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1

Proportionally more deleterious genetic variation in European than in African populations

Lohmueller, Kirk E., Indap, Amit R., Schmidt, Steffen, Boyko, Adam R., Hernandez, Ryan D., Hubisz, Melissa J., Sninsky, John J., White, Thomas J., Sunyaev, Shamil R., Nielsen, Rasmus

Journal:

Year:

2008

Language:

english

File:

PDF, 302 KB

english, 2008

2

A method and server for predicting damaging missense mutations

Adzhubei, Ivan A, Schmidt, Steffen, Peshkin, Leonid, Ramensky, Vasily E, Gerasimova, Anna, Bork, Peer, Kondrashov, Alexey S, Sunyaev, Shamil R

Journal:

Year:

2010

Language:

english

File:

PDF, 244 KB

english, 2010

3

Metabolites: a helping hand for pathway evolution?

Steffen Schmidt, Shamil Sunyaev, Peer Bork, Thomas Dandekar

Journal:

Trends in Biochemical Sciences

Year:

2003

Language:

english

File:

PDF, 853 KB

english, 2003

4

Sequencing studies in human genetics: design and interpretation

Goldstein, David B., Allen, Andrew, Keebler, Jonathan, Margulies, Elliott H., Petrou, Steven, Petrovski, Slavé, Sunyaev, Shamil

Journal:

Nature Reviews Genetics

Year:

2013

Language:

english

File:

PDF, 610 KB

english, 2013

5

Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair

Polak, Paz, Lawrence, Michael S, Haugen, Eric, Stoletzki, Nina, Stojanov, Petar, Thurman, Robert E, Garraway, Levi A, Mirkin, Sergei, Getz, Gad, Stamatoyannopoulos, John A, Sunyaev, Shamil R

Journal:

Nature Biotechnology

Year:

2013

Language:

english

File:

PDF, 541 KB

english, 2013

6

Quantification of frequency-dependent genetic architectures in 25 UK Biobank traits reveals action of negative selection

Schoech, Armin P., Jordan, Daniel M., Loh, Po-Ru, Gazal, Steven, O’Connor, Luke J., Balick, Daniel J., Palamara, Pier F., Finucane, Hilary K., Sunyaev, Shamil R., Price, Alkes L.

Journal:

Nature Communications

Year:

2019

Language:

english

File:

PDF, 807 KB

english, 2019

7

Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types?

Shamil R. Sunyaev, Frank Eisenhaber, Patrick Argos, Eugene N. Kuznetsov, Vladimir G. Tumanyan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1998

Language:

english

File:

PDF, 421 KB

english, 1998

8

Protein identification pipeline for the homology-driven proteomics

Magno Junqueira, Victor Spirin, Tiago Santana Balbuena, Henrik Thomas, Ivan Adzhubei, Shamil Sunyaev, Andrej Shevchenko

Journal:

Journal of Proteomics

Year:

2008

Language:

english

File:

PDF, 1.23 MB

english, 2008

9

Homology-based functional proteomics by mass spectrometry: Application to the Xenopus microtubule-associated proteome

Adam J. Liska, Andrei V. Popov, Shamil Sunyaev, Peg Coughlin, Bianca Habermann, Anna Shevchenko, Peer Bork, Eric Karsenti, Andrej Shevchenko

Journal:

Year:

2004

Language:

english

File:

PDF, 203 KB

english, 2004

10

Error-tolerant EST database searches by tandem mass spectrometry and multiTag software

Adam J. Liska, Shamil Sunyaev, Ignat N. Shilov, Dan A. Schaeffer, Andrej Shevchenko

Journal:

Year:

2005

Language:

english

File:

PDF, 90 KB

english, 2005

11

Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing

Patrice Waridel, Ari Frank, Henrik Thomas, Vineeth Surendranath, Shamil Sunyaev, Pavel Pevzner, Andrej Shevchenko

Journal:

Year:

2007

Language:

english

File:

PDF, 578 KB

english, 2007

12

From analysis of protein structural alignments toward a novel approach to align protein sequences

Shamil R. Sunyaev, Gennady A. Bogopolsky, Natalia V. Oleynikova, Peter K. Vlasov, Alexei V. Finkelstein, Mikhail A. Roytberg

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 756 KB

english, 2004

13

Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes

Shamil Sunyaev, Jens Hanke, Atakan Aydin, Ute Wirkner, Inga Zastrow, Jens Reich, Peer Bork

Journal:

Journal of Molecular Medicine

Year:

1999

Language:

english

File:

PDF, 87 KB

english, 1999

14

SNP2RFLP: a computational tool to facilitate genetic mapping using benchtop analysis of SNPs

Wesley A. Beckstead, Bryan C. Bjork, Rolf W. Stottmann, Shamil Sunyaev, David R. Beier

Journal:

Mammalian Genome

Year:

2008

Language:

english

File:

PDF, 190 KB

english, 2008

15

Positive selection at sites of multiple amino acid replacements since rat–mouse divergence

Bazykin, Georgii A., Kondrashov, Fyodor A., Ogurtsov, Aleksey Y., Sunyaev, Shamil, Kondrashov, Alexey S.

Journal:

Year:

2004

Language:

english

File:

PDF, 148 KB

english, 2004

16

A universal trend of amino acid gain and loss in protein evolution

Jordan, I. King, Kondrashov, Fyodor A., Adzhubei, Ivan A., Wolf, Yuri I., Koonin, Eugene V., Kondrashov, Alexey S., Sunyaev, Shamil

Journal:

Year:

2005

Language:

english

File:

PDF, 242 KB

english, 2005

17

Corrigendum: A universal trend of amino acid gain and loss in protein evolution

Jordan, I. King, Kondrashov, Fyodor A., Adzhubei, Ivan A., Wolf, Yuri I., Koonin, Eugene V., Kondrashov, Alexey S., Sunyaev, Shamil

Journal:

Year:

2005

Language:

english

File:

PDF, 56 KB

english, 2005

18

Human mutation rate associated with DNA replication timing

Stamatoyannopoulos, John A, Adzhubei, Ivan, Thurman, Robert E, Kryukov, Gregory V, Mirkin, Sergei M, Sunyaev, Shamil R

Journal:

Nature Genetics

Year:

2009

Language:

english

File:

PDF, 205 KB

english, 2009

19

Large-Scale Identification and Evolution Indexing of Tyrosine Phosphorylation Sites from Murine Brain

Ballif, Bryan A., Carey, G. Richard, Sunyaev, Shamil R., Gygi, Steven P.

Journal:

Journal of Proteome Research

Year:

2008

Language:

english

File:

PDF, 1.22 MB

english, 2008

20

Pooled Association Tests for Rare Variants in Exon-Resequencing Studies

Alkes L. Price, Gregory V. Kryukov, Paul I.W. de Bakker, Shaun M. Purcell, Jeff Staples, Lee-Jen Wei, Shamil R. Sunyaev

Journal:

The American Journal of Human Genetics

Year:

2010

Language:

english

File:

PDF, 232 KB

english, 2010

21

Pooled Association Tests for Rare Variants in Exon-Resequencing Studies

Alkes L. Price, Gregory V. Kryukov, Paul I.W. de Bakker, Shaun M. Purcell, Jeff Staples, Lee-Jen Wei, Shamil R. Sunyaev

Journal:

The American Journal of Human Genetics

Year:

2010

Language:

english

File:

PDF, 26 KB

english, 2010

22

Development and Validation of a Computational Method for Assessment of Missense Variants in Hypertrophic Cardiomyopathy

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 R. Sunyaev

Journal:

The American Journal of Human Genetics

Year:

2011

Language:

english

File:

PDF, 509 KB

english, 2011

23

Human allelic variation: perspective from protein function, structure, and evolution

Daniel M Jordan, Vasily E Ramensky, Shamil R Sunyaev

Journal:

Current Opinion in Structural Biology

Year:

2010

Language:

english

File:

PDF, 513 KB

english, 2010

24

A limited role for balancing selection

Saurabh Asthana, Steffen Schmidt, Shamil Sunyaev

Journal:

Trends in Genetics

Year:

2005

Language:

english

File:

PDF, 79 KB

english, 2005

25

Towards a structural basis of human non-synonymous single nucleotide polymorphisms

Shamil Sunyaev, Vasily Ramensky, Peer Bork

Journal:

Trends in Genetics

Year:

2000

Language:

english

File:

PDF, 284 KB

english, 2000

26

SNP frequencies in human genes: an excess of rare alleles and differing modes of selection

Shamil R. Sunyaev, Warren C. Lathe III, Vasily E. Ramensky, Peer Bork

Journal:

Trends in Genetics

Year:

2000

Language:

english

File:

PDF, 218 KB

english, 2000

27

Increase of functional diversity by alternative splicing

Evgenia V. Kriventseva, Ina Koch, Rolf Apweiler, Martin Vingron, Peer Bork, Mikhail S. Gelfand, Shamil Sunyaev

Journal:

Trends in Genetics

Year:

2003

Language:

english

File:

PDF, 494 KB

english, 2003

28

Integration of genome data and protein structures: prediction of protein folds, protein interactions and ‘molecular phenotypes’ of single nucleotide polymorphisms

Shamil Sunyaev, Warren Lathe, Peer Bork

Journal:

Current Opinion in Structural Biology

Year:

2001

Language:

english

File:

PDF, 156 KB

english, 2001

29

Homology-based fold predictions for Mycoplasma genitalium proteins

Martijn Huynen, Tobias Doerks, Frank Eisenhaber, Christine Orengo, Shamil Sunyaev, Yanping Yuan, Peer Bork

Journal:

Journal of Molecular Biology

Year:

1998

Language:

english

File:

PDF, 169 KB

english, 1998

30

Shifting Paradigm of Association Studies: Value of Rare Single-Nucleotide Polymorphisms

Ivan P. Gorlov, Olga Y. Gorlova, Shamil R. Sunyaev, Margaret R. Spitz, Christopher I. Amos

Journal:

The American Journal of Human Genetics

Year:

2008

Language:

english

File:

PDF, 977 KB

english, 2008

31

A Model for Statistical Significance of Local Similarities in Structure

Alexander Stark, Shamil Sunyaev, Robert B. Russell

Journal:

Journal of Molecular Biology

Year:

2003

Language:

english

File:

PDF, 1.04 MB

english, 2003

32

Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies

Gregory V. Kryukov, Len A. Pennacchio, Shamil R. Sunyaev

Journal:

The American Journal of Human Genetics

Year:

2007

Language:

english

File:

PDF, 1.71 MB

english, 2007

33

Common Single-Nucleotide Polymorphisms Act in Concert to Affect Plasma Levels of High-Density Lipoprotein Cholesterol

Victor Spirin, Steffen Schmidt, Alexander Pertsemlidis, Richard S. Cooper, Jonathan C. Cohen, Shamil R. Sunyaev

Journal:

The American Journal of Human Genetics

Year:

2007

Language:

english

File:

PDF, 837 KB

english, 2007

34

Differential Relationship of DNA Replication Timing to Different Forms of Human Mutation and Variation

Amnon Koren, Paz Polak, James Nemesh, Jacob J. Michaelson, Jonathan Sebat, Shamil R. Sunyaev, Steven A. McCarroll

Journal:

The American Journal of Human Genetics

Year:

2012

Language:

english

File:

PDF, 770 KB

english, 2012

35

Charting the Proteomes of Organisms with Unsequenced Genomes by MALDI-Quadrupole Time-of-Flight Mass Spectrometry and BLAST Homology Searching

Shevchenko, Andrej, Sunyaev, Shamil, Loboda, Alexander, Shevchenko, Anna, Bork, Peer, Ens, Werner, Standing, Kenneth G.

Journal:

Analytical Chemistry

Year:

2001

Language:

english

File:

PDF, 214 KB

english, 2001

36

Computational and statistical approaches to analyzing variants identified by exome sequencing

Nathan O Stitziel, Adam Kiezun, Shamil Sunyaev

Journal:

Year:

2011

Language:

english

File:

PDF, 213 KB

english, 2011

37

Genome-wide association study reveals class I MHC–restricted T cell–associated molecule gene (CRTAM) variants interact with vitamin D levels to affect asthma exacerbations

Du, Rose, Litonjua, Augusto A., Tantisira, Kelan G., Lasky-Su, Jessica, Sunyaev, Shamil R., Klanderman, Barbara J., Celedón, Juan C., Avila, Lydiana, Soto-Quiros, Manuel E., Weiss, Scott T.

Journal:

Journal of Allergy and Clinical Immunology

Year:

2012

Language:

english

File:

PDF, 561 KB

english, 2012

38

Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection

Schmidt, Steffen, Gerasimova, Anna, Kondrashov, Fyodor A., Adzuhbei, Ivan A., Kondrashov, Alexey S., Sunyaev, Shamil, Schierup, Mikkel H.

Journal:

Year:

2008

Language:

english

File:

PDF, 133 KB

english, 2008

39

Biocomputing enters its adolescence

Journal:

Year:

2005

Language:

english

File:

PDF, 51 KB

english, 2005

40

Evaluating empirical bounds on complex disease genetic architecture

Agarwala, Vineeta, Flannick, Jason, Sunyaev, Shamil, Altshuler, David

Journal:

Nature Genetics

Year:

2013

Language:

english

File:

PDF, 1.31 MB

english, 2013

41

Clinically Relevant Variants - Identifying, Collecting, Interpreting, and Disseminating: The 2013 Annual Scientific Meeting of the Human Genome Variation Society

Stanley, Christine M., Sunyaev, Shamil R., Greenblatt, Marc S., Oetting, William S.

Journal:

Year:

2014

Language:

english

File:

PDF, 154 KB

english, 2014

42

Systems biology and the analysis of genetic variation

Sunyaev, Shamil R, Roth, Frederick P

Journal:

Current Opinion in Genetics & Development

Year:

2013

Language:

english

File:

PDF, 127 KB

english, 2013

43

MultiTag: Multiple Error-Tolerant Sequence Tag Search for the Sequence-Similarity Identification of Proteins by Mass Spectrometry

Sunyaev, Shamil, Liska, Adam J., Golod, Alexander, Shevchenko, Anna, Shevchenko, Andrej

Journal:

Analytical Chemistry

Year:

2003

Language:

english

File:

PDF, 129 KB

english, 2003

44

Separating the Wheat from the Chaff: Unbiased Filtering of Background Tandem Mass Spectra Improves Protein Identification

Junqueira, Magno, Spirin, Victor, Santana Balbuena, Tiago, Waridel, Patrice, Surendranath, Vineeth, Kryukov, Grigoriy, Adzhubei, Ivan, Thomas, Henrik, Sunyaev, Shamil, Shevchenko, Andrej

Journal:

Journal of Proteome Research

Year:

2008

Language:

english

File:

PDF, 1.32 MB

english, 2008

45

No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans

Do, Ron, Balick, Daniel, Li, Heng, Adzhubei, Ivan, Sunyaev, Shamil, Reich, David

Journal:

Nature Genetics

Year:

2015

Language:

english

File:

PDF, 708 KB

english, 2015

46

Cell-of-origin chromatin organization shapes the mutational landscape of cancer

Polak, Paz, Karlić, Rosa, Koren, Amnon, Thurman, Robert, Sandstrom, Richard, Lawrence, Michael S., Reynolds, Alex, Rynes, Eric, Vlahoviček, Kristian, Stamatoyannopoulos, John A., Sunyaev, Shamil R.

Journal:

Year:

2015

Language:

english

File:

PDF, 6.55 MB

english, 2015

47

Identification of cis-suppression of human disease mutations by comparative genomics

Jordan, Daniel M., Frangakis, Stephan G., Golzio, Christelle, Cassa, Christopher A., Kurtzberg, Joanne, Davis, Erica E., Sunyaev, Shamil R., Katsanis, Nicholas

Journal:

Year:

2015

Language:

english

File:

PDF, 2.35 MB

english, 2015

48

Adaptive Mutations in the JC Virus Protein Capsid Are Associated with Progressive Multifocal Leukoencephalopathy (PML)

Sunyaev, Shamil R., Lugovskoy, Alexey, Simon, Kenneth, Gorelik, Leonid, Malik, Harmit S.

Journal:

Year:

2009

Language:

english

File:

PDF, 3.66 MB

english, 2009

49

Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome

Boyko, Adam R., Williamson, Scott H., Indap, Amit R., Degenhardt, Jeremiah D., Hernandez, Ryan D., Lohmueller, Kirk E., Adams, Mark D., Schmidt, Steffen, Sninsky, John J., Sunyaev, Shamil R., White, T

Journal:

Year:

2008

Language:

english

File:

PDF, 409 KB

english, 2008

50

Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence

Gokcumen, Omer, Zhu, Qihui, Mulder, Lubbertus C. F., Iskow, Rebecca C., Austermann, Christian, Scharer, Christopher D., Raj, Towfique, Boss, Jeremy M., Sunyaev, Shamil, Price, Alkes, Stranger, Barbara

Journal:

Year:

2013

Language:

english

File:

PDF, 1.53 MB

english, 2013