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Publications

2012

Breen MS, Kemena C, Vlasov PK, Notredame C, Kondrashov FA.  2012.  Epistasis as the primary factor in molecular evolution. Nature. 490:535–538.
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Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, Dunham I, Kundaje A, Aldred SF, Collins PJ et al..  2012.  An integrated encyclopedia of DNA elements in the human genome. Nature. 489:57–74.
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Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG et al..  2012.  The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res.. 22:1775–1789.
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Chang JM, Di Tommaso P, Taly JF, Notredame C.  2012.  Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee.. BMC Bioinformatics. 13 Suppl 4:S1. Abstract
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Torrent M, Di Tommaso P, Pulido D, Nogués MV, Notredame C, Boix E, Andreu D.  2012.  AMPA: an automated web server for prediction of protein antimicrobial regions.. Bioinformatics. 28:130–131. Abstract
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Erb I, González-Vallinas JR, Bussotti G, Blanco E, Eyras E, Notredame C.  2012.  Use of ChIP-Seq data for the design of a multiple promoter-alignment method.. Nucleic Acids Res.. 40:e52. Abstract
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2011

Taly JF, Magis C, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Kemena C, Notredame C.  2011.  Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures.. Nat Protoc. 6:1669–1682. Abstract
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Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C.  2011.  BlastR–fast and accurate database searches for non-coding RNAs.. Nucleic Acids Res.. 39:6886–6895. Abstract
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Merhej V, Notredame C, Royer-Carenzi M, Pontarotti P, Raoult D.  2011.  The rhizome of life: the sympatric Rickettsia felis paradigm demonstrates the random transfer of DNA sequences.. Mol. Biol. Evol.. 28:3213–3223. Abstract
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Kemena C, Taly JF, Kleinjung J, Notredame C.  2011.  STRIKE: evaluation of protein MSAs using a single 3D structure.. Bioinformatics. 27:3385–3391. Abstract
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Cedric Notredame

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