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Number of Projects : 397

ID	Project Title	Applicant	Topics	Type	Status	Department
14968	Analysis of microbiota in Anopheles mosquitoes	P. BALDACCI			New	Department of Parasites and Insect Vectors
14967	Transcriptional regulation of bacterial physiology during host-pathogen interaction	A. FIRON	Differential analysis RNA-seq	Medium	New	Department of Microbiology
14680	Modulation of cellular pathways involved in neuropathology of rabies infection	F. LARROUS	Differential analysis RNA-seq	Medium	In Progress	Department of Infection & Epidemiology
14672	Flemmingsome: A Midbody Remnant Proteome Database	N. Gupta-Rossi	Cell biology and developmental biology Web development		Pending	Department of Cell Biology & Infection
14671	Functinal analysis of proteome and phopshoproteome changes in murin intestine – mechanism of Streptococcus gallolyticus-induced carcinogenesis	E. Pasquereau			New	Department of Microbiology
14667	improvement of new methodology for oral infection on mice	A. DERBISE	Biostatistics	Short	Closed	Department of Microbiology
14643	Plasmodium vivax Invasion Pathways into Human Reticulocytes – VIPers	D. Menard	Population genetics	Coaching	Pending	Other
14612	Implementation of the ViroScreen workflow in Galaxy	L. Dacheux	Galaxy		In Progress	Department of Infection & Epidemiology
14611	Deciphering the transcriptome profil during rabies infection in brain in mouse and in human	L. Dacheux	Biostatistics Functional Analysis Microarray Transcriptomics	Short	New	Department of Infection & Epidemiology
14608	Integration and advanced statistical analyses of complex datasets for host factor identification involved in Salmonella and Shigella intracellular niche formation	J. Enninga	Proteomics		Pending	Department of Cell Biology & Infection
14607	Récupération des données associées aux séquences de génomes de Klebsiella pneumoniae téléchargées du NCBI	N. CABANEL	Data management		Pending
14589	Development and design of new functionalities for MEMHDX, a web application dedicated to the statistical analysis and vizualization of large HDX-MS datasets.	S. BRIER	Statistics Web development	Short	In Progress
14587	Off-target sites of Cas endonucleases targeted to trinucleotide repeats	G. RICHARD	Genomics		New	Department of Genome & Genetics
14555	Identification of non-coding RNAs under the control of the PerR regulators	N. Benaroudj	Non coding RNA RNA-seq Transcriptomics	Short	In Progress	Department of Microbiology
14510	Shigella targeting of human colonic Lamina Propria Mononuclear Cells	K. Brunner			New	Department of Cell Biology & Infection
14386	Cartography of the expansion of pathogenic Yersinia in Vietnam	G. Mas Fiol	Statistics	Short	Pending
14385	Evaluation of the mutation rate per site and dN/dS in the genomes of Yersinia enterocolitica	C. Savin	Phylogenetics	Short	In Progress	Department of Microbiology
14337	Long-term preservation of a Campylobacter fetus strain and genomic stability	D. Clermont	Read mapping Sequence analysis	Short	In Progress
14332	Proteomic analysis of the intracellular compartments containing Brucella abortus	J. Pizarro-Cerda	Differential analysis	Short	In Progress	Department of Microbiology
14331	Spatial analysis of cysticercosis seroprevalence in villages of Ivory Coast	R. JAMBOU	Statistics	Short	Pending
14328	SHERLOCK4HAT – WP1.1	B. Rotureau	Motifs and patterns detection	Short	In Progress
14231	Implementation of the ViroScreen workflow in Galaxy	L. Dacheux	Galaxy Workflow and pipeline development	Short	Closed	Department of Infection & Epidemiology
14071	MacSyFinder 2.0	E. Rocha	Data Visualization Parallel computing Program development Scientific computing Sofware development and engineering Tool Development	Long	Pending	Department of Genome & Genetics
13980	MLST versus Short Tandem repeats (Microsatellites) for Pneumocystis jirovecii genotyping	M. Gits-Muselli	Biostatistics Evolution Genetics Genotyping Graph theory and analysis Population genetics	Short	Pending	Department of Mycology
13848	Secretome Analysis of OIS IL6KO SASP	M. von Joest	Proteomics	Short	Pending	Department of Developmental & Stem Cell Biology
13699	DNMT and RNMT in Leishmania	G. Spaeth	Phylogenetics Sequence homology analysis	Short	In Progress	Department of Parasites and Insect Vectors
13672	Impact of APC gene mutations on anti-tumoral immune responses	V. Di Bartolo	Biostatistics	Short	Pending	Department of Immunology
13654	Role of Tunneling nanotubes in Glioblastoma	G. Pinto	Statistics	Short	In Progress	Department of Cell Biology & Infection
13522	CRISPR design tools on crispr.pasteur.fr	D. Bikard	CRISPR Web development	Medium	In Progress	Department of Microbiology
13496	Microscystis transcriptome	M. Gugger	Differential analysis	Medium	Pending	Department of Microbiology
13471	Bioinformatic analysis of paired alpha and beta T cell receptor sequences obtained at the single cell level by illumina sequencing	L. Chakrabarti	Immunogenetics Program development Single Cell Tool Development Transcriptomics		In Progress	Department of Virology
13458	Assessing the role of gut microbiota in spondyloarthritis patients and impact of anti-TNF treament on its composition	C. RICHARD-MICELI	Machine learning Targeted metagenomics		Pending	Department of Immunology
13429	Uncovering diversity and improving gene annotation of Leptospira sppo	M. PICARDEAU	Annotation		Pending	Department of Microbiology
13426	ICARE	N. Rosine	Clustering Exploratory data analysis Flow cytometry/cell sorting Program development Sofware development and engineering Statistics	Short	In Progress	Department of Immunology
13412	Analysis of the clinical manifestations of Lyme borreliosis in France from 2003 to 2011	V. Choumet	Epidemiology and public health Statistics	Short	In Progress	Department of Infection & Epidemiology
13408	Proteome remodeling induces by the Cytotoxic Necrotizing Factors 1	L. TSOUMTSA	Functional Analysis	Short	Pending
13406	Multiparametric immunophenotyping of whole blood in IFN-treated multiple sclerosis patients	P. Devi	Biostatistics Functional Analysis Transcriptomics	Short	In Progress	Department of Immunology
13401	Identification of mouse skin macrophage subpopulations	D. OBINO	Single Cell	Medium	Pending
13393	Excess calorie intake early in life increases susceptibility to colitis in the adult	Z. Al Nabhani	Biostatistics	Short	In Progress	Department of Immunology
13391	Finding SNPs associated with Dengue infection in the mosquito Aedes aegypti	M. Sarah	Transcriptomics Variant analysis	Short	In Progress	Department of Genome & Genetics
13387	Distribution of Cytotoxic necrotizing factor 1 among the sequence type 131 emergent multidrug resistant lineage of Escherichia coli	T. Landry Laure	Statistics	Short	In Progress
13382	Mechanisms of HIV-1-infected cells susceptibility to Fc effector functions	T. Bruel	Biostatistics CRISPR	Short	In Progress	Department of Virology
13376	Antiviral activities of anti-HIV-1 antibodies	T. Bruel	Microarray Transcriptomics	Short	Closed	Department of Virology
13341	Serpentine: a flexible 2D binning method for differential Hi-C analysis	V. Scolari	Biostatistics Chromatin conformation capture	Short	In Progress	Department of Genome & Genetics
13324	Defining the differential contributions of CD4+ and CD8+ anti-CD19 CAR T cells to tumor outcome, immune recruitment and toxicity	M. Cazaux	RNA-seq Single Cell	Short	Pending	Department of Immunology
13305	Characterization of the bacterial and fungal microbiota in Aedes aegypti natural breeding sites and larvae	L. LAMBRECHTS	Shotgun metagenomics		Pending	Department of Genome & Genetics
13296	Quality controls for human plasmas and serums stored in biobanks	H. LAUDE	Statistics	Short	Pending	Department of Microbiology
13292	The anti-IgE antibody Omalizumab induces adverse reactions through engagement of Fc gamma receptors	B. Balbino	Biostatistics	Short	Awaiting Publication	Department of Immunology
13287	Targetting the function of a hypothetical protein	D. Czernecki	Sequence analysis	Short	Pending	Department of Structural Biology & Chemistry
13267	Analysis of Internal Deletions in EV71	B. Meyer	Sequence analysis	Short	Pending	Department of Virology
13264	maintenance du site de la Collection des cyanobactéries	B. BENEDIC	Web development	Short	Pending	Department of Microbiology
13260	Heterogeneity of the skeletal muscle microenvironment	L. Peduto	RNA-seq Single Cell	Short	In Progress	Other
13259	Defective interfering viral genomes of shrimps’ viruses	A. Komarova	Sequence design Workflow and pipeline development	Short	Awaiting Publication	Department of Virology
13205	Optimisation of freeze and conservation method of peripherical blood mononucleated cells	S. Vallier	Biostatistics Exploratory data analysis Flow cytometry/cell sorting	Medium	Pending	Other
13204	Early transcriptional signature of T-cell memory after dengue vaccination	C. Roth	Differential analysis RNA-seq	Short	Pending	Department of Genome & Genetics
13196	Chikungunya virus adaptation to a low temperature in a French population Ae. albopictus	R. Bellone	Data Visualization Variant analysis		Pending	Department of Virology
13174	Characterization of Yolk Sac Derived Progenitors in the Fetal Liver	L. Freyer	Single Cell	Medium	Pending	Department of Developmental & Stem Cell Biology
13146	Intégration d’outils bioinformatique dans Galaxy pour identification bactérienne	A. LE FLECHE	Galaxy	Short	Closed
13141	3D PATH	M. RINCEL	Association studies Biostatistics Genetics Multidimensional data analysis Statistics		Pending	Department of Immunology
13128	Remettre les servers Genolist comme LegioList, TuberclListe, Colibri etc en service	C. Buchrieser	Web development		Closed	Department of Genome & Genetics
13125	Move of the DISCO-BAC server VM to the new DSI infrastructure	B. Schwikowski	Web development	Short	Closed	Department of Genome & Genetics
13116	Targeted search of specific commensals in 16S databases	P. Schnupf	Targeted metagenomics	Short	In Progress	Department of Cell Biology & Infection
13081	Hamper cell-to-cell variation to enhance drug-mediated killing	G. MANINA	Biostatistics	Short	Pending	Department of Cell Biology & Infection
13078	Determination of the transcriptome controlled by the two-component system BvrR/BvrS using dominant positive and negative BvrR mutants	J. PIZARRO-CERDA	Differential analysis	Coaching	Pending	Department of Microbiology
13043	Build a software to decipher Gephyrin alternative transcripts obtained with long read sequencing	a. eric	Tool Development	Long	In Progress	Department of Developmental & Stem Cell Biology
12997	Identifying subpopulation-specific signatures of tuberculosis persistence for enhanced diagnostics.	G. MANINA	Differential analysis RNA-seq	Coaching	Pending	Department of Cell Biology & Infection
12996	Analyse transcriptionnelle du cellules cancéreuse intestinal vs normales après co-culture avec la bactérie associée au cancer Streptococcus gallolyticus	E. Pasquereau	Pathway Analysis		Awaiting Publication	Department of Microbiology
12992	Genomic DNA sequencing of Burkholderia ambifaria Q53 strain isolated from peanut rizospheric soil	M. BEN ASSAYA	Annotation Variant analysis		In Progress	Department of Structural Biology & Chemistry
12991	Role of RNA primary and secondary structure in non-homologous recombination	B. Meyer	Statistics		Declined	Department of Virology
12988	LGP2 binds PACT to regulate RIG-I- and MDA5-mediated antiviral response	A. Komarova	Biostatistics	Short	Closed	Department of Virology
12987	Afribiota-Neuro	P. Vonaesch	Biostatistics	Short	In Progress	Department of Cell Biology & Infection
12963	Gene expression and its regulation during and after inpatient detoxification of cocaine: a link to relapse?	R. Icick	RNA-seq	Medium	In Progress	Department of Neuroscience
12929	Single nucleotide polymorphisms and genome organization in members of the genus Yersinia	J. PIZARRO-CERDA	Comparative Genomics Data Visualization	Short	Pending	Department of Microbiology
12920	Séquençage à haut débit (NGS) et traitement de séquences ADN des domaines variables d’anticorps simple chaine d’alpaga (domaines VHH ou Nanobodies®)	M. Gomes	Sequence homology analysis Sequencing Workflow and pipeline development	Short	In Progress	Department of Structural Biology & Chemistry
12913	Genetic and statistical analysis of data produced with the Collaborative Cross at the Institut Pasteur	X. MONTAGUTELLI	Genetics Variant analysis	Long	In Progress
12901	crispr.pasteur.fr	D. Bikard	Data Visualization Web development	Short	Awaiting Publication	Department of Microbiology
12897	Comparative genomics of Listeria monocytogenes isolates	M. Lecuit	Sequence analysis	Medium	Awaiting Publication	Department of Cell Biology & Infection
12891	Identification d’une mémoire épigénomique à Streptococcus pneumoniae	C. CHEVALIER	ChIP-seq Differential analysis	Medium	In Progress	Department of Cell Biology & Infection
12853	Impact des contraintes biomécanistiques sur la dynamique des macro-ouverture induits par l’EDIN de Staphylococcus aureus.	C. MOREL	Biostatistics	Short	In Progress
12833	Training project for bacterial ChIP-seq Analysis on Streptococcus agalactiae	M. Mazzuoli	ChIP-seq Workflow and pipeline development	Coaching	Closed	Department of Microbiology
12775	Determination of host response elicited by different Salmonella lifestyles	C. LUK	RNA-seq Statistics	Coaching	Declined	Department of Cell Biology & Infection
12771	Tissue-resident stromal cell heterogeneity	L. Peduto	Single Cell	Medium	In Progress	Department of Immunology
12767	Comparative genomics of Helicobacter pylori bismuth resistant strains	H. DE REUSE	Comparative Genomics Variant analysis	Short	Pending	Department of Microbiology
12765	Viral Host Range Databank	L. Debarbieux	Data integration Data management Data Visualization Web development	Medium	In Progress	Department of Microbiology
12674	DNMT orthologs in Leishmania	S. Lamotte	Sequence homology analysis	Short	Closed	Department of Parasites and Insect Vectors
12670	Genome-wide interactions between HP1g and RNA.	C. Rachez	ChIP-seq RNA-seq	Short	Closed	Department of Developmental & Stem Cell Biology
12647	Sequence analysis of Mycobacterium marinum mutants	M. Cimino	Annotation Genome assembly Variant analysis	Short	In Progress
12641	Functional interactomics of SKAP2	J. Bureau	Functional Analysis	Short	Pending	Department of Genome & Genetics
12627	Role of small non coding RNAs in the adaptive response to oxidative stress in pathogenic Leptospira	N. BENAROUDJ	RNA-seq	Short	In Progress	Department of Microbiology
12619	Asymptomatic pathogen carriage in stunted and non-stunted children living in Antananarivo, Madagascar	P. Vonaesch	Biostatistics Data and text mining Data integration Exploratory data analysis	Short	In Progress	Department of Cell Biology & Infection
12618	Cellular plasticity during mammary gland development	H. LI	RNA-seq Single Cell	Short	Declined	Department of Developmental & Stem Cell Biology
12591	Rainfalls and water contamination in Antananarivo over 25 years	J. Ronan	Statistics	Short	Awaiting Publication	Other
12571	Role of the Topoisomerase 1 and Guanine quadruplexes as transcriptional regulators	M. LAVIGNE	Transcriptomics	Medium	Awaiting Publication	Department of Virology
12502	Toxin induced dephosphorylation of H3S10	M. Hamon	ChIP-seq		Declined	Department of Cell Biology & Infection
12497	Genome annotation of sequenced bacteria of the Culture Collection of the Pasteur Institut	M. Pina	Annotation		Pending	Department of Microbiology
12401	Comparison of matrices of antibody gene usage	P. BRUHNS	Biostatistics Data Visualization Parallel computing Statistical inference	Medium	Pending	Department of Immunology
12288	High content screening of mitochondrial morphology defects in mitochondrial genetic diseases	T. Wai	Biostatistics Image analysis Machine learning	Short	Pending
12261	Identification of eukaryotic 5’UTRs	A. ECHARD	Motifs and patterns detection Transcriptomics	Short	Closed	Department of Cell Biology & Infection
12260	Pasteur MLST: Institut Pasteur genomic taxonomy database of microbial strains	S. Brisse	Comparative Genomics Comparative Genomics Database Web development	Medium	Pending	Other
12257	Analysis of neuronal population dynamics in rodents during virtual navigation	C. Schmidt-Hieber	Neuroimaging and computational neuroscience Program development Sofware development and engineering Tool Development	Short	Pending
12246	functional enrichment of RNA processing factors associated with proteins of influenza viruses	C. Demeret	Databases and ontologies	Short	Awaiting Publication	Department of Virology
12231	Identification of immune response signatures that correlate with therapeutic responses to TNF inhibitors using machine-learning algorithms	L. Rogge	Biostatistics Machine learning	Short	In Progress	Department of Immunology
12220	The Flemmingsome: the proteome of intact cytokinetic midbodies	N. GUPTA-ROSSI	Cell biology and developmental biology Database Proteomics Web development	Short	Awaiting Publication	Department of Cell Biology & Infection
12193	Automated merging of CSV documents.	M. Mistretta	Data management	Short	Closed	Department of Cell Biology & Infection
12128	Transcriptomics of Anopheles – Plasmodium vivax interactions towards identification of malaria transmission blocking targets	C. Bourgouin	Annotation Differential analysis Non coding RNA RNA-seq Transcriptome assembly	Long	In Progress	Department of Genome & Genetics
12107	Ecological evolution in Klebsiella	J. Lopez Fernandez	Biostatistics Phylogenetics	Short	In Progress	Department of Infection & Epidemiology
12106	An Aedes albopictus-driven epidemiological prediction for arboviral diseases outbreak in Europe	P. Yen	Epidemiology and public health		Closed	Department of Virology
12069	Heterogeneity of tissue resident stromal cells	D. Al-Dhahri	Single Cell	Medium	In Progress	Department of Immunology
12068	Antimalarial drug resistance in Africa: A comprehensive molecular analysis of the emergence of artemisinin resistant parasites in Africa	D. Menard	Phylogenetics Population genetics Variant analysis	Short	Pending	Department of Parasites and Insect Vectors
12049	Understanding the pathways of small RNA production during Meiotic Silencing by Unpaired DNA (MSUD) in the fungus Neurospora crassa	E. Gladyshev	Non coding RNA Workflow and pipeline development	Long	In Progress	Other
12041	Characterization of Yolk Sac Derived Progenitors in the Fetal Liver	L. Freyer	Single Cell	Long	In Progress	Department of Developmental & Stem Cell Biology
12018	Assessing the integrations of viral sequences into the genomes of Aedes albopictus and Aedes aegypti	V. Houé	Genomics Host-pathogen interactions	Short	Pending	Department of Virology
11988	Phage infection dynamics in the gut of gnotobiotic mice	M. Mansos Lourenco	Biostatistics qPCR	Short	In Progress	Department of Microbiology
11975	Analyse d’expression de gènes de la réponse immune par voies fonctionnelles	F. Michel	Pathway Analysis	Short	In Progress	Other
11966	Dynamic and integrative multidimensional OMICs analysis of the cellular senescence fate	O. Bischof	ATAC-seq ChIP-seq Data integration Epigenomics Modeling Motifs and patterns detection Transcriptomics	Long	In Progress	Department of Cell Biology & Infection
11936	Dissecting Peptidoglycan pathways in human near-haploid cells	M. Fanton d\’Andon	Genomics	Medium	Pending	Department of Microbiology
11931	High-throuput nanobodies (VHH) screening and sequencing	M. Marinozzi	Sequence analysis		Declined	Department of Structural Biology & Chemistry
11885	Development of a Software tool to integrate Bottomp-up, Middle-down and Top-down proteomics data	M. Matondo	Data Visualization User centered design Web development	Medium	Pending
11805	Implémentation d’un algorithme rapide de génotypage cgMLST	V. BOUCHEZ	Algorithmics	Short	In Progress	Department of Infection & Epidemiology
11793	ChIP-seq analysis of the majour regulator of GBS virulence	m. mazzuoli	ChIP-seq	Short	Awaiting Publication	Department of Microbiology
11691	Fusion proteins in mammals and yeasts	F. Rey	Phylogenetics Sequence analysis	Short	Closed	Department of Virology
11681	Genetic traits involved in the regulation of NK cell and ILC homeostasis and NK cell-mediated anti-tumor functions	C. Vosshenrich	Biostatistics Genotyping Statistics	Short	In Progress	Department of Immunology
11642	Defining Shigella-targeting of human lamina propria mononuclear cells using CyTOF technology	K. Brunner	Cytometry Differential analysis Single Cell	Short	Closed	Department of Cell Biology & Infection
11593	Search for non-annotated transcripts in zebrafish lymphocytes	J. Levraud			Pending	Department of Developmental & Stem Cell Biology
11514	Exploring immunological mechanisms of human graft-verus-host disease after hematopoietic stem cell transplantation	E. Latis	Differential analysis	Short	Closed	Department of Immunology
11491	MOODel: Modeling Mood Disorders	A. A. Dargél	Clustering Statistical inference	Long	In Progress	Department of Neuroscience
11317	Role of ATM in EBV latency	M. Lecuit	Differential analysis RNA-seq Statistics	Short	Awaiting Publication	Department of Cell Biology & Infection
11315	Next Generation Surveillance of Salmonella and Shigella infections	F. Weill	Genome analysis Phylogenetics		Pending	Department of Infection & Epidemiology
11308	Transcriptome of epithelial cells challenged with different serotypes of S. pneumoniae	M. Connor	Transcriptomics		Declined	Department of Cell Biology & Infection
11305	Modulation of neutrophil cytosolic proteome in GCSF-treated patients. Impact of sample treatment	M. Benoit	Proteomics		In Progress	Department of Cell Biology & Infection
11290	Analyse statistique d’interactions protéine-protéine	G. Edith	Interactomics Statistical inference	Short	Awaiting Publication	Department of Cell Biology & Infection
11226	Extracting spatiotemporal gene expression activity from live biological tissues	T. Gregor	Applied mathematics Biophysics Modeling Systems Biology	Medium	Pending
11221	State and parameter inference for stochastic models of gene expression	J. Ruess	Applied mathematics Modeling Single Cell Statistical inference Systems Biology	Long	Pending	Other
11123	Identification of the mouse and/or rat orthologues of the human gene ANOS1, responsible for the X-chromosome-linked form of Kallmann syndrome	J. HARDELIN	Annotation Genomics	Short	In Progress	Department of Neuroscience
11075	characterization of RNA virus populations from untargeted NGS in natural infections samples	E. Simon-Loriere	RNA-seq		Closed	Department of Virology
11074	Evaluation de la représentativité génétique d’un pool de souches	E. Sitterlé	Statistics	Short	In Progress	Department of Mycology
10966	Analysis of methylation for HIV patients with co-infections	Y. Madec	Biostatistics Data integration Epidemiology and public health Epigenomics Genotyping Statistics	Short	In Progress	Department of Infection & Epidemiology
10958	BD-CheM – Development of a chemical database to store structural and physico-chemistry data	O. Sperandio	Database Web development	Short	Awaiting Publication	Department of Structural Biology & Chemistry
10948	Insight into the Immune System: A bioresource and data-sharing platform to study chronic inflammatory diseases (IsIShare)	h. laude	Biostatistics Data integration Data management		Closed	Other
10940	CRC related Dysbiosis	S. Iradj	Metagenomics		Declined	Other
10939	Microbiota dysbiosis in human colon cancer	I. SOBHANI	Metagenomics	Medium	Pending	Other
10938	Implication du plasmide pKOBEG dans le génome d’Escherechia coli 55989	E. Gasiorowski	Escherichia coli	Short	In Progress	Department of Microbiology
10937	Physical Contact between human and non human primates in Southeastern Cameroon	V. Narat	Clustering Statistical inference	Short	Closed	Department of Infection & Epidemiology
10934	Mechanisms of phage resistance in Vibrio cholerae O1 biotype classic	P. Kaminski	Sequence analysis	Short	New	Department of Microbiology
10928	DNA encapsulation of human resources for research projects on immune system and inflammatory diseases	h. laude	Microarray SNP	Short	Closed	Other
10921	Analysis of DNA methylation in the presence and absence of antibiotics in wt and mutant V. cholerae	B. Zeynep	Bisulfite-seq Vibrio cholerae	Medium	Closed	Department of Genome & Genetics
10920	Phylogenetic analysis of HHD-PDZ containing proteins	N. Wolff	Phylogeny Sequence analysis Phylogeny/phylogenetics Sequence analysis	Short	Awaiting Publication	Department of Neuroscience
10913	Finding and Predicting CRISPR-Cas9 Efficiency	J. Wong Ng	Data Visualization Tool Development Web development	Short	Closed	Department of Microbiology
10906	Identification of APOBEC3 mutations in cancer genoms	V. CAVAL	Galaxy	Short	Closed	Department of Virology
10896	Prediction of Congenital Infection in Tunisian Pregnant Women	B. Imene	Metagenomics		Pending	Other
10895	CNF-domain containing toxin family	E. Lemichez	Comparative Genomics	Short	In Progress	Department of Microbiology
10893	Impact of gut microbiota on lipid metabolism	G. Chevalier	Metagenomics Metabolomics	Short	Closed	Department of Immunology
10841	Duplications in bacteriophage genomes.	L. De Sordi	Assembly	Medium	Awaiting Publication	Department of Microbiology
10840	Identification of Ago2-bound nuclear transcripts and genomic loci in adult zebrafish neural stem cells	B. Laure	ChIP-seq RNA-seq	Coaching	In Progress	Department of Developmental & Stem Cell Biology
10825	Characterization of the role of Argonaute proteins in regulating germline gene expression at the transcriptional and the post-transcriptional levels.	G. CECERE	Differential analysis Epigenomics Non coding RNA Program development Ribosome profiling RNA-seq Transcriptomics Workflow and pipeline development	Long	In Progress
10791	Mapping of Enhancers from transcriptome data	C. MUCHARDT	Epigenomics Transcriptomics	Long	In Progress	Department of Developmental & Stem Cell Biology
10781	Analysis of IFITM RNA levels in vraious cell types and tissues	O. Schwartz	Differential analysis RNA-seq Statistics Transcriptomics	Medium	Closed	Department of Virology
10757	Evolutionary approach to protein thermal stability	N. Reyes	Sequence analysis	Medium	In Progress	Department of Structural Biology & Chemistry
10712	VCF filtering script	N. Elisabeth	Variant analysis	Short	Closed	Department of Infection & Epidemiology
10700	Genomic determinants for initiation and length of natural antisense transcripts in a compact eukaryotic genome and phylogenetic analysis of related Entamoeba species	N. GUILLEN	Non coding RNA Phylogenetics RNA-seq Sequence analysis Transcriptomics	Long	In Progress	Department of Parasites and Insect Vectors
10674	Channels in metagenomics data	D. Marc	Metagenomics	Short	Closed	Department of Structural Biology & Chemistry
10570	Phylogenetic analysis of insect-specific flaviviruses	A. Baidaliuk	Phylogeny/phylogenetics	Short	Awaiting Publication	Department of Genome & Genetics
10540	Characterization of a Salmonella mutant carrying a single amino-acid substitution in the stress sigma factor RpoS	F. NOREL	RNA-seq	Short	Closed	Department of Structural Biology & Chemistry
10508	Genotype to phenotype analysis of immune responses in chronic inflammatory diseases	E. Bianchi	Genotyping Immunogenetics Machine learning Statistics Transcriptomics	Long	In Progress	Department of Immunology
10502	The resurgence of a neglected disease, Yellow fever: from jungle to urban environments	A. FAILLOUX	Variant analysis	Medium	Closed	Department of Virology
10357	Environmental and human surveillance of polioviruses, VDPVs, and other enteroviruses in Madagascar and the impact during the switch from tOPV to bOPV	P. Polston	Metagenomics	Long	In Progress	Department of Virology
10344	Amélioration des techniques permettant la détection de poliovirus dans l’environnement.	M. Bessaud	Poliovirus		Declined	Department of Virology
10343	Détection et assemblage d’entérovirus dans des échantillons cliniques et environnementaux	M. Bessaud	Assembly Metagenomics Enteroviruses Poliovirus	Medium	In Progress	Department of Virology
10315	De novo sequencing and analysis of three unassigned species of non tuberculous mycobacteria.	R. GHARBI	Assembly	Short	Awaiting Publication	Department of Genome & Genetics
10297	viral evolution around Ebola Treatment Center in Macenta	C. Picard	Phylogenetics Variant analysis	Short	In Progress	Department of Virology
10209	identification of sRNA in Leptospira biflexa and influence of a putative Hfq on the transcriptome	M. PICARDEAU	RNA-seq	Short	Closed	Department of Microbiology
10143	AIMyc: Analysis of the Impact of antibiotics, antifungals on the Mycobiome of allogeneic stem cell recipients.	A. Alexandre	Metagenomics	Short	Closed	Department of Mycology
9762	Trichosporon asahii NGS analysis	M. Desnos-Ollivier	Comparative Genomics Genome assembly Variant analysis	Short	In Progress	Department of Mycology
9635	Assembly of insect virus genome	K. Eiglmeier	Galaxy	Short	In Progress	Department of Parasites and Insect Vectors
9210	Effects of expanded-spectrum cephalosporins ( ceftriaxone or céfotaxime) on the human gut Mycobiome	M. Bougnoux	Targeted metagenomics	Short	In Progress	Department of Mycology
8806	Characterizaion of the microbiome of lab colonies of Aedes aegypti	L. Dickson	Metagenomics	Short	Closed	Department of Genome & Genetics
8788	Super-resolution imaging and reconstructions of human cell chromosome architecture	X. Hao	3C Genomics	Short	In Progress	Department of Cell Biology & Infection
8727	Functional interactions between HP1 proteins and RNA.	C. RACHEZ	Differential analysis RNA-seq Transcriptomics	Short	Closed	Department of Developmental & Stem Cell Biology
8657	Biomarqueurs d’identification précoce du sepsis aux urgences (BIPS)	J. Cavaillon	Statistics	Short	In Progress	Department of Infection & Epidemiology
8565	Multi-traits GWAS in Malaria	A. Sakuntabhai	Statistics		Declined	Department of Genome & Genetics
8543	the role of host defense in female genital tract infection by Chlamydia trachomatis	y. wu	Differential analysis qPCR Statistical inference	Short	Closed	Department of Cell Biology & Infection
8528	Comparing V-J gene usage for specific antibody generation	P. Bruhns	Statistical inference	Short	Awaiting Publication	Department of Immunology
8521	Relationships between ESBL-producing Escherichia coli from food and healthy mothers in Phnom Penh, Cambodia	M. Nadimpalli	Annotation Assembly Phylogeny Escherichia coli	Short	Closed	Department of Infection & Epidemiology
8494	NOXO1 interacting partners in intestinal epithelial cells under inflammatory and infectious conditions	B. MARTEYN	Proteomics	Short	Closed	Department of Cell Biology & Infection
8491	Investigating developmental defects of a C. trachomatis mutant strain	A. Subtil	Statistical inference	Short	Closed	Department of Cell Biology & Infection
8453	Heritability of the melatonin synthesis pathway in Autism Spectrum Disorders	M. Benabou	Genetics Statistics	Short	Closed	Department of Neuroscience
8392	Transcriptional profile of Nod2+ neurons upon MDP signaling	G. CHEVALIER	Differential analysis RNA-seq	Short	Closed	Department of Immunology
8364	Assess possible correlations between enteric viruses found in sewage waste water and healthy Roma children in Romania in the period 2016-2017	A. Baidjoe	Metagenomics	Short	Awaiting Publication	Department of Virology
8363	Analyse génomique de corynebacterie	M. BEN ASSAYA	Sequence analysis Variant analysis	Short	Closed	Department of Structural Biology & Chemistry
8340	Infection of Ixodes ricinus by Borrelia burgdorferi sensu lato by in peri-urban forests of France	V. Choumet	Modeling Statistics	Short	Closed	Department of Infection & Epidemiology
8328	Experimental evolution of Chikungunya and Zika viruses’ strains to study emerging variants.	M. Vignuzzi	CNV SNP Data Visualization Phylogeny/phylogenetics	Medium	In Progress	Department of Virology
8318	Salmonella CRISPR database	L. Fabre	CRISPR Tool Development	Short	Closed	Department of Infection & Epidemiology
8302	Metabolic characterization of ILCs under homeostatic or stress conditions	L. Surace	Data integration Data management Data Visualization Metabolomics Pathway Analysis Statistics	Short	Awaiting Publication	Department of Immunology
8290	Common and phylogenetically widespread coding for peptides by bacterial small RNAs – Follow up of a project regarding its journal review	B. Schwikowski	Database Systems Biology Web development		Closed	Department of Genome & Genetics
8263	Performing Gene Ontology Analysis on RNAseq data in Aedes aegypti	S. Merkling	RNA-seq	Short	Awaiting Publication	Department of Genome & Genetics
8239	INNOV DIAG HPV VALOEXPRESS	P. Pérot	Diff. Expression Statistics Tool Development	Short	Closed	Department of Cell Biology & Infection
8232	Looking for the SNPs in evolved Corynebacterium diphtheriae genomes	S. BRISSE	CNV SNP		Pending	Department of Infection & Epidemiology
8227	TB drugs and host response	L. Tailleux	RNA-seq	Short	Awaiting Publication	Department of Genome & Genetics
8217	Evaluation of the GO annotation of the Leishmania donovani genome	G. Spaeth	Annotation		Declined	Department of Parasites and Insect Vectors
8202	Transcriptomic analysis of blood cells from ebola infected patients	S. REYNARD	Differential analysis Microarray Pathway Analysis Statistics	Short	Closed	Department of Virology
8130	Genomic analysis of catheter-related Escherichia coli infection	C. BELOIN	Comparative Genomics Genome assembly	Short	In Progress	Department of Microbiology
8125	Lipid-binding domains in Vaccinia virus proteins	E. Quemin	Sequence analysis	Short	Closed	Department of Cell Biology & Infection
8117	Histone Methyltransferase and Demethylase in Leishmania	S. Lamotte	Phylogenetics Sequence analysis	Short	Awaiting Publication	Department of Parasites and Insect Vectors
8094	ModeMood: Modeling Mood Disorders	A. Ayub Dargél	Statistics	Short	Awaiting Publication	Department of Neuroscience
8067	Bioinformatic analysis of the adenylate cyclase CyaA toxin	A. Chenal	Sequence analysis Structural bioinformatics	Short	Awaiting Publication	Department of Structural Biology & Chemistry
8002	Genetic profile of patients with dyslexia	C. Leblond	Genetics Genotyping Statistics	Medium	In Progress	Department of Neuroscience
8001	Characterization of an RNA binding protein of Listeria monocytogenes	A. Pagliuso	RNA-seq	Short	Awaiting Publication	Department of Cell Biology & Infection
7990	MacSyDBCapsule	E. Rocha	Tool Development	Short	Closed	Department of Genome & Genetics
7968	Extraction of sequence information from published genomes of commensal bacteria	P. Schnupf	Comparative Genomics Orthology and paralogy analysis Sequence homology analysis	Short	Closed	Department of Cell Biology & Infection
7965	Statistical analysis of PI survey for the scientific direction	G. Chevalier	Clustering Dimensional reduction Statistics	Short	Closed	Other
7964	Identification de SNP entre 2 souches bactériennes	L. Debarbieux	Assembly Comparative Genomics Omics SNP	Short	In Progress	Department of Microbiology
7930	Gene expression profiling in Kupffer cells	Y. Wei	Pathway Analysis	Short	In Progress	Department of Virology
7917	Recombination among enteroviruses	M. Bessaud	Tool Development	Short	Pending	Department of Virology
7901	Automatic detection of antibiotic resistance genes	O. Chesneau	Sequence analysis	Short	In Progress	Other
7841	Research of SNPs to explain the non virulent phenotype of a mutant of L. interrogans serovar Manilae L495 affecting the expression of a protein not involved in virulence	C. WERTS	Variant analysis	Short	Closed	Department of Microbiology
7836	Graphical representation of co-expressed genes in various datasets	P. Jean-Jacques	Microarray	Short	Closed	Department of Developmental & Stem Cell Biology
7834	Role of PerR-regulated oxidative stress response in pathogen Leptospira virulence	N. Benaroudj	Variant analysis	Short	Pending	Department of Microbiology
7829	Discovery of non-annotated transcripts in RNAseq data from Aedes Aegypti	S. Merkling	Annotation RNA-seq Transcriptome assembly Transcriptomics	Short	Closed	Department of Genome & Genetics
7820	Study of the early pathogenesis during Lassa fever in cynomolgus monkeys and its correlation with the outcome	S. Baize	Differential analysis Pathway Analysis RNA-seq	Long	In Progress	Department of Virology
7810	Quantitative temporal analysis of cellular proteins regulated by HBV in primary human hepatocytes	C. Neuveut	Differential analysis Proteomics	Short	Declined	Department of Virology
7789	Caractéristiques génomiques de souches d’Escherichia coli productrices de BLSE associées à un portage persistant après un voyage en zone tropicale	L. Armand	Statistics		Declined	Department of Genome & Genetics
7757	Comparative analysis of transcriptomic and proteomic data to study RNA and protein expression regulation during RVFV infection in mice.	B. Magali	Differential analysis Microarray	Short	Pending	Department of Developmental & Stem Cell Biology
7750	Gene ontology analysis of RNAseq data from uninfected and Leishmania-infected mouse macrophages	E. Prina	Pathway Analysis	Short	Closed	Department of Parasites and Insect Vectors
7721	Comparative analysis of gene expression pattern between samples of tumor and normal mice tissue	E. CHALATSI	Differential analysis Microarray Pathway Analysis		Declined	Department of Cell Biology & Infection
7704	Comparative analysis of gene expression in different human cell clones	P. GARCIA GUTIERREZ	Differential analysis	Short	Awaiting Publication	Department of Cell Biology & Infection
7631	Differentiation of Shigella species from Escherichia coli by MALDI-TOF mass spectrometry	S. Lefèvre	Proteomics	Short	Awaiting Publication	Department of Infection & Epidemiology
7608	Single cell analysis of HIV-specific CD4+ T cell differentiation	L. Chakrabarti	Single Cell	Medium	Awaiting Publication	Department of Virology
7607	JASS: an online tool for the joint analysis of GWAS summary statistics	H. Aschard	Data Visualization Genetics Statistics Tool Development Web development	Medium	Awaiting Publication	Centers
7596	Immune control of the gut microbiota and lifespan of A. stephensi.	E. Bischoff	Shotgun metagenomics	Short	Awaiting Publication	Department of Parasites and Insect Vectors
7528	Characterization of the specific TCR repertoire preferentially expressed in spontaneously controlled HIV infection	V. Libri	Annotation RNA-seq Single Cell		Declined	Centers
7437	Utilize mouse models to study infection by HIV-1	V. Libri	qPCR Sequence analysis	Short	Closed	Centers
7429	A novel MacSyFinder module for detection of bacterial capsule systems on the future Galaxy platform.	E. Rocha	Tool Development	Short	Closed	Department of Genome & Genetics
7427	Add unit tests to IntegronFinder	E. Rocha	Tool Development	Short	In Progress	Department of Genome & Genetics
7419	Development of a new web interface for ARIA	B. Bardiaux	Galaxy Structural bioinformatics Web development	Long	In Progress	Department of Structural Biology & Chemistry
7413	In silico analyses of a novel LincRNA potentially involved in type I IFN response	E. Rubino	Non coding RNA Transcriptomics	Short	Closed	Department of Immunology
7409	Development of top-down proteomics for clinical microbiology	J. Chamot-Rooke	Proteomics Tool Development	Short	In Progress	Department of Structural Biology & Chemistry
7331	Analysis of DNA methylation in the presence and absence of antibiotics in wt and mutant V. cholerae.	z. Baharoglu	Bisulfite-seq Epigenomics	Medium	Closed	Department of Genome & Genetics
7283	Detection of virulence Genes and genes of interest in Bacillus cereus	D. Clermont	Comparative Genomics	Short	Closed	Department of Microbiology
7277	optimisation d\’un programme sous R	P. Commere	Cytometry Statistics	Short	Closed	Other
7213	Activation of plasmacytoïd dendritic cells by arenaviruses : transcriptomic analysis	J. Schaeffer	Differential analysis Pathway Analysis	Short	Closed	Department of Virology
7198	Genomic analysis of bacterial evolution	L. Debarbieux	Comparative Genomics SNP		Pending	Department of Microbiology
7188	Genomic differences of the same strains preserved in different culture collections	D. Clermont	Variant analysis		Closed	Department of Microbiology
7143	Modeling mitochondrial metabolism dormant Cryptococcus neoformans	B. Hommel	Genomics Proteomics Systems Biology Transcriptomics		In Progress	Department of Mycology
7142	Development of a web application and new functionalities for the maintenance and curation of iPPI-DB	O. Sperandio	Database Galaxy Structural bioinformatics Web development	Long	In Progress	Centers
7121	Determination of phage termini using NGS	D. Bikard	Sequence analysis Statistics		Declined	Department of Microbiology
7089	Cytokinesis study	N. GUPTA	Proteomics	Medium	Declined	Department of Cell Biology & Infection
7074	Gene Ontology and sequence analysis of proteomics data on mycolactone effects on dendritic cells.	J. Morel	Proteomics Sequence analysis	Short	Closed	Department of Immunology
7072	RNA analysis underlying phenotype of mouse model for autism	B. Thomas	RNA-seq Statistics	Medium	Awaiting Publication	Department of Neuroscience
7069	Mapping the genomic architecture of human neuroanatomical diversity	R. Toro	Statistics Variant analysis	Long	In Progress	Department of Neuroscience
7066	Insect Vector Genomics	K. Vernick	Genetics Genomics Population genetics Transcriptomics WGS metagenomics	Long	In Progress	Department of Parasites and Insect Vectors
7046	Transcriptional regulation of innate lymphoid cell plasticity versus differentiation	R. GOLUB	Single Cell Statistics	Short	In Progress	Department of Immunology
6952	PhageTermini: a Fast and User-friendly Software to Determine Bacteriophage Packaging Mode and Termini	M. Monot	Galaxy	Short	Closed	Department of Microbiology
6826	Regulation of HIV-1 integration selectivity by chromatin	M. LAVIGNE	Sequence analysis Statistics	Short	In Progress	Department of Virology
6818	Identification of genes involved in the attenuation of virulence of rough M. abscessus Tn5 mutants in zebrafish	A. Pawlik	Variant analysis	Short	Closed	Department of Genome & Genetics
6803	Identification of promoteur-overlaping antisense transcription	G. Badis-Bréard	Transcriptomics	Short	Closed	Department of Genome & Genetics
6783	Tac4, a new RNA helicase involved in translation control?	M. Fromont-Racine	Transcriptomics	Short	Closed	Department of Genome & Genetics
6761	Impact of hepatic inflammation on microbiota	Y. Wei	Shotgun metagenomics	Short	Awaiting Publication	Department of Virology
6759	Measles virus protein C interplay with cellular apoptotic pathways; applications for cancer treatment	A. Meignié	Data Visualization Systems Biology Transcriptomics	Short	In Progress	Department of Virology
6721	Regulation of Sirtuin 2-dependent histone deacetylation during bacterial infection	J. Pereira	ChIP-seq	Short	Closed	Department of Cell Biology & Infection
6701	Identification of Tac4 mRNA targets	M. Fromont-Racine	RNA-seq	Short	Awaiting Publication	Department of Genome & Genetics
6699	Deciphering the composition dynamics of infant gut microbiome	X. GAO	Shotgun metagenomics	Short	Closed	Department of Infection & Epidemiology
6667	Analysis of the transcriptome of malaria parasites	S. Vembar	Differential analysis RNA-seq Transcriptome assembly	Medium	Closed	Department of Parasites and Insect Vectors
6579	Novel protein interaction in the assembly of photosynthetic prokaryotic complexes	G. Kufryk	Phylogenetics	Short	Pending	Department of Structural Biology & Chemistry
6535	Dissecting the peptidoglycan trafficking machinery using gene trap mutagenesis in near-haploid human cells	C. Brenner	Genome assembly Statistics	Medium	Closed	Department of Microbiology
6510	IgBlast on Galaxy	T. Hieu	Galaxy	Short	Closed	Department of Immunology
6333	Identification of new or unexpected pathogens, including viruses, bacteria, fungi and parasites associated with acute or progressive diseases	M. ELOIT	Phylogenetics Shotgun metagenomics Tool Development	Long	In Progress	Department of Cell Biology & Infection
6325	Diffusion des mutations de résistance du VIH : modèles et méthodes d’estimation	O. Gascuel	Phylogenetics	Medium	In Progress	Department of Genome & Genetics
6313	Molecular analysis of muscle stem cells	F. Pala	Microarray	Medium	Closed	Department of Developmental & Stem Cell Biology
6311	Nanotherapeutics for multidrug-resistant tuberculosis	L. Tailleux	RNA-seq	Short	Closed	Department of Genome & Genetics
6272	Host gene regulation in response to Listeria monocytogenes infection	D. RIBET	Differential analysis Microarray Statistics	Short	Closed	Department of Cell Biology & Infection
6040	Deconvolution of synthetic chromosomes in 3D	R. Koszul	Chromatin conformation capture		Pending	Department of Genome & Genetics
5740	Methylome analysis of a human progeroid disease for the detection of progeroid-specific alterations and their link with regular ageing	M. Ricchetti	Epigenomics	Medium	Awaiting Publication	Department of Developmental & Stem Cell Biology
5679	Collaboration with the hub to develop ChiPseq and ATACseq analysis pipelines	J. Coppee	ATAC-seq ChIP-seq	Medium	Closed	Department of Genome & Genetics
5667	Comparative analysis of the virulence plasmids of Shigella Spp. and entero-invasive Escherichia coli	C. Parsot	Data Visualization Variant analysis	Short	Closed	Department of Cell Biology & Infection
5583	Label-free quantitative proteomics of Human Macrophages infected by M. tuberculosis	M. Matondo	Proteomics		Declined	Department of Structural Biology & Chemistry
5567	Rift valley fever NSm protein functional study	B. Magali	Differential analysis Pathway Analysis Proteomics	Short	Awaiting Publication	Department of Virology
5489	Zebrafish microbiota	F. Stressmann	Shotgun metagenomics	Short	Awaiting Publication	Department of Microbiology
5412	Comparative genomic and phylogenetic analysis of Clostridium botulinum strains	M. Christelle	Comparative Genomics Phylogenetics		Declined	Department of Microbiology
5310	Patho-evolution of mycobacterial strains	E. Boritsch	Variant analysis	Short	Awaiting Publication	Department of Genome & Genetics
5121	Deciphering dormancy in Cryptocococcus neoformans	B. Hommel	Statistics	Medium	Awaiting Publication	Department of Mycology
5034	Environmental and human surveillance of polioviruses, VDPVs, and other enteroviruses in Madagascar during the switch from tOPV to bOPV	P. Polston	Shotgun metagenomics	Medium	Closed	Department of Virology
4863	Recherche de SNP chez une souche de leptospira biflexa d’interêt	B. Pascale	Comparative Genomics Data Visualization Variant analysis	Short	Closed	Department of Microbiology
4711	Genomic analysis of small orfs of unknown function	F. Norel	Comparative Genomics Sequence analysis	Short	Closed	Department of Microbiology
4541	Prediction of RNA-RNA interactions between a family of GC-rich ncRNAs and nascent transcripts of virulence genes in Plasmodium falciparum	A. Barcons Simon	Non coding RNA	Short	Closed	Department of Parasites and Insect Vectors
4489	HSC3D	P. Clerc	Genomics Single Cell	Short	In Progress	Department of Developmental & Stem Cell Biology
4336	Comparative genomic and phylogenetic analysis of Clostridium baratii strains	C. MAZUET	Phylogenetics Sequence analysis	Short	Closed	Department of Microbiology
4173	Gene Expression analysis	D. Sophie	Differential analysis Microarray Statistics	Short	Closed	Department of Immunology
4109	BrainEvo	G. Dumas	Data Visualization		Declined	Department of Neuroscience
4108	Bioinformatic analysis of phospholipase A2 (PLA2) from P. falciparum	A. Alaganan	Phylogenetics Structural bioinformatics	Short	Closed	Department of Parasites and Insect Vectors
3936	mechanism of toxin production by Klesiella pneumoniae	R. TOURNEBIZE	Genome assembly Variant analysis	Short	Awaiting Publication	Department of Cell Biology & Infection
3907	secretome analysis of human intestinal cells during shigella invasion	n. sauvonnet	Statistics		In Progress	Department of Cell Biology & Infection
3905	Development and use of statistical programs to analyze RNA-Seq data produced at the Transcriptome & Epigenome Platform	J. Coppée	Differential analysis RNA-seq Single Cell Statistics	Mis-a-disposition	Closed	Department of Genome & Genetics
3883	Development and use of statistical programs to analyze RNA-Seq data produced at the Transcriptome & Epigenome Platform	J. Coppée	Differential analysis miRNA Statistics	Mis-a-disposition	Closed	Department of Genome & Genetics
3826	Analysis of sequencing data from a Leishmania donovani cosmid library	P. Pescher	Sequence analysis	Medium	In Progress	Department of Parasites and Insect Vectors
3564	Mining the Plasmodium genome to identify novel blood stage antigens for use as malaria vaccine candidates	C. Chitnis	Genomics		Pending	Department of Parasites and Insect Vectors
3475	Development of a bioinformatics workflow dedicated to the analysis of the viral metagenome: from NGS raw data to the identification of novel viruses	L. Dacheux	Shotgun metagenomics Taxonomy	Short	In Progress	Department of Infection & Epidemiology
3456	individual-nucleotide resolution Cross-Linking and ImmunoPrecipitation (iCLIP) of Argonaute proteins in C. elegans	G. CECERE	RNA-seq		Declined	Department of Developmental & Stem Cell Biology
3442	Reconstruction of archaeal genomes from environmental metagenomic data	s. gribaldo	Shotgun metagenomics	Long	In Progress	Department of Microbiology
3346	Systems Biology of Cell Infection by the Bacterial Pathogen Listeria monocytogenes	J. PIZARRO-CERDA	miRNA Systems Biology	Medium	In Progress	Department of Cell Biology & Infection
3327	Listeriomics – Development of a web platform for visualization and analysis of Listeria omics data	P. Cossart	Data Visualization Genomics Proteomics Tool Development Transcriptomics	Medium	Closed	Department of Cell Biology & Infection
3322	Host Range Database	L. Debarbieux	Data Visualization		Declined	Department of Microbiology
3312	Determination of SNPs in 6 genomes of Leptospira kirschneri serovar grippotyphosa	P. hugon	Data Visualization Variant analysis	Short	In Progress	Department of Microbiology
3257	Factors determining HIV seeding in CD4+ T cell subpopulations	S. Asier	Differential analysis Statistics	Medium	Closed	Department of Virology
3255	ANALYSIS OF TRANSCRIPTIONNAL MODULATIONS INDUCED IN C57BL/6 BONE-MARROW DERIVED MACROPHAGES INFECTED BY LEISHMANIA AMAZONENSIS IN PRESENCE OR ABSENCE OF INFLAMMASOME-ACTIVATING CONDITIONS	H. LECOEUR	Differential analysis RNA-seq	Short	Closed	Department of Parasites and Insect Vectors
3254	ANALYSIS OF TRANSCRIPTIONAL MODULATIONS RELATED TO CELL DEATH PROCESSES IN MURINE BONE-MARROW DERIVED MACROPHAGES AND DENDRITIC CELLS INFECTED BY LEISHMANIA AMAZONENSIS	H. Lecoeur	Differential analysis Microarray Statistics	Short	Closed	Department of Parasites and Insect Vectors
3223	Transciptomic analysis of dendritic cell response during Lassa virus infection	J. Schaeffer	Differential analysis Transcriptomics		Closed	Department of Virology
3127	Interactions and dynamics of fungal and bacterial microbiome in healthy people	M. Bougnoux	Shotgun metagenomics	Short	Closed	Department of Mycology
3103	Massive amplification at an unselected locus accompanies complex chromosomal rearrangements in yeast	B. DUJON	Variant analysis	Mis-a-disposition	Closed	Department of Genome & Genetics
3100	SNP based analysis of French Bordetella pertussis isolates: comparison of isolates producing all the vaccine antigens to isolates producing only some of them.	V. Bouchez	Comparative Genomics Variant analysis	Medium	Closed	Department of Infection & Epidemiology
3086	Bio-informatics support for the LeiSHield project	G. Spaeth	Sequence analysis	Long	In Progress	Department of Parasites and Insect Vectors
3035	Immunovax	G. Barba Spaeth	Statistics	Short	Declined	Department of Virology
3030	RNAseq analysis-gene ontology enrichment Clostridium tetani	D. Chapeton Montes	Differential analysis Statistics	Medium	In Progress	Department of Microbiology
2976	Meta-analysis of dengue transcriptomic data	I. Nikolayeva	Systems Biology	Medium	In Progress	Department of Genome & Genetics
2944	Antibody sequencing by MS: Automation of analysis	B. Saunier	Proteomics Sequence analysis Tool Development	Long	In Progress	Department of Virology
2937	The contribution of ecological variation to the microbiome of Ae. aegypti	L. Dickson	Shotgun metagenomics	Short	Closed	Department of Genome & Genetics
2936	A long-term mission for an assigned CIH-embedded bioinformatician to provide bioinformatic support to the CIH community	M. Hasan	Differential analysis Microarray RNA-seq Sequence analysis Single Cell Systems Biology Tool Development	Mis-a-disposition	In Progress	Department of Immunology
2933	Variant effects on influenza virus proteins	C. Barbezange	Sequence analysis Statistics Variant analysis	Medium	In Progress	Department of Virology
2922	Comparative genomic and phylogenetic analysis of 14 Clostridium tetani strains	D. Chapeton Montes	Comparative Genomics Phylogenetics	Short	Closed	Department of Microbiology
2920	Un workflow pour l’analyses des polymorphismes des souches de grippe saisonnier.	V. Enouf	Sequence analysis Tool Development Variant analysis	Short	In Progress	Department of Virology
2919	L’analyses phylogénétique par séquence protéique, temporal et géographical	N. Naffakh	Phylogenetics	Long	In Progress	Department of Virology
2918	Analyses fonctionnel des protéines humains de type ubiquitin.	C. Demeret	Proteomics Sequence analysis	Medium	In Progress	Department of Virology
2917	Analyses protéine-protéine interactions	Y. Jacob	Proteomics Structural bioinformatics	Mis-a-disposition	In Progress	Department of Virology
2905	Deciphering dormancy in Cryptocococcus neoformans	h. benjamin	Statistics	Short	Closed	Department of Mycology
2904	Variant detection on NGS data	L. DEBARBIEUX	Variant analysis	Medium	Closed	Department of Microbiology
2892	The Physiological Consequences of Altering Bacterial Cell Wall Synthesis	J. Berry	Annotation Differential analysis Genomics Proteomics Transcriptomics	Medium	Closed	Department of Microbiology
2889	Genome On Rails	E. Rocha	Comparative Genomics		Declined	Department of Genome & Genetics
2882	Deciphering the global response of human macrophages against M. tuberculosis	L. Tailleux	Genomics Statistics	Medium	Awaiting Publication	Department of Genome & Genetics
2881	Re-annotation and HTseq analysis of the Sudanese L. donovani strain LdS1	G. Spaeth	Sequence analysis	Long	In Progress	Department of Parasites and Insect Vectors
2875	Do faecal microbiome phages facilitate antibiotic resistance?	E. Rocha	Shotgun metagenomics	Coaching	In Progress	Department of Genome & Genetics
2873	Transcriptome du fibroblaste cutané humain: une approche pré-expérimentale	B. David-Watine	Differential analysis		Declined	Department of Cell Biology & Infection
2871	Mise a disposition d’un(e) bioinformaticien(ne) du hub pour les analyses bioinformatiques du transcriptome et de l epigenome	J. Coppee	ATAC-seq ChIP-seq Non coding RNA RNA-seq Single Cell	Mis-a-disposition	Closed	Department of Genome & Genetics
2850	Horizontal gene transfer in mycobacteria	E. Boritsch	Data Visualization Genome assembly Variant analysis	Long	Closed	Department of Genome & Genetics
2829	Yeast comparative genomics	B. Dujon	Annotation Comparative Genomics Genome assembly Variant analysis	Long	Awaiting Publication	Department of Genome & Genetics
2827	N/A	N. Rachidi	Phylogenetics Sequence analysis	Short	Closed	Department of Parasites and Insect Vectors
2822	sequence conservation in the vicinity of Gli3 binding sites in the mouse genome	R. Benoit	Sequence analysis	Short	Closed	Other
2760	Pasteur International Bioresources Network (PIBnet) bioinformatics: whole-genome sequencing of microbial agents for disease surveillance, outbreak investigation, epidemiology and population biology	S. BRISSE	Genome assembly Phylogenetics Statistics Taxonomy Tool Development Variant analysis	Embedded	In Progress	Department of Genome & Genetics
2741	A reference panel of dengue vector genomes	L. Lambrechts	Annotation Genome assembly Tool Development	Medium	Closed	Department of Genome & Genetics
2720	How ribosomal protein gene position impacts in the genome evolution during a long term evolution experiment.	A. SOLER	Genome assembly Genome rearrangements Variant analysis	Medium	Pending	Department of Genome & Genetics
2712	Regulation by phase variation and attenuation: looking for leader peptides containing repeats in the intergenic regions of streptococcal genomes	S. Dramsi	Annotation Phylogenetics	Medium	Closed	Department of Microbiology
2622	MicrocystOmics	C. Pancrace	Data Visualization Genomics Statistics Transcriptomics	Medium	Closed	Department of Microbiology
2598	Updating the Topo IB gene tree	P. Forterre	Data Visualization Phylogenetics Taxonomy	Medium	Closed	Department of Microbiology
2596	Assemblage de novo d’une souche d’E. coli	L. DEBARBIEUX	Genome assembly	Short	Closed	Department of Microbiology
2595	A program to identify integrons, attC sites and gene cassettes	E. Rocha	Tool Development	Medium	Closed	Department of Genome & Genetics
2561	Identification of Transcription Start Sites and small RNAs in Leptospira interrogans by transcriptome analysis	M. Picardeau	Differential analysis miRNA Transcriptomics	Medium	Closed	Department of Microbiology
2552	Role of SUMO, a new epigenetic mark, in stress response	A. DEJEAN	ATAC-seq ChIP-seq Differential analysis Epigenomics RNA-seq Transcriptomics	Long	Awaiting Publication	Department of Cell Biology & Infection
2548	INNOV DIAG HPV	P. Pérot	Differential analysis Statistics Tool Development	Medium	Closed	Department of Cell Biology & Infection
2535	Influence of chromatin dynamics on genomic stability during replication	L. Lazar Stefanita	Data Visualization Variant analysis	Medium	Closed	Department of Genome & Genetics
2533	Transcriptome analyis of two human T cell subsets	F. MICHEL	Diff. Expression		Declined	Department of Immunology
2529	a web interface for MacSyFinder (a tool to detect macromolecular systems in genomes).	E. Rocha	Tool Development	Medium	Closed	Department of Genome & Genetics
2528	Analysis of host epitranscriptional modifications upon colonisation with commensals and infection by bacterial pathogens	P. Cossart	ChIP-seq Differential analysis	Long	In Progress	Department of Cell Biology & Infection
2527	Deconvolution of synthetic homologous chromosomes in 3D	R. Koszul	Chromatin conformation capture	Short	Closed	Department of Genome & Genetics
2526	Analyse de données de microarray	Y. Wei	Differential analysis Microarray Statistics	Medium	Closed	Department of Virology
2525	Characterization of an unusual Leishmania major HSP70-related protein	G. Spaeth	Data Visualization Phylogenetics Tool Development	Short	Closed	Department of Parasites and Insect Vectors
2512	Single cell gene expression profiling of HIV-specific CD8+ T cells associated with HIV control	A. Saez-Cirion	Differential analysis Single Cell	Long	Awaiting Publication	Department of Virology
2510	Implementation of a statistical tool for HDX-MS data analyses	S. BRIER	Proteomics	Long	Closed	Department of Structural Biology & Chemistry
2506	Analyse de séquence 16S	L. DEBARBIEUX	Taxonomy	Medium	Closed	Department of Microbiology
2504	Analyse de données de miRNA	F. Michel	miRNA	Short	Closed	Department of Immunology
2497	Methods to identify and characterize orthologs of genes encoding small proteins	F. Norel	Phylogenetics	Long	Closed	Department of Microbiology
2490	Analyses of SNP diversity of Legionella pneumophila strains	C. Buchrieser	Comparative Genomics Data Visualization Variant analysis	Medium	Closed	Department of Genome & Genetics
2485	Interactive web interfaces and Analysis Tools of Bacterial NGS data for Postgenomics Life Scientist	M. Monot	Tool Development		Declined	Department of Microbiology
2484	Genomic analyses of E. coli strains	A. Wessel	Genome assembly Variant analysis	Medium	Closed	Department of Microbiology
2479	Molecular analysis of muscle stem cells	S. Tajbakhsh	Differential analysis Genomics Proteomics Transcriptomics	Long	Closed	Department of Developmental & Stem Cell Biology
2456	Transfert annotations	C. Bouchier	Annotation	Short	Closed	Department of Genome & Genetics
2436	Identification of new cellular parameters involved in HIV-1 integration selectivity	M. LAVIGNE	Sequence analysis Statistics Structural bioinformatics	Medium	Closed	Department of Virology
2426	Formatage et soumission de données à l’EBI	G. JANBON	Databank submission	Short	Closed	Department of Mycology
2418	Détection de variants dans des données NGS (miSeq) de phage	L. DEBARBIEUX	Variant analysis	Short	Closed	Department of Microbiology
2417	Whole-genome sequencing of microbial agents for disease surveillance, outbreak investigation, epidemiology and population biology	S. Brisse	Genome assembly Phylogenetics Statistics Taxonomy Tool Development Variant analysis	Long	Closed	Department of Genome & Genetics
2416	Fast and accurate implementation of the raw read coverage homogenization technique	A. Criscuolo	Tool Development	Medium	In Progress	Centers
2409	Systems wide analysis of amastigote and promastigote stages of Leishmania donovani	P. Pescher	Data Visualization Differential analysis Genomics Metabolomics Proteomics Transcriptomics	Long	In Progress	Department of Parasites and Insect Vectors
2405	Study of lncRNAs in Cryptococcus neoformans	G. Janbon	Differential analysis Sequence analysis Transcriptome assembly Transcriptomics	Long	In Progress	Department of Mycology
2391	gRNA library design	P. Navarro Gil	CRISPR Sequence analysis	Medium	Awaiting Publication	Department of Developmental & Stem Cell Biology
2318	Novel regulators of cell wall maintenance in Aspergillus fumigatus	S. Raj	Transcriptomics		Declined	Department of Mycology
2314	Host microbiota modification by the pathogen Listeria monocytogenes	J. Pizarro-Cerda	Shotgun metagenomics	Medium	Closed	Department of Cell Biology & Infection
2309	Mapping of research themes and fields of expertise available in the Institut Pasteur international Network	A. Fontanet	Data Visualization Tool Development	Medium	In Progress	Department of Infection & Epidemiology
2303	Development of analysis tools for mate-paired data.	C. Axel			Declined	Department of Genome & Genetics
2294	Gene regulation in yeast quiescence	G. Badis-Breard	Transcriptomics		Declined	Department of Genome & Genetics
2286	viral evolution around Ebola Treatment Centre in Macenta and according to disease outcomes	C. Picard	Genome assembly Variant analysis	Short	Closed	Department of Virology
2277	Transcriptome of Human sperm	D. Marie-Charlotte	RNA-seq	Medium	Closed	Department of Developmental & Stem Cell Biology
2267	Systems Biology Data Management and Analysis Platform (SYSMAP)	B. Schwikowski	Tool Development		Declined	Department of Genome & Genetics
2266	Impact des facteurs épidemiologiques et strategiques sur l’incidence du paludisme à Thiès	A. SOW			Declined	Other
2263	HIghthroughput CRISPR-Cas9 screen in bacteria	D. Bikard	CRISPR Differential analysis	Long	Closed	Department of Microbiology
2254	MacSyFinder development: models data structure	E. Rocha	Tool Development		Closed	Department of Genome & Genetics
2250	Genome-wide replication lanscape of Candida glabrata	G. Richard	Sequence analysis	Long	Closed	Department of Genome & Genetics
2249	Phylogenetic analysis of the Leishmania HSP70 protein family	G. Spaeth	Data Visualization Phylogenetics	Short	Closed	Department of Parasites and Insect Vectors
2243	Characterisation of skeletal muscle stem cell properties in distinct physiological states	F. Pala	Differential analysis Statistics	Short	Closed	Department of Developmental & Stem Cell Biology
2240	search for transcrition factors upregulating Tgfb1 expression in FHL2-/- cells	Y. Wei	Annotation	Short	Closed	Department of Virology
2239	Characterization of microevolution in Candida albicans isolates	C. d’Enfert	Comparative Genomics Data Visualization Genome assembly Variant analysis	Long	In Progress	Department of Mycology
2237	Candida albicans population genomics	C. d’Enfert	Genome assembly Phylogenetics Tool Development Variant analysis	Long	In Progress	Department of Mycology
2178	Evolutionary relationships between giant viruses and eukaryotes	P. Forterre	Phylogenetics Sequence analysis	Long	Awaiting Publication	Department of Microbiology
1320	An automatic pipeline to call SNPs from RNA-seq reads	V. Raquin	Variant analysis	Medium	Awaiting Publication	Department of Genome & Genetics
601	développement d’un logiciel danalyse sur la base de spade et visne	P. Commere	Sofware development and engineering		Declined	Other
526	Regulation of HIV replication by cellular DNA topology	M. Lavigne	Structural bioinformatics	Short	Declined	Department of Virology
380	Genomic approach for the identification of new targets of antimycobacterial drugs	M. BUCHIERI	Variant analysis	Short	Closed	Department of Genome & Genetics
244	Mapping the cell surface signature of the developing mouse heart	M. Valente	Differential analysis Statistics	Short	Closed	Department of Immunology
150	Sequence alignment – implement algorithm in C	C. MacPherson	Algorithmics		Declined	Other
148	Image-based siRNA and drug screens of infection by the pathogen Listeria monocytogenes	J. Pizarro-Cerda	Statistics	Medium	Declined	Department of Cell Biology & Infection
131	Linking Phenotype to genotype in C. neoformans clinical isolates	A. Alexandre	Statistics Variant analysis	Medium	Closed	Department of Mycology