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Keywords
Last Name
Institution

Shamil R. Sunyaev, PH.D.

TitleAssociate Professor of Medicine
InstitutionBrigham and Women's Hospital
DepartmentMedicine
AddressHarvard Medical School
NRB 466b (BWH Genetics)
77 Avenue Louis Pasteur
Boston MA 02115
Phone617/525-6675
Fax617/525-4705
Other Positions
TitleAssistant Professor of Health Sciences and Technology
InstitutionHarvard Medical School
DepartmentHealth Sciences and Technology


 Research 
 research resources
This researcher has shared information about their research resources
in the eagle-i Network. To update or add resource records, contact
eagle-i@hms.harvard.edu.
Sunyaev Lab - Protocols (2) and Software (5)

 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Polak P, Lawrence MS, Haugen E, Stoletzki N, Stojanov P, Thurman RE, Garraway LA, Mirkin S, Getz G, Stamatoyannopoulos JA, Sunyaev SR. Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair. Nat Biotechnol. 2014 Jan; 32(1):71-5.
    View in: PubMed
  2. Sunyaev SR, Roth FP. Systems biology and the analysis of genetic variation. Curr Opin Genet Dev. 2013 Dec; 23(6):599-601.
    View in: PubMed
  3. Agarwala V, Flannick J, Sunyaev S, Altshuler D. Evaluating empirical bounds on complex disease genetic architecture. Nat Genet. 2013 Dec; 45(12):1418-27.
    View in: PubMed
  4. Seim I, Fang X, Xiong Z, Lobanov AV, Huang Z, Ma S, Feng Y, Turanov AA, Zhu Y, Lenz TL, Gerashchenko MV, Fan D, Hee Yim S, Yao X, Jordan D, Xiong Y, Ma Y, Lyapunov AN, Chen G, Kulakova OI, Sun Y, Lee SG, Bronson RT, Moskalev AA, Sunyaev SR, Zhang G, Krogh A, Wang J, Gladyshev VN. Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii. Nat Commun. 2013 Aug 20; 4:2212.
    View in: PubMed
  5. Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Lee RS, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CW, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013 Jul 11; 499(7457):214-8.
    View in: PubMed
  6. Goldstein DB, Allen A, Keebler J, Margulies EH, Petrou S, Petrovski S, Sunyaev S. Sequencing studies in human genetics: design and interpretation. Nat Rev Genet. 2013 Jul; 14(7):460-70.
    View in: PubMed
  7. Gokcumen O, Zhu Q, Mulder LC, Iskow RC, Austermann C, Scharer CD, Raj T, Boss JM, Sunyaev S, Price A, Stranger B, Simon V, Lee C. Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence. PLoS Genet. 2013 Apr; 9(4):e1003404.
    View in: PubMed
  8. Coste B, Houge G, Murray MF, Stitziel N, Bandell M, Giovanni MA, Philippakis A, Hoischen A, Riemer G, Steen U, Steen VM, Mathur J, Cox J, Lebo M, Rehm H, Weiss ST, Wood JN, Maas RL, Sunyaev SR, Patapoutian A. Gain-of-function mutations in the mechanically activated ion channel PIEZO2 cause a subtype of Distal Arthrogryposis. Proc Natl Acad Sci U S A. 2013 Mar 19; 110(12):4667-72.
    View in: PubMed
  9. Kiezun A, Pulit SL, Francioli LC, van Dijk F, Swertz M, Boomsma DI, van Duijn CM, Slagboom PE, van Ommen GJ, Wijmenga C, de Bakker PI, Sunyaev SR. Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency. PLoS Genet. 2013 Feb; 9(2):e1003301.
    View in: PubMed
  10. McFarland CD, Korolev KS, Kryukov GV, Sunyaev SR, Mirny LA. Impact of deleterious passenger mutations on cancer progression. Proc Natl Acad Sci U S A. 2013 Feb 19; 110(8):2910-5.
    View in: PubMed
  11. Adzhubei I, Jordan DM, Sunyaev SR. Predicting Functional Effect of Human Missense Mutations Using PolyPhen-2. Curr Protoc Hum Genet. 2013 Jan; Chapter 7:Unit7.20.
    View in: PubMed
  12. Diogo D, Kurreeman F, Stahl EA, Liao KP, Gupta N, Greenberg JD, Rivas MA, Hickey B, Flannick J, Thomson B, Guiducci C, Ripke S, Adzhubey I, Barton A, Kremer JM, Alfredsson L, Sunyaev S, Martin J, Zhernakova A, Bowes J, Eyre S, Siminovitch KA, Gregersen PK, Worthington J, Klareskog L, Padyukov L, Raychaudhuri S, Plenge RM. Rare, Low-Frequency, and Common Variants in the Protein-Coding Sequence of Biological Candidate Genes from GWASs Contribute to Risk of Rheumatoid Arthritis. Am J Hum Genet. 2013 Jan 10; 92(1):15-27.
    View in: PubMed
  13. Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P. Genomic variation landscape of the human gut microbiome. Nature. 2013 Jan 3; 493(7430):45-50.
    View in: PubMed
  14. Koren A, Polak P, Nemesh J, Michaelson JJ, Sebat J, Sunyaev SR, McCarroll SA. Differential relationship of DNA replication timing to different forms of human mutation and variation. Am J Hum Genet. 2012 Dec 7; 91(6):1033-40.
    View in: PubMed
  15. Thompson BA, Greenblatt MS, Vallee MP, Herkert JC, Tessereau C, Young EL, Adzhubey IA, Li B, Bell R, Feng B, Mooney SD, Radivojac P, Sunyaev SR, Frebourg T, Hofstra RM, Sijmons RH, Boucher K, Thomas A, Goldgar DE, Spurdle AB, Tavtigian SV. Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions. Hum Mutat. 2013 Jan; 34(1):255-65.
    View in: PubMed
  16. Nusinow DP, Kiezun A, O'Connell DJ, Chick JM, Yue Y, Maas RL, Gygi SP, Sunyaev SR. Network-based inference from complex proteomic mixtures using SNIPE. Bioinformatics. 2012 Dec 1; 28(23):3115-22.
    View in: PubMed
  17. Sunyaev SR. Inferring causality and functional significance of human coding DNA variants. Hum Mol Genet. 2012 Oct 15; 21(R1):R10-7.
    View in: PubMed
  18. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6; 489(7414):75-82.
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  19. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, Stamatoyannopoulos JA. Systematic localization of common disease-associated variation in regulatory DNA. Science. 2012 Sep 7; 337(6099):1190-5.
    View in: PubMed
  20. Kiezun A, Garimella K, Do R, Stitziel NO, Neale BM, McLaren PJ, Gupta N, Sklar P, Sullivan PF, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Lehner T, Shugart YY, Price AL, de Bakker PI, Purcell SM, Sunyaev SR. Exome sequencing and the genetic basis of complex traits. Nat Genet. 2012 Jun; 44(6):623-30.
    View in: PubMed
  21. Pasaniuc B, Rohland N, McLaren PJ, Garimella K, Zaitlen N, Li H, Gupta N, Neale BM, Daly MJ, Sklar P, Sullivan PF, Bergen S, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Purcell SM, Haas DW, Liang L, Sunyaev S, Patterson N, de Bakker PI, Reich D, Price AL. Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat Genet. 2012 Jun; 44(6):631-5.
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  22. 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. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science. 2012 Jul 6; 337(6090):64-9.
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  23. Leshchiner I, Alexa K, Kelsey P, Adzhubei I, Austin-Tse CA, Cooney JD, Anderson H, King MJ, Stottmann RW, Garnaas MK, Ha S, Drummond IA, Paw BH, North TE, Beier DR, Goessling W, Sunyaev SR. Mutation mapping and identification by whole-genome sequencing. Genome Res. 2012 Aug; 22(8):1541-8.
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  24. Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci. 2012 Jun; 21(6):769-85.
    View in: PubMed
  25. Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y, Lewis L, Han Y, Voight BF, Lim E, Rossin E, Kirby A, Flannick J, Fromer M, Shakir K, Fennell T, Garimella K, Banks E, Poplin R, Gabriel S, DePristo M, Wimbish JR, Boone BE, Levy SE, Betancur C, Sunyaev S, Boerwinkle E, Buxbaum JD, Cook EH, Devlin B, Gibbs RA, Roeder K, Schellenberg GD, Sutcliffe JS, Daly MJ. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 2012 May 10; 485(7397):242-5.
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  26. Zuk O, Hechter E, Sunyaev SR, Lander ES. The mystery of missing heritability: Genetic interactions create phantom heritability. Proc Natl Acad Sci U S A. 2012 Jan 24; 109(4):1193-8.
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  27. Du R, Litonjua AA, Tantisira KG, Lasky-Su J, Sunyaev SR, Klanderman BJ, Celedón JC, Avila L, Soto-Quiros ME, Weiss ST. Genome-wide association study reveals class I MHC-restricted T cell-associated molecule gene (CRTAM) variants interact with vitamin D levels to affect asthma exacerbations. J Allergy Clin Immunol. 2012 Feb; 129(2):368-73, 373.e1-5.
    View in: PubMed
  28. Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, Marino SM, Sun X, Turanov AA, Yang P, Yim SH, Zhao X, Kasaikina MV, Stoletzki N, Peng C, Polak P, Xiong Z, Kiezun A, Zhu Y, Chen Y, Kryukov GV, Zhang Q, Peshkin L, Yang L, Bronson RT, Buffenstein R, Wang B, Han C, Li Q, Chen L, Zhao W, Sunyaev SR, Park TJ, Zhang G, Wang J, Gladyshev VN. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature. 2011 Nov 10; 479(7372):223-7.
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  29. Stitziel NO, Kiezun A, Sunyaev S. Computational and statistical approaches to analyzing variants identified by exome sequencing. Genome Biol. 2011; 12(9):227.
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  30. Gorelik L, Reid C, Testa M, Brickelmaier M, Bossolasco S, Pazzi A, Bestetti A, Carmillo P, Wilson E, McAuliffe M, Tonkin C, Carulli JP, Lugovskoy A, Lazzarin A, Sunyaev S, Simon K, Cinque P. Progressive multifocal leukoencephalopathy (PML) development is associated with mutations in JC virus capsid protein VP1 that change its receptor specificity. J Infect Dis. 2011 Jul 1; 204(1):103-14.
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  31. Spirin V, Shpunt A, Seebacher J, Gentzel M, Shevchenko A, Gygi S, Sunyaev S. Assigning spectrum-specific P-values to protein identifications by mass spectrometry. Bioinformatics. 2011 Apr 15; 27(8):1128-34.
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  32. Jordan DM, Kiezun A, Baxter SM, Agarwala V, Green RC, Murray MF, Pugh T, Lebo MS, Rehm HL, Funke BH, Sunyaev SR. Development and validation of a computational method for assessment of missense variants in hypertrophic cardiomyopathy. Am J Hum Genet. 2011 Feb 11; 88(2):183-92.
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  33. Jordan DM, Ramensky VE, Sunyaev SR. Human allelic variation: perspective from protein function, structure, and evolution. Curr Opin Struct Biol. 2010 Jun; 20(3):342-50.
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  34. Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ, Sunyaev SR. Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet. 2010 Jun 11; 86(6):832-8.
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  35. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods. 2010 Apr; 7(4):248-9.
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  36. Molla M, Delcher A, Sunyaev S, Cantor C, Kasif S. Triplet repeat length bias and variation in the human transcriptome. Proc Natl Acad Sci U S A. 2009 Oct 6; 106(40):17095-100.
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  37. Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, Church GM. Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res. 2009 Sep; 19(9):1606-15.
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  38. Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR. Human mutation rate associated with DNA replication timing. Nat Genet. 2009 Apr; 41(4):393-5.
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  39. Sunyaev SR, Lugovskoy A, Simon K, Gorelik L. Adaptive mutations in the JC virus protein capsid are associated with progressive multifocal leukoencephalopathy (PML). PLoS Genet. 2009 Feb; 5(2):e1000368.
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  40. Kryukov GV, Shpunt A, Stamatoyannopoulos JA, Sunyaev SR. Power of deep, all-exon resequencing for discovery of human trait genes. Proc Natl Acad Sci U S A. 2009 Mar 10; 106(10):3871-6.
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  41. Schmidt S, Gerasimova A, Kondrashov FA, Adzhubei IA, Kondrashov AS, Sunyaev S. Erratum. PLoS Genet. 2008 Dec; 4(12).
    View in: PubMed
  42. Schmidt S, Gerasimova A, Kondrashov FA, Adzhubei IA, Adzuhbei IA, Kondrashov AS, Sunyaev S. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genet. 2008 Nov; 4(11):e1000281.
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  43. Beckstead WA, Bjork BC, Stottmann RW, Sunyaev S, Beier DR. SNP2RFLP: a computational tool to facilitate genetic mapping using benchtop analysis of SNPs. Mamm Genome. 2008 Oct-Dec; 19(10-12):687-90.
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  44. Junqueira M, Spirin V, Balbuena TS, Thomas H, Adzhubei I, Sunyaev S, Shevchenko A. Protein identification pipeline for the homology-driven proteomics. J Proteomics. 2008 Aug 21; 71(3):346-56.
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  45. Junqueira M, Spirin V, Santana Balbuena T, Waridel P, Surendranath V, Kryukov G, Adzhubei I, Thomas H, Sunyaev S, Shevchenko A. Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification. J Proteome Res. 2008 Aug; 7(8):3382-95.
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  46. Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, Lohmueller KE, Adams MD, Schmidt S, Sninsky JJ, Sunyaev SR, White TJ, Nielsen R, Clark AG, Bustamante CD. Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet. 2008 May; 4(5):e1000083.
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  47. Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante CD. Proportionally more deleterious genetic variation in European than in African populations. Nature. 2008 Feb 21; 451(7181):994-7.
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  48. Gorlov IP, Gorlova OY, Sunyaev SR, Spitz MR, Amos CI. Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms. Am J Hum Genet. 2008 Jan; 82(1):100-12.
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  49. Spirin V, Schmidt S, Pertsemlidis A, Cooper RS, Cohen JC, Sunyaev SR. Common single-nucleotide polymorphisms act in concert to affect plasma levels of high-density lipoprotein cholesterol. Am J Hum Genet. 2007 Dec; 81(6):1298-303.
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  50. Ballif BA, Carey GR, Sunyaev SR, Gygi SP. Large-scale identification and evolution indexing of tyrosine phosphorylation sites from murine brain. J Proteome Res. 2008 Jan; 7(1):311-8.
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  51. Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S. Analysis of sequence conservation at nucleotide resolution. PLoS Comput Biol. 2007 Dec; 3(12):e254.
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  52. Asthana S, Noble WS, Kryukov G, Grant CE, Sunyaev S, Stamatoyannopoulos JA. Widely distributed noncoding purifying selection in the human genome. Proc Natl Acad Sci U S A. 2007 Jul 24; 104(30):12410-5.
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  53. Waridel P, Frank A, Thomas H, Surendranath V, Sunyaev S, Pevzner P, Shevchenko A. Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing. Proteomics. 2007 Jul; 7(14):2318-29.
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  54. Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14; 447(7146):799-816.
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  55. Ilyinskii PO, Gabai VL, Sunyaev SR, Thoidis G, Shneider AM. Toxicity of influenza A virus matrix protein 2 for mammalian cells is associated with its intrinsic proton-channeling activity. Cell Cycle. 2007 Aug 15; 6(16):2043-7.
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  56. Kryukov GV, Pennacchio LA, Sunyaev SR. Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet. 2007 Apr; 80(4):727-39.
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  57. Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Martin J, Hebert S, Doelle H, Ersoy B, Kryukov G, Schmidt S, Yosef N, Ruppin E, Sharan R, Vaisse C, Sunyaev S, Dent R, Cohen J, McPherson R, Pennacchio LA. Medical sequencing at the extremes of human body mass. Am J Hum Genet. 2007 Apr; 80(4):779-91.
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  58. Liska AJ, Sunyaev S, Shilov IN, Schaeffer DA, Shevchenko A. Error-tolerant EST database searches by tandem mass spectrometry and multiTag software. Proteomics. 2005 Nov; 5(16):4118-22.
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  59. Keightley PD, Kryukov GV, Sunyaev S, Halligan DL, Gaffney DJ. Evolutionary constraints in conserved nongenic sequences of mammals. Genome Res. 2005 Oct; 15(10):1373-8.
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  60. Kryukov GV, Schmidt S, Sunyaev S. Small fitness effect of mutations in highly conserved non-coding regions. Hum Mol Genet. 2005 Aug 1; 14(15):2221-9.
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  61. Sunyaev S. Biocomputing enters its adolescence. Genome Biol. 2005; 6(6):325.
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  62. Jordan IK, Kondrashov FA, Adzhubei IA, Wolf YI, Koonin EV, Kondrashov AS, Sunyaev S. A universal trend of amino acid gain and loss in protein evolution. Nature. 2005 Feb 10; 433(7026):633-8.
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  63. Dimmic MW, Sunyaev S, Bustamante CD. Inferring SNP function using evolutionary, structural, and computational methods. Pac Symp Biocomput. 2005; 382-4.
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  64. Asthana S, Schmidt S, Sunyaev S. A limited role for balancing selection. Trends Genet. 2005 Jan; 21(1):30-2.
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  65. Liska AJ, Popov AV, Sunyaev S, Coughlin P, Habermann B, Shevchenko A, Bork P, Karsenti E, Shevchenko A. Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome. Proteomics. 2004 Sep; 4(9):2707-21.
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  66. Ogurtsov AY, Sunyaev S, Kondrashov AS. Indel-based evolutionary distance and mouse-human divergence. Genome Res. 2004 Aug; 14(8):1610-6.
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  67. Bazykin GA, Kondrashov FA, Ogurtsov AY, Sunyaev S, Kondrashov AS. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. 2004 Jun 3; 429(6991):558-62.
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  68. Sunyaev SR, Bogopolsky GA, Oleynikova NV, Vlasov PK, Finkelstein AV, Roytberg MA. From analysis of protein structural alignments toward a novel approach to align protein sequences. Proteins. 2004 Feb 15; 54(3):569-82.
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  69. Habermann B, Oegema J, Sunyaev S, Shevchenko A. The power and the limitations of cross-species protein identification by mass spectrometry-driven sequence similarity searches. Mol Cell Proteomics. 2004 Mar; 3(3):238-49.
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  70. Sunyaev S, Kondrashov FA, Bork P, Ramensky V. Impact of selection, mutation rate and genetic drift on human genetic variation. Hum Mol Genet. 2003 Dec 15; 12(24):3325-30.
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  71. Schmidt S, Sunyaev S, Bork P, Dandekar T. Metabolites: a helping hand for pathway evolution? Trends Biochem Sci. 2003 Jun; 28(6):336-41.
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  72. Sunyaev S, Liska AJ, Golod A, Shevchenko A, Shevchenko A. MultiTag: multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry. Anal Chem. 2003 Mar 15; 75(6):1307-15.
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  73. Stark A, Sunyaev S, Russell RB. A model for statistical significance of local similarities in structure. J Mol Biol. 2003 Mar 7; 326(5):1307-16.
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  74. Kriventseva EV, Koch I, Apweiler R, Vingron M, Bork P, Gelfand MS, Sunyaev S. Increase of functional diversity by alternative splicing. Trends Genet. 2003 Mar; 19(3):124-8.
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  75. Shevchenko A, Sunyaev S, Liska A, Bork P, Shevchenko A. Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes. Methods Mol Biol. 2003; 211:221-34.
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  76. Kondrashov AS, Sunyaev S, Kondrashov FA. Dobzhansky-Muller incompatibilities in protein evolution. Proc Natl Acad Sci U S A. 2002 Nov 12; 99(23):14878-83.
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  77. Ramensky V, Bork P, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 2002 Sep 1; 30(17):3894-900.
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  78. Shevchenko A, Sunyaev S, Loboda A, Shevchenko A, Bork P, Ens W, Standing KG. Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching. Anal Chem. 2001 May 1; 73(9):1917-26.
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  79. Sunyaev S, Ramensky V, Koch I, Lathe W, Kondrashov AS, Bork P. Prediction of deleterious human alleles. Hum Mol Genet. 2001 Mar 15; 10(6):591-7.
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  80. Sunyaev S, Lathe W, Bork P. Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms. Curr Opin Struct Biol. 2001 Feb; 11(1):125-30.
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  81. Sunyaev SR, Lathe WC, Ramensky VE, Bork P. SNP frequencies in human genes an excess of rare alleles and differing modes of selection. Trends Genet. 2000 Aug; 16(8):335-7.
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  82. Sunyaev S, Ramensky V, Bork P. Towards a structural basis of human non-synonymous single nucleotide polymorphisms. Trends Genet. 2000 May; 16(5):198-200.
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  83. Sunyaev S, Hanke J, Brett D, Aydin A, Zastrow I, Lathe W, Bork P, Reich J. Individual variation in protein-coding sequences of human genome. Adv Protein Chem. 2000; 54:409-37.
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  84. Sunyaev S, Hanke J, Aydin A, Wirkner U, Zastrow I, Reich J, Bork P. Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes. J Mol Med (Berl). 1999 Nov; 77(11):754-60.
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  85. Sunyaev SR, Eisenhaber F, Rodchenkov IV, Eisenhaber B, Tumanyan VG, Kuznetsov EN. PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng. 1999 May; 12(5):387-94.
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  86. Huynen M, Doerks T, Eisenhaber F, Orengo C, Sunyaev S, Yuan Y, Bork P. Homology-based fold predictions for Mycoplasma genitalium proteins. J Mol Biol. 1998 Jul 17; 280(3):323-6.
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  87. Sunyaev SR, Eisenhaber F, Argos P, Kuznetsov EN, Tumanyan VG. Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types? Proteins. 1998 May 15; 31(3):225-46.
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  88. Sunyaev S, Kuznetsov E, Rodchenkov I, Tumanyan V. Protein sequence-structure compatibility criteria in terms of statistical hypothesis testing. Protein Eng. 1997 Jun; 10(6):635-46.
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