• 2024
  Hafner L, Gadin E, Huang L, Frouin A, Laporte F, Gaultier C, Vieira A, Maudet C, Varet H, Moura A, Bracq-Dieye H, Tessaud-Rita N, Maury M, Dazas M, Legendre R, Gastineau P, Tsai YH, Coppée JY, Charlier C, Patin E, Chikhi R, Rocha EPC, Leclercq A, Disson O, Aschard H, Lecuit M, Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes., Nat Microbiol 2024 Dec; 9(12): 3345-3361.
• 2024
  Grégoire Davignon, Natalia Pietrosemoli, Nadia Benaroudj, Marie-Estelle Soupé-Gilbert, Julie Cagliero, Élodie Turc, Mathieu Picardeau, Linda Guentas, Cyrille Goarant, Roman Thibeaux, Leptospira interrogans biofilm transcriptome highlights adaption to starvation and general stress while maintaining virulence., npj Biofilms and Microbiomes, 2024, 10 (1), pp.95. ⟨10.1038/s41522-024-00570-0⟩.
• 2024
  Coppolino F, De Gaetano GV, Claverie C, Sismeiro O, Varet H, Legendre R, Pellegrini A, Berbiglia A, Tavella L, Lentini G, Famà A, Barbieri G, Pietrocola G, Teti G, Firon A, Beninati C, The SaeRS two-component system regulates virulence gene expression in group B Streptococcus during invasive infection., mBio 2024 Sep; 15(9): e0197524.
• 2024
  Hamdi Y, Boujemaa M, Ben Aissa-Haj J, Radouani F, Khyatti M, Mighri N, Hannachi M, Ghedira K, Souiai O, Hkimi C, Kammoun MS, Mejri N, Bouaziz H, Beloufa MA, Charoute H, Barakat A, Najjar I, Taniguchi H, Pietrosemoli N, , Dellagi K, Abdelhak S, Boubaker MS, Chica C, Rouleau E, A regionally based precision medicine implementation initiative in North Africa:The PerMediNA consortium., Transl Oncol 2024 Jun; 44(): 101940.
• 2024
  Aouadi W, Najburg V, Legendre R, Varet H, Kergoat L, Tangy F, Larrous F, Komarova AV, Bourhy H, Comparative analysis of rabies pathogenic and vaccine strains detection by RIG-I-like receptors., Microbes Infect 2024 ; 26(4): 105321.
• 2024
  Labusch M, Thetiot M, Than-Trong E, Morizet D, Coolen M, Varet H, Legendre R, Ortica S, Mancini L, Bally-Cuif L, Prosaposin maintains adult neural stem cells in a state associated with deep quiescence., Stem Cell Reports 2024 Apr; 19(4): 515-528.
• 2023
  de Castro RJA, Marina CL, Sturny-Leclère A, Hoffmann C, Bürgel PH, Wong SSW, Aimanianda V, Varet H, Agrawal R, Bocca AL, Alanio A, Kicking sleepers out of bed: Macrophages promote reactivation of dormant Cryptococcus neoformans by extracellular vesicle release and non-lytic exocytosis., PLoS Pathog 2023 Nov; 19(11): e1011841.
• 2023
  Pasquereau-Kotula E, du Merle L, Sismeiro O, Pietrosemoli N, Varet H, Legendre R, Trieu-Cuot P, Dramsi S, Transcriptome profiling of human col\onic cells exposed to the gut pathobiont Streptococcus gallolyticus subsp. gallolyticus., PLoS One 2023 ; 18(11): e0294868.
• 2023
  Di Carlo SE, Raffenne J, Varet H, Ode A, Granados DC, Stein M, Legendre R, Tuckermann J, Bousquet C, Peduto L, Depletion of slow-cycling PDGFRα+ADAM12+ mesenchymal cells promotes antitumor immunity by restricting macrophage efferocytosis., Nat Immunol 2023 Oct; (): .
• 2023
  Mateo M, Reynard S, Pietrosemoli N, Perthame E, Journeaux A, Noy K, Germain C, Carnec X, Picard C, Borges-Cardoso V, Hortion J, Lopez-Maestre H, Regnard P, Fellmann L, Vallve A, Barron S, Jourjon O, Lacroix O, Duthey A, Dirheimer M, Daniau M, Legras-Lachuer C, Carbonnelle C, Raoul H, Tangy F, Baize S, Rapid protection induced by a single-shot Lassa vaccine in male cynomolgus monkeys., Nat Commun 2023 Mar; 14(1): 1352.
• 2023
  Altamirano-Silva P, Meza-Torres J, Zúñiga-Pereira AM, Zamora-Jaen S, Pietrosemoli N, Cantos G, Peltier J, Pizarro-Cerdá J, Moreno E, Chacón-Díaz C, Guzmán-Verri C, Chaves-Olarte E, Phenotypes controlled by the Brucella abortus two component system BvrR/BvrS are differentially impacted by BvrR phosphorylation., Front Microbiol 2023 ; 14(): 1148233.
• 2023
  Guillaume Dugied, Estelle Mn Laurent, Mikaël Attia, Jean-Pascal Gimeno, Kamel Bachiri, Payman Samavarchi-Tehrani, Flora Donati, Yannis Rahou, Sandie Munier, Faustine Amara, Mélanie dos Santos, Nicolas Soler, Stevenn Volant, Natalia Pietrosemoli, Anne-Claude Gingras, Georgios Pavlopoulos, Sylvie van der Werf, Pascal Falter-Braun, Patrick Aloy, Yves Jacob, Anastassia Komarova, Yorgos Sofianatos, Caroline Demeret, Etienne Coyaud, Multi-Modal SARS-CoV-2 Proteins Interactomics Unveil Spatial Patterns of Invasion Featuring 151 Contacts with Human Proteins Essential for Infection, 2023.
• 2023
  Dumont L, Lopez Maestre H, Chalmel F, Huber L, Rives-Feraille A, Moutard L, Bateux F, Rondanino C, Rives N, Throughout in vitro first spermatogenic wave: Next-generation sequencing gene expression patterns of fresh and cryopreserved prepubertal mice testicular tissue explants., Front Endocrinol (Lausanne) 2023 ; 14(): 1112834.
• 2022
  Mateo M, Hortion J, Perthame E, Picard C, Reynard S, Journeaux A, Germain C, Carnec X, Baillet N, Borges-Cardoso V, Pietrosemoli N, Vallve A, Barron S, Jourjon O, Lacroix O, Duthey A, Dirheimer M, Daniau M, Legras-Lachuer C, Jouvion G, Carbonnelle C, Raoul H, Baize S, , Pathogenesis of recent Lassa virus isolates from lineages II and VII in cynomolgus monkeys., Virulence 2022 12; 13(1): 654-669.
• 2022
  Foresto E, Revale S, Primo E, Nievas F, Carezzano E, Puente M, Alzari P, Martínez M, Ben-Assaya M, Mornico D, Santoro M, Martínez-Abarca F, Giordano W, Bogino P, , Complete Genome Sequence of Mesorhizobium ciceri Strain R30, a Rhizobium Used as a Commercial Inoculant for Chickpea in Argentina., Microbiol Resour Announc 2022 Nov; 11(11): e0077922.
• 2022
  Nievas F, Revale S, Foresto E, Cossovich S, Puente M, Alzari P, Martínez M, Ben-Assaya M, Mornico D, Santoro M, Martínez-Abarca F, Giordano W, Bogino P, , Complete Genome Sequence of Bradyrhizobium sp. Strain C-145, a Nitrogen-Fixing Rhizobacterium Used as a Peanut Inoculant in Argentina., Microbiol Resour Announc 2022 Aug; 11(8): e0050522.
• 2022
  Collard JM, Andrianonimiadana L, Habib A, Rakotondrainipiana M, Andriantsalama P, Randriamparany R, Rabenandrasana MAN, Weill FX, Sauvonnet N, Randremanana RV, Guillemot V, Vonaesch P, Sansonetti PJ, High prevalence of small intestine bacteria overgrowth and asymptomatic carriage of enteric pathogens in stunted children in Antananarivo, Madagascar., PLoS Negl Trop Dis 2022 May; 16(5): e0009849.
• 2022
  Mekki Y, Guillemot V, Lemaître H, Carrión-Castillo A, Forkel S, Frouin V, Philippe C, , The genetic architecture of language functional connectivity., Neuroimage 2022 Apr; 249(): 118795.
• 2022
  Senol AD, Pinto G, Beau M, Guillemot V, Dupree JL, Stadelmann C, Ranft J, Lubetzki C, Davenne M, , Alterations of the axon initial segment in multiple sclerosis grey matter., Brain Commun 2022 ; 4(6): fcac284.
• 2021
  Surace L, Doisne JM, Croft CA, Thaller A, Escoll P, Marie S, Petrosemoli N, Guillemot V, Dardalhon V, Topazio D, Cama A, Buchrieser C, Taylor N, Amit I, Musumeci O, Di Santo JP, , Dichotomous metabolic networks govern human ILC2 proliferation and function., Nat Immunol 2021 Nov; 22(11): 1367-1374.
• 2021
  Tenenhaus A, Guillemot V, Gidrol X, Frouin V, , Gene association networks from microarray data using a regularized estimation of partial correlation based on PLS regression., IEEE/ACM Trans Comput Biol Bioinform 2010 ; 7(2): 251-62.
• 2021
  Julienne H, Laville V, McCaw ZR, He Z, Guillemot V, Lasry C, Ziyatdinov A, Nerin C, Vaysse A, Lechat P, Ménager H, Le Goff W, Dube MP, Kraft P, Ionita-Laza I, Vilhjálmsson BJ, Aschard H, Multitrait GWAS to connect disease variants and biological mechanisms., PLoS Genet 2021 Aug; 17(8): e1009713.
• 2021
  Menegatti S, Guillemot V, Latis E, Yahia-Cherbal H, Mittermüller D, Rouilly V, Mascia E, Rosine N, Koturan S, Millot GA, Leloup C, Duffy D, Gleizes A, Hacein-Bey-Abina S, , Sellam J, Berenbaum F, Miceli-Richard C, Dougados M, Bianchi E, Rogge L, Immune response profiling of patients with spondyloarthritis reveals signalling networks mediating TNF-blocker function in vivo., Ann Rheum Dis 2021 Apr; 80(4): 475-486.
• 2021
  Dupont MSJ, Guillemot V, Campagne P, Serafini N, Marie S, Montagutelli X, Di Santo JP, Vosshenrich CAJ, , Host genetic control of natural killer cell diversity revealed in the Collaborative Cross., Proc Natl Acad Sci U S A 2021 Mar; 118(10): .
• 2020
  Mornico D, Hon CC, Koutero M, Weber C, Coppee JY, Dillies MA, Guillen N, , Genomic determinants for initiation and length of natural antisense transcripts in Entamoeba histolytica., Sci Rep 2020 11; 10(1): 20190.
• 2020
  Declercq M, Biquand E, Karim M, Pietrosemoli N, Jacob Y, Demeret C, Barbezange C, van der Werf S, , Influenza A virus co-opts ERI1 exonuclease bound to histone mRNA to promote viral transcription., Nucleic Acids Res. 2020 Sep; (): .
• 2020
  Coulibaly S, Cimino M, Ouattara M, Lecoutey C, Buchieri MV, Alonso-Rodriguez N, Briffotaux J, Mornico D, Gicquel B, Rochais C, Dallemagne P, , Phenanthrolinic analogs of quinolones show antibacterial activity against M. tuberculosis., Eur J Med Chem 2020 Sep; 207(): 112821.
• 2020
  Julienne H, Lechat P, Guillemot V, Lasry C, Yao C, Araud R, Laville V, Vilhjalmsson B, Ménager H, Aschard H, JASS: command line and web interface for the joint analysis of GWAS results., NAR Genom Bioinform 2020 Mar; 2(1): lqaa003.
• 2020
  Lecoeur H, Prina E, Rosazza T, Kokou K, N'Diaye P, Aulner N, Varet H, Bussotti G, Xing Y, Milon G, Weil R, Meng G, Späth GF, Targeting Macrophage Histone H3 Modification as a Leishmania Strategy to Dampen the NF-κB/NLRP3-Mediated Inflammatory Response., Cell Rep 2020 Feb; 30(6): 1870-1882.e4.
• 2019
  Boité MC, Späth GF, Bussotti G, Porrozzi R, Morgado FN, Llewellyn M, Schwabl P, Cupolillo E, , Trans-Atlantic Spill Over: Deconstructing the Ecological Adaptation of Leishmania infantum in the Americas., Genes (Basel) 2019 12; 11(1): .
• 2019
  Dahl A, Guillemot V, Mefford J, Aschard H, Zaitlen N, , Adjusting for Principal Components of Molecular Phenotypes Induces Replicating False Positives., Genetics 2019 Apr; 211(4): 1179-1189.
• 2019
  Schaeffer J, Reynard S, Carnec X, Pietrosemoli N, Dillies MA, Baize S, Non-Pathogenic Mopeia Virus Induces More Robust Activation of Plasmacytoid Dendritic Cells than Lassa Virus, Viruses 2019 03;11(3).
• 2019
  Heurtier V, Owens N, Gonzalez I, Mueller F, Proux C, Mornico D, Clerc P, Dubois A, Navarro P, The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells, Nat Commun 2019 03;10(1):1109.
• 2019
  Reynard S, Journeaux A, Gloaguen E, Schaeffer J, Varet H, Pietrosemoli N, Mateo M, Baillet N, Laouenan C, Raoul H, Mullaert J, Baize S, Immune parameters and outcomes during Ebola virus disease, JCI Insight 2019 Jan;4(1).
• 2019
  Guillemot V, Beaton D, Gloaguen A, Löfstedt T, Levine B, Raymond N, Tenenhaus A, Abdi H, , A constrained singular value decomposition method that integrates sparsity and orthogonality., PLoS One 2019 ; 14(3): e0211463.
• 2019
  Batrancourt B, Lecouturier K, Ferrand-Verdejo J, Guillemot V, Azuar C, Bendetowicz D, Migliaccio R, Rametti-Lacroux A, Dubois B, Levy R, , Exploration Deficits Under Ecological Conditions as a Marker of Apathy in Frontotemporal Dementia., Front Neurol 2019 ; 10(): 941.
• 2018
  Garali I, Adanyeguh IM, Ichou F, Perlbarg V, Seyer A, Colsch B, Moszer I, Guillemot V, Durr A, Mochel F, Tenenhaus A, , A strategy for multimodal data integration: application to biomarkers identification in spinocerebellar ataxia., Brief Bioinform 2018 Nov; 19(6): 1356-1369.
• 2018
  Bussotti G, Gouzelou E, Côrtes Boité M, Kherachi I, Harrat Z, Eddaikra N, Mottram JC, Antoniou M, Christodoulou V, Bali A, Guerfali FZ, Laouini D, Mukhtar M, Dumetz F, Dujardin JC, Smirlis D, Lechat P, Pescher P, El Hamouchi A, Lemrani M, Chicharro C, Llanes-Acevedo IP, Botana L, Cruz I, Moreno J, Jeddi F, Aoun K, Bouratbine A, Cupolillo E, Späth GF, , Leishmania Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification., mBio 2018 11; 9(6): .
• 2018
  Schor IE, Bussotti G, Maleš M, Forneris M, Viales RR, Enright AJ, Furlong EEM, Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis, Curr. Biol. 2018 11;28(22):3547-3561.e9.
• 2018
  Schaeffer J, Carnec X, Reynard S, Mateo M, Picard C, Pietrosemoli N, Dillies MA, Baize S, , Lassa virus activates myeloid dendritic cells but suppresses their ability to stimulate T cells., PLoS Pathog 2018 Nov; 14(11): e1007430.
• 2018
  Hadj-Selem F, Lofstedt T, Dohmatob E, Frouin V, Dubois M, Guillemot V, Duchesnay E, , Continuation of Nesterov’s Smoothing for Regression With Structured Sparsity in High-Dimensional Neuroimaging., IEEE Trans Med Imaging 2018 Nov; 37(11): 2403-2413.
• 2018
  Morel JD, Paatero AO, Wei J, Yewdell JW, Guenin-Macé L, Van Haver D, Impens F, Pietrosemoli N, Paavilainen VO, Demangel C, Proteomics reveals scope of mycolactone-mediated Sec61 blockade and distinctive stress signature, Mol. Cell Proteomics 2018 Jun;.
• 2018
  Pietrosemoli N, Dobay MP, Optimized Protein-Protein Interaction Network Usage with Context Filtering, Methods Mol. Biol. 2018;1819:33-50.
• 2017
  Pietrosemoli N, Mella S, Yennek S, Baghdadi MB, Sakai H, Sambasivan R, Pala F, Di Girolamo D, Tajbakhsh S, Comparison of multiple transcriptomes exposes unified and divergent features of quiescent and activated skeletal muscle stem cells., Skelet Muscle 2017 Dec; 7(1): 28.
• 2017
  Aschard H, Guillemot V, Vilhjalmsson B, Patel CJ, Skurnik D, Ye CJ, Wolpin B, Kraft P, Zaitlen N, , Covariate selection for association screening in multiphenotype genetic studies., Nat Genet 2017 Dec; 49(12): 1789-1795.
• 2017
  Prieto Barja P, Pescher P, Bussotti G, Dumetz F, Imamura H, Kedra D, Domagalska M, Chaumeau V, Himmelbauer H, Pages M, Sterkers Y, Dujardin JC, Notredame C, Späth GF, Haplotype selection as an adaptive mechanism in the protozoan pathogen Leishmania donovani, Nat Ecol Evol 2017 Dec;1(12):1961-1969.
• 2017
  Ibrahim EC, Guillemot V, Comte M, Tenenhaus A, Zendjidjian XY, Cancel A, Belzeaux R, Sauvanaud F, Blin O, Frouin V, Fakra E, , Modeling a linkage between blood transcriptional expression and activity in brain regions to infer the phenotype of schizophrenia patients., NPJ Schizophr 2017 Sep; 3(1): 25.
• 2017
  Hurtado-Ortiz R, Nazimoudine A, Criscuolo A, Hugon P, Mornico D, Brisse S, Bizet C, Clermont D, , Psychrobacter pasteurii and Psychrobacter piechaudii sp. nov., two novel species within the genus Psychrobacter., Int J Syst Evol Microbiol 2017 Sep; 67(9): 3192-3197.
• 2017
  Grotzke JE, Kozik P, Morel JD, Impens F, Pietrosemoli N, Cresswell P, Amigorena S, Demangel C, Sec61 blockade by mycolactone inhibits antigen cross-presentation independently of endosome-to-cytosol export, Proc. Natl. Acad. Sci. U.S.A. 2017 07;114(29):E5910-E5919.
• 2017
  Romero-Soriano V, Modolo L, Lopez-Maestre H, Mugat B, Pessia E, Chambeyron S, Vieira C, Garcia Guerreiro MP, Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids., Genome Biol Evol 2017 Jun; 9(6): 1450-1470.
• 2017
  Dumetz F, Imamura H, Sanders M, Seblova V, Myskova J, Pescher P, Vanaerschot M, Meehan CJ, Cuypers B, De Muylder G, Späth GF, Bussotti G, Vermeesch JR, Berriman M, Cotton JA, Volf P, Dujardin JC, Domagalska MA, Modulation of Aneuploidy in during Adaptation to Different and Environments and Its Impact on Gene Expression, mBio 2017 05;8(3).
• 2017
  Davis MP, Carrieri C, Saini HK, van Dongen S, Leonardi T, Bussotti G, Monahan JM, Auchynnikava T, Bitetti A, Rappsilber J, Allshire RC, Shkumatava A, O'Carroll D, Enright AJ, Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution, EMBO Rep. 2017 07;18(7):1231-1247.
• 2017
  El Behi M, Sanson C, Bachelin C, Guillot-Noël L, Fransson J, Stankoff B, Maillart E, Sarrazin N, Guillemot V, Abdi H, Cournu-Rebeix I, Fontaine B, Zujovic V, , Adaptive human immunity drives remyelination in a mouse model of demyelination., Brain 2017 Apr; 140(4): 967-980.
• 2017
  Lerat E, Fablet M, Modolo L, Lopez-Maestre H, Vieira C, TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes., Nucleic Acids Res 2017 Feb; 45(4): e17.
• 2017
  Lopez-Maestre H, Carnelossi EA, Lacroix V, Burlet N, Mugat B, Chambeyron S, Carareto CM, Vieira C, Identification of misexpressed genetic elements in hybrids between Drosophila-related species., Sci Rep 2017 Jan; 7(): 40618.
• 2017
  Lima L, Sinaimeri B, Sacomoto G, Lopez-Maestre H, Marchet C, Miele V, Sagot MF, Lacroix V, Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads., Algorithms Mol Biol 2017 ; 12(): 2.
• 2016
  Lopez-Maestre H, Brinza L, Marchet C, Kielbassa J, Bastien S, Boutigny M, Monnin D, Filali AE, Carareto CM, Vieira C, Picard F, Kremer N, Vavre F, Sagot MF, Lacroix V, SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence., Nucleic Acids Res 2016 Nov; 44(19): e148.
• 2016
  Kraemmer J, Smith K, Weintraub D, Guillemot V, Nalls MA, Cormier-Dequaire F, Moszer I, Brice A, Singleton AB, Corvol JC, , Clinical-genetic model predicts incident impulse control disorders in Parkinson’s disease., J Neurol Neurosurg Psychiatry 2016 Oct; 87(10): 1106-11.
• 2016
  Gonzalez-Hilarion S, Paulet D, Lee KT, Hon CC, Lechat P, Mogensen E, Moyrand F, Proux C, Barboux R, Bussotti G, Hwang J, Coppée JY, Bahn YS, Janbon G, Intron retention-dependent gene regulation in Cryptococcus neoformans, Sci Rep 2016 08;6:32252.
• 2016
  Pasi M, Mornico D, Volant S, Juchet A, Batisse J, Bouchier C, Parissi V, Ruff M, Lavery R, Lavigne M, DNA minicircles clarify the specific role of DNA structure on retroviral integration, Nucleic Acids Res. 2016 Jul;.
• 2016
  Bussotti G, Leonardi T, Clark MB, Mercer TR, Crawford J, Malquori L, Notredame C, Dinger ME, Mattick JS, Enright AJ, Improved definition of the mouse transcriptome via targeted RNA sequencing, Genome Res. 2016 05;26(5):705-16.
• 2016
  Richard A, Corvol JC, Debs R, Reach P, Tahiri K, Carpentier W, Gueguen J, Guillemot V, Labeyrie C, Adams D, Viala K, Cohen Aubart F, , Transcriptome Analysis of Peripheral Blood in Chronic Inflammatory Demyelinating Polyradiculoneuropathy Patients Identifies TNFR1 and TLR Pathways in the IVIg Response., Medicine (Baltimore) 2016 May; 95(19): e3370.
• 2015
  Nava C, Rupp J, Boissel JP, Mignot C, Rastetter A, Amiet C, Jacquette A, Dupuits C, Bouteiller D, Keren B, Ruberg M, Faudet A, Doummar D, Philippe A, Périsse D, Laurent C, Lebrun N, Guillemot V, Chelly J, Cohen D, Héron D, Brice A, Closs EI, Depienne C, , Hypomorphic variants of cationic amino acid transporter 3 in males with autism spectrum disorders., Amino Acids 2015 Dec; 47(12): 2647-58.
• 2015
  Chatzou M, Magis C, Chang JM, Kemena C, Bussotti G, Erb I, Notredame C, Multiple sequence alignment modeling: methods and applications, Brief. Bioinformatics 2016 11;17(6):1009-1023.
• 2015
  Allaïli N, Valabrègue R, Auerbach EJ, Guillemot V, Yahia-Cherif L, Bardinet E, Jabourian M, Fossati P, Lehéricy S, Marjańska M, , Single-voxel (1)H spectroscopy in the human hippocampus at 3 T using the LASER sequence: characterization of neurochemical profile and reproducibility., NMR Biomed 2015 Oct; 28(10): 1209-17.
• 2015
  Ounzain S, Micheletti R, Arnan C, Plaisance I, Cecchi D, Schroen B, Reverter F, Alexanian M, Gonzales C, Ng SY, Bussotti G, Pezzuto I, Notredame C, Heymans S, Guigó R, Johnson R, Pedrazzini T, CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis, J. Mol. Cell. Cardiol. 2015 Dec;89(Pt A):98-112.
• 2015
  Paquet ER, Cui J, Davidson D, Pietrosemoli N, Hassan HH, Tsofack SP, Maltais A, Hallett MT, Delorenzi M, Batist G, Aloyz R, Lebel M, A 12-gene signature to distinguish colon cancer patients with better clinical outcome following treatment with 5-fluorouracil or FOLFIRI, J Pathol Clin Res 2015 Jul;1(3):160-72.
• 2015
  Clark MB, Mercer TR, Bussotti G, Leonardi T, Haynes KR, Crawford J, Brunck ME, Cao KA, Thomas GP, Chen WY, Taft RJ, Nielsen LK, Enright AJ, Mattick JS, Dinger ME, Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing, Nat. Methods 2015 Apr;12(4):339-42.
• 2015
  Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See LH, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR, Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression, Nat Commun 2015 Jan;6:5903.
• 2015
  Vidalain PO, Jacob Y, Hagemeijer MC, Jones LM, Neveu G, Roussarie JP, Rottier PJ, Tangy F, de Haan CA, A field-proven yeast two-hybrid protocol used to identify coronavirus-host protein-protein interactions, Methods Mol. Biol. 2015;1282:213-29.
• 2014
  Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B, , Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP, Principles of regulatory information conservation between mouse and human, Nature 2014 Nov;515(7527):371-375.
• 2014
  Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, , A comparative encyclopedia of DNA elements in the mouse genome, Nature 2014 Nov;515(7527):355-64.
• 2014
  Tenenhaus A, Philippe C, Guillemot V, Le Cao KA, Grill J, Frouin V, , Variable selection for generalized canonical correlation analysis., Biostatistics 2014 Jul; 15(3): 569-83.
• 2014
  Di Tommaso P, Bussotti G, Kemena C, Capriotti E, Chatzou M, Prieto P, Notredame C, SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments, Nucleic Acids Res. 2014 Jul;42(Web Server issue):W356-60.
• 2014
  Magis C, Taly JF, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Notredame C, T-Coffee: Tree-based consistency objective function for alignment evaluation, Methods Mol. Biol. 2014;1079:117-29.
• 2013
  Bussotti G, Notredame C, Enright AJ, Detecting and comparing non-coding RNAs in the high-throughput era, Int J Mol Sci 2013 Jul;14(8):15423-58.
• 2013
  Kemena C, Bussotti G, Capriotti E, Marti-Renom MA, Notredame C, Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package, Bioinformatics 2013 May;29(9):1112-9.
• 2013
  Guillemot V, Bender A, Boulesteix AL, , Iterative reconstruction of high-dimensional Gaussian Graphical Models based on a new method to estimate partial correlations under constraints., PLoS One 2013 ; 8(4): e60536.
• 2012
  Le Floch E, Guillemot V, Frouin V, Pinel P, Lalanne C, Trinchera L, Tenenhaus A, Moreno A, Zilbovicius M, Bourgeron T, Dehaene S, Thirion B, Poline JB, Duchesnay E, , Significant correlation between a set of genetic polymorphisms and a functional brain network revealed by feature selection and sparse Partial Least Squares., Neuroimage 2012 Oct; 63(1): 11-24.
• 2012
  , An integrated encyclopedia of DNA elements in the human genome, Nature 2012 Sep;489(7414):57-74.
• 2012
  Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R, The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression, Genome Res. 2012 Sep;22(9):1775-89.
• 2012
  Erb I, González-Vallinas JR, Bussotti G, Blanco E, Eyras E, Notredame C, Use of ChIP-Seq data for the design of a multiple promoter-alignment method, Nucleic Acids Res. 2012 Apr;40(7):e52.
• 2011
  Esteve-Codina A, Kofler R, Palmieri N, Bussotti G, Notredame C, Pérez-Enciso M, Exploring the gonad transcriptome of two extreme male pigs with RNA-seq, BMC Genomics 2011 Nov;12:552.
• 2011
  Taly JF, Magis C, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Kemena C, Notredame C, Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures, Nat Protoc 2011 Nov;6(11):1669-82.
• 2011
  Boulesteix AL, Guillemot V, Sauerbrei W, , Use of pretransformation to cope with extreme values in important candidate features., Biom J 2011 Jul; 53(4): 673-88.
• 2011
  Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C, BlastR–fast and accurate database searches for non-coding RNAs, Nucleic Acids Res. 2011 Sep;39(16):6886-95.
• 2011
  Guillemot V, Tenenhaus A, Le Brusquet L, Frouin V, , Graph constrained discriminant analysis: a new method for the integration of a graph into a classification process., PLoS One 2011 ; 6(10): e26146.
• 2010
  Heride C, Ricoul M, Kiêu K, von Hase J, Guillemot V, Cremer C, Dubrana K, Sabatier L, , Distance between homologous chromosomes results from chromosome positioning constraints., J Cell Sci 2010 Dec; 123(Pt 23): 4063-75.
• 2010
  Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R, Long noncoding RNAs with enhancer-like function in human cells, Cell 2010 Oct;143(1):46-58.
• 2010
  Jelizarow M, Guillemot V, Tenenhaus A, Strimmer K, Boulesteix AL, , Over-optimism in bioinformatics: an illustration., Bioinformatics 2010 Aug; 26(16): 1990-8.
• 2010
  Coll O, Villalba A, Bussotti G, Notredame C, Gebauer F, A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis, Genes Dev. 2010 Jan;24(2):129-34.
• 2008
  Marcatili P, Bussotti G, Tramontano A, The MoVIN server for the analysis of protein interaction networks, BMC Bioinformatics 2008 Mar;9 Suppl 2:S11.