Notredame C - Search Results

1

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.

2

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.

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

T-Coffee: Tree-based consistency objective function for alignment evaluation.

Magis C, Taly JF, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Notredame C. Magis C, et al. Among authors: notredame c. Methods Mol Biol. 2014;1079:117-29. doi: 10.1007/978-1-62703-646-7_7. Methods Mol Biol. 2014. PMID: 24170398

5

TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction.

Chang JM, Di Tommaso P, Notredame C. Chang JM, et al. Among authors: notredame c. Mol Biol Evol. 2014 Jun;31(6):1625-37. doi: 10.1093/molbev/msu117. Epub 2014 Apr 1. Mol Biol Evol. 2014. PMID: 24694831

6

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.

Chang JM, Di Tommaso P, Lefort V, Gascuel O, Notredame C. Chang JM, et al. Among authors: notredame c. Nucleic Acids Res. 2015 Jul 1;43(W1):W3-6. doi: 10.1093/nar/gkv310. Epub 2015 Apr 8. Nucleic Acids Res. 2015. PMID: 25855806 Free PMC article.

7

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.

8

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

9

Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words.

Lin HN, Notredame C, Chang JM, Sung TY, Hsu WL. Lin HN, et al. Among authors: notredame c. PLoS One. 2011;6(12):e27872. doi: 10.1371/journal.pone.0027872. Epub 2011 Dec 2. PLoS One. 2011. PMID: 22163274 Free PMC article.

10

Use of ChIP-Seq data for the design of a multiple promoter-alignment method.

Erb I, González-Vallinas JR, Bussotti G, Blanco E, Eyras E, Notredame C. Erb I, et al. Among authors: notredame c. Nucleic Acids Res. 2012 Apr;40(7):e52. doi: 10.1093/nar/gkr1292. Epub 2012 Jan 9. Nucleic Acids Res. 2012. PMID: 22230796 Free PMC article.

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