Table of Contents

Publications

Selected Recent Papers

  1. Nazeen S, Wang X, Morrow AR, Strom R, Ethier E, Ritter D, Henderson ABH, Afroz J, Cassa CS, Stitziel NO, Gupta RM, Luk KC, Studer L, Khurana V, Sunyaev SR. NERINE reveals rare variant associations in gene networks across phenotypes and implicates an SNCA-PRL-LRRK2 subnetwork in Parkinson's disease. Cell Genom. 2026 Jun 22:101284. doi: 10.1016/j.xgen.2026.101284.
    [PMID: 42330948] [DOI: 10.1016/j.xgen.2026.101284] [ScienceDirect]
  2. Kar P, Moldovan MA, Guez J, Nazeen S, Goodrich JK, Karani T, Samocha KE, Karczewski KJ, Koch E, Seplyarskiy V, Sunyaev SR. Inference of elevated mutation rates and variant effects using 700k exomes. bioRxiv [Preprint]. 2026 Jun 10:2026.06.09.730991. doi: 10.64898/2026.06.09.730991.
    [PMID: 42327107] [PMCID: 13278075] [DOI: 10.64898/2026.06.09.730991] [ScienceDirect]
  3. Guez J, Goodrich JK, Moldovan MA, Chao KR, Kar P, Panchal R, Wilson MW, Laricchia KM, Rohlicek G, Biba D, Marten D, He Q, Darnowsky PW, Grant R, Weisburd B, Baxter SM, Nadeau J, Lu W, Jahl S, Parsa S, Lamane A, DiTroia S, Fu J, Zhao X, Alarmani E, Tolonen C, Novod S, Bryant S, Stevens C, Chapman SB, Cusick C, Vittal C, Gauthier LD, Goldstein JI, Goldstein D, King D, Poterba T, Tiao G, Tranchero M, Lotter W, MacArthur DG, Brand H, Seplyarskiy V, Koch E, Talkowski ME, Solomonson M, Neale BM, O'Donnell-Luria A, Finucane HK, Sunyaev SR, Daly MJ, Rehm HL, Samocha KE, Karczewski KJ, gnomAD Project Consortium. Integrating 730,947 exome sequences with clinical literature improves gene discovery. medRxiv [Preprint]. 2026 Mar 25:2026.03.23.26349081. doi: 10.64898/2026.03.23.26349081.
    [PMID: 41929314] [PMCID: 13042128] [DOI: 10.64898/2026.03.23.26349081] [ScienceDirect]
  4. Connally NJ, Sunyaev S. Farm animal evolution demonstrates hidden molecular basis of human traits. bioRxiv [Preprint]. 2026 Feb 3:2026.02.02.703413. doi: 10.64898/2026.02.02.703413.
    [PMID: 41676459] [PMCID: 12889581] [DOI: 10.64898/2026.02.02.703413] [ScienceDirect]
  5. McGinty RJ, Balick DJ, Mirkin SM, Sunyaev SR. Inherent instability of simple DNA repeats shapes an evolutionarily stable distribution of repeat lengths. Nat Commun. 2025 Dec 9;17(1):93. doi: 10.1038/s41467-025-66725-5.
    [PMID: 41365873] [PMCID: 12769509] [DOI: 10.1038/s41467-025-66725-5] [ScienceDirect]
  6. Seplyarskiy V, Moldovan MA, Koch E, Kar P, Neville MDC, Rahbari R, Sunyaev S. Hotspots of human mutation point to clonal expansions in spermatogonia. Nature. 2025 Nov;647(8089):429-435. doi: 10.1038/s41586-025-09579-7. Epub 2025 Oct 8.
    [PMID: 41062699] [PMCID: 12714578] [DOI: 10.1038/s41586-025-09579-7] [ScienceDirect]
  7. Kobren SN, Moldovan MA, Reimers R, Traviglia D, Li X, Barnum D, Veit A, Corona RI, Carvalho Neto GdV, Willett J, Berselli M, Ronchetti W, Nelson SF, Martinez-Agosto JA, Sherwood R, Krier J, Kohane IS, Sunyaev SR, Undiagnosed Diseases Network. Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations. Nat Commun. 2025 Aug 7;16(1):7267. doi: 10.1038/s41467-025-61712-2.
    [PMID: 40770127] [PMCID: 12328722] [DOI: 10.1038/s41467-025-61712-2] [ScienceDirect]
  8. Maury EA, Jones A, Seplyarskiy V, Nguyen TTL, Rosenbluh C, Bae T, Wang Y, Abyzov A, Khoshkhoo S, Chahine Y, Zhao S, Venkatesh S, Root E, Voloudakis G, Roussos P, Park PJ, Akbarian S, Brennand K, Reilly S, Lee EA, Sunyaev SR, Walsh CA, Chess A, Brain Somatic Mosaicism Network‡. Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes. Science. 2024 Oct 11;386(6718):217-224. doi: 10.1126/science.adq1456. Epub 2024 Oct 10.
    [PMID: 39388546] [PMCID: 11490355] [DOI: 10.1126/science.adq1456] [ScienceDirect]
  9. Seplyarskiy V, Koch EM, Lee DJ, Lichtman JS, Luan HH, Sunyaev SR. A mutation rate model at the basepair resolution identifies the mutagenic effect of polymerase III transcription. Nat Genet. 2023 Dec;55(12):2235-2242. doi: 10.1038/s41588-023-01562-0. Epub 2023 Nov 30.
    [PMID: 38036792] [PMCID: 11348951] [DOI: 10.1038/s41588-023-01562-0] [ScienceDirect]
  10. McGinty RJ, Sunyaev SR. Revisiting mutagenesis at non-B DNA motifs in the human genome. Nat Struct Mol Biol. 2023 Apr;30(4):417-424. doi: 10.1038/s41594-023-00936-6. Epub 2023 Mar 13.
    [PMID: 36914796] [PMCID: 10225297] [DOI: 10.1038/s41594-023-00936-6] [ScienceDirect]
  11. Connally NJ, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S, Cotsapas C, Cassa CA, Sunyaev SR. The missing link between genetic association and regulatory function. Elife. 2022 Dec 14;11:e74970. doi: 10.7554/eLife.74970.
    [PMID: 36515579] [PMCID: 9842386] [DOI: 10.7554/eLife.74970] [ScienceDirect]
  12. Seplyarskiy VB, Sunyaev S. The origin of human mutation in light of genomic data. Nat Rev Genet. 2021 Oct;22(10):672-686. doi: 10.1038/s41576-021-00376-2. Epub 2021 Jun 23.
    [PMID: 34163020] [DOI: 10.1038/s41576-021-00376-2] [ScienceDirect]
  13. Koch EM, Sunyaev SR. Maintenance of Complex Trait Variation: Classic Theory and Modern Data. Front Genet. 2021 Nov 12;12:763363. doi: 10.3389/fgene.2021.763363. eCollection 2021.
    [PMID: 34868244] [PMCID: 8636146] [DOI: 10.3389/fgene.2021.763363] [ScienceDirect]
  14. Seplyarskiy VB, Soldatov RA, Koch E, McGinty RJ, Goldmann JM, Hernandez RD, Barnes K, Correa A, Burchard EG, Ellinor PT, McGarvey ST, Mitchell BD, Vasan RS, Redline S, Silverman E, Weiss ST, Arnett DK, Blangero J, Boerwinkle E, He J, Montgomery C, Rao DC, Rotter JI, Taylor KD, Brody JA, Chen YI, de las Fuentes L, Hwu C, Rich SS, Manichaikul AW, Mychaleckyj JC, Palmer ND, Smith JA, Kardia SLR, Peyser PA, Bielak LF, O'Connor TD, Emery LS, Gilissen C, Wong WSW, Kharchenko PV, Sunyaev S, TOPMed Population Genetics Working Group. Population sequencing data reveal a compendium of mutational processes in the human germ line. Science. 2021 Aug 27;373(6558):1030-1035. doi: 10.1126/science.aba7408. Epub 2021 Aug 12.
    [PMID: 34385354] [PMCID: 9217108] [DOI: 10.1126/science.aba7408] [ScienceDirect]
  15. Radke DW, Sul JH, Balick DJ, Akle S, Green RC, Sunyaev SR, Alzheimer's Disease Neuroimaging Initiative. Purifying selection on noncoding deletions of human regulatory loci detected using their cellular pleiotropy. Genome Res. 2021 Jun;31(6):935-946. doi: 10.1101/gr.275263.121. Epub 2021 May 7.
    [PMID: 33963077] [PMCID: 8168579] [DOI: 10.1101/gr.275263.121] [ScienceDirect]
  16. Dietlein F, Weghorn D, Taylor-Weiner A, Richters A, Reardon B, Liu D, Lander ES, Van Allen EM, Sunyaev SR. Identification of cancer driver genes based on nucleotide context. Nat Genet. 2020 Feb;52(2):208-218. doi: 10.1038/s41588-019-0572-y. Epub 2020 Feb 3.
    [PMID: 32015527] [PMCID: 7031046] [DOI: 10.1038/s41588-019-0572-y] [ScienceDirect]
  17. 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 Jul 2;107(1):46-59. doi: 10.1016/j.ajhg.2020.05.004. Epub 2020 May 28.
    [PMID: 32470373] [PMCID: 7332650] [DOI: 10.1016/j.ajhg.2020.05.004] [ScienceDirect]
  18. Weghorn D, Balick DJ, Cassa C, Kosmicki JA, Daly MJ, Beier DR, Sunyaev SR. Applicability of the Mutation-Selection Balance Model to Population Genetics of Heterozygous Protein-Truncating Variants in Humans. Mol Biol Evol. 2019 Aug 1;36(8):1701-1710. doi: 10.1093/molbev/msz092.
    [PMID: 31004148] [PMCID: 6738481] [DOI: 10.1093/molbev/msz092] [ScienceDirect]
  19. Sohail M, Maier RM, Ganna A, Bloemendal A, Martin AR, Turchin MC, Chiang CW, Hirschhorn J, Daly MJ, Patterson N, Neale B, Mathieson I, Reich D, Sunyaev SR. Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies. Elife. 2019 Mar 21;8:e39702. doi: 10.7554/eLife.39702.
    [PMID: 30895926] [PMCID: 6428571] [DOI: 10.7554/eLife.39702] [ScienceDirect]
  20. Seplyarskiy VB, Akkuratov EE, Akkuratova N, Andrianova MA, Nikolaev SI, Bazykin GA, Adameyko I, Sunyaev SR. Error-prone bypass of DNA lesions during lagging-strand replication is a common source of germline and cancer mutations. Nat Genet. 2019 Jan;51(1):36-41. doi: 10.1038/s41588-018-0285-7. Epub 2018 Dec 3.
    [PMID: 30510240] [PMCID: 6317876] [DOI: 10.1038/s41588-018-0285-7] [ScienceDirect]
  21. Weghorn D, Sunyaev S. Bayesian inference of negative and positive selection in human cancers. Nat Genet. 2017 Dec;49(12):1785-1788. doi: 10.1038/ng.3987. Epub 2017 Nov 6.
    [PMID: 29106416] [DOI: 10.1038/ng.3987] [ScienceDirect]
  22. Sohail M, Vakhrusheva OA, Sul JH, Pulit SL, Francioli LC, van den Berg LH, Veldink JH, de Bakker PIW, Bazykin GA, Kondrashov AS, Sunyaev SR, Alzheimer’s Disease Neuroimaging Initiative. Negative selection in humans and fruit flies involves synergistic epistasis. Science. 2017 May 5;356(6337):539-542. doi: 10.1126/science.aah5238.
    [PMID: 28473589] [PMCID: 6200135] [DOI: 10.1126/science.aah5238] [ScienceDirect]
  23. 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. 2017 May;49(5):806-810. doi: 10.1038/ng.3831. Epub 2017 Apr 3.
    [PMID: 28369035] [PMCID: 5618255] [DOI: 10.1038/ng.3831] [ScienceDirect]
  24. 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 Apr;49(4):600-605. doi: 10.1038/ng.3795. Epub 2017 Feb 20.
    [PMID: 28218759] [PMCID: 5374036] [DOI: 10.1038/ng.3795] [ScienceDirect]
  25. Polak P, Karlić R, Koren A, Thurman R, Sandstrom R, Lawrence M, Reynolds A, Rynes E, Vlahoviček K, Stamatoyannopoulos JA, Sunyaev SR. Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature. 2015 Feb 19;518(7539):360-364. doi: 10.1038/nature14221.
    [PMID: 25693567] [PMCID: 4405175] [DOI: 10.1038/nature14221] [ScienceDirect]
  26. Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Ye K, Guryev V, Arndt PF, Kloosterman WP, de Bakker PIW, Sunyaev SR, Genome of the Netherlands Consortium. Genome-wide patterns and properties of de novo mutations in humans. Nat Genet. 2015 Jul;47(7):822-826. doi: 10.1038/ng.3292. Epub 2015 May 18.
    [PMID: 25985141] [PMCID: 4485564] [DOI: 10.1038/ng.3292] [ScienceDirect]
  27. 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] [PMCID: 4552954] [DOI: 10.1371/journal.pgen.1005436] [ScienceDirect]
  28. Jordan DM, Frangakis SG, Golzio C, Cassa CA, Kurtzberg J, Davis EE, Sunyaev SR, Katsanis N, Task Force for Neonatal Genomics. 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.
    [PMID: 26123021] [PMCID: 4537371] [DOI: 10.1038/nature14497] [ScienceDirect]

Other Papers

  1. Leitão E, Santini A, Cogne B, Essid M, Athanasiadou M, LaFlamme CW, Marijon P, Bernard V, Jousselin K, Chatron N, Barcia G, Keren B, Mignot C, Charles P, Besnard T, Paluch R, de Sainte Agathe J, Almanza Fuerte EP, Sengupta S, Milh M, Ramond F, Allan T, An I, Araujo C, Arpin S, Austin-Tse C, Auvin S, Baer S, Bahi-Buisson N, Bak M, Barth M, Baulac S, Bednarek-Weirauch N, Begemann M, Bennett MF, Bensabath U, Bézieau S, Bhouri R, Biehler M, Hammer TB, Bogoin J, Bonanno E, Boussion S, Bris C, Brosseau-Beauvir A, Bruel A, Briand-Suleau A, Buratti J, Celse T, Chambon P, Chemaly N, Chesneau B, Colin E, Colmard M, Colson C, Conrad S, Courtin T, Creveaux I, Cullier A, Dang LT, de Saint Martin A, de Vanssay de Blavous Legendre C, Demeer B, Denommé-Pichon A, Diekhoff P, DiTroia S, Doco-Fenzy M, Dubourg C, Dubucs C, Ducreux S, Dufour L, Duquet R, Durand B, El Chehadeh S, Elbracht M, Faivre L, Faoucher M, Faudet A, Forlani S, Fradin M, Gaignard P, Ganne B, Garde A, Géraud J, Gill D, Goldenberg A, Grabli D, Grisel C, Gueden S, Gueguen P, Guerrot A, Guichet A, Haack TB, Härting N, Häusler MG, Heide S, Herget T, Héron B, Héron D, Herwig J, Heulin M, Holling T, Houdayer C, Isidor B, Jacquette A, Januel L, Jean-Marçais N, Kaiser FJ, Kaya S, King C, Konyukh M, Kraft F, Krause J, Kirstetter R, Kuechler A, Kurth I, Kutsche K, Labalme A, Laloy J, Laugel V, Le Bricquir F, Lèbre A, Lebrun M, Leguern E, Levy J, Lieffering N, Lyonnet S, Lüthy K, Macdonald SMW, Mansour-Hendili L, Maraval J, Marquardt I, Mattausch C, Mercier S, Messaoud O, Morel G, Mortreux J, Munnich A, Nabbout R, Nambot S, Navarro V, Neale A, Nguyen L, Nizon M, Nowak F, O'Leary MC, Odent S, Ojeda NM, Olin V, Olivieri S, Õunap K, Pais LS, Panagiotakaki E, Patat O, Perrin-Sabourin L, Petit F, Philippe C, Piton A, Planes M, Poirsier C, Pouzet A, Prouteau C, Quéméner-Redon S, Renaud M, Richard A, Rio M, Rivier C, Robin-Renaldo F, Rollier P, Rossi M, Roubertie A, Ruault V, Rupin-Mas M, Saugier-Veber P, Saunier A, Saneto R, Sarrazin E, Sarret C, Schaefer E, Schluth-Bolard C, Schneider A, Schumann I, Seplyarskiy VB, Spranger S, Smol T, Sturm M, Sunyaev SR, Sperelakis-Beedham B, Stenton SL, Stock F, Tharreau M, Torun D, Toulouse J, Thiyagarajah H, Valence S, Valleix S, Van-Gils J, Villard L, Ville D, Villeneuve N, Vitobello A, Waernessyckle A, Wagner J, Weber Y, Wieczorek D, Witkowski T, Yadavilli M, Yammine T, Zaafrane-Khachnaoui K, Zaki MS, Ziegler A, Bramswig NC, Lermine A, Nicolas G, Gleeson JG, Sadleir LG, Hildebrand MS, Scheffer IE, Whiffin N, O'Donnell-Luria A, Mefford HC, Blanc P, Thevenon J, Charbonnier C, Charenton C, Depienne C, Lesca G, Nava C. Systematic analysis of snRNA genes reveals frequent RNU2-2 variants in dominant and recessive developmental and epileptic encephalopathies. Nat Genet. 2026 Apr;58(4):782-797. doi: 10.1038/s41588-026-02547-5. Epub 2026 Mar 30.
    [PMID: 41912934] [PMCID: 13083260] [DOI: 10.1038/s41588-026-02547-5] [ScienceDirect]
  2. Isakov O, Fluss R, Marek-Yagel D, Sunyaev S, Ben-Shachar S. Incorporation of Clinical and Molecular Variant Properties Improves the Performance of in silico Pathogenicity Prediction Tools. Genet Med. 2026 Mar 25:102557. doi: 10.1016/j.gim.2026.102557.
    [PMID: 41904679] [DOI: 10.1016/j.gim.2026.102557] [ScienceDirect]
  3. Buianova AA, Adzhubei IA, Kryukova OV, Kost OA, Mironenko IV, Kozuch AS, Ilyina GA, Kuznetsova AA, Repinskaia ZA, Churov AV, Dudek SM, Rebrikov DV, Danilov SM. ACE-Dependent Alzheimer's Disease: Blood ACE Phenotyping of the Most Prevalent and Damaging ACE Missense Mutation-Y215C (rs3730025). Biomedicines. 2026 Jan 26;14(2):275. doi: 10.3390/biomedicines14020275.
    [PMID: 41751174] [PMCID: 12937726] [DOI: 10.3390/biomedicines14020275] [ScienceDirect]
  4. Zhou H, Verma V, Li X, Li Z, Shedd N, Li TC, Yang H, Zhang A, Borsari B, Buyske S, Gerstein M, Matise T, Zody MC, Neale B, Weng Z, Sunyaev SR, Lin X. FAVOR 2.0: A reengineered functional annotation of variants online resource for interpreting genomic variation. Nucleic Acids Res. 2026 Jan 6;54(D1):D1405-D1414. doi: 10.1093/nar/gkaf1217.
    [PMID: 41335103] [PMCID: 12807660] [DOI: 10.1093/nar/gkaf1217] [ScienceDirect]
  5. Fazal S, Dashnow H, Dohrn MF, Raposo J, Hiatt L, Danzi MC, Xu IRL, Toro C, Adams DR, Usdin K, Hayward B, Kobren SN, Sunyaev SR, Spillmann RC, Shashi V, Rebelo A, Bademci G, Tekin M, Quinlan AR, Zuchner S, Undiagnosed Diseases Network. A genome-wide approach for the discovery of novel repeat expansion disorders in the Undiagnosed Diseases Network cohort. Genet Med. 2025 Aug;27(8):101462. doi: 10.1016/j.gim.2025.101462. Epub 2025 May 22.
    [PMID: 40417743] [PMCID: 12318663] [DOI: 10.1016/j.gim.2025.101462] [ScienceDirect]
  6. Hakim A, Connally NJ, Schnitzler GR, Cho MH, Jiang ZG, Sunyaev SR, Gupta RM. Missing Regulation Between Genetic Association and Transcriptional Abundance for Hypercholesterolemia Genes. Genes (Basel). 2025 Jan 15;16(1):84. doi: 10.3390/genes16010084.
    [PMID: 39858631] [PMCID: 11764661] [DOI: 10.3390/genes16010084] [ScienceDirect]
  7. Hajheidari M, Sunyaev S, de Meaux J. Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression. Plant Cell Physiol. 2025 May 17;66(4):444-460. doi: 10.1093/pcp/pcae140.
    [PMID: 39626022] [PMCID: 12085094] [DOI: 10.1093/pcp/pcae140] [ScienceDirect]
  8. Lake NJ, Ma K, Liu W, Battle SL, Laricchia KM, Tiao G, Puiu D, Ng KK, Cohen J, Compton AG, Cowie S, Christodoulou J, Thorburn DR, Zhao H, Arking DE, Sunyaev SR, Lek M. Quantifying constraint in the human mitochondrial genome. Nature. 2024 Nov;635(8038):390-397. doi: 10.1038/s41586-024-08048-x. Epub 2024 Oct 16.
    [PMID: 39415008] [PMCID: 11646341] [DOI: 10.1038/s41586-024-08048-x] [ScienceDirect]
  9. Li TC, Zhou H, Verma V, Tang X, Shao Y, Van Buren E, Weng Z, Gerstein M, Neale B, Sunyaev SR, Lin X. FAVOR-GPT: a generative natural language interface to whole genome variant functional annotations. Bioinform Adv. 2024 Sep 28;4(1):vbae143. doi: 10.1093/bioadv/vbae143. eCollection 2024.
    [PMID: 39387060] [PMCID: 11461909] [DOI: 10.1093/bioadv/vbae143] [ScienceDirect]
  10. Yu T, Fife JD, Bhat V, Adzhubey I, Sherwood R, Cassa CA. FUSE: Improving the estimation and imputation of variant impacts in functional screening. Cell Genom. 2024 Oct 9;4(10):100667. doi: 10.1016/j.xgen.2024.100667.
    [PMID: 39389016] [PMCID: 11602636] [DOI: 10.1016/j.xgen.2024.100667] [ScienceDirect]
  11. Lincoln MR, Connally N, Axisa P, Gasperi C, Mitrovic M, van Heel D, Wijmenga C, Withoff S, Jonkers IH, Padyukov L, Rich SS, Graham RR, Gaffney PM, Langefeld CD, Vyse TJ, Hafler DA, Chun S, Sunyaev SR, Cotsapas C, International Multiple Sclerosis Genetics Consortium. Genetic mapping across autoimmune diseases reveals shared associations and mechanisms. Nat Genet. 2024 May;56(5):838-845. doi: 10.1038/s41588-024-01732-8. Epub 2024 May 13.
    [PMID: 38741015] [PMCID: 13095137] [DOI: 10.1038/s41588-024-01732-8] [ScienceDirect]
  12. Bendapudi PK, Nazeen S, Ryu J, Söylemez O, Robbins A, Rouaisnel B, O'Neil JK, Pokhriyal R, Yang M, Colling M, Pasko B, Bouzinier M, Tomczak L, Collier L, Barrios D, Ram S, Toth-Petroczy A, Krier J, Fieg E, Dzik WH, Hudspeth JC, Pozdnyakova O, Nardi V, Knight J, Maas R, Sunyaev S, Losman J. Low-frequency inherited complement receptor variants are associated with purpura fulminans. Blood. 2024 Mar 14;143(11):1032-1044. doi: 10.1182/blood.2023021231.
    [PMID: 38096369] [PMCID: 10950473] [DOI: 10.1182/blood.2023021231] [ScienceDirect]
  13. Nazeen S, Wang X, Zielinski D, Lam I, Hallacli E, Xu P, Ethier E, Strom R, Zanella CA, Nithianandam V, Ritter D, Henderson A, Saurat N, Afroz J, Nutter-Upham A, Benyamini H, Copty J, Ravishankar S, Morrow A, Mitchel J, Neavin D, Gupta R, Farbehi N, Grundman J, Myers RH, Scherzer CR, Trojanowski JQ, Van Deerlin VM, Cooper AA, Lee EB, Erlich Y, Lindquist S, Peng J, Geschwind DH, Powell J, Studer L, Feany MB, Sunyaev SR, Khurana V. Deep sequencing of proteotoxicity modifier genes uncovers a Presenilin-2/beta-amyloid-actin genetic risk module shared among alpha-synucleinopathies. bioRxiv [Preprint]. 2024 Mar 7:2024.03.03.583145. doi: 10.1101/2024.03.03.583145.
    [PMID: 38496508] [PMCID: 10942362] [DOI: 10.1101/2024.03.03.583145] [ScienceDirect]
  14. Critical Assessment of Genome Interpretation Consortium. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biol. 2024 Feb 22;25(1):53. doi: 10.1186/s13059-023-03113-6.
    [PMID: 38389099] [PMCID: 10882881] [DOI: 10.1186/s13059-023-03113-6] [ScienceDirect]
  15. Fazal S, Danzi MC, Xu I, Kobren SN, Sunyaev S, Reuter C, Marwaha S, Wheeler M, Dolzhenko E, Lucas F, Wuchty S, Tekin M, Züchner S, Aguiar-Pulido V. RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci. Genome Biol. 2024 Jan 31;25(1):39. doi: 10.1186/s13059-024-03171-4.
    [PMID: 38297326] [PMCID: 10832122] [DOI: 10.1186/s13059-024-03171-4] [ScienceDirect]
  16. Danilov SM, Adzhubei IA, Kozuch AJ, Petukhov PA, Popova IA, Choudhury A, Sengupta D, Dudek SM. Carriers of Heterozygous Loss-of-Function ACE Mutations Are at Risk for Alzheimer's Disease. Biomedicines. 2024 Jan 12;12(1):162. doi: 10.3390/biomedicines12010162.
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  146. 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. doi: 10.1002/prot.10503.
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  147. 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. doi: 10.1093/hmg/ddg359. Epub 2003 Oct 21.
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  148. Schmidt S, Sunyaev S, Bork P, Dandekar T. Metabolites: a helping hand for pathway evolution?. Trends Biochem Sci. 2003 Jun;28(6):336-41. doi: 10.1016/S0968-0004(03)00114-2.
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  149. 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. doi: 10.1021/ac026199a.
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  150. 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. doi: 10.1016/s0022-2836(03)00045-7.
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  151. 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. doi: 10.1016/S0168-9525(03)00023-4.
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  152. 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. doi: 10.1385/1-59259-342-9:221.
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  153. 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. doi: 10.1073/pnas.232565499. Epub 2002 Oct 28.
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  154. Ramensky V, Bork P, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 2002 Sep 1;30(17):3894-900. doi: 10.1093/nar/gkf493.
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  155. 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. doi: 10.1021/ac0013709.
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  156. Sunyaev S, Ramensky V, Koch I, Lathe W3, Kondrashov AS, Bork P. Prediction of deleterious human alleles. Hum Mol Genet. 2001 Mar 15;10(6):591-7. doi: 10.1093/hmg/10.6.591.
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  157. Sunyaev S, Lathe W3, 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. doi: 10.1016/s0959-440x(00)00175-5.
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  158. Sunyaev SR, Lathe WC3, 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. doi: 10.1016/s0168-9525(00)02058-8.
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  159. 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. doi: 10.1016/s0168-9525(00)01988-0.
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  160. 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. doi: 10.1016/s0065-3233(00)54012-1.
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