Predicting Functional Effect of Human Missense Mutations Using PolyPhen-2

Masatoshi Nei, Sudhir Kumar, None, Molecular Evolution and Phylogenetics ,(2000)

Michael J. Bamshad, Joshua M. Akey, , , , Jacob A. Tennessen, Abigail W. Bigham, Timothy D. O’Connor, Wenqing Fu, Eimear E. Kenny, Simon Gravel, Sean McGee, Ron Do, Xiaoming Liu, Goo Jun, Hyun Min Kang, Daniel Jordan, Suzanne M. Leal, Stacey Gabriel, Mark J. Rieder, Goncalo Abecasis, David Altshuler, Deborah A. Nickerson, Eric Boerwinkle, Shamil Sunyaev, Carlos D. Bustamante, Evolution and functional impact of rare coding variation from deep sequencing of human exomes Science. ,vol. 337, pp. 64- 69 ,(2012) , 10.1126/SCIENCE.1219240

Daniel Chasman, R.Mark Adams, Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation. Journal of Molecular Biology. ,vol. 307, pp. 683- 706 ,(2001) , 10.1006/JMBI.2001.4510

Adam R. Boyko, Scott H. Williamson, Amit R. Indap, Jeremiah D. Degenhardt, Ryan D. Hernandez, Kirk E. Lohmueller, Mark D. Adams, Steffen Schmidt, John J. Sninsky, Shamil R. Sunyaev, Thomas J. White, Rasmus Nielsen, Andrew G. Clark, Carlos D. Bustamante, Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome PLoS Genetics. ,vol. 4, pp. e1000083- ,(2008) , 10.1371/JOURNAL.PGEN.1000083

Stephanie Hicks, David A. Wheeler, Sharon E. Plon, Marek Kimmel, Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Human Mutation. ,vol. 32, pp. 661- 668 ,(2011) , 10.1002/HUMU.21490

Ivan A Adzhubei, Steffen Schmidt, Leonid Peshkin, Vasily E Ramensky, Anna Gerasimova, Peer Bork, Alexey S Kondrashov, Shamil R Sunyaev, A method and server for predicting damaging missense mutations Nature Methods. ,vol. 7, pp. 248- 249 ,(2010) , 10.1038/NMETH0410-248

Michael J. Bamshad, Sarah B. Ng, Abigail W. Bigham, Holly K. Tabor, Mary J. Emond, Deborah A. Nickerson, Jay Shendure, Exome sequencing as a tool for Mendelian disease gene discovery Nature Reviews Genetics. ,vol. 12, pp. 745- 755 ,(2011) , 10.1038/NRG3031

J. Thompson, The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research. ,vol. 25, pp. 4876- 4882 ,(1997) , 10.1093/NAR/25.24.4876

Euan A Ashley, Atul J Butte, Matthew T Wheeler, Rong Chen, Teri E Klein, Frederick E Dewey, Joel T Dudley, Kelly E Ormond, Aleksandra Pavlovic, Alexander A Morgan, Dmitry Pushkarev, Norma F Neff, Louanne Hudgins, Li Gong, Laura M Hodges, Dorit S Berlin, Caroline F Thorn, Katrin Sangkuhl, Joan M Hebert, Mark Woon, Hersh Sagreiya, Ryan Whaley, Joshua W Knowles, Michael F Chou, Joseph V Thakuria, Abraham M Rosenbaum, Alexander Wait Zaranek, George M Church, Henry T Greely, Stephen R Quake, Russ B Altman, Clinical assessment incorporating a personal genome The Lancet. ,vol. 375, pp. 1525- 1535 ,(2010) , 10.1016/S0140-6736(10)60452-7

P. C. Ng, J. G. Henikoff, S. Henikoff, PHAT: a transmembrane-specific substitution matrix german conference on bioinformatics. ,vol. 16, pp. 760- 766 ,(2000) , 10.1093/BIOINFORMATICS/16.9.760