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Items: 1 to 20 of 119

1.

Automated inference of molecular mechanisms of disease from amino acid substitutions.

Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, Mooney SD, Radivojac P.

Bioinformatics. 2009 Nov 1;25(21):2744-50. doi: 10.1093/bioinformatics/btp528. Epub 2009 Sep 3.

2.

In silico functional profiling of human disease-associated and polymorphic amino acid substitutions.

Mort M, Evani US, Krishnan VG, Kamati KK, Baenziger PH, Bagchi A, Peters BJ, Sathyesh R, Li B, Sun Y, Xue B, Shah NH, Kann MG, Cooper DN, Radivojac P, Mooney SD.

Hum Mutat. 2010 Mar;31(3):335-46. doi: 10.1002/humu.21192.

3.

Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro-fuzzy classifiers.

Barenboim M, Masso M, Vaisman II, Jamison DC.

Proteins. 2008 Jun;71(4):1930-9. doi: 10.1002/prot.21838.

PMID:
18186470
4.

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.

5.

Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease.

Xin F, Myers S, Li YF, Cooper DN, Mooney SD, Radivojac P.

Bioinformatics. 2010 Aug 15;26(16):1975-82. doi: 10.1093/bioinformatics/btq319. Epub 2010 Jun 15.

6.

Assessment of computational methods for predicting the effects of missense mutations in human cancers.

Gnad F, Baucom A, Mukhyala K, Manning G, Zhang Z.

BMC Genomics. 2013;14 Suppl 3:S7. doi: 10.1186/1471-2164-14-S3-S7. Epub 2013 May 28.

7.

Sequence feature-based prediction of protein stability changes upon amino acid substitutions.

Teng S, Srivastava AK, Wang L.

BMC Genomics. 2010 Nov 2;11 Suppl 2:S5. doi: 10.1186/1471-2164-11-S2-S5.

8.

Predicting deleterious amino acid substitutions.

Ng PC, Henikoff S.

Genome Res. 2001 May;11(5):863-74.

10.

Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis.

Masso M, Vaisman II.

Bioinformatics. 2008 Sep 15;24(18):2002-9. doi: 10.1093/bioinformatics/btn353. Epub 2008 Jul 16.

PMID:
18632749
11.
12.

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.

13.

Correlating protein function and stability through the analysis of single amino acid substitutions.

Bromberg Y, Rost B.

BMC Bioinformatics. 2009 Aug 27;10 Suppl 8:S8. doi: 10.1186/1471-2105-10-S8-S8.

14.

When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants.

Pagel KA, Pejaver V, Lin GN, Nam HJ, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P.

Bioinformatics. 2017 Jul 15;33(14):i389-i398. doi: 10.1093/bioinformatics/btx272.

PMID:
28882004
15.

Correlated mutations: a hallmark of phenotypic amino acid substitutions.

Kowarsch A, Fuchs A, Frishman D, Pagel P.

PLoS Comput Biol. 2010 Sep 16;6(9). pii: e1000923. doi: 10.1371/journal.pcbi.1000923.

16.

Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

Mathe E, Olivier M, Kato S, Ishioka C, Hainaut P, Tavtigian SV.

Nucleic Acids Res. 2006 Mar 6;34(5):1317-25. Print 2006.

17.

The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease.

Lugo-Martinez J, Pejaver V, Pagel KA, Jain S, Mort M, Cooper DN, Mooney SD, Radivojac P.

PLoS Comput Biol. 2016 Aug 26;12(8):e1005091. doi: 10.1371/journal.pcbi.1005091. eCollection 2016 Aug.

18.

Prediction of RNA binding sites in proteins from amino acid sequence.

Terribilini M, Lee JH, Yan C, Jernigan RL, Honavar V, Dobbs D.

RNA. 2006 Aug;12(8):1450-62. Epub 2006 Jun 21.

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