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Items: 1 to 20 of 133

1.

SIFT Indel: predictions for the functional effects of amino acid insertions/deletions in proteins.

Hu J, Ng PC.

PLoS One. 2013 Oct 23;8(10):e77940. doi: 10.1371/journal.pone.0077940. eCollection 2013.

2.

Predicting the effects of frameshifting indels.

Hu J, Ng PC.

Genome Biol. 2012 Feb 9;13(2):R9. doi: 10.1186/gb-2012-13-2-r9.

3.

Predicting the functional effect of amino acid substitutions and indels.

Choi Y, Sims GE, Murphy S, Miller JR, Chan AP.

PLoS One. 2012;7(10):e46688. doi: 10.1371/journal.pone.0046688. Epub 2012 Oct 8.

4.

Discriminating between deleterious and neutral non-frameshifting indels based on protein interaction networks and hybrid properties.

Zhang N, Huang T, Cai YD.

Mol Genet Genomics. 2015 Feb;290(1):343-52. doi: 10.1007/s00438-014-0922-5. Epub 2014 Sep 24.

PMID:
25248637
5.

DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels.

Zhao H, Yang Y, Lin H, Zhang X, Mort M, Cooper DN, Liu Y, Zhou Y.

Genome Biol. 2013 Mar 13;14(3):R23. doi: 10.1186/gb-2013-14-3-r23.

6.

DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels.

Folkman L, Yang Y, Li Z, Stantic B, Sattar A, Mort M, Cooper DN, Liu Y, Zhou Y.

Bioinformatics. 2015 May 15;31(10):1599-606. doi: 10.1093/bioinformatics/btu862. Epub 2015 Jan 7.

7.

A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i).

Bermejo-Das-Neves C, Nguyen HN, Poch O, Thompson JD.

BMC Bioinformatics. 2014 Apr 17;15:111. doi: 10.1186/1471-2105-15-111.

8.
9.

Dindel: accurate indel calls from short-read data.

Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R.

Genome Res. 2011 Jun;21(6):961-73. doi: 10.1101/gr.112326.110. Epub 2010 Oct 27.

10.

SIFT web server: predicting effects of amino acid substitutions on proteins.

Sim NL, Kumar P, Hu J, Henikoff S, Schneider G, Ng PC.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W452-7. doi: 10.1093/nar/gks539. Epub 2012 Jun 11.

11.

Large-scale parsimony analysis of metazoan indels in protein-coding genes.

Belinky F, Cohen O, Huchon D.

Mol Biol Evol. 2010 Feb;27(2):441-51. doi: 10.1093/molbev/msp263. Epub 2009 Oct 28.

12.

Exploring the selective constraint on the sizes of insertions and deletions in 5' untranslated regions in mammals.

Chen CH, Liao BY, Chen FC.

BMC Evol Biol. 2011 Jul 5;11:192. doi: 10.1186/1471-2148-11-192.

13.

Equivalent indels--ambiguous functional classes and redundancy in databases.

Assmus J, Kleffe J, Schmitt AO, Brockmann GA.

PLoS One. 2013 May 2;8(5):e62803. doi: 10.1371/journal.pone.0062803. Print 2013.

14.

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.

Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J; 1000 Genomes Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G.

Genome Res. 2013 May;23(5):749-61. doi: 10.1101/gr.148718.112. Epub 2013 Mar 11.

15.

Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins.

Hsing M, Cherkasov A.

BMC Bioinformatics. 2008 Jun 25;9:293. doi: 10.1186/1471-2105-9-293.

16.

Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication.

Guo B, Zou M, Wagner A.

Mol Biol Evol. 2012 Oct;29(10):3005-22. Epub 2012 Apr 4.

17.

Impact of indels on the flanking regions in structural domains.

Zhang Z, Huang J, Wang Z, Wang L, Gao P.

Mol Biol Evol. 2011 Jan;28(1):291-301. doi: 10.1093/molbev/msq196. Epub 2010 Jul 29.

18.

Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes.

Boschiero C, Gheyas AA, Ralph HK, Eory L, Paton B, Kuo R, Fulton J, Preisinger R, Kaiser P, Burt DW.

BMC Genomics. 2015 Jul 31;16:562. doi: 10.1186/s12864-015-1711-1.

19.

PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels.

Choi Y, Chan AP.

Bioinformatics. 2015 Aug 15;31(16):2745-7. doi: 10.1093/bioinformatics/btv195. Epub 2015 Apr 6.

20.

Accurate indel prediction using paired-end short reads.

Grimm D, Hagmann J, Koenig D, Weigel D, Borgwardt K.

BMC Genomics. 2013 Feb 27;14:132. doi: 10.1186/1471-2164-14-132.

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