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publications [2017/01/27 10:39]
schun [Selected Recent Publications]
publications [2017/05/05 12:36]
ivan [Selected Recent Publications]
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 ===== Selected Recent Publications ===== ===== Selected Recent Publications =====
  
- +  - Cassa CA, Weghorn D, Balick DJ, Jordan DM, Nusinow D, Samocha KE, O'​Donnell-Luria A, MacArthur DG, Daly 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]]. 
-  - 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. ​in press.  +  - 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. ​49(4):​600-605 (2017) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​28218759|PMID:​28218759]]. 
-  - 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.3493. PMID: 26808112  +  - Sul JH, Cade BE, Cho MH, Qiao D, Silverman EK, Redline S, Sunyaev S. Increasing Generality and Power of Rare-Variant Tests by Utilizing Extended Pedigrees.\\ Am J Hum Genet. 99(4):​846-859 (2016) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​27666371|PMID:​27666371]]
-  - 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 +  - 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.3493. ​PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​26808112|PMID:​26808112]].  
-  - 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. PMID: 26378430 +  - 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. PMID: 26317225 +  - 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]]. 
-  - 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 +  - 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]]. 
-  - 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+  - 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]].
   - 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 Genet. 47(7):822-6 (2015). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25985141|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]].   - 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]].
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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. 2016 Oct;33(10):​2555-64. doi: 10.1093/​molbev/​msw127. Epub 2016 Jun 28. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​27436009|PMID:​ 27436009]] +  - 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]]. 
-  - 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. ​2015 Dec 3;97(6):​775-89. doi10.1016/j.ajhg.2015.10.006. Epub 2015 Nov 12. PMID: 26581902+  - 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]].
   - 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   - 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
-  - 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]]+  - 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]]
   - 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 Med. 2015 Sep;​3(5):​413-23. doi: 10.1002/​mgg3.152. Epub 2015 May 10. PMID: 26436107   - 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 Med. 2015 Sep;​3(5):​413-23. doi: 10.1002/​mgg3.152. Epub 2015 May 10. PMID: 26436107
-  - 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]] ​+  - 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]] ​
   - MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio LA, Stamatoyannopoulos JA, Sunyaev SR, Valle D, Voight BF, Winckler W, Gunter C. Guidelines for investigating causality of sequence variants in human disease.\\ Nature. 508(7497):​469-76 (2014) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24759409|PMID:​24759409]].   - MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio LA, Stamatoyannopoulos JA, Sunyaev SR, Valle D, Voight BF, Winckler W, Gunter C. Guidelines for investigating causality of sequence variants in human disease.\\ Nature. 508(7497):​469-76 (2014) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24759409|PMID:​24759409]].
   - Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, ... Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.\\ Genome Biol. 15(3):R53 (2014) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24667040|PMID:​24667040]].   - Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, ... Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.\\ Genome Biol. 15(3):R53 (2014) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24667040|PMID:​24667040]].