Resumé

Dmitri Pervouchine was born in 1974 in Moscow Russia. He graduated from Moscow State University with two degrees, in Mathematics and in Chemistry, and continued his education at the Bioinformatics program at Boston University. In 2002 he defended his PhD in Mathematics under the supervision of Dr. Ernest B. Vinberg and joined the group of Dr. Nancy Kopell at the Center for BioDynamics and Department of Mathematics and Statistics at Boston University, working on neuronal dynamics, memory, and learning. In 2005 he joined the group of Drs. Mikhail Gelfand and Andrei Mironov, where he worked on computational RNA structure prediction and evolution. Dmitry found a class of RNA structures in introns of eukaryotic genes that impact splicing of pre-mRNAs. In 2011 Dmitry joined transcriptomics research at the group of Dr. Roderic Guigo in the Center for Genomic Regulation in Barcelona. Dmitry works in close collaboration with Dr. Thomas Gingeras from Cold Spring Harbor Laboratory and particularly he was involved in mouse ENCODE consortium where he and colleagues identified a group of genes with constrained expression across mammalian evolution and described distinct properties of this group of genes.

PUBLICATIONS 2012-2016

  • Morozov D, Morozova O, Budnik I, Pervouchine D, Pimenova E, Zakharova N. Urinary cytokines as markers of latent inflammation in children with chronic pyelonephritis and anorectal malformations. J Pediatr Urol. 2016 Feb 16. pii: S1477-5131(16)00045-0
  • Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J. Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction. BMC Genomics. 2015;16 Suppl 8:S2. doi: 10.1186/1471-2164-16-S8-S2
  • Melé M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ, Johnson R, Segrè AV, Djebali S, Niarchou A; GTEx Consortium, Wright FA, Lappalainen T, Calvo M, Getz G, Dermitzakis ET, Ardlie KG, Guigó R. Human genomics. The human transcriptome across tissues and individuals. Science. 2015 May 8; 348(6235):660-5. doi: 10.1126/science.aaa0355.
  • Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See LH, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. "Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression." Nat Commun. 2015 Jan 13; 6:5903. doi: 10.1038/ncomms6903
  • Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; Mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. Principles of regulatory information conservation between mouse and human. Nature. 2014 Nov 20;515(7527):371-5. doi: 10.1038/nature13985.
  • Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium. "A comparative encyclopedia of DNA elements in the mouse genome." Nature 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992
  • Pervouchine DD. IRBIS: a systematic search for conserved complementarity. RNA. 2014 Oct;20(10):1519-31. doi: 10.1261/rna.045088.114.
  • Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. "Comparative analysis of the transcriptome across distant species" Nature. 2014 Aug 28;512(7515):445-8
  • Pervouchine, DD, Knowles, DG, Guigó, R (2013). Intron-centric estimation of alternative splicing from RNA-seq data. Bioinformatics, 29, 2:273-4.
  • Pervouchine, DD, Khrameeva, EE, Pichugina, MY, Nikolaienko, OV, Gelfand, MS, Rubtsov, PM, Mironov, AA (2012). Evidence for widespread association of mammalian splicing and conserved long-range RNA structures. RNA, 18, 1:1-15.
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