The Department of Computational Biology at Institut Pasteur is a multidisciplinary community of researchers dedicated to better understanding complex biological mechanisms and systems, from bacteria to human. We conduct research in computational biology, algorithms, biostatistics, and systems biology, using large, complex, heterogeneous data. Our activities focus on the development of mathematical and statistical models, their implementation in computer programs, and highly collaborative applications.
About
Teams
Laboratory
Statistical Genetics
Hugues Aschard
Laboratory
InBio: Experimental and Computational Methods for Modeling Cellular Processes
Grégory Batt
Laboratory
G5
Sequence Bioinformatics
Rayan Chikhi
Platform
Bioinformatics and Biostatistics HUB
Marie-Agnès Dillies
Laboratory
Decision and Bayesian Computation
Jean-Baptiste Masson
Laboratory
Computational Systems Biomedicine
Benno Schwikowski
Laboratory
Imaging and Modeling
Christophe Zimmer
Laboratory
G5
Machine Learning for integrative genomics
Laura Cantini
Laboratory
G5
Evolutionary dynamics of infectious diseases
Sebastian Duchene
Associated teams
Laboratory
UMR
G5
Comparative Functional Genomics
Camille Berthelot
Laboratory
Human Genetics and Cognitive Functions
Thomas Bourgeron
Laboratory
Mathematical Modelling Of Infectious Diseases
Simon Cauchemez
Laboratory
Architecture and Dynamics of Biological Macromolecules
Marc Delarue
Group
Synapse and Circuit Dynamics
David DiGregorio
Laboratory
Physics of Biological Function
Thomas Gregor
Laboratory
Spatial Regulation of Genomes
Romain Koszul
Laboratory
Structural Bioinformatics
Michael Nilges
Laboratory
Biological Image Analysis
Jean-Christophe Olivo-Marin
Laboratory
Human Evolutionary Genetics
Lluis Quintana-Murci
Laboratory
G5
Microbial Paleogenomics Unit
Nicolás Rascovan
Laboratory
Microbial Evolutionary Genomics
Eduardo Rocha
Group
Neural circuits for spatial navigation and memory
Christoph Schmidt-Hieber
Management
Grégory Batt
Head of Structure
Director
Jobs
Partners
Featured Projects
Featured Publications
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2021Fast-track virtual reality for cardiac imaging in congenital heart disease., J Card Surg 2021 Mar; (): .
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2021Partial breast resection for multifocal lower quadrant breast tumour using virtual reality., BMJ Case Rep 2021 Mar; 14(3): .
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2021Deciphering the state of immune silence in fatal COVID-19 patients., Nat Commun 2021 03; 12(1): 1428.
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2021Germline inherited small RNAs facilitate the clearance of untranslated maternal mRNAs in C. elegans embryos., Nat Commun 2021 03; 12(1): 1441.
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2021A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport., Nat Commun 2021 Mar; 12(1): 1352.
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2021Clustering and reverse transcription of HIV-1 genomes in nuclear niches of macrophages., EMBO J 2021 Jan; 40(1): e105247.
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2020Origin, evolution and global spread of SARS-CoV-2, Comptes Rendus Biologies 2020; 20 p.
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2020COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM., Bioinformatics 2020 Oct; (): .
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2020Genuage: visualize and analyze multidimensional single-molecule point cloud data in virtual reality., Nat. Methods 2020 Sep; (): .
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2020A bacterial size law revealed by a coarse-grained model of cell physiology, PLoS Comput Biol 2020 09; 16(9): e1008245.
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2020Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients., Cell 2020 Jun; 181(7): 1475-1488.e12.
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2020DIVA: Natural Navigation inside 3D Images Using Virtual Reality., J. Mol. Biol. 2020 Jun; (): .
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2020Efficiently Analysing Large Viral Data Sets in Computational Phylogenomics, In Phylogenetics in the Genomic Era, Scornavacca C Delsuc F & Galtier N (eds). 2020; 5.3:1--5.3:43.
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2020JASS: command line and web interface for the joint analysis of GWAS results., NAR Genom Bioinform 2020 Mar; 2(1): lqaa003.
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2020Bystander IFN-γ activity promotes widespread and sustained cytokine signaling altering the tumor microenvironment., Nat Cancer 2020 Mar; 1(3): 302-314.
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2019ImJoy: an open-source computational platform for the deep learning era, Nat. Methods 2019 Dec;16(12):1199-1200.
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2019RAISS: robust and accurate imputation from summary statistics., Bioinformatics 2019 11; 35(22): 4837-4839.
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2019A comprehensive study of metabolite genetics reveals strong pleiotropy and heterogeneity across time and context., Nat Commun 2019 10; 10(1): 4788.
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2019A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios, Mol. Biol. Evol. 2019 Sep;36(9):2069-2085.
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2019NGPhylogeny.fr: new generation phylogenetic services for non-specialists, Nucleic Acids Res. 2019 Jul;47(W1):W260-W265.
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2019Molecular noise of innate immunity shapes bacteria-phage ecologies, PLoS Comput. Biol. 2019 07;15(7):e1007168.
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2019Optimal control of an artificial microbial differentiation system for protein bioproduction, ECC 2019, pp. 2663-2668.
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2019Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data, Brief. Bioinformatics 2019 Jun;.
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2019Parallel decompression of gzip-compressed files and random access to DNA sequences, HiCOMB'19, Proceedings of IPDPS 2019.
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2019Graph analysis of fragmented long-read bacterial genome assemblies, Bioinformatics 2019 Mar;.
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2019Genetic effects on the commensal microbiota in inflammatory bowel disease patients., PLoS Genet 2019 03; 15(3): e1008018.
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2019Joint Analysis of Multiple Interaction Parameters in Genetic Association Studies., Genetics 2019 02; 211(2): 483-494.
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2018A computational framework to study sub-cellular RNA localization, Nature Communications, 2018, 9 (1), pp.4584. ⟨10.1038/s41467-018-06868-w⟩.
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2018VarExp: estimating variance explained by genome-wide GxE summary statistics., Bioinformatics 2018 10; 34(19): 3412-3414.
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2018A Blood RNA Signature Detecting Severe Disease in Young Dengue Patients at Hospital Arrival., J Infect Dis 2018 May; 217(11): 1690-1698.
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2018Renewing Felsenstein’s phylogenetic bootstrap in the era of big data, Nature 2018 Apr;.
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2018Deep learning massively accelerates super-resolution localization microscopy, Nat. Biotechnol. 2018 Jun;36(5):460-468.
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2017Balancing a genetic toggle switch by real-time feedback control and periodic forcing, Nat Commun. 2017 Nov 17;8(1):1671.
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2017Covariate selection for association screening in multiphenotype genetic studies., Nat Genet 2017 Dec; 49(12): 1789-1795.
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2017Shaping bacterial population behavior through computer-interfaced control of individual cells, Nat Commun. 2017 Nov 16;8(1):1535.
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2017Network module identification-A widespread theoretical bias and best practices, Methods 2018 01;132:19-25.
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2017Common and phylogenetically widespread coding for peptides by bacterial small RNAs, BMC Genomics 2017 07;18(1):553.
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2015InferenceMAP: mapping of single-molecule dynamics with Bayesian inference, Nat. Methods 2015 Jul;12(7):594-5.
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