Simossis VA - Search Results

1

The PRALINE online server: optimising progressive multiple alignment on the web.

Simossis VA, Heringa J. Simossis VA, et al. Comput Biol Chem. 2003 Oct;27(4-5):511-9. doi: 10.1016/j.compbiolchem.2003.09.002. Comput Biol Chem. 2003. PMID: 14642759

2

An overview of multiple sequence alignment.

Simossis V, Kleinjung J, Heringa J. Simossis V, et al. Curr Protoc Bioinformatics. 2003 Nov;Chapter 3:Unit 3.7. doi: 10.1002/0471250953.bi0307s03. Curr Protoc Bioinformatics. 2003. PMID: 18428699 Review.

3

PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information.

Simossis VA, Heringa J. Simossis VA, et al. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W289-94. doi: 10.1093/nar/gki390. Nucleic Acids Res. 2005. PMID: 15980472 Free PMC article.

4

Homology-extended sequence alignment.

Simossis VA, Kleinjung J, Heringa J. Simossis VA, et al. Nucleic Acids Res. 2005 Feb 7;33(3):816-24. doi: 10.1093/nar/gki233. Print 2005. Nucleic Acids Res. 2005. PMID: 15699183 Free PMC article.

5

The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods.

Simossis VA, Heringa J. Simossis VA, et al. Comput Biol Chem. 2004 Dec;28(5-6):351-66. doi: 10.1016/j.compbiolchem.2004.09.005. Comput Biol Chem. 2004. PMID: 15556476

6

Integrating protein secondary structure prediction and multiple sequence alignment.

Simossis VA, Heringa J. Simossis VA, et al. Curr Protein Pept Sci. 2004 Aug;5(4):249-66. doi: 10.2174/1389203043379675. Curr Protein Pept Sci. 2004. PMID: 15320732 Review.

7

DIANA-microT web server: elucidating microRNA functions through target prediction.

Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG. Maragkakis M, et al. Among authors: simossis va. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W273-6. doi: 10.1093/nar/gkp292. Epub 2009 Apr 30. Nucleic Acids Res. 2009. PMID: 19406924 Free PMC article.

8

A simple and fast secondary structure prediction method using hidden neural networks.

Lin K, Simossis VA, Taylor WR, Heringa J. Lin K, et al. Among authors: simossis va. Bioinformatics. 2005 Jan 15;21(2):152-9. doi: 10.1093/bioinformatics/bth487. Epub 2004 Sep 17. Bioinformatics. 2005. PMID: 15377504

9

The database of experimentally supported targets: a functional update of TarBase.

Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG. Papadopoulos GL, et al. Among authors: simossis va. Nucleic Acids Res. 2009 Jan;37(Database issue):D155-8. doi: 10.1093/nar/gkn809. Epub 2008 Oct 27. Nucleic Acids Res. 2009. PMID: 18957447 Free PMC article.

10

Accurate microRNA target prediction correlates with protein repression levels.

Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG. Maragkakis M, et al. Among authors: simossis va. BMC Bioinformatics. 2009 Sep 18;10:295. doi: 10.1186/1471-2105-10-295. BMC Bioinformatics. 2009. PMID: 19765283 Free PMC article.

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