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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
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Posts
Future Blog Post
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Blog Post number 4
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Blog Post number 1
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portfolio
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publications
MarkUs: An Open-Source Web Application to Annotate Student Papers On-Line
Published in , 1900
Recommended citation: 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
Three-dimensional modeling of the m P. m falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression
Published in , 1900
Recommended citation: 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
A statistical approach for inferring the 3D structure of the genome
Published in , 1900
Recommended citation: N. Varoquaux, F. Ay, W. S. Noble, J.-P. Vert. A statistical approach for inferring the 3D structure of the genome, Bioinformatics, 2014
A community effort to assess and improve drug sensitivity prediction algorithms
Published in , 1900
Recommended citation: 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 https://www.nature.com/articles/nbt.2877?report=reader
Multiple dimensions of epigenetic gene regulation in the malaria parasite m Plasmodium m falciparum
Published in , 1900
Recommended citation: 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 https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201400145
Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C
Published in , 1900
Recommended citation: 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 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1236-7
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
Published in , 1900
Recommended citation: 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 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0831-x
Accurate identification of centromere locations in yeast genomes using Hi-C
Published in , 1900
Recommended citation: N. Varoquaux, I. Liachko, F. Ay, J. N. Burton et al.. Accurate identification of centromere locations in yeast genomes using Hi-C, NAR, 2015 https://academic.oup.com/nar/article/43/11/5331/1171025?login=true
Measuring Cluster Stability for Bayesian non-Parametrics Using the Linear Bootstrap
Published in , 1900
Recommended citation: 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 https://arxiv.org/abs/1712.01435
Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages
Published in , 1900
Recommended citation: 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 https://www.nature.com/articles/s41467-018-04295-5
The types, roles, and practices of documentation in Data Analytics Open Source Software Libraries: A Collaborative Ethnography of Documentation Work
Published in , 1900
Recommended citation: 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 https://link.springer.com/article/10.1007/s10606-018-9333-1
Unfolding the Genome: the case study of m P. falciparum
Published in , 1900
Recommended citation: N. Varoquaux. Unfolding the Genome: the case study of \em P. falciparum, The International Journal of Biostatistics, May 2018 https://www.degruyter.com/document/doi/10.1515/ijb-2017-0061/html
Effective normalization for copy number variation in Hi-C cancer data
Published in , 1900
Recommended citation: 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 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2256-5
Inferring Diploid 3D Chromatin Structures from Hi-C Data
Published in , 1900
Recommended citation: A. G. Cauer, G. Yardimci, J.-P. Vert, N. Varoquaux et al.. Inferring Diploid 3D Chromatin Structures from Hi-C Data, 2019 http://drops.dagstuhl.de/opus/volltexte/2019/11041/
iced: fast and memory efficient normalization of contact maps
Published in , 1900
Recommended citation: N. Varoquaux, N. Servant. iced: fast and memory efficient normalization of contact maps, Journal of Open Source Software, 4 2019 http://dx.doi.org/10.21105/joss.01286
Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses
Published in , 1900
Recommended citation: 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 http://www.pnas.org/lookup/doi/10.1073/pnas.1907500116
circHiC: circular visualization of Hi-C data and integration of genomic data
Published in , 1900
Recommended citation: I. Junier, N. Varoquaux. circHiC: circular visualization of Hi-C data and integration of genomic data, August 2020 http://biorxiv.org/lookup/doi/10.1101/2020.08.13.249110
A pipeline to analyse time-course gene expression data
Published in , 1900
Recommended citation: N. Varoquaux, E. Purdom. A pipeline to analyse time-course gene expression data, F1000Research, December 2020 https://f1000research.com/articles/9-1447/v1
Cell Wall Compositions of Sorghum bicolor Leaves and Roots Remain Relatively Constant Under Drought Conditions
Published in , 1900
Recommended citation: 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 https://www.frontiersin.org/articles/10.3389/fpls.2021.747225/full
Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation
Published in , 1900
Recommended citation: 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 https://www.nature.com/articles/s41467-021-25462-1
Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics
Published in , 1900
Recommended citation: 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 http://www.nature.com/articles/s41467-021-23553-7
Computational Tools for the Multiscale Analysis of Hi-C Data in Bacterial Chromosomes
Published in , 1900
Recommended citation: N. Varoquaux, V. S. Lioy, F. Boccard, I. Junier. Computational Tools for the Multiscale Analysis of Hi-C Data in Bacterial Chromosomes, 2022 https://link.springer.com/10.1007/978-1-0716-1390-0_10
Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression
Published in , 1900
Recommended citation: 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 https://onlinelibrary.wiley.com/doi/10.1111/mec.16343
Community, Time, and (Con)text: A Dynamical Systems Analysis of Online Communication and Community Health among Open‐Source Software Communities
Published in , 1900
Recommended citation: 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 https://onlinelibrary.wiley.com/doi/10.1111/cogs.13134
Unveiling the Links Between Peptide Identification and Differential Analysis FDR Controls by Means of a Practical Introduction to Knockoff Filters
Published in , 1900
Recommended citation: 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 https://link.springer.com/10.1007/978-1-0716-1967-4_1
Inference of 3D genome architecture by modeling overdispersion of Hi-C data
Published in , 1900
Recommended citation: N. Varoquaux, W. S. Noble, J.-P. Vert. Inference of 3D genome architecture by modeling overdispersion of Hi-C data, Bioinformatics, January 2023 https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btac838/6967433
Diversification of ubiquinone biosynthesis via gene duplications, transfers, losses, and parallel evolution
Published in , 1900
Recommended citation: 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 https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msad219/7288468
talks
Talk 1 on Relevant Topic in Your Field
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This is a description of your talk, which is a markdown files that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
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This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.