Shamil Sunyaev

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Protein identification pipeline for the homology-driven proteomics
    Magno Junqueira
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    J Proteomics 71:346-56. 2008
  2. pmc Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency
    Adam Kiezun
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
    PLoS Genet 9:e1003301. 2013
  3. pmc Inferring causality and functional significance of human coding DNA variants
    Shamil R Sunyaev
    Genetics Division, Brigham and Women s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Hum Mol Genet 21:R10-7. 2012
  4. pmc Biocomputing enters its adolescence
    Shamil Sunyaev
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Genome Biol 6:325. 2005
  5. ncbi request reprint Impact of selection, mutation rate and genetic drift on human genetic variation
    Shamil Sunyaev
    Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Hum Mol Genet 12:3325-30. 2003
  6. ncbi request reprint MultiTag: multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry
    Shamil Sunyaev
    European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Anal Chem 75:1307-15. 2003
  7. pmc Computational and statistical approaches to analyzing variants identified by exome sequencing
    Nathan O Stitziel
    Division of Cardiovascular Medicine, Brigham and Women s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
    Genome Biol 12:227. 2011
  8. pmc Hypermutable non-synonymous sites are under stronger negative selection
    Steffen Schmidt
    Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 4:e1000281. 2008
  9. pmc Triplet repeat length bias and variation in the human transcriptome
    Michael Molla
    Department of Biomedical Engineering and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 106:17095-100. 2009
  10. pmc Assigning spectrum-specific P-values to protein identifications by mass spectrometry
    Victor Spirin
    Division of Genetics, Brigham and Women s Hospital, Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Bioinformatics 27:1128-34. 2011

Detail Information

Publications30

  1. pmc Protein identification pipeline for the homology-driven proteomics
    Magno Junqueira
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    J Proteomics 71:346-56. 2008
    ..All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download...
  2. pmc Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency
    Adam Kiezun
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
    PLoS Genet 9:e1003301. 2013
    ..The results confirm the abundance of slightly deleterious coding variation in humans...
  3. pmc Inferring causality and functional significance of human coding DNA variants
    Shamil R Sunyaev
    Genetics Division, Brigham and Women s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Hum Mol Genet 21:R10-7. 2012
    ..In spite of many successes of recent studies, functional characterization of human allelic variants remains problematic...
  4. pmc Biocomputing enters its adolescence
    Shamil Sunyaev
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Genome Biol 6:325. 2005
    ..A report on the tenth Pacific Symposium on Biocomputing, Big Island, Hawaii, USA, 4-8 January 2005...
  5. ncbi request reprint Impact of selection, mutation rate and genetic drift on human genetic variation
    Shamil Sunyaev
    Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Hum Mol Genet 12:3325-30. 2003
    ..Evolutionary and medical implications of the impact of selection on human polymorphisms are discussed...
  6. ncbi request reprint MultiTag: multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry
    Shamil Sunyaev
    European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Anal Chem 75:1307-15. 2003
    ..This feature facilitates the identification of low abundance proteins, since noisy and low-intensity tandem mass spectra can be utilized...
  7. pmc Computational and statistical approaches to analyzing variants identified by exome sequencing
    Nathan O Stitziel
    Division of Cardiovascular Medicine, Brigham and Women s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
    Genome Biol 12:227. 2011
    ..New sequencing technology has enabled the identification of thousands of single nucleotide polymorphisms in the exome, and many computational and statistical approaches to identify disease-association signals have emerged...
  8. pmc Hypermutable non-synonymous sites are under stronger negative selection
    Steffen Schmidt
    Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 4:e1000281. 2008
    ..Thus, sites with different mutation rates are not necessarily selectively equivalent. This suggests that the mutation rate may complement sequence conservation as a characteristic predictive of functional importance of nucleotide sites...
  9. pmc Triplet repeat length bias and variation in the human transcriptome
    Michael Molla
    Department of Biomedical Engineering and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 106:17095-100. 2009
    ....
  10. pmc Assigning spectrum-specific P-values to protein identifications by mass spectrometry
    Victor Spirin
    Division of Genetics, Brigham and Women s Hospital, Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Bioinformatics 27:1128-34. 2011
    ....
  11. pmc Analysis of sequence conservation at nucleotide resolution
    Saurabh Asthana
    Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Comput Biol 3:e254. 2007
    ..A small subset of these fragmented positions may be identified with high confidence...
  12. doi request reprint Evaluating empirical bounds on complex disease genetic architecture
    Vineeta Agarwala
    1 Harvard MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 2 Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 3 Program in Biophysics, Graduate School of Arts and Sciences, Harvard University, Cambridge, Massachusetts, USA 4
    Nat Genet 45:1418-27. 2013
    ....
  13. pmc Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence
    Omer Gokcumen
    Department of Pathology, Brigham and Women s Hospital, Boston, Massachusetts, United States of America
    PLoS Genet 9:e1003404. 2013
    ..We postulate that the variation observed at this locus predates Human-Neandertal divergence and is evolving under balancing selection, especially among European populations...
  14. pmc Human non-synonymous SNPs: server and survey
    Vasily Ramensky
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 30:3894-900. 2002
    ..The strongest selective pressure was detected for proteins involved in transcription regulation...
  15. ncbi request reprint Small fitness effect of mutations in highly conserved non-coding regions
    Gregory V Kryukov
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Hum Mol Genet 14:2221-9. 2005
    ..Our results suggest that most individual mutations in conserved non-coding regions are only slightly deleterious but are numerous and may have a significant cumulative impact on fitness...
  16. pmc Rare, low-frequency, and common variants in the protein-coding sequence of biological candidate genes from GWASs contribute to risk of rheumatoid arthritis
    Dorothée Diogo
    Division of Rheumatology, Immunology, and Allergy, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Am J Hum Genet 92:15-27. 2013
    ..Further, we have demonstrated that very large sample sizes will be required for comprehensively identifying the independent alleles contributing to the missing heritability of RA...
  17. pmc Patterns and rates of exonic de novo mutations in autism spectrum disorders
    Benjamin M Neale
    Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
    Nature 485:242-5. 2012
    ..Despite the challenge posed by such models, results from de novo events and a large parallel case-control study provide strong evidence in favour of CHD8 and KATNAL2 as genuine autism risk factors...
  18. pmc Widely distributed noncoding purifying selection in the human genome
    Saurabh Asthana
    Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 104:12410-5. 2007
    ..This finding suggests the existence of a large complement of human noncoding variants that may impact gene expression and phenotypic traits, the majority of which will escape detection with current approaches to genome analysis...
  19. ncbi request reprint A model for statistical significance of local similarities in structure
    Alexander Stark
    EMBL, Structural and Computational Biology Programme, Meyerhofstrasse 1, 69117, Heidelberg, Germany
    J Mol Biol 326:1307-16. 2003
    ..The approach is highly complementary to fold comparison for providing functional clues for new structures, and is key for the detection of recurrences of any new pattern...
  20. ncbi request reprint Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes
    Anna Shevchenko
    European Molecular Biology Laboratory, Heidelberg, Germany
    Methods Mol Biol 211:221-34. 2003
  21. ncbi request reprint The power and the limitations of cross-species protein identification by mass spectrometry-driven sequence similarity searches
    Bianca Habermann
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Mol Cell Proteomics 3:238-49. 2004
    ..We also estimated phylogenetic distances between organisms under study and related reference organisms with completely sequenced genomes that allow substantial coverage of unknown proteomes...
  22. ncbi request reprint A universal trend of amino acid gain and loss in protein evolution
    I King Jordan
    National Center for Biotechnology Information, NIH, Bethesda, Maryland 20894, USA
    Nature 433:633-8. 2005
    ..Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day...
  23. pmc Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification
    Magno Junqueira
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    J Proteome Res 7:3382-95. 2008
    ....
  24. ncbi request reprint Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing
    Patrice Waridel
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Proteomics 7:2318-29. 2007
    ..This approach enabled a completely automated identification of novel proteins that were, otherwise, missed by conventional database searches...
  25. ncbi request reprint Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome
    Adam J Liska
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Proteomics 4:2707-21. 2004
    ..These findings were made possible due to the application of sequence-similarity methods, which extended mass spectrometric protein identification capabilities by 2-fold compared to conventional methods...
  26. ncbi request reprint Increase of functional diversity by alternative splicing
    Evgenia V Kriventseva
    European Bioinformatics Institute EMBL EBI, Hinxton Wellcome Trust Genome Campus, Hinxton, Cambridge, UK CB10 1SD
    Trends Genet 19:124-8. 2003
    ..Thus, it seems that positive selection has had a major role in the evolution of alternative splicing...
  27. ncbi request reprint Error-tolerant EST database searches by tandem mass spectrometry and multiTag software
    Adam J Liska
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Proteomics 5:4118-22. 2005
    ..The MultiTag outperformed conventional database searching software that only utilizes stringent matching of tandem mass spectra to nucleotide sequences of ESTs...
  28. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  29. pmc Dobzhansky-Muller incompatibilities in protein evolution
    Alexey S Kondrashov
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Proc Natl Acad Sci U S A 99:14878-83. 2002
    ..Data on protein structures and on cooccurrence of amino acids at different sites of multiple orthologous proteins often make it possible to provisionally identify the substitution that compensates a particular CPD...

Research Grants14

  1. New Methods and Enhanced Software for Predicting Functional SNPs
    Shamil Sunyaev; Fiscal Year: 2010
    ..This new version of PolyPhen will be incorporated into the Clinical Research Chart developed by I2b2 National Center of Biomedical Computing and integrated with VISTA visualization tools. ..
  2. Statistical Methods for the Design and Interpretation of Deep Resequencing Studie
    Shamil Sunyaev; Fiscal Year: 2010
    ....
  3. Approaches to Multiorganismal Comparative Proteomics
    Shamil Sunyaev; Fiscal Year: 2006
    ....
  4. Statistical Methods for the Design and Interpretation of Deep Resequencing Studie
    Shamil Sunyaev; Fiscal Year: 2009
    ....
  5. New Methods and Enhanced Software for Predicting Functional SNPs
    Shamil Sunyaev; Fiscal Year: 2009
    ..This new version of PolyPhen will be incorporated into the Clinical Research Chart developed by I2b2 National Center of Biomedical Computing and integrated with VISTA visualization tools. ..
  6. Approaches to Multiorganismal Comparative Proteomics
    Shamil Sunyaev; Fiscal Year: 2009
    ....
  7. New Methods and Enhanced Software for Predicting Functional SNPs
    Shamil Sunyaev; Fiscal Year: 2007
    ..This new version of PolyPhen will be incorporated into the Clinical Research Chart developed by I2b2 National Center of Biomedical Computing and integrated with VISTA visualization tools. ..
  8. Approaches to Multiorganismal Comparative Proteomics
    Shamil Sunyaev; Fiscal Year: 2007
    ....
  9. Statistical Methods for the Design and Interpretation of Deep Resequencing Studie
    Shamil Sunyaev; Fiscal Year: 2010
    ..abstract_text> ..