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Sunyaev Lab: Publications

Original Articles:

  1. 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.
  2. Gorlov IP, Gorlova OY, Sunyaev SR, Spitz MR, Amos CI. Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms. Am J Hum Genet (2008) 82(1):100-12.
  3. Ballif BA, Carey GR, Sunyaev SR, Gygi SP. Large-scale identification and evolution indexing of tyrosine phosphorylation sites from murine brain. J Proteome Res (2008) 7(1):311-8.
  4. Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S. Analysis of sequence conservation at nucleotide resolution. PLoS Comput Biol (2007) 3(12):e254.
  5. Spirin V, Schmidt S, Pertsemlidis A, Cooper RS, Cohen JC, Sunyaev SR. Common Single-Nucleotide Polymorphisms Act in Concert to Affect Plasma Levels of High-Density Lipoprotein Cholesterol. Am J Hum Genet (2007) 81(6):1298-1303.
  6. 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(16):2043-7.
  7. Asthana S, Noble WS, Kryukov G, Grant CE, Sunyaev S, Stamatoyannopoulos JA. Widely distributed noncoding purifying selection in the human genome. Proc Natl Acad Sci USA (2007) 104(30):12410-5.
  8. 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. [PDF]
  9. 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(14):2318-29.
  10. 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. Am J Hum Genet (2007) 80(4):779-91.
  11. Kryukov GV, Pennacchio LA, Sunyaev SR. Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet (2007) 80(4):727-39.
  12. Jordan IK, Kondrashov FA, Adzhubei IA, Wolf YI, Koonin EV, Kondrashov AS, Sunyaev S. Protein evolution: Causes of trends in amino-acid gain and loss (Reply). Nature (2006) 442(7105):E12.
  13. 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(16):4118-22.
  14. Keightly PD, Kryukov GV, Sunyaev S, Halligan DL, Gaffney DJ. Evolutionary constraints in conserved nongenic sequences of mammals. Genome Research (2005) 15(10):1373-8.
  15. Kryukov GV, Schmidt S, Sunyaev S. Small Fitness Effect of Mutations in Highly Conserved Non-coding Regions. Hum Mol Genet (2005) 14(15):2221-9.
  16. Asthana S, Schmidt S, Sunyaev S. A limited role for long-term balancing selection. Trends Genet (2005) 21(1):30-32.
  17. Jordan IK, 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(7026):633-638.
  18. Liska AJ, Popov AV, Sunyaev S, Coughlin P, Habermann B, Shevchenko A, Bork P, Karsenti E, Shevchenko A. Homology-based functional proteomics by tandem mass spectrometry: application to the Xenopus microtubule-associate proteome. Proteomics (2004) 4(9):2707-2721.
  19. Ogurtsov A, Sunyaev S, Kondrashov A. Indel-based evolutionary distance and mouse-human divergence. Genome Res (2004) 14(8):1610-1616.
  20. 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(6991):558-562.
  21. 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.
  22. Sunyaev SR, Bogopolsky GA, Oleynikova NV, Vlasov PK, Finkelstein AV, Roytberg MA. From analysis of protein structural alignments towards a novel approach to align protein sequences. Proteins (2004) 54:569-582.
  23. 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.
  24. Schmidt S, Sunyaev S, Bork P, Dandekar T. Metabolites: A helping hand for pathway evolution? Trends Biochem Sci (2003) 28:336-341.
  25. Stark A, Sunyaev S, Russell RB. A model for statistical significance of local similarities in structure. J Mol Biol (2003) 326:1307-1316.
  26. Sunyaev S, Liska A, 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) 75:1307-1315.
  27. Kriventseva EV, Koch I, Apweiler R, Vingron M, Bork P, Gelfand MS, Sunyaev S. Increase of functional diversity by alternative splicing. Trends Genet (2003) 19:124-128.
  28. Eisenhaber F, Sunyaev S, Tumanyan V, Kuznetsov E. Measuring Generality of Knowledge-Based Potentials Extracted from Protein Structure Sets. In Frontiers in Computational Genomics, 2003, Caister Academic Press, Wynmondham, UK, pp. 57-87.
  29. Kondrashov AS, Sunyaev S, Kondrashov FA. Dobzhansky-Muller incompatibilities in protein evolution. Proc Natl Acad Sci USA (2002) 99:14878-14883.
  30. 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.
  31. Ramensky V, Bork P, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res (2002) 30:3894-3900.