A statistical approach for inferring the 3D structure of the genome

di Varoquaux, Nelle, Ay, Ferhat, Noble, William Stafford, Vert, Jean-Philippe
Pubblicato in Bioinformatics (2014)

Effective normalization for copy number variation in Hi-C data

di Servant, Nicolas, Varoquaux, Nelle, Heard, Edith, Barillot, Emmanuel, Vert, Jean-Philippe
Pubblicato in BMC Bioinformatics (2018)

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: Gene regulation via histone modifications, nucleosome positioning and nuclear archi...

di Ay, Ferhat, Bunnik, Evelien M., Varoquaux, Nelle, Vert, Jean-Philippe, Noble, William Stafford, Le Roch, Karine G.
Pubblicato in Bioessays (2014)

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

di Varoquaux, Nelle, Liachko, Ivan, Ay, Ferhat, Burton, Joshua N., Shendure, Jay, Dunham, Maitreya J., Vert, Jean-Philippe, Noble, William S.
Pubblicato in Nucleic Acids Res (2015)

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

di Ay, Ferhat, Vu, Thanh H, Zeitz, Michael J, Varoquaux, Nelle, Carette, Jan E, Vert, Jean-Philippe, Hoffman, Andrew R, Noble, William S
Pubblicato in BMC Genomics (2015)

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

di Servant, Nicolas, Varoquaux, Nelle, Lajoie, Bryan R., Viara, Eric, Chen, Chong-Jian, Vert, Jean-Philippe, Heard, Edith, Dekker, Job, Barillot, Emmanuel
Pubblicato in Genome Biol (2015)

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

di Ay, Ferhat, Bunnik, Evelien M., Varoquaux, Nelle, Bol, Sebastiaan M., Prudhomme, Jacques, Vert, Jean-Philippe, Noble, William Stafford, Le Roch, Karine G.
Pubblicazione 2014

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

di Bunnik, Evelien M., Cook, Kate B., Varoquaux, Nelle, Batugedara, Gayani, Prudhomme, Jacques, Cort, Anthony, Shi, Lirong, Andolina, Chiara, Ross, Leila S., Brady, Declan, Fidock, David A., Nosten, Francois, Tewari, Rita, Sinnis, Photini, Ay, Ferhat, Vert, Jean-Philippe, Noble, William Stafford, Le Roch, Karine G.
Pubblicato in Nat Commun (2018)

Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics

di Xu, Ling, Dong, Zhaobin, Chiniquy, Dawn, Pierroz, Grady, Deng, Siwen, Gao, Cheng, Diamond, Spencer, Simmons, Tuesday, Wipf, Heidi M.-L., Caddell, Daniel, Varoquaux, Nelle, Madera, Mary A., Hutmacher, Robert, Deutschbauer, Adam, Dahlberg, Jeffery A., Guerinot, Mary Lou, Purdom, Elizabeth, Banfield, Jillian F., Taylor, John W., Lemaux, Peggy G., Coleman-Derr, Devin
Pubblicato in Nat Commun (2021)

Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses

di Varoquaux, Nelle, Cole, Benjamin, Gao, Cheng, Pierroz, Grady, Baker, Christopher R., Patel, Dhruv, Madera, Mary, Jeffers, Tim, Hollingsworth, Joy, Sievert, Julie, Yoshinaga, Yuko, Owiti, Judith A., Singan, Vasanth R., DeGraaf, Stephanie, Xu, Ling, Blow, Matthew J., Harrison, Maria J., Visel, Axel, Jansson, Christer, Niyogi, Krishna K., Hutmacher, Robert, Coleman-Derr, Devin, O’Malley, Ronan C., Taylor, John W., Dahlberg, Jeffery, Vogel, John P., Lemaux, Peggy G., Purdom, Elizabeth
Pubblicato in Proc Natl Acad Sci U S A (2019)