Publications

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

I. Junier, E. Ghobadpour, O. Espeli, R. Everaers. DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling, Frontiers in Microbiology, October 2023

I. Boulas, L. Bruno, S. Rimsky, O. Espeli et al.. Assessing in vivo the impact of gene context on transcription through DNA supercoiling, Nucleic Acids Research, September 2023

A. Kranjc, T. J. Narwani, S. S. Abby, A. G. De Brevern. Structural Space of the Duffy Antigen/Receptor for Chemokines’ Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations, International Journal of Molecular Sciences, August 2023

N. Sturm, M. Roger-Margueritat, F. Pierrel, P. Lehours et al.. Spatial heterogeneity for APRIL production by eosinophils in the small intestine, Journal of Leukocyte Biology, March 2023

B. Néron, R. Denise, C. Coluzzi, M. Touchon et al.. MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes, Peer Community Journal, March 2023

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

S. S. Abby, R. Denise, E. P. Rocha. Identification of protein secretion systems in bacterial genomes using MacSyFinder version 2, 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

R. Launay, E. Teppa, C. Martins, S. S. Abby et al.. Towards Molecular Understanding of the Functional Role of UbiJ-UbiK2 Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies, International Journal of Molecular Sciences, September 2022

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. Etourneau & T. Burger. Challenging Targets or Describing Mismatches? A Comment on Common Decoy Distribution by Madej et al., Journal of Proteome Research, 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

V. S. Lioy, I. Junier, F. Boccard. Multiscale Dynamic Structuring of Bacterial Chromosomes, Annual Review of Microbiology, October 2021

M. Kerou, R. I. Ponce-Toledo, R. Zhao, S. S. Abby et al.. Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages, The ISME Journal, September 2021

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, August 2021

J.-C. Walter, T. Lepage, J. Dorignac, F. Geniet et al.. Supercoiled DNA and non-equilibrium formation of protein complexes: A quantitative model of the nucleoprotein ParBS partition complex, PLOS Computational Biology, April 2021

R. Zhao, J. M. Mogollón, S. S. Abby, C. Schleper et al.. Geochemical transition zone powering microbial growth in subsurface sediments, Proceedings of the National Academy of Sciences, December 2020

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

C. Reyes, L. H. Hodgskiss, M. Kerou, T. Pribasnig et al.. Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation, The ISME Journal, November 2020

V. S. Lioy, I. Junier, V. Lagage, I. Vallet et al.. Distinct Activities of Bacterial Condensins for Chromosome Management in Pseudomonas aeruginosa, Cell Reports, November 2020

S. S. Abby, K. Kazemzadeh, C. Vragniau, L. Pelosi et al.. Advances in bacterial pathways for the biosynthesis of ubiquinone, Biochimica et Biophysica Acta (BBA) - Bioenergetics, November 2020

S. S. Abby, M. Kerou, C. Schleper. Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments, mBio, October 2020

M. Joyeux, I. Junier. Requirements for DNA-Bridging Proteins to Act as Topological Barriers of the Bacterial Genome, Biophysical Journal, September 2020

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

R. Denise, S. S. Abby, E. P. Rocha. The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries, Trends in Microbiology, May 2020

J.-C. Walter, T. Lepage, J. Dorignac, F. Geniet et al.. Modeling supercoiled DNA interacting with an anchored cluster of proteins: towards a quantitative estimation of chromosomal DNA supercoiling, arXiv:2002.00111 [physics, q-bio], April 2020

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 Plasmodium falciparum, Bioessays, 2015

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

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

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

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

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

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

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

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

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

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

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

A. Alemany, A. Mossa, I. Junier, F. Ritort. Experimental free-energy measurements of kinetic molecular states using fluctuation theorems, Nature Physics, September 2012

S. S. Abby, E. P. C. Rocha. The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems, PLoS Genetics, September 2012

V. Daubin, S. Abby. Les transferts horizontaux de gènes et l’arbre de la vie, médecine/sciences, August 2012

F. Képès, B. C. Jester, T. Lepage, N. Rafiei et al.. The layout of a bacterial genome, FEBS Letters, July 2012

I. Junier, J. Hérisson, F. Képès. Genomic Organization of Evolutionarily Correlated Genes in Bacteria: Limits and Strategies, Journal of Molecular Biology, June 2012

S. S. Abby, E. Tannier, M. Gouy, V. Daubin. Lateral gene transfer as a support for the tree of life, Proceedings of the National Academy of Sciences, March 2012

J. A. Gama, S. S. Abby, S. Vieira-Silva, F. Dionisio et al.. Immune Subversion and Quorum-Sensing Shape the Variation in Infectious Dose among Bacterial Pathogens, PLoS Pathogens, February 2012

S. Vieira-Silva, M. Touchon, S. S. Abby, E. P. C. Rocha. Investment in rapid growth shapes the evolutionary rates of essential proteins, Proceedings of the National Academy of Sciences, December 2011

M. Elati, R. Fekih, R. Nicolle, I. Junier et al.. Boosting Binding Sites Prediction Using Gene’s Positions, 2011

I. Junier, J. Hérisson, F. Képès. Periodic pattern detection in sparse boolean sequences, Algorithms for Molecular Biology, December 2010

S. S. Abby, E. Tannier, M. Gouy, V. Daubin. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests, BMC Bioinformatics, December 2010

I. Junier, O. Martin, F. Képès. Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization, PLoS Computational Biology, February 2010

I. Junier, A. Mossa, M. Manosas, F. Ritort. Recovery of Free Energy Branches in Single Molecule Experiments, Physical Review Letters, February 2009

S. Abby, V. Daubin. Comparative genomics and the evolution of prokaryotes, Trends in Microbiology, March 2007