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A simple method for analyzing exome sequencing data shows distinct levels of nonsynonymous variation for human immune and nervous system genes.

Freudenberg J, Gregersen PK, Freudenberg-Hua Y.

PLoS One. 2012;7(6):e38087. doi: 10.1371/journal.pone.0038087. Epub 2012 Jun 6.


Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.

Wu J, Li Y, Jiang R.

PLoS Genet. 2014 Mar 20;10(3):e1004237. doi: 10.1371/journal.pgen.1004237. eCollection 2014 Mar.


dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs.

Liu X, Wu C, Li C, Boerwinkle E.

Hum Mutat. 2016 Mar;37(3):235-41. doi: 10.1002/humu.22932. Epub 2016 Jan 5.


On transition bias in mitochondrial genes of pocket gophers.

Xia X, Hafner MS, Sudman PD.

J Mol Evol. 1996 Jul;43(1):32-40.


dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations.

Liu X, Jian X, Boerwinkle E.

Hum Mutat. 2013 Sep;34(9):E2393-402. doi: 10.1002/humu.22376. Epub 2013 Jul 10.


Single nucleotide variation analysis in 65 candidate genes for CNS disorders in a representative sample of the European population.

Freudenberg-Hua Y, Freudenberg J, Kluck N, Cichon S, Propping P, Nöthen MM.

Genome Res. 2003 Oct;13(10):2271-6.


Evolution and functional impact of rare coding variation from deep sequencing of human exomes.

Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Kang HM, Jordan D, Leal SM, Gabriel S, Rieder MJ, Abecasis G, Altshuler D, Nickerson DA, Boerwinkle E, Sunyaev S, Bustamante CD, Bamshad MJ, Akey JM; Broad GO; Seattle GO; NHLBI Exome Sequencing Project.

Science. 2012 Jul 6;337(6090):64-9. doi: 10.1126/science.1219240. Epub 2012 May 17.


Whole-exome sequencing in obsessive-compulsive disorder identifies rare mutations in immunological and neurodevelopmental pathways.

Cappi C, Brentani H, Lima L, Sanders SJ, Zai G, Diniz BJ, Reis VN, Hounie AG, Conceição do Rosário M, Mariani D, Requena GL, Puga R, Souza-Duran FL, Shavitt RG, Pauls DL, Miguel EC, Fernandez TV.

Transl Psychiatry. 2016 Mar 29;6:e764. doi: 10.1038/tp.2016.30.


Not so different after all: a comparison of methods for detecting amino acid sites under selection.

Kosakovsky Pond SL, Frost SD.

Mol Biol Evol. 2005 May;22(5):1208-22. Epub 2005 Feb 9.


Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants.

Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ; NHLBI Exome Sequencing Project, Akey JM.

Nature. 2013 Jan 10;493(7431):216-20. doi: 10.1038/nature11690. Epub 2012 Nov 28. Erratum in: Nature. 2013 Mar 14;495(7440):270. Rieder, Mark J [added].


Using the plurality of codon positions to identify deleterious variants in human exomes.

Subramanian S.

Bioinformatics. 2015 Feb 1;31(3):301-5. doi: 10.1093/bioinformatics/btu653. Epub 2014 Oct 4.


Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences.

Ngandu NK, Scheffler K, Moore P, Woodman Z, Martin D, Seoighe C.

Virol J. 2008 Dec 23;5:160. doi: 10.1186/1743-422X-5-160. Review.


Predicting mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies.

Li MX, Kwan JS, Bao SY, Yang W, Ho SL, Song YQ, Sham PC.

PLoS Genet. 2013;9(1):e1003143. doi: 10.1371/journal.pgen.1003143. Epub 2013 Jan 17.


Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans.

Keightley PD, Halligan DL.

Genetics. 2011 Aug;188(4):931-40. doi: 10.1534/genetics.111.128355. Epub 2011 May 19.


A flexible method for estimating the fraction of fitness influencing mutations from large sequencing data sets.

Moon S, Akey JM.

Genome Res. 2016 Jun;26(6):834-43. doi: 10.1101/gr.203059.115. Epub 2016 Apr 14.


Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates.

Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T.

Bioinformatics. 2007 Jul 1;23(13):i319-27.


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.


Next generation exome sequencing of paediatric inflammatory bowel disease patients identifies rare and novel variants in candidate genes.

Christodoulou K, Wiskin AE, Gibson J, Tapper W, Willis C, Afzal NA, Upstill-Goddard R, Holloway JW, Simpson MA, Beattie RM, Collins A, Ennis S.

Gut. 2013 Jul;62(7):977-84. doi: 10.1136/gutjnl-2011-301833. Epub 2012 Apr 28.


Variations in the exome of the LNCaP prostate cancer cell line.

Spans L, Atak ZK, Van Nieuwerburgh F, Deforce D, Lerut E, Aerts S, Claessens F.

Prostate. 2012 Sep 1;72(12):1317-27. doi: 10.1002/pros.22480. Epub 2011 Dec 27.


Variation in the pattern of synonymous and nonsynonymous difference between two fungal genomes.

Hughes AL, Friedman R.

Mol Biol Evol. 2005 May;22(5):1320-4. Epub 2005 Mar 2.


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