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Shamil Sunyaev

Research Profile

Genes & Molecular Sequences

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Evolution, Molecular

Chemicals & Drugs

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Publications

TOP 3
Omer Gokcumen; Rebecca C Iskow; Christian Austermann; Jeremy M Boss; Lubbertus C F Mulder; Alkes Price; Towfique Raj; Christopher D Scharer; Viviana Simon; Barbara Stranger; Shamil Sunyaev; Qihui Zhu; Charles Lee
Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence.
Bertrand Coste; James Cox; Monica A Giovanni; Alexander Hoischen; Gunnar Houge; Matthew Lebo; Richard L Maas; Jayanti Mathur; Michael F Murray; Anthony Philippakis; Heidi Rehm; Gunnar Riemer; Unni Steen; Vidar Martin Steen; Nathan Stitziel; Shamil Sunyaev; Scott T Weiss; John N Wood; Michael Bandell; Ardem Patapoutian
Gain-of-function mutations in the mechanically activated ion channel PIEZO2 cause a subtype of Distal Arthrogryposis.
Christopher D McFarland; Kirill S Korolev; Gregory V Kryukov; Shamil Sunyaev; Leonid A Mirny
Impact of deleterious passenger mutations on cancer progression.

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All Publications

2013: Omer Gokcumen; Rebecca C Iskow; Christian Austermann; Jeremy M Boss; Lubbertus C F Mulder; Alkes Price; Towfique Raj; Christopher D Scharer; Viviana Simon; Barbara Stranger; Shamil Sunyaev; Qihui Zhu; Charles Lee
Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence.
PLoS genetics 2013;9(4):e1003404.
2013: Bertrand Coste; James Cox; Monica A Giovanni; Alexander Hoischen; Gunnar Houge; Matthew Lebo; Richard L Maas; Jayanti Mathur; Michael F Murray; Anthony Philippakis; Heidi Rehm; Gunnar Riemer; Unni Steen; Vidar Martin Steen; Nathan Stitziel; Shamil Sunyaev; Scott T Weiss; John N Wood; Michael Bandell; Ardem Patapoutian
Gain-of-function mutations in the mechanically activated ion channel PIEZO2 cause a subtype of Distal Arthrogryposis.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(12):4667-72.
2013: Christopher D McFarland; Kirill S Korolev; Gregory V Kryukov; Shamil Sunyaev; Leonid A Mirny
Impact of deleterious passenger mutations on cancer progression.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(8):2910-5.
2013: Adam Kiezun; Sara L Pulit; P Eline Slagboom; Morris Swertz; Freerk van Dijk; Cornelia M van Duijn; G J B van Ommen; Cisca Wijmenga; Dorret I Boomsma; Paul I W de Bakker; Laurent C Francioli; Shamil Sunyaev
Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency.
PLoS genetics 2013;9(2):e1003301.
2013: Dorothée Diogo; Steve Eyre; Jason Flannick; Jeffrey D Greenberg; Peter K Gregersen; Candace Guiducci; Namrata Gupta; Brendan Hickey; Lars Klareskog; Joel M Kremer; Fina Kurreeman; Katherine P Liao; Javier Martin; Leonid Padyukov; Soumya Raychaudhuri; Stephan Ripke; Manuel A Rivas; Katherine A Siminovitch; Eli A Stahl; Shamil Sunyaev; Brian Thomson; Jane Worthington; Alexandra Zhernakova; Ivan Adzhubey; Lars Alfredsson; Anne Barton; John Bowes; Robert M Plenge
Rare, low-frequency, and common variants in the protein-coding sequence of biological candidate genes from GWASs contribute to risk of rheumatoid arthritis.
American journal of human genetics 2013;92(1):15-27.
2013: Siegfried Schloissnig; Shinichi Sunagawa; Shamil Sunyaev; Julien Tap; Alison Waller; George M Weinstock; Ana Zhu; Karthik Kota; Jens Roat Kultima; John Martin; Daniel R Mende; Makedonka Mitreva; Manimozhiyan Arumugam; Peer Bork
Genomic variation landscape of the human gut microbiome.
Nature 2013;493(7430):45-50.
2013: Ivan Adzhubei; Daniel M Jordan; Shamil Sunyaev
Predicting functional effect of human missense mutations using PolyPhen-2.
Current protocols in human genetics / editorial board, Jonathan L. Haines ... [et al.] 2013;Chapter 7():Unit7.20.
2013: Bryony A Thompson; Maxime P Vallee; Erin L Young; Chloe Tessereau; Alun Thomas; Ivan A Adzhubey; Russell Bell; Ken Boucher; Bingjian Feng; Thierry Frebourg; David E Goldgar; Marc S Greenblatt; Johanna C Herkert; Robert M W Hofstra; Biao Li; Sean D Mooney; Predrag Radivojac; Rolf H Sijmons; Amanda B Spurdle; Shamil Sunyaev; Sean V Tavtigian
Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions.
Human mutation 2013;34(1):255-65.
2012: Amnon Koren; Jacob J Michaelson; James Nemesh; Paz Polak; Jonathan Sebat; Shamil Sunyaev; Steven A McCarroll
Differential relationship of DNA replication timing to different forms of human mutation and variation.
American journal of human genetics 2012;91(6):1033-40.
2012: David P Nusinow; Daniel J O'Connell; Yingzi Yue; Joel M Chick; Steven P Gygi; Adam Kiezun; Richard L Maas; Shamil Sunyaev
Network-based inference from complex proteomic mixtures using SNIPE.
Bioinformatics (Oxford, England) 2012;28(23):3115-22.
2012: Jacob A Tennessen; Goncalo Abecasis; Joshua M Akey; David Altshuler; Michael Bamshad; Abigail W Bigham; Eric Boerwinkle; Carlos D Bustamante; Ron Do; Wenqing Fu; Stacey Gabriel; Simon Gravel; Daniel Jordan; Goo Jun; Hyun Min Kang; Eimear E Kenny; Suzanne M Leal; Xiaoming Liu; Sean McGee; Deborah A Nickerson; Timothy D O'Connor; Mark J Rieder; Shamil Sunyaev
Evolution and functional impact of rare coding variation from deep sequencing of human exomes.
Science (New York, N.Y.) 2012;337(6090):64-9.
2012: Adam Kiezun; Thomas Lehner; Paul Lichtenstein; Patrik Magnusson; Paul J McLaren; Jennifer L Moran; Benjamin M Neale; Alkes L Price; Shaun M Purcell; Yin Yao Shugart; Pamela Sklar; Nathan O Stitziel; Patrick F Sullivan; Paul I W de Bakker; Ron Do; Kiran Garimella; Namrata Gupta; Christina M Hultman; Shamil Sunyaev
Exome sequencing and the genetic basis of complex traits.
Nature genetics 2012;44(6):623-30.
2012: Bogdan Pasaniuc; Nick Patterson; Shaun M Purcell; David Reich; Nadin Rohland; Pamela Sklar; Patrick F Sullivan; Shamil Sunyaev; Noah Zaitlen; Sarah Bergen; Mark J Daly; Paul I W de Bakker; Kiran Garimella; Namrata Gupta; David W Haas; Christina M Hultman; Heng Li; Liming Liang; Paul Lichtenstein; Patrik Magnusson; Paul J McLaren; Jennifer L Moran; Benjamin M Neale; Alkes L Price
Extremely low-coverage sequencing and imputation increases power for genome-wide association studies.
Nature genetics 2012;44(6):631-5.
2011: Leonid Gorelik; Carl Reid; Manuela Testa; Margot Brickelmaier; Simona Bossolasco; Annamaria Pazzi; Arabella Bestetti; Paul Carmillo; Ewa Wilson; Michele McAuliffe; Christopher Tonkin; John P Carulli; Alexey Lugovskoy; Adriano Lazzarin; Shamil Sunyaev; Kenneth Simon; Paola Cinque
Progressive multifocal leukoencephalopathy (PML) development is associated with mutations in JC virus capsid protein VP1 that change its receptor specificity.
The Journal of infectious diseases 2011;204(1):103-14.
2011: Victor Spirin; Alexander Shpunt; Jan Seebacher; Marc Gentzel; Andrej Shevchenko; Steven Gygi; Shamil Sunyaev
Assigning spectrum-specific P-values to protein identifications by mass spectrometry.
Bioinformatics (Oxford, England) 2011;27(8):1128-34.
2011: Daniel M Jordan; Adam Kiezun; Samantha M Baxter; Vineeta Agarwala; Robert C Green; Michael F Murray; Trevor Pugh; Matthew S Lebo; Heidi L Rehm; Birgit H Funke; Shamil Sunyaev
Development and validation of a computational method for assessment of missense variants in hypertrophic cardiomyopathy.
American journal of human genetics 2011;88(2):183-92.
2011: Nathan O Stitziel; Adam Kiezun; Shamil Sunyaev
Computational and statistical approaches to analyzing variants identified by exome sequencing.
Genome biology 2011;12(9):227.
2009: Michael Molla; Arthur Delcher; Shamil Sunyaev; Charles Cantor; Simon Kasif
Triplet repeat length bias and variation in the human transcriptome.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(40):17095-100.
2009: Gregory V Kryukov; Alexander Shpunt; John A Stamatoyannopoulos; Shamil Sunyaev
Power of deep, all-exon resequencing for discovery of human trait genes.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(10):3871-6.
2009: Shamil Sunyaev; Alexey Lugovskoy; Kenneth Simon; Leonid Gorelik
Adaptive mutations in the JC virus protein capsid are associated with progressive multifocal leukoencephalopathy (PML).
PLoS genetics 2009;5(2):e1000368.
2008: Steffen Schmidt; Anna Gerasimova; Fyodor A Kondrashov; Ivan A Adzhubei; Ivan A Adzuhbei; Alexey S Kondrashov; Shamil Sunyaev
Hypermutable non-synonymous sites are under stronger negative selection.
PLoS genetics 2008;4(11):e1000281.
2008: Magno Junqueira; Victor Spirin; Tiago Santana Balbuena; Henrik Thomas; Ivan Adzhubei; Shamil Sunyaev; Andrej Shevchenko
Protein identification pipeline for the homology-driven proteomics.
Journal of proteomics 2008;71(3):346-56.
2008: Magno Junqueira; Victor Spirin; Tiago Santana Balbuena; Patrice Waridel; Vineeth Surendranath; Grigoriy Kryukov; Ivan Adzhubei; Henrik Thomas; Shamil Sunyaev; Andrej Shevchenko
Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification.
Journal of proteome research 2008;7(8):3382-95.
2008: Kirk E Lohmueller; Amit R Indap; Steffen Schmidt; Adam R Boyko; Ryan D Hernandez; Melissa J Hubisz; John J Sninsky; Thomas J White; Shamil Sunyaev; Rasmus Nielsen; andrew clark; Carlos Bustamante
Proportionally more deleterious genetic variation in European than in African populations.
Nature 2008;451(7181):994-7.
2008: Ivan P Gorlov; Olga Y Gorlova; Shamil Sunyaev; Margaret R Spitz; Christopher I Amos
Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.
American journal of human genetics 2008;82(1):100-12.
2008: Bryan A Ballif; G Richard Carey; Shamil Sunyaev; Steven P Gygi
Large-scale identification and evolution indexing of tyrosine phosphorylation sites from murine brain.
Journal of proteome research 2008;7(1):311-8.
2007: Saurabh Asthana; Mikhail Roytberg; John A Stamatoyannopoulos; Shamil Sunyaev
Analysis of sequence conservation at nucleotide resolution.
PLoS computational biology 2007;3(12):e254.
2007: Petr O Ilyinskii; Vladimir L Gabai; Shamil Sunyaev; Galini Thoidis; Alexander M Shneider
Toxicity of influenza A virus matrix protein 2 for mammalian cells is associated with its intrinsic proton-channeling activity.
Cell cycle (Georgetown, Tex.) 2007;6(16):2043-7.
2007: Saurabh Asthana; William Stafford Noble; Gregory V Kryukov; Charles E Grant; Shamil Sunyaev; John A Stamatoyannopoulos
Widely distributed noncoding purifying selection in the human genome.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(30):12410-5.
2007: Patrice Waridel; Ari Frank; Henrik Thomas; Vineeth Surendranath; Shamil Sunyaev; Pavel Pevzner; Andrej Shevchenko
Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing.
Proteomics 2007;7(14):2318-29.
2007: Nadav Ahituv; Nihan Kavaslar; Wendy Schackwitz; Anna Ustaszewska; Joel Martin; Sybil Hebert; Heather Doelle; Baran Ersoy; Gregory V Kryukov; Steffen Schmidt; Nir Yosef; Eytan Ruppin; Roded Sharan; Christian Vaisse; Shamil Sunyaev; Robert Dent; Jonathan Cohen; Ruth McPherson; Len A Pennacchio
Medical sequencing at the extremes of human body mass.
American journal of human genetics 2007;80(4):779-91.
2007: Gregory V Kryukov; Len A Pennacchio; Shamil Sunyaev
Most rare missense alleles are deleterious in humans: implications for complex disease and association studies.
American journal of human genetics 2007;80(4):727-39.
2005: Adam J Liska; Shamil Sunyaev; Ignat N Shilov; Dan A Schaeffer; Andrej Shevchenko
Error-tolerant EST database searches by tandem mass spectrometry and multiTag software.
Proteomics 2005;5(16):4118-22.
2005: Peter D Keightley; Gregory V Kryukov; Shamil Sunyaev; Daniel L Halligan; Daniel J Gaffney
Evolutionary constraints in conserved nongenic sequences of mammals.
Genome research 2005;15(10):1373-8.
2005: Gregory V Kryukov; Steffen Schmidt; Shamil Sunyaev
Small fitness effect of mutations in highly conserved non-coding regions.
Human molecular genetics 2005;14(15):2221-9.
2005: I King Jordan; Fyodor A Kondrashov; Ivan A Adzhubei; Yuri I Wolf; Eugene V Koonin; Alexey S Kondrashov; Shamil Sunyaev
A universal trend of amino acid gain and loss in protein evolution.
Nature 2005;433(7026):633-8.
2005: Shamil Sunyaev
Biocomputing enters its adolescence.
Genome biology 2005;6(6):325.
2005: Matthew W Dimmic; Shamil Sunyaev; Carlos Bustamante
Inferring SNP function using evolutionary, structural, and computational methods.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005;():382-4.
2005: Saurabh Asthana; Steffen Schmidt; Shamil Sunyaev
A limited role for balancing selection.
Trends in genetics : TIG 2005;21(1):30-2.
2004: Adam J Liska; Andrei V Popov; Shamil Sunyaev; Peg Coughlin; Bianca Habermann; Andrej Shevchenko; Peer Bork; Eric Karsenti; Andrej Shevchenko
Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome.
Proteomics 2004;4(9):2707-21.
2004: Aleksey Y Ogurtsov; Shamil Sunyaev; Alexey S Kondrashov
Indel-based evolutionary distance and mouse-human divergence.
Genome research 2004;14(8):1610-6.
2004: Georgii A Bazykin; Fyodor A Kondrashov; Aleksey Y Ogurtsov; Shamil Sunyaev; Alexey S Kondrashov
Positive selection at sites of multiple amino acid replacements since rat-mouse divergence.
Nature 2004;429(6991):558-62.
2004: Bianca Habermann; Jeffrey Oegema; Shamil Sunyaev; Andrej Shevchenko
The power and the limitations of cross-species protein identification by mass spectrometry-driven sequence similarity searches.
Molecular & cellular proteomics : MCP 2004;3(3):238-49.
2004: Shamil Sunyaev; Gennady A Bogopolsky; Natalia V Oleynikova; Peter K Vlasov; Alexei V Finkelstein; Mikhail A Roytberg
From analysis of protein structural alignments toward a novel approach to align protein sequences.
Proteins 2004;54(3):569-82.
2003: Shamil Sunyaev; Fyodor A Kondrashov; Peer Bork; Vasily Ramensky
Impact of selection, mutation rate and genetic drift on human genetic variation.
Human molecular genetics 2003;12(24):3325-30.
2003: Steffen Schmidt; Shamil Sunyaev; Peer Bork; Thomas Dandekar
Metabolites: a helping hand for pathway evolution?
Trends in biochemical sciences 2003;28(6):336-41.
2003: Shamil Sunyaev; Adam J Liska; Alexander Golod; Andrej Shevchenko; Andrej Shevchenko
MultiTag: multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry.
Analytical chemistry 2003;75(6):1307-15.
2003: Alexander Stark; Shamil Sunyaev; Robert B Russell
A model for statistical significance of local similarities in structure.
Journal of molecular biology 2003;326(5):1307-16.
2003: Evgenia Kriventseva; Ina Koch; Rolf Apweiler; Martin Vingron; Peer Bork; Mikhail S Gelfand; Shamil Sunyaev
Increase of functional diversity by alternative splicing.
Trends in genetics : TIG 2003;19(3):124-8.
2003: Andrej Shevchenko; Shamil Sunyaev; Adam J Liska; Peer Bork; Andrej Shevchenko
Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes.
Methods in molecular biology (Clifton, N.J.) 2003;211():221-34.
2002: Alexey S Kondrashov; Shamil Sunyaev; Fyodor A Kondrashov
Dobzhansky-Muller incompatibilities in protein evolution.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(23):14878-83.
2002: Vasily Ramensky; Peer Bork; Shamil Sunyaev
Human non-synonymous SNPs: server and survey.
Nucleic acids research 2002;30(17):3894-900.
2001: Andrej Shevchenko; Shamil Sunyaev; Alexander Loboda; A Shevchenko; Peer Bork; Werner Ens; Kenneth G Standing
Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching.
Analytical chemistry 2001;73(9):1917-26.
2001: Shamil Sunyaev; Vasily Ramensky; I Koch; warren lathe; Alexey S Kondrashov; Peer Bork
Prediction of deleterious human alleles.
Human molecular genetics 2001;10(6):591-7.
2001: Shamil Sunyaev; warren lathe; Peer Bork
Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms.
Current opinion in structural biology 2001;11(1):125-30.
2000: Shamil Sunyaev; warren lathe; Vasily Ramensky; Peer Bork
SNP frequencies in human genes an excess of rare alleles and differing modes of selection.
Trends in genetics : TIG 2000;16(8):335-7.
2000: Shamil Sunyaev; Vasily Ramensky; Peer Bork
Towards a structural basis of human non-synonymous single nucleotide polymorphisms.
Trends in genetics : TIG 2000;16(5):198-200.
2000: Shamil Sunyaev; J Hanke; David Brett; Atakan Aydin; I Zastrow; warren lathe; Peer Bork; Jens Reich
Individual variation in protein-coding sequences of human genome.
Advances in protein chemistry 2000;54():409-37.
1999: Shamil Sunyaev; J Hanke; Atakan Aydin; U Wirkner; I Zastrow; Jens Reich; Peer Bork
Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes.
Journal of molecular medicine (Berlin, Germany) 1999;77(11):754-60.
1999: Shamil Sunyaev; Frank Eisenhaber; I V Rodchenkov; Birgit Eisenhaber; V G Tumanyan; E N Kuznetsov
PSIC: profile extraction from sequence alignments with position-specific counts of independent observations.
Protein engineering 1999;12(5):387-94.
1998: M Huynen; Tobias Doerks; Frank Eisenhaber; C Orengo; Shamil Sunyaev; Y Yuan; P Bork
Homology-based fold predictions for Mycoplasma genitalium proteins.
Journal of molecular biology 1998;280(3):323-6.
1998: Shamil Sunyaev; Frank Eisenhaber; P Argos; E N Kuznetsov; V G Tumanyan
Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types?
Proteins 1998;31(3):225-46.