Selected Sunyaev Lab PublicationsSunyaev S, Kuznetsov E, Rodchenkov I, Tumanyan V. “Protein sequence-structure compatibility criteria in terms of statistical hypothesis testing.” Protein Eng 1997;10(6):635-646. PubMed Link
Sunyaev S, Eisenhaber F, Argos P, Kuznetsov EN, Tumanyan VG. “Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types?” Proteins 1998;31(3):225-246. PubMed Link
Huynen M, Doerks T, Eisenhaber F, Orengo C, Sunyaev S, Yuan Y, Bork P. “Homology-based fold predictions for Mycoplasma genitalium proteins.” J Mol Biol 1998;280(3):323-326. PubMed Link
Sunyaev S, Eisenhaber F, Rodchenkov IV, Eisenhaber B, Tumanyan VG, Kuznetsov EN. “PSIC: profile extraction from sequence alignments with position-specific counts of independent observations.” Protein Eng 1999;12(5):387-394. PubMed Link
Sunyaev S, Hanke J, Aydin A, Wirkner U, Zastrow I, Reich J, Bork P. “Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associate genes.” J Mol Med 1999;77(11) 754-760. PubMed Link
Sunyaev S, Ramensky V, Bork P. “Towards a structural basis of human non-synonymous single nucleotide polymorphisms.” Trends Genet 2000;16(5): 198-200. (Original report in the Genome Analysis section.) PubMed Link
Sunyaev S, Hanke J, Brett D, Aydin A, Zastrow I, Lathe III W, Bork P, Reich J. “Individual variation in protein-coding sequences of human genome.” Advances in Protein Chemistry. 2000;54:409-37. PubMed Link
Sunyaev S, Lathe III W, Ramensky V, Bork P. “SNP frequencies in human genes: an excess of rare alleles and differing modes of selection.” Trends Genet 2000;16(8): 335-337. (Original report in the Genome Analysis section.) PubMed Link
Shevchenko A, Sunyaev S, Loboda A, Shevchenko A, Bork P, Ens W, Standing K. “Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching” Anal Chem 2001;73(10):1917-1926. PubMed Link
Sunyaev S, Lathe III W, Bork P. “Integration of genome data and protein structures: Prediction of protein folds, protein interactions and “molecular phenotypes of SNPs” Curr Opin Struct Biol 2001;11(1):125-130. PubMed Link
Sunyaev S, Ramensky V, Koch I, Lathe III W, Kondrashov A, Bork P. "Prediction of Deleterious Alleles" Hum Mol Genet 2001;10(6): 591-597. PubMed Link
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 2002;211: 221-234. PubMed Link
Ramensky V, Bork P, Sunyaev S. "Human non-synonymous SNPs: server and survey" Nucleic Acids Res 2002;30:3894-3900. PubMed Link
Kondrashov A, Sunyaev S, Kondrashov F. Dobzhansky-Muller incompatibilites in preotein evolution. Proc Natl Acad Sci (2002) Nov 12; 99(23):14878-83. PubMed Link
Kriventseva E, Koch I, Apweiler R, Vingron M, Bork P, Gelfand M, Sunyaev* S. Increase of functional diversity by alternative splicing. Trends Genet 2003;19(3):124-128. (Original report in the Genome Analysis section.) PubMed Link
Stark A, Sunyaev S, Russel RB. A model for statistical significance of local similarities in structure. J Mol Biol 2003;326(5):1307-1316. PubMed Link
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. Analytical Chem 2003;75:1307-1315. PubMed Link
Schmidt S, Sunyaev S, Bork P, Dandekar T. Metabolites: a helping hand for pathway evolution? Trends Biochem Sci (2003) 28:336-341. PubMed Link
Sunyaev S, Kondrashov FA, Bork P, Ramensky V. Impact of selection, mutation rate and genetic drift on human genetic variation. Hum Mol Genet (2003) 12:3325-3330. PubMed Link
Sunyaev S, Bogopolsky G, Oleinikova N, Vlasov P, Finkelstein A, Roytberg M. From analysis of protein structural alignments towards a novel approach to align protein sequences. Proteins (2004) 54:569-582. PubMed Link
Habermann B, Oegema J, Sunyaev S, Shevchenko A. The power and the limitations of cross-species protein identification by mass spectrometry driven sequence similarity searches. Mol Cell Proteomics (2004) 3:238-249. PubMed Link
Ogurtsov A, Sunyaev S, Kondrashov A. Indel-based evolutionary distance and mouse-human divergence. Genome Research (2004) 14(8):1610-1616. PubMed Link
Liska A, Popov A, Sunyaev S, Shevchenko A, Habermann B, Bork P, Karsenti E and Shevchenko A. Homology-based proteomics by tandem mass spectrometry: Application to the Xenopus microtubule-associate proteome. Proteomics (2004) 4(9):2707-2721. PubMed Link
Bazykin GA, Kondrashov FA, Ogurtsov AY, Sunyaev S, Kondrashov AS. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature (2004) 429:558-562. PubMed Link
King Jordan I, Kondrashov FA, Adzhubei IA, Wolf YI, Koonin EV, Kondrashov* AS, Sunyaev* S.A universal trend of amino acid gain and loss in protein evolution. Nature (2005) 433: 633 - 638. PubMed Link
Asthana S, Schmidt S, Sunyaev* S.A limited role for long-term balancing selection. Trends in Genetics (2005) 21:30-32 (Original report in the Genome Analysis section.). PubMed Link
Kryukov GV, Schmidt S, Sunyaev* S. Small fitness effect of mutations in conserved non-coding regions. Human Molecular Genetics (2005) 14:2221-2229 PubMed Link
Liska AJ, Sunyaev S, Shilov IN, Schaeffer DA, Shevchenko A. Error-tolerant EST database searches by tandem mass spectrometry and multiTag software. Proteomics. (2005) 5:4118-4122. PubMed Link
Keightley PD, Kryukov GV, Sunyaev S, Halligan DL, Gaffney DJ. Evolutionary constraints in conserved nongenic sequences of mammals. Genome Research (2005) 15:1373-1378. PubMed Link
Kryukov GV, Pennacchio LA, Sunyaev SR. Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. American Journal of Human Genetics (2007) 80:727-39 PubMed Link
Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Martin J, Hebert S, Doelle H, Ersoy B, Kryukov G, Schmidt S, Yosef N, Ruppin E, Sharan R, Vaisse C, Sunyaev S, Dent R, Cohen J, McPherson R, Pennacchio LA. Medical sequencing at the extremes of human body mass. American Journal of Human Genetics (2007) 80:779-91 PubMed Link
Asthana S, Noble WS, Kryukov GV, Grant CE, Sunyaev S, Stamatoyannopoulos JA. Widely distributed non-coding purifying selection in the human genome. Proc. Natl. Acad. Sci. (2007) 104:12410-12415 Pubmed Link
Spirin V, Schmidt S, Pertsemlidis A, Cooper RS, Cohen JC, Sunyaev SR. Common SNPs act in concert to affect plasma levels of HDL-Cholesterol. American Journal of Human Genetics (2007) 81:1298-1303 Pubmed Link
Waridel P, Frank A, Thomas H, Surendranath V, Sunyaev S, Pevzner P, Shevchenko A. Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing. Proteomics (2007) 7: 2318-29 Pubmed Link
Ilyinskii PO, Gabai VL, Sunyaev SR, Thoidis G, Shneider AM. Toxicity of influenza A virus matrix protein 2 for mammalian cells is associated with its intrinsic proton-channeling activity. Cell Cycle (2007) 6: 2043-7 Pubmed Link
ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007 447(7146):799-816 Pubmed Link
Asthana S, Roytberg MA, Stamatoyannopoulos JA, Sunyaev SR. Analysis of sequence conservation at single-nucleotide resolution. PLoS Computational Biology (2007) 3: e254 Pubmed Link
Baliff BA, Carey RG, Sunyaev SR, Gygi SP. Large-scale identification and evolution indexing of tyrosine phosphorylation sites from murine brain. J. Proteome Res. (2007) 7: 311-318 Pubmed Link
Gorlov I, Gorlova O, Sunyaev S, Amos C. Shifting Paradigm of AssociationStudies: Value of Rare Single-Nucleotide Polymorphisms. American Journal of Human Genetics (2008) 82: 100-112 Pubmed Link
Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante CD. Proportionally more deleterious genetic variation in European than in African populations. Nature (2008) 451(7181):994-7 Pubmed Link
Reviews, Chapters and Editorials:
Eisenhaber F, Sunyaev S, Tumanyan V, Kuznetsov E. Measuring Generality of Knowledge- Based Potentials Extracted from Protein Structure Sets. In: Galperin MY, Koonin EV, editors. Frontiers in Computational Genomics. Wynmondham, UK: Caister Academic Press; 2003. p. 57-87
Asthana S, Sunyaev S. Understanding the functional importance of human single nucleotide polymorphism. In Eisenhaber F, editor. Discovering Biomolecular Mechanisms with Computational Biology. New York: Springer Science + Business Media; 2006; Georgetown, TX: Landes Bioscience. p. 126-30
Dimmic MW, Sunyaev S, Bustamante CD. “Inferring SNP function using evolutionary, structural, and computational methods” (2005) in Pac Symp Biocomput. 2005:382-4. PubMed Link
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