015, [link]

"Accurate identification of centromere locations in yeast genomes using Hi-C" *N. Varoquaux, I. Liachko, F. Ay, J. N. Burton, J. Shendure, M. J. Dunham, J.-P. Vert, W. S. Noble, NAR 2015 [link]

"Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C" *F. Ay, T. H. Vu, M. J. Zeitz, N. Varoquaux, J. E. Carette, J.-P. Vert, A. R. Hoffman and W. S. Noble, BMC Genomics 2015, 16:121 [link]

"Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum" *F. Ay, *E. M. Bunnik, N. Varoquaux, J.-P. Vert, W. S. Noble and K. G. Le Roch, Bioessays, 36, 0000-0000 [link]

"A statistical approach for inferring the three-dimensional structure of the genome" *N. Varoquaux, F. Ay, W. S. Noble and J.-P. Vert, Bioinformatics 30 (12), i26-i33 [link]

"Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression" *N. Varoquaux, *F. Ay, *E. M. Bunnik, S. M. Bol, J. Prudhomme, J.-P. Vert, W. S. Noble, and K. G. Le Roch, Genome Res 2014 0: gr.169417.113v1-gr.169417.113 [link]

"A community effort to assess and improve drug sensitivity prediction algorithms" *Costello J.C., Heiser L.M., Georgii E., Gönen M., Menden M.P., Wang N.J., Bansal M., Ammad-Ud-Din M., Hintsanen P., Khan S.A., Mpindi J.P., Kallioniemi O., Honkela A., Aittokallio T., Wennerberg K., NCI DREAM Community, Collins J.J., Gallahan D., Singer D., Saez-Rodriguez J., Kaski S., Gray J.-W., Stolovitzky G., Nature Biotechnology [link]

Scientific computing activities

I am a contributor in a number of scientific computing libraries in Python including:

I am also involved in the French speaking Python association, AFPy, and Software Carpentry.