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Items: 1 to 20 of 23

1.

Classification of Paediatric Inflammatory Bowel Disease using Machine Learning.

Mossotto E, Ashton JJ, Coelho T, Beattie RM, MacArthur BD, Ennis S.

Sci Rep. 2017 May 25;7(1):2427. doi: 10.1038/s41598-017-02606-2.

2.

Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples.

Peterson TA, Gauran IIM, Park J, Park D, Kann MG.

PLoS Comput Biol. 2017 Apr 20;13(4):e1005428. doi: 10.1371/journal.pcbi.1005428. eCollection 2017 Apr.

3.

Blind prediction of deleterious amino acid variations with SNPs&GO.

Capriotti E, Martelli PL, Fariselli P, Casadio R.

Hum Mutat. 2017 Sep;38(9):1064-1071. doi: 10.1002/humu.23179. Epub 2017 May 2.

4.

An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology.

Li J, Batcha AM, GrĂ¼ning B, Mansmann UR.

Cancer Inform. 2016 Apr 10;14(Suppl 5):87-107. doi: 10.4137/CIN.S30793. eCollection 2015. Review.

5.

A Molecular Evolutionary Reference for the Human Variome.

Liu L, Tamura K, Sanderford M, Gray VE, Kumar S.

Mol Biol Evol. 2016 Jan;33(1):245-54. doi: 10.1093/molbev/msv198. Epub 2015 Oct 13.

6.

Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel).

Douville C, Masica DL, Stenson PD, Cooper DN, Gygax DM, Kim R, Ryan M, Karchin R.

Hum Mutat. 2016 Jan;37(1):28-35. doi: 10.1002/humu.22911. Epub 2015 Oct 26.

7.

Computational methods and resources for the interpretation of genomic variants in cancer.

Tian R, Basu MK, Capriotti E.

BMC Genomics. 2015;16 Suppl 8:S7. doi: 10.1186/1471-2164-16-S8-S7. Epub 2015 Jun 18. Review.

8.

Identifying Highly Penetrant Disease Causal Mutations Using Next Generation Sequencing: Guide to Whole Process.

Erzurumluoglu AM, Rodriguez S, Shihab HA, Baird D, Richardson TG, Day IN, Gaunt TR.

Biomed Res Int. 2015;2015:923491. doi: 10.1155/2015/923491. Epub 2015 Apr 6. Review.

9.

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.

Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH; UniProt Consortium.

Bioinformatics. 2015 Mar 15;31(6):926-32. doi: 10.1093/bioinformatics/btu739. Epub 2014 Nov 13.

10.

ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples.

Tian R, Basu MK, Capriotti E.

Bioinformatics. 2014 Sep 1;30(17):i572-8. doi: 10.1093/bioinformatics/btu466.

11.

Use of long term molecular dynamics simulation in predicting cancer associated SNPs.

Kumar A, Purohit R.

PLoS Comput Biol. 2014 Apr 10;10(4):e1003318. doi: 10.1371/journal.pcbi.1003318. eCollection 2014 Apr.

12.

Interaction-based discovery of functionally important genes in cancers.

Ghersi D, Singh M.

Nucleic Acids Res. 2014 Feb;42(3):e18. doi: 10.1093/nar/gkt1305. Epub 2013 Dec 19.

13.

Status quo of annotation of human disease variants.

Venselaar H, Camilli F, Gholizadeh S, Snelleman M, Brunner HG, Vriend G.

BMC Bioinformatics. 2013 Dec 4;14:352. doi: 10.1186/1471-2105-14-352.

14.

Computational approaches to identify functional genetic variants in cancer genomes.

Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N; International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group.

Nat Methods. 2013 Aug;10(8):723-9. doi: 10.1038/nmeth.2562.

15.

Identifying Mendelian disease genes with the variant effect scoring tool.

Carter H, Douville C, Stenson PD, Cooper DN, Karchin R.

BMC Genomics. 2013;14 Suppl 3:S3. doi: 10.1186/1471-2164-14-S3-S3. Epub 2013 May 28.

16.

Collective judgment predicts disease-associated single nucleotide variants.

Capriotti E, Altman RB, Bromberg Y.

BMC Genomics. 2013;14 Suppl 3:S2. doi: 10.1186/1471-2164-14-S3-S2. Epub 2013 May 28.

17.

WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation.

Capriotti E, Calabrese R, Fariselli P, Martelli PL, Altman RB, Casadio R.

BMC Genomics. 2013;14 Suppl 3:S6. doi: 10.1186/1471-2164-14-S3-S6. Epub 2013 May 28.

18.

Predicting the functional consequences of cancer-associated amino acid substitutions.

Shihab HA, Gough J, Cooper DN, Day IN, Gaunt TR.

Bioinformatics. 2013 Jun 15;29(12):1504-10. doi: 10.1093/bioinformatics/btt182. Epub 2013 Apr 25.

19.

Knowledge discovery in variant databases using inductive logic programming.

Nguyen H, Luu TD, Poch O, Thompson JD.

Bioinform Biol Insights. 2013 Mar 18;7:119-31. doi: 10.4137/BBI.S11184. Print 2013.

20.

Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models.

Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, Day IN, Gaunt TR.

Hum Mutat. 2013 Jan;34(1):57-65. doi: 10.1002/humu.22225. Epub 2012 Nov 2.

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