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publications [2016/01/14 15:40]
cassa [Selected Recent Publications]
publications [2017/05/05 12:33]
ivan [Selected Recent Publications]
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 ===== Selected Recent Publications ===== ===== Selected Recent Publications =====
  
-  - Palamara PFFrancioli LCWilton PRGenovese GGusev A, Finucane HKSankararaman S; Genome of the Netherlands Consortium**Sunyaev SR**de Bakker PIWakeley JPe'er IPrice ALLeveraging Distant Relatedness to Quantify Human Mutation ​and Gene-Conversion Rates. \\ Am J Hum Genet. ​2015 Dec 3;97(6):775-89. doi: 10.1016/​j.ajhg.2015.10.006Epub 2015 Nov 12. PMID: 26581902 +  - Cassa CAWeghorn DBalick DJJordan DMNusinow D, Samocha KE, O'​Donnell-Luria ​A, MacArthur DGDaly MJ, Beier DR, Sunyaev SR. Estimating ​the selective effects of heterozygous protein-truncating variants from human exome data.\\ Nat Genet. 49(5):​806-810 (2017) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​28369035|PMID:​28369035]]. 
-  - Kazanov MD, Roberts SA, Polak P, Stamatoyannopoulos J, Klimczak LJ, Gordenin DA, **Sunyaev SR**. APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating,​ Gene-Dense, and Active Chromatin Regions. \\ Cell Rep. 2015 Nov 10;​13(6):​1103-9. doi: 10.1016/​j.celrep.2015.09.077. Epub 2015 Oct 29. PMID: 26527001 +  - Chun S, Casparino A, Patsopoulos NA, Croteau-Chonka DC, Raby BA, De Jager PL, Sunyaev SR, Cotsapas C. Limited statistical evidence for shared genetic effects of eQTLs and autoimmune disease-associated loci in three major immune cell types. \\ Nat Genet. 2017 Feb 20. doi: 10.1038/​ng.3795. PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​28218759|PMID:​28218759]]. 
-  - Akle S, Chun S, Jordan DM, **Cassa CA**. Mitigating false-positive associations in rare disease gene discovery.\\ Hum Mutat. 2015 Oct;​36(10):​998-1003. doi: 10.1002/​humu.22847. ​PMID26378430 +  - Sul JHCade BECho MHQiao D, Silverman EK, Redline S, Sunyaev SIncreasing Generality ​and Power of Rare-Variant Tests by Utilizing Extended Pedigrees. \\ Am J Hum Genet. ​2016 Oct 6;99(4):846-859. doi: 10.1016/​j.ajhg.2016.08.015. PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​27666371|PMID:​27666371]]. 
-  - Cassa CA, Smith SE, Docken W, Hoffman E, McLaughlin H, Chun S, Leshchiner I, Miraoui H, Raychaudhuri S, Frank NY, Wilson BJ, **Sunyaev SR**, Maas RL; Brigham Genomic Medicine, Vuzman D. An argument for early genomic sequencing in atypical cases: a WISP3 variant leads to diagnosis of progressive pseudorheumatoid arthropathy of childhood. \\ Rheumatology (Oxford). 2015 Oct 22. pii: kev367. PMID: 26493744 +  - Savova V, Chun S, Sohail M, McCole RB, Witwicki R, Gai L, Lenz TL, Wu CT, Sunyaev SR, Gimelbrant AA. Genes with monoallelic expression contribute disproportionately to genetic diversity in humans. \\ Nat Genet. 2016 Mar;​48(3):​231-7. doi: 10.1038/ng.3493PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​26808112|PMID:26808112]]. ​ 
-  - Chopra SS, Leshchiner I, Duzkale H, McLaughlin H, Giovanni M, Zhang C, Stitziel N, Fingeroth J, Joyce RM, Lebo M, Rehm H, Vuzman D, Maas R, **Sunyaev SR**, Murray M, Cassa CA. Inherited CHST11/MIR3922 deletion is associated with a novel recessive syndrome presenting with skeletal malformation and malignant lymphoproliferative disease.\\ Mol Genet Genomic Med2015 Sep;​3(5):​413-23doi: 10.1002/mgg3.152. Epub 2015 May 10. PMID: 26436107 +  - Kazanov MD, Roberts SA, Polak P, Stamatoyannopoulos J, Klimczak LJ, Gordenin DA, Sunyaev SR. APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating,​ Gene-Dense, and Active Chromatin Regions. \\ Cell Rep. 2015 Nov 10;​13(6):​1103-9. doi: 10.1016/​j.celrep.2015.09.077. Epub 2015 Oct 29. PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​26527001|PMID:​26527001]]. 
-  - Balick DJ, Do R, Cassa CA, Reich D, **Sunyaev SR**. Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck.\\ PLoS Genet. 2015 Aug 28;​11(8):​e1005436. doi: 10.1371/​journal.pgen.1005436. eCollection 2015 Aug. PMID26317225 +  - Akle S, Chun S, Jordan DM, Cassa CA. Mitigating false-positive associations in rare disease gene discovery.\\ Hum Mutat. 2015 Oct;​36(10):​998-1003. doi: 10.1002/​humu.22847. ​PubMed [[http://www.ncbi.nlm.nih.gov/pubmed/​26378430|PMID:26378430]]. 
-  - Lenz TL, Deutsch AJ, Han B, Hu X, Okada Y, Eyre S, Knapp M, Zhernakova A, Huizinga TW, Abecasis G, Becker J, Boeckxstaens GE, Chen WM, Franke A, Gladman DD, Gockel I, Gutierrez-Achury J, Martin J, Nair RP, Nöthen MM, Onengut-Gumuscu S, Rahman P, Rantapää-Dahlqvist S, Stuart PE, Tsoi LC, van Heel DA, Worthington J, Wouters MM, Klareskog L, Elder JT, Gregersen PK, Schumacher J, Rich SS, Wijmenga C, **Sunyaev SR**, de Bakker PI, Raychaudhuri SWidespread non-additive and interaction effects within HLA loci modulate the risk of autoimmune diseases\\ Nat Genet2015 Sep;​47(9):​1085-90doi: 10.1038/ng.3379. Epub 2015 Aug 10. PMID: 26258845 +  - Balick DJ, Do R, Cassa CA, Reich D, Sunyaev SR. Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck.\\ PLoS Genet. 2015 Aug 28;​11(8):​e1005436. doi: 10.1371/​journal.pgen.1005436. eCollection 2015 Aug. PubMed [[http://www.ncbi.nlm.nih.gov/pubmed/​26317225|PMID:26317225]]
-  - van Leeuwen EM, Kanterakis A, Deelen P, Kattenberg MV; Genome of the Netherlands Consortium, Slagboom PE, de Bakker PI, Wijmenga C, Swertz MA, Boomsma DI, van Duijn CM, Karssen LC, Hottenga JJPopulation-specific genotype imputations using minimac or IMPUTE2.\\ Nat Protoc. 2015 Sep;​10(9):​1285-96. doi: 10.1038/​nprot.2015.077. Epub 2015 Jul 30. PMID: 26226460 +  - Jordan DM, Frangakis SG, Golzio C, Cassa CA, Kurtzberg J; Task Force for Neonatal Genomics, Davis EE, Sunyaev SR, Katsanis N. Identification of cis-suppression of human disease mutations by comparative genomics. \\ Nature. 2015 Aug 13;​524(7564):​225-9. doi: 10.1038/​nature14497. Epub 2015 Jun 29. PubMed [[http://www.ncbi.nlm.nih.gov/pubmed/​26123021|PMID:26123021]]
-  - Jordan DM, Frangakis SG, Golzio C, Cassa CA, Kurtzberg J; Task Force for Neonatal Genomics, Davis EE, **Sunyaev SR**, Katsanis N. Identification of cis-suppression of human disease mutations by comparative genomics. \\ Nature. 2015 Aug 13;​524(7564):​225-9. doi: 10.1038/​nature14497. Epub 2015 Jun 29. PMID26123021 +  - Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I; Genome of the Netherlands Consortium, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Ye K, Guryev V, Arndt PF, Kloosterman WP, de Bakker PI, Sunyaev SR. Genome-wide patterns and properties of de novo mutations in humans.\\ Nat Genet. 47(7):822-6 (2015). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25985141|PMID:​25985141]]. 
-  - Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I; Genome of the Netherlands Consortium, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Ye K, Guryev V, Arndt PF, Kloosterman WP, de Bakker PI, **Sunyaev SR**Genome-wide patterns and properties of de novo mutations in humans.\\ Nat Genet2015 Jul;​47(7):​822-6doi: 10.1038/ng.3292. Epub 2015 May 18. PMID: 25985141 +  - Do R, Balick D, Li H, Adzhubei I, Sunyaev S, Reich D. No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans.\\ Nat Genet. 47(2):​126-31 (2015). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25581429|PMID:​25581429]]. 
-  - Auer PL, Nalls M, Meschia JF, Worrall BB, Longstreth WT Jr, Seshadri S, Kooperberg C, Burger KM, Carlson CS, Carty CL, Chen WM, Cupples LA, DeStefano AL, Fornage M, Hardy J, Hsu L, Jackson RD, Jarvik GP, Kim DS, Lakshminarayan K, Lange LA, Manichaikul A, Quinlan AR, Singleton AB, Thornton TA, Nickerson DA, Peters U, Rich SS; National Heart, Lung, and Blood Institute Exome Sequencing ProjectRare and Coding Region Genetic Variants Associated With Risk of Ischemic Stroke: The NHLBI Exome Sequence Project.\\ JAMA Neurol. 2015 Jul;​72(7):​781-8. doi: 10.1001/​jamaneurol.2015.0582. PMID: 25961151 +  - Polak P, Karlić R, Koren A, Thurman R, Sandstrom R, Lawrence MS, Reynolds A, Rynes E, Vlahoviček K, Stamatoyannopoulos JA, Sunyaev SR. Cell-of-origin chromatin organization shapes the mutational landscape of cancer.\\ Nature 518(7539):​360-4 (2015). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25693567|PMID:​25693567]]. 
-  - Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I; Genome of the Netherlands Consortium, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Ye K, Guryev V, Arndt PF, Kloosterman WP, de Bakker PI, **Sunyaev SR**. Genome-wide patterns and properties of de novo mutations in humans.\\ Nat Genet. 47(7):822-6 (2015). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25985141|PMID:​25985141]]. +  - Zuk O, Schaffner SF, Samocha K, Do R, Hechter E, Kathiresan S, Daly MJ, Neale BM, Sunyaev SR, Lander ES.\\ Proc Natl Acad Sci. 111(4):​E455-64 (2014). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24443550|PMID:​24443550]]. 
-  - Do R, Balick D, Li H, Adzhubei I, **Sunyaev S**, Reich D. No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans.\\ Nat Genet. 47(2):​126-31 (2015). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25581429|PMID:​25581429]]. +  - 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. 32(1):71-5 (2014). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24336318|PMID:​24336318]]. 
-  - Polak P, Karlić R, Koren A, Thurman R, Sandstrom R, Lawrence MS, Reynolds A, Rynes E, Vlahoviček K, Stamatoyannopoulos JA, **Sunyaev SR**. Cell-of-origin chromatin organization shapes the mutational landscape of cancer.\\ Nature 518(7539):​360-4 (2015). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25693567|PMID:​25693567]]. +  - 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 14(7):​460-70 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23752795|PMID:​23752795]]. 
-  - Zuk O, Schaffner SF, Samocha K, Do R, Hechter E, Kathiresan S, Daly MJ, Neale BM, **Sunyaev SR**, Lander ES.\\ Proc Natl Acad Sci. 111(4):​E455-64 (2014). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24443550|PMID:​24443550]]. +  - 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 110(12):​4667-72 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23487782|PMID:​23487782]]. 
-  - 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. 32(1):71-5 (2014). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24336318|PMID:​24336318]]. +  - Kiezun A, Pulit SL, Francioli LC, van Dijk F, Swertz M, Boomsma DI, van Duijn CM, Slagboom PE, van Ommen GJ, Wijmenga C; Genome of the Netherlands Consortium, de Bakker PI, Sunyaev SR. Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency.\\ PLoS Genet 9(2):​e1003301 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​3468643|PMID:​3468643]]. 
-  - 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 14(7):​460-70 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23752795|PMID:​23752795]]. +  - Cassa CA, Tong MY, Jordan DM. Large numbers of genetic variants considered to be pathogenic are common in asymptomatic individuals.\\ Hum Mutat 34(9):​1216-20 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23818451|PMID:​23818451]]. 
-  - 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 110(12):​4667-72 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23487782|PMID:​23487782]]. +  - 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 28(23):​3115-22 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23060611|PMID:​23060611]]. 
-  - Kiezun A, Pulit SL, Francioli LC, van Dijk F, Swertz M, Boomsma DI, van Duijn CM, Slagboom PE, van Ommen GJ, Wijmenga C; Genome of the Netherlands Consortium, de Bakker PI, **Sunyaev SR**. Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency.\\ PLoS Genet 9(2):​e1003301 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​3468643|PMID:​3468643]]. +  - 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. 44(6):​623-30 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22641211|PMID:​22641211]]. 
-  - **Cassa CA**, Tong MY, Jordan DM. Large numbers of genetic variants considered to be pathogenic are common in asymptomatic individuals.\\ Hum Mutat 34(9):​1216-20 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23818451|PMID:​23818451]]. +  - 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 22(8):​1541-8 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22555591|PMID:​22555591]]. 
-  - 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 28(23):​3115-22 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23060611|PMID:​23060611]]. +  - 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. 109(4):​1193-8 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22223662|PMID:​22223662]] 
-  - 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. 44(6):​623-30 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22641211|PMID:​22641211]]. +  - 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. 27(8):​1128-34 (2011). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​21349864|PMID:​21349864]]. 
-  - 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 22(8):​1541-8 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22555591|PMID:​22555591]]. +  - 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. 88(2):​183-92 (2011). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​21310275|PMID:​21310275]]. 
-  - 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. 109(4):​1193-8 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22223662|PMID:​22223662]] +  - 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. 86(6):832-8 (2010). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​20471002|PMID:​20471002]]. 
-  - 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. 27(8):​1128-34 (2011). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​21349864|PMID:​21349864]]. +  - 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. 7(4):248-9 (2010). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​20354512|PMID:​20354512]].  
-  - 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. 88(2):​183-92 (2011). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​21310275|PMID:​21310275]]. +  - Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR. Human mutation rate associated with DNA replication timing.\\ Nat Genet. 41(4):393-5 (2009). ​ PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19287383|PMID:​19287383]]. 
-  - 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. 86(6):832-8 (2010). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​20471002|PMID:​20471002]]. +  - 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. 10;​106(10):​3871-6 (2009) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19202052|PMID:​19202052]]. 
-  - 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. 7(4):248-9 (2010). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​20354512|PMID:​20354512]].  +  - 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. 5(2):​e1000368 (2009) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19197354|PMID:​19197354]].
-  - Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, **Sunyaev SR**. Human mutation rate associated with DNA replication timing.\\ Nat Genet. 41(4):393-5 (2009). ​ PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19287383|PMID:​19287383]]. +
-  - 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. 10;​106(10):​3871-6 (2009) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19202052|PMID:​19202052]]. +
-  - **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. 5(2):​e1000368 (2009) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19197354|PMID:​19197354]].+
  
  
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 ===== All Other Publications Since 2012 ===== ===== All Other Publications Since 2012 =====
  
- +  - Savova V, Pearl EJ, Boke E, Nag A, Adzhubei I, Horb ME, Peshkin L. Transcriptomic insights into genetic diversity of protein-coding genes in X. laevis.\\ Dev Biol. 424(2):​181-188 (2017) PubMed [[https://​www.ncbi.nlm.nih.gov/​pubmed/​28283406|PMID:​28283406]]. 
- +  - Lenz TL, Spirin V, Jordan DM, Sunyaev SR. Excess of deleterious mutations around HLA genes reveals evolutionary cost of balancing selection.\\ Mol Biol Evol. 33(10):​2555-64 (2016) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​27436009|PMID:​27436009]]. 
-  - Lenz TL, Deutsch AJ, Han B, Hu X, Okada Y, Eyre S, Knapp M, Zhernakova A, Huizinga TWJ, Abecasis G, Becker J, Boeckxstaens,​ GE, Chen W-M, Franke A, Gladman DD, Gockel I, Gutierrez-Achury J, Martin J, Nair RP, Nöthen MM, Onengut-Gumuscu S, Rahman P, Rantapää-Dahlqvist S, Stuart PE, Tsoi LC, Van Heel DA, Worthington J, Wouters MM, Klareskog L, Elder JT, Gregersen P, Schumacher J, Rich SS, Wijmenga C, Sunyaev SR, de Bakker PIW, Raychaudhuri S. Widespread non-additive and interaction effects within HLA loci modulate the risk of autoimmune diseases. \\ Nat Genet. 47(9): 1085-1090 (2015) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​26258845|PMID:​26258845]] +  - Palamara PF, Francioli LC, Wilton PR, Genovese G, Gusev A, Finucane HK, Sankararaman S; Genome of the Netherlands Consortium, Sunyaev SR, de Bakker PI, Wakeley J, Pe'er I, Price AL. Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates.\\ Am J Hum Genet. 97(6):​775-89 (2015) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​26581902|PMID:​26581902]]. 
-  - Genome of the Netherlands Consortium. Whole-genome sequence variation, population structure and demographic history of the Dutch population. \\ Nat Genet. 46(8):​818-25 (2014) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24974849|PMID:​24974849]] ​+  - Cassa CA, Smith SE, Docken W, Hoffman E, McLaughlin H, Chun S, Leshchiner I, Miraoui H, Raychaudhuri S, Frank NY, Wilson BJ, Sunyaev SR, Maas RL; Brigham Genomic Medicine, Vuzman D. An argument for early genomic sequencing in atypical cases: a WISP3 variant leads to diagnosis of progressive pseudorheumatoid arthropathy of childhood. \\ Rheumatology (Oxford). 2015 Oct 22. pii: kev367. PMID: 2649374444 
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