Publications

C. Planchenault, M. C. Pons, C. Schiavon, P. Siguier et al.. Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells, Journal of Molecular Biology, February 2020

2020

J. Cury, S. S. Abby, O. Doppelt-Azeroual, B. Néron et al.. Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan, 2020

2019

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

2019

L. Pelosi, C.-D.-T. Vo, S. S. Abby, L. Loiseau et al.. Ubiquinone Biosynthesis over the Entire O2 Range: Characterization of a Conserved O2-Independent Pathway, mBio, August 2019

2019

T. Lepage, I. Junier. A polymer model of bacterial supercoiled DNA including structural transitions of the double helix, Physica A: Statistical Mechanics and its Applications, August 2019

2019

R. Denise, S. S. Abby, E. P. C. Rocha. Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility, PLOS Biology, July 2019

2019

R. J. E. Alves, M. Kerou, A. Zappe, R. Bittner et al.. Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures, Frontiers in Microbiology, July 2019

2019

A. F. Schober, A. D. Mathis, C. Ingle, J. O. Park et al.. A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism, Cell Reports, June 2019

2019

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

2019

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

2018

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

2018

A. C. Pozzi, H. H. Bautista-Guerrero, S. S. Abby, A. Herrera-Belaroussi et al.. Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size, Systematic and Applied Microbiology, July 2018

2018

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

2018

I. Junier, P. Frémont, O. Rivoire. Universal and idiosyncratic characteristic lengths in bacterial genomes, Physical Biology, March 2018

2018

S. S. Abby, M. Melcher, M. Kerou, M. Krupovic et al.. Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome, Frontiers in Microbiology, January 2018

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

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

2017

N. Leisch, N. Pende, P. M. Weber, H. R. Gruber-Vodicka et al.. Asynchronous division by non-ring FtsZ in the gammaproteobacterial symbiont of Robbea hypermnestra, Nature Microbiology, January 2017

2017

T. Lepage, I. Junier. Modeling Bacterial DNA: Simulation of Self-Avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix, 2017

2017

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

2017

S. S. Abby, E. P. C. Rocha. Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder, 2017

2016

M. Kerou, P. Offre, L. Valledor, S. S. Abby et al.. Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers, Proceedings of the National Academy of Sciences, December 2016

2016

A. Behdenna, J. Pothier, S. S. Abby, A. Lambert et al.. Testing for Independence between Evolutionary Processes, Systematic Biology, September 2016

2016

L. Pelosi, A.-L. Ducluzeau, L. Loiseau, F. Barras et al.. Evolution of Ubiquinone Biosynthesis: Multiple Proteobacterial Enzymes with Various Regioselectivities To Catalyze Three Contiguous Aromatic Hydroxylation Reactions, mSystems, August 2016

2016

I. Junier, E. Unal, E. Yus, V. Lloréns-Rico et al.. Insights into the Mechanisms of Basal Coordination of Transcription Using a Genome-Reduced Bacterium, Cell Systems, June 2016

2016

I. Junier, O. Rivoire. Conserved Units of Co-Expression in Bacterial Genomes: An Evolutionary Insight into Transcriptional Regulation, PLOS ONE, May 2016

2016

S. S. Abby, J. Cury, J. Guglielmini, B. Néron et al.. Identification of protein secretion systems in bacterial genomes, Scientific Reports, March 2016

2015

M. C. Lagomarsino, O. Espéli, I. Junier. From structure to function of bacterial chromosomes: Evolutionary perspectives and ideas for new experiments, FEBS Letters, October 2015

2015

I. Junier, Y. G. Spill, M. A. Marti-Renom, M. Beato et al.. On the demultiplexing of chromosome capture conformation data, FEBS Letters, October 2015

2015

T. Lepage, F. Képès, I. Junier. Thermodynamics of Long Supercoiled Molecules: Insights from Highly Efficient Monte Carlo Simulations, Biophysical Journal, July 2015

2015

M. Trussart, F. Serra, D. Baù, I. Junier et al.. Assessing the limits of restraint-based 3D modeling of genomes and genomic domains, Nucleic Acids Research, April 2015

2015

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

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

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

2015

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

2014

I. Junier. Conserved patterns in bacterial genomes: A conundrum physically tailored by evolutionary tinkering, Computational Biology and Chemistry, December 2014

2014

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

2014

S. S. Abby, M. Touchon, A. De Jode, N. Grimsley et al.. Bacteria in Ostreococcus tauri cultures - friends, foes or hitchhikers?, Frontiers in Microbiology, November 2014

2014

S. S. Abby, B. Néron, H. Ménager, M. Touchon et al.. MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems, PLoS ONE, October 2014

2014

J. Guglielmini, B. Néron, S. S. Abby, M. P. Garcillán-Barcia et al.. Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion, Nucleic Acids Research, May 2014

2014

I. Junier, F. Boccard, O. Espéli. Polymer modeling of the E. coli genome reveals the involvement of locus positioning and macrodomain structuring for the control of chromosome conformation and segregation, Nucleic Acids Research, February 2014

2014

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

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

2013

I. Junier, O. Rivoire. Synteny in Bacterial Genomes: Inference, Organization and Evolution, arXiv:1307.4291 [q-bio], July 2013

2013

M. Elati, R. Nicolle, I. Junier, D. Fernández et al.. PreCisIon: PREdiction of CIS-regulatory elements improved by gene’s positION, Nucleic Acids Research, February 2013

2013

M. Seifi, I. Junier, J.-B. Rouquier, S. Iskrov et al.. Stable Community Cores in Complex Networks, 2013

2012

G. J. Szollosi, B. Boussau, S. S. Abby, E. Tannier et al.. Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations, Proceedings of the National Academy of Sciences, October 2012

2012

N. N. Nickerson, S. S. Abby, E. P. C. Rocha, M. Chami et al.. A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin, Journal of Bacteriology, September 2012

2012

I. Junier, R. K. Dale, C. Hou, F. Képès et al.. CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus, Nucleic Acids Research, September 2012