Balick DJ, Jordan DM, Sunyaev S, Do R. Overcoming constraints on the detection of recessive selection in human genes from population frequency data.
Am J Hum Genet. 2022 Jan 6;109(1):33-49. doi: 10.1016/j.ajhg.2021.12.001. PMID: 34951958

Chun S, Imakaev M, Hui D, Patsopoulos NA, Neale BM, Kathiresan S, Stitziel NO, Sunyaev SR. Non-parametric Polygenic Risk Prediction via Partitioned GWAS Summary Statistics.
Am J Hum Genet. 2020 May 21. doi: 10.1016/j.ajhg.2020.05.004. PubMed PMID: 32470373.

Cassa CA, Jordan DM, Adzhubei I, Sunyaev SR. A literature review at genome scale: improving clinical variant assessment.
Genet Med. 2018 Feb 1. doi: 10.1038/gim.2017.230. PubMed PMID:29388949. View article at SharedIt

Weghorn D, Sunyaev SR. Bayesian inference of negative and positive selection in human cancers.
Nat Genet. 49(12):1785-1788 (2017). PubMed PMID:29106416. View article at SharedIt.

Sohail M, Vakhrusheva OA, Sul JH, Pulit SL, Francioli LC; Genome of the Netherlands Consortium; Alzheimer’s Disease Neuroimaging Initiative, van den Berg LH, Veldink JH, de Bakker PIW, Bazykin GA, Kondrashov AS, Sunyaev SR. Negative selection in humans and fruit flies involves synergistic epistasis.
Science 356(6337):539-542 (2017). PubMed PMID:28473589.

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 PMID:28369035. PMC: https://www.ncbi.nlm.nih.gov/pubmed/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. 49(4):600-605 (2017) PubMed PMID:28218759.

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 PMID:27666371.

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 PMID:26808112.

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 PMID:26527001.

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 PMID:26378430.

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 PMID:26317225.

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 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 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 PMID:25581429.

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 PMID:25693567.

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 PMID:24443550.

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 PMID:24336318.

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 PMID:23752795.

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 PMID:23487782.

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 PMID:3468643.

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 PMID:23818451.

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 PMID:23060611.

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 PMID:22641211.

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 PMID:22555591.

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 PMID:22223662

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 PMID:21349864.

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 PMID:21310275.

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 PMID:20471002.

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 PMID:20354512.

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 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 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 PMID:19197354.

Chun S, Akle S, Teodosiadis A, Cade BE, Wang H, Sofer T, Evans DS, Stone KL, Gharib SA, Mukherjee S, Palmer LJ, Hillman D, Rotter JI, Hanis CL, Stamatoyannopoulos JA, Redline S, Cotsapas C, Sunyaev SR. Leveraging pleiotropy to discover and interpret GWAS results for sleep-associated traits.
BioRxiv. 2022. doi: 10.1101/832162 (preprint).

D’Antonio M, Weghorn D, D’Antonio-Chronowska A, Coulet F, Olson KM, DeBoever C, Drees F, Arias A, Alakus H, Richardson AL, Schwab RB, Farley EK, Sunyaev SR, Frazer KA. Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer.
Nat Commun. 8 (2017) PubMed PMID:28874753.

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 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 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. 97(6):775-89 (2015) PubMed 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

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 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

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 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 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 PMID:24667040.

Stanley CM, Sunyaev SR, Greenblatt MS, Oetting WS. Clinically relevant variants - identifying, collecting, interpreting, and disseminating: the 2013 annual scientific meeting of the Human Genome Variation Society.
Hum Mutat. 35(4):505-10 (2014) PubMed PMID:24470180.

Sunyaev SR, Roth FP. Systems biology and the analysis of genetic variation.
Curr Opin Genet Dev. 23(6):599-601 (2013). PubMed PMID:24291212.

Agarwala V, Flannick J, Sunyaev S; GoT2D Consortium, Altshuler D. Evaluating empirical bounds on complex disease genetic architecture.
Nat Genet. 45(12):1418-27 (2013). PubMed PMID:24141362.

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 4:2212 (2013). PubMed PMID:23962925.

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 499(7457):214-8 (2013). PubMed PMID:23770567.

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 9(4):e1003404 (2013). PubMed PMID:23593015.

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; Consortium of Rheumatology Researchers of North America; Rheumatoid Arthritis Consortium International, 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 92(1):15-27 (2013). PubMed PMID:23261300.

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 493(7430):45-50 (2013). PubMed PMID:23222524.

Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2.
Curr Protoc Hum Genet. Chapter 7:Unit7.20 (2013). PubMed PMID:23315928.

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 110(8):2910-5 (2013). PubMed PMID:23388632.

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 34(1):255-65 (2013). PubMed PMID:22949387.

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 91(6):1033-40 (2012). PubMed PMID:23176822.

Sunyaev SR. Inferring causality and functional significance of human coding DNA variants.
Hum Mol Genet 21(R1):R10-7 (2012). Review. PubMed PMID:22990389.

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 337(6099):1190-5 (2012). PubMed PMID:22955828.

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 489(7414):75-82 (2012). PubMed PMID:22955617.