Ruslan Sadreyev

Molbio Department


Director of Bioinformatics


Email

Publications
    2017
  1. Walsh RM, Shen EY, Bagot RC, Anselmo A, Jiang Y, Javidfar B, Wojtkiewicz GJ, Cloutier J, Chen JW, Sadreyev R, Nestler EJ, Akbarian S, Hochedlinger K. Phf8 loss confers resistance to depression-like and anxiety-like behaviors in mice. Nat Commun 2017 May 09; 8:15142.

  2. Pym E, Sasidharan N, Thompson-Peer KL, Simon DJ, Anselmo A, Sadreyev R, Hall Q, Nurrish S, Kaplan JM. Shank is a dose-dependent regulator of Cav1 calcium current and CREB target expression. Elife 2017 May 06; 6

  3. Hulsmans M, Clauss S, Xiao L, Aguirre AD, King KR, Hanley A, Hucker WJ, Wülfers EM, Seemann G, Courties G, Iwamoto Y, Sun Y, Savol AJ, Sager HB, Lavine KJ, Fishbein GA, Capen DE, Da Silva N, Miquerol L, Wakimoto H, Seidman CE, Sadreyev RI, Naxerova K, Mitchell RN, Brown D, Libby P, Weissleder R, Swirski FK, Kohl P, Vinegoni C, Milan DJ, Ellinor PT, Nahrendorf M. Macrophages Facilitate Electrical Conduction in the Heart. Cell 2017 Apr 20; 169(3):510-522.e20.

  4. Mueller B, Mieczkowski J, Kundu S, Wang P, Sadreyev R, Tolstorukov MY, Kingston RE. Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction. Genes Dev. 2017 Mar 29.

  5. Choi J, Clement K, Huebner AJ, Webster J, Rose CM, Brumbaugh J, Walsh RM, Lee S, Savol A, Etchegaray JP, Gu H, Boyle P, Elling U, Mostoslavsky R, Sadreyev R, Park PJ, Gygi SP, Meissner A, Hochedlinger K. DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells. Cell Stem Cell 2017 Mar 29.

  6. Lau MS, Schwartz MG, Kundu S, Savol AJ, Wang PI, Marr SK, Grau DJ, Schorderet P, Sadreyev RI, Tabin CJ, Kingston RE. Mutation of a nucleosome compaction region disrupts Polycomb-mediated axial patterning. Science 2017 Mar 10; 355(6329):1081-1084.

  7. Kundu S, Ji F, Sunwoo H, Jain G, Lee JT, Sadreyev RI, Dekker J, Kingston RE. Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. Mol. Cell 2017 Feb 02; 65(3):432-446.e5.

  8. Strle K, Sulka KB, Pianta A, Crowley JT, Arvikar SL, Anselmo A, Sadreyev R, Steere AC. TH17 Cytokine Responses in Lyme Disease Correlate with Borreliaburgdorferi Antibodies During Early Infection in Patients with Erythema Migrans and with Autoantibodies Late in the Illness in Patients with Antibiotic-Refractory Lyme Arthritis. Clin. Infect. Dis. 2017 Jan 11.

  9. Lehrbach NJ, Ji F, Sadreyev R. Next-Generation Sequencing for Identification of EMS-Induced Mutations in Caenorhabditis elegans. Curr Protoc Mol Biol 2017 Jan 05; 117:7.29.1-7.29.12.

  10. Fusco DN, Pratt H, Kandilas S, Cheon SS, Lin W, Cronkite DA, Basavappa M, Jeffrey KL, Anselmo A, Sadreyev R, Yapp C, Shi X, O'Sullivan JF, Gerszten RE, Tomaru T, Yoshino S, Satoh T, Chung RT. HELZ2 Is an IFN Effector Mediating Suppression of Dengue Virus. Front Microbiol 2017; 8:240.

  11. 2016
  12. Gregory KE, Samuel BS, Houghteling P, Shan G, Ausubel FM, Sadreyev RI, Walker WA. Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants. Microbiome 2016 Dec 30; 4(1):68.

  13. Joh RI, Khanduja JS, Calvo IA, Mistry M, Palmieri CM, Savol AJ, Ho Sui SJ, Sadreyev RI, Aryee MJ, Motamedi M. Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs. Mol. Cell 2016 Dec 15; 64(6):1088-1101.

  14. McEwan DL, Feinbaum RL, Stroustrup N, Haas W, Conery AL, Anselmo A, Sadreyev R, Ausubel FM. Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway. BMC Biol. 2016 Dec 07; 14(1):105.

  15. Moore JC, Tang Q, Yordán NT, Garcia EG, Lobbardi R, Ramakrishnan A, Marvin DL, Anselmo A, Sadreyev RI, Langenau DM. Single-cell imaging of normal and malignant cell engraftment into optically clear prkdc-null SCID zebrafish. J. Exp. Med. 2016 Nov 14; 213(12):2575-2589.

  16. Wein MN, Liang Y, Goransson O, Sundberg TB, Wang J, Williams EA, O'Meara MJ, Govea N, Beqo B, Nishimori S, Nagano K, Brooks DJ, Martins JS, Corbin B, Anselmo A, Sadreyev R, Wu JY, Sakamoto K, Foretz M, Xavier RJ, Baron R, Bouxsein ML, Gardella TJ, Divieti-Pajevic P, Gray NS, Kronenberg HM. SIKs control osteocyte responses to parathyroid hormone. Nat Commun 2016 Oct 19; 7:13176.

  17. Sykes DB, Kfoury YS, Mercier FE, Wawer MJ, Law JM, Haynes MK, Lewis TA, Schajnovitz A, Jain E, Lee D, Meyer H, Pierce KA, Tolliday NJ, Waller A, Ferrara SJ, Eheim AL, Stoeckigt D, Maxcy KL, Cobert JM, Bachand J, Szekely BA, Mukherjee S, Sklar LA, Kotz JD, Clish CB, Sadreyev RI, Clemons PA, Janzer A, Schreiber SL, Scadden DT. Inhibition of Dihydroorotate Dehydrogenase Overcomes Differentiation Blockade in Acute Myeloid Leukemia. Cell 2016 Sep 14.

  18. Moore JC, Mulligan TS, Torres Yordán N, Castranova D, Pham VN, Tang Q, Lobbardi R, Anselmo A, Liwski RS, Berman JN, Sadreyev RI, Weinstein BM, Langenau DM. T cell immune deficiency in zap70 mutant zebrafish. Mol. Cell. Biol. 2016 Sep 6.

  19. Sarkar A, Huebner AJ, Sulahian R, Anselmo A, Xu X, Flattery K, Desai N, Sebastian C, Yram MA, Arnold K, Rivera M, Mostoslavsky R, Bronson R, Bass AJ, Sadreyev R, Shivdasani RA, Hochedlinger K. Sox2 Suppresses Gastric Tumorigenesis in Mice. Cell Rep 2016 Aug 3.

  20. Ray MK, Wiskow O, King MJ, Ismail N, Ergun A, Wang Y, Plys AJ, Davis CP, Kathrein K, Sadreyev R, Borowsky ML, Eggan K, Zon L, Galloway JL, Kingston RE. CAT7 and cat7l long non-coding RNAs Tune Polycomb Repressive Complex 1 Function During Human and Zebrafish Development. J. Biol. Chem. 2016 Jul 12.

  21. Deaton AM, Mieczkowski J, Tolstorukov MY, Kundu S, Sadreyev RI, Jansen LE, Kingston RE. Enhancer regions show high histone H3.3 turnover that changes during differentiation. Elife 2016 Jun 15; 5

  22. Kugel S, Sebastián C, Fitamant J, Ross KN, Saha SK, Jain E, Gladden A, Arora KS, Kato Y, Rivera MN, Ramaswamy S, Sadreyev RI, Goren A, Deshpande V, Bardeesy N, Mostoslavsky R. SIRT6 Suppresses Pancreatic Cancer through Control of Lin28b. Cell 2016 May 11.

  23. Moore FE, Garcia EG, Lobbardi R, Jain E, Tang Q, Cortes M, Molodtsov A, Kasheta M, Luo CC, Mylvaganam R, Yoder JA, Blackburn JS, Sadreyev RI, Ceol CJ, North TE, Langenau DM. Single-cell transcriptional analysis of normal, aberrant, and malignant hematopoiesis in zebrafish. J. Exp. Med. 2016 May 2.

  24. Bukhari SI, Truesdell SS, Lee S, Kollu S, Classon A, Boukhali M, Jain E, Mortensen RD, Yanagiya A, Sadreyev RI, Haas W, Vasudevan S. A Specialized Mechanism of Translation Mediated by FXR1a-Associated MicroRNP in Cellular Quiescence. Mol. Cell 2016 Mar 3; 61(5):760-73.

  25. Hata AN, Niederst MJ, Archibald HL, Gomez-Caraballo M, Siddiqui FM, Mulvey HE, Maruvka YE, Ji F, Bhang HE, Siravegna G, Hu H, Raoof S, Lockerman E, Kalsy A, Lee D, Keating CL, Ruddy DA, Damon LJ, Crystal AS, Costa C, Piotrowska Z, Bardelli A, Iafrate AJ, Sadreyev RI, Stegmeier F, Getz G, Sequist LV, Faber AC, Engelman JA. Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition. Nat. Med. 2016 Mar; 22(3):262-9.

  26. Nishikawa JL, Boeszoermenyi A, Vale-Silva LA, Torelli R, Posteraro B, Sohn YJ, Ji F, Gelev V, Sanglard D, Sanguinetti M, Sadreyev RI, Mukherjee G, Bhyravabhotla J, Buhrlage SJ, Gray NS, Wagner G, Näär AM, Arthanari H. Inhibiting fungal multidrug resistance by disrupting an activator-Mediator interaction. Nature 2016 Feb 25; 530(7591):485-9.

  27. Wani AH, Boettiger AN, Schorderet P, Ergun A, Münger C, Sadreyev RI, Zhuang X, Kingston RE, Francis NJ. Chromatin topology is coupled to Polycomb group protein subnuclear organization. Nat Commun 2016; 7:10291.

  28. 2015
  29. Varmeh S, Borre PV, Gunda V, Brauner E, Holm T, Wang Y, Sadreyev RI, Parangi S. Genome-wide analysis of differentially expressed miRNA in PLX4720-resistant and parental human thyroid cancer cell lines. Surgery 2015 Oct 5.

  30. Tong J, Sadreyev RI, Pei J, Kinch LN, Grishin NV. Using homology relations within a database markedly boosts protein sequence similarity search. Proc. Natl. Acad. Sci. U.S.A. 2015 Jun 2; 112(22):7003-8.

  31. Pinter SF, Colognori D, Beliveau BJ, Sadreyev RI, Payer B, Yildirim E, Wu CT, Lee JT. Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome. Genetics 2015 Jun; 200(2):537-49.

  32. Sadreyev IR, Ji F, Cohen E, Ruvkun G, Tabach Y. PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles. Nucleic Acids Res. 2015 May 9.

  33. Guo S, Ergun A, Lu L, Walker WA, Ganguli K. Secreted Metabolites of Bifidobacterium infantis and Lactobacillus acidophilus Protect Immature Human Enterocytes from IL-1?-Induced Inflammation: A Transcription Profiling Analysis. PLoS ONE 2015; 10(4):e0124549.

  34. 2014
  35. Sarma K, Cifuentes-Rojas C, Ergun A, Del Rosario A, Jeon Y, White F, Sadreyev R, Lee JT. ATRX Directs Binding of PRC2 to Xist RNA and Polycomb Targets. Cell 2014 Nov 6; 159(4):869-83.

  36. West JA, Davis CP, Sunwoo H, Simon MD, Sadreyev RI, Wang PI, Tolstorukov MY, Kingston RE. The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. Mol. Cell 2014 Sep 4; 55(5):791-802.

  37. Broering TJ, Alavattam KG, Sadreyev RI, Ichijima Y, Kato Y, Hasegawa K, Camerini-Otero RD, Lee JT, Andreassen PR, Namekawa SH. BRCA1 establishes DNA damage signaling and pericentric heterochromatin of the X chromosome in male meiosis. J. Cell Biol. 2014 Jun 9; 205(5):663-75.

  38. Sadreyev RI. Informatics for molecular biologists. Curr Protoc Mol Biol 2014; 106:19.0.1-2.

  39. Bowman SK, Deaton AM, Domingues H, Wang PI, Sadreyev RI, Kingston RE, Bender W. H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex. Elife 2014; 3:e02833.

  40. 2013
  41. Sadreyev RI, Yildirim E, Pinter SF, Lee JT. Bimodal quantitative relationships between histone modifications for X-linked and autosomal loci. Proc. Natl. Acad. Sci. U.S.A. 2013 Apr 23; 110(17):6949-54.

  42. Yildirim E, Kirby JE, Brown DE, Mercier FE, Sadreyev RI, Scadden DT, Lee JT. Xist RNA is a potent suppressor of hematologic cancer in mice. Cell 2013 Feb 14; 152(4):727-42.

  43. 2012
  44. Pinter SF, Sadreyev RI, Yildirim E, Jeon Y, Ohsumi TK, Borowsky M, Lee JT. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. Genome Res. 2012 Oct; 22(10):1864-76.

  45. Anguera MC, Sadreyev R, Zhang Z, Szanto A, Payer B, Sheridan SD, Kwok S, Haggarty SJ, Sur M, Alvarez J, Gimelbrant A, Mitalipova M, Kirby JE, Lee JT. Molecular signatures of human induced pluripotent stem cells highlight sex differences and cancer genes. Cell Stem Cell 2012 Jul 6; 11(1):75-90.

  46. Yildirim E, Sadreyev RI, Pinter SF, Lee JT. X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription. Nat. Struct. Mol. Biol. 2012 Jan; 19(1):56-61.

  47. 2011
  48. Spencer RJ, del Rosario BC, Pinter SF, Lessing D, Sadreyev RI, Lee JT. A boundary element between Tsix and Xist binds the chromatin insulator Ctcf and contributes to initiation of X-chromosome inactivation. Genetics 2011 Oct; 189(2):441-54.

  49. Sun S, Fukue Y, Nolen L, Sadreyev R, Lee JT. Characterization of Xpr (Xpct) reveals instability but no effects on X-chromosome pairing or Xist expression. Transcription ; 1(1):46-56.

  50. 2009
  51. Sadreyev RI, Feramisco JD, Tsao H, Grishin NV. Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways. Bioinformatics 2009 Nov 15; 25(22):2891-6.

  52. Feramisco JD, Sadreyev RI, Murray ML, Grishin NV, Tsao H. Phenotypic and genotypic analyses of genetic skin disease through the Online Mendelian Inheritance in Man (OMIM) database. J. Invest. Dermatol. 2009 Nov; 129(11):2628-36.

  53. Wang Y, Sadreyev RI, Grishin NV. PROCAIN server for remote protein sequence similarity search. Bioinformatics 2009 Aug 15; 25(16):2076-7.

  54. Sadreyev RI, Tang M, Kim BH, Grishin NV. COMPASS server for homology detection: improved statistical accuracy, speed and functionality. Nucleic Acids Res. 2009 Jul; 37(Web Server issue):W90-4.

  55. Sadreyev RI, Kim BH, Grishin NV. Discrete-continuous duality of protein structure space. Curr. Opin. Struct. Biol. 2009 Jun; 19(3):321-8.

  56. Wang Y, Sadreyev RI, Grishin NV. PROCAIN: protein profile comparison with assisting information. Nucleic Acids Res. 2009 Jun; 37(11):3522-30.

  57. Sadreyev RI, Shi S, Baker D, Grishin NV. Structure similarity measure with penalty for close non-equivalent residues. Bioinformatics 2009 May 15; 25(10):1259-63.

  58. Sadreyev RI, Wang Y, Grishin NV. Considering scores between unrelated proteins in the search database improves profile comparison. BMC Bioinformatics 2009; 10:399.

  59. Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Das R, Grishin NV, Baker D. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins 2009; 77 Suppl 9:89-99.

  60. 2008
  61. Sadreyev RI, Grishin NV. Accurate statistical model of comparison between multiple sequence alignments. Nucleic Acids Res. 2008 Apr; 36(7):2240-8.

  62. 2007
  63. Sadreyev RI, Tang M, Kim BH, Grishin NV. COMPASS server for remote homology inference. Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W653-8.

  64. Qi Y, Sadreyev RI, Wang Y, Kim BH, Grishin NV. A comprehensive system for evaluation of remote sequence similarity detection. BMC Bioinformatics 2007; 8:314.

  65. 2006
  66. Krishna SS, Sadreyev RI, Grishin NV. A tale of two ferredoxins: sequence similarity and structural differences. BMC Struct. Biol. 2006; 6:8.

  67. Sadreyev RI, Grishin NV. Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds. BMC Struct. Biol. 2006; 6:6.

  68. 2005
  69. Kim BH, Sadreyev R, Grishin NV. COG4849 is a novel family of nucleotidyltransferases. J. Mol. Recognit. ; 18(5):422-5.

  70. 2004
  71. Sadreyev RI, Grishin NV. Estimates of statistical significance for comparison of individual positions in multiple sequence alignments. BMC Bioinformatics 2004 Aug 5; 5:106.

  72. Sadreyev RI, Grishin NV. Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs. Bioinformatics 2004 Apr 12; 20(6):818-28.

  73. 2003
  74. Sadreyev RI, Baker D, Grishin NV. Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Sci. 2003 Oct; 12(10):2262-72.

  75. Mittelman D, Sadreyev R, Grishin N. Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinformatics 2003 Aug 12; 19(12):1531-9.

  76. Pei J, Sadreyev R, Grishin NV. PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics 2003 Feb 12; 19(3):427-8.

  77. Sadreyev R, Grishin N. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol. 2003 Feb 7; 326(1):317-36.

  78. Kinch LN, Wrabl JO, Krishna SS, Majumdar I, Sadreyev RI, Qi Y, Pei J, Cheng H, Grishin NV. CASP5 assessment of fold recognition target predictions. Proteins 2003; 53 Suppl 6:395-409.

  79. 2002
  80. Sadreyev RI, Panchin YV. Effects of glutamate agonists on the isolated neurons from the locomotor network of the mollusc Clione limacina. Neuroreport 2002 Dec 3; 13(17):2235-9.

  81. 2000
  82. Sadreyev RI, Panchin YV. The role of putative glutamatergic neurons and their connections in the locomotor central pattern generator of the mollusk, Clione limacina. Comp. Biochem. Physiol., Part A Mol. Integr. Physiol. 2000 Jun; 126(2):193-202.

  83. 1998
  84. Arshavsky YI, Deliagina TG, Orlovsky GN, Panchin YV, Popova LB, Sadreyev RI. Analysis of the central pattern generator for swimming in the mollusk Clione. Ann. N. Y. Acad. Sci. 1998 Nov 16; 860:51-69.

  85. 1997
  86. Panchin YV, Sadreyev RI. Effects of acetylcholine and glutamate on isolated neurons of locomotory network of Clione. Neuroreport 1997 Sep 8; 8(13):2897-901.

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