• 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 in the Americas, Genes (Basel) 2019 12;11(1).
• 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).
• 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 11;14(11):e1007430.
• 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, 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
  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 12;7(1):28.
• 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
  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
  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 Jul;114(29):E5910-E5919.
• 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.
• 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.
• 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
  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
  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.
• 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
  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.
• 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
  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.