Notredame C - Search Results

1

Upcoming challenges for multiple sequence alignment methods in the high-throughput era.

Kemena C, Notredame C. Kemena C, et al. Among authors: notredame c. Bioinformatics. 2009 Oct 1;25(19):2455-65. doi: 10.1093/bioinformatics/btp452. Epub 2009 Jul 30. Bioinformatics. 2009. PMID: 19648142 Free PMC article. Review.

2

Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures.

Taly JF, Magis C, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Kemena C, Notredame C. Taly JF, et al. Among authors: notredame c. Nat Protoc. 2011 Nov;6(11):1669-82. doi: 10.1038/nprot.2011.393. Nat Protoc. 2011. PMID: 21979275

3

STRIKE: evaluation of protein MSAs using a single 3D structure.

Kemena C, Taly JF, Kleinjung J, Notredame C. Kemena C, et al. Among authors: notredame c. Bioinformatics. 2011 Dec 15;27(24):3385-91. doi: 10.1093/bioinformatics/btr587. Epub 2011 Oct 28. Bioinformatics. 2011. PMID: 22039207 Free PMC article.

4

Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package.

Kemena C, Bussotti G, Capriotti E, Marti-Renom MA, Notredame C. Kemena C, et al. Among authors: notredame c. Bioinformatics. 2013 May 1;29(9):1112-9. doi: 10.1093/bioinformatics/btt096. Epub 2013 Feb 28. Bioinformatics. 2013. PMID: 23449094

5

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments.

Di Tommaso P, Bussotti G, Kemena C, Capriotti E, Chatzou M, Prieto P, Notredame C. Di Tommaso P, et al. Among authors: notredame c. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W356-60. doi: 10.1093/nar/gku459. Epub 2014 Jun 27. Nucleic Acids Res. 2014. PMID: 24972831 Free PMC article.

6

Multiple sequence alignment modeling: methods and applications.

Chatzou M, Magis C, Chang JM, Kemena C, Bussotti G, Erb I, Notredame C. Chatzou M, et al. Among authors: notredame c. Brief Bioinform. 2016 Nov;17(6):1009-1023. doi: 10.1093/bib/bbv099. Epub 2015 Nov 27. Brief Bioinform. 2016. PMID: 26615024 Review.

7

Epistasis as the primary factor in molecular evolution.

Breen MS, Kemena C, Vlasov PK, Notredame C, Kondrashov FA. Breen MS, et al. Among authors: notredame c. Nature. 2012 Oct 25;490(7421):535-8. doi: 10.1038/nature11510. Epub 2012 Oct 14. Nature. 2012. PMID: 23064225

8

Alignathon: a competitive assessment of whole-genome alignment methods.

Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, Hou M, Herrero J, Kent WJ, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D, Paten B. Earl D, et al. Among authors: notredame c. Genome Res. 2014 Dec;24(12):2077-89. doi: 10.1101/gr.174920.114. Epub 2014 Oct 1. Genome Res. 2014. PMID: 25273068 Free PMC article.

9

Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud.

Di Tommaso P, Orobitg M, Guirado F, Cores F, Espinosa T, Notredame C. Di Tommaso P, et al. Among authors: notredame c. Bioinformatics. 2010 Aug 1;26(15):1903-4. doi: 10.1093/bioinformatics/btq304. Epub 2010 Jul 6. Bioinformatics. 2010. PMID: 20605929 Free PMC article.

10

Segment-based multiple sequence alignment.

Rausch T, Emde AK, Weese D, Döring A, Notredame C, Reinert K. Rausch T, et al. Among authors: notredame c. Bioinformatics. 2008 Aug 15;24(16):i187-92. doi: 10.1093/bioinformatics/btn281. Bioinformatics. 2008. PMID: 18689823

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