Dmitry Davidovich Pervouchine

No editorial board membership but frequently asked for peer review

1. 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: 10.1186/1471216416S8S2

2. 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):6605. doi: 10.1126/science.aaa0355.

3. 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

4. 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):3715. doi: 10.1038/nature13985.

5. 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, FisherAylor 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):35564. doi: 10.1038/nature13992

6. Pervouchine DD. IRBIS: a systematic search for conserved complementarity. RNA . 2014 Oct;20(10):151931. doi: 10.1261/rna.045088.114.

7. 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):4458

8. Pervouchine, DD, Knowles, DG, Guigó, R (2013) . Introncentric estimation of alternative splicing from RNAseq data. Bioinformatics , 29, 2:2734.

9. Pervouchine, DD, Khrameeva, EE, Pichugina, MY, Nikolaienko, OV, Gelfand, MS, Rubtsov, PM, Mironov, AA (2012) . Evidence for widespread association of mammalian splicing and conserved longrange RNA structures. RNA , 18, 1:115.

10. N. Kopell, C. Börgers, D. Pervouchine, P. Malerba, and A. B.L.Tort. “Gamma and Theta Rhythms in Biophysical Models of Hippocampal Circuits”, Hippocampal Microcircuits: A Computational Modellers Resource Book. Eds. V. Cutsuridis, B.P. Graham, S. Cobb, I. Vida. Springer 2010. Ch. 15.

11. Raker, VA, Mironov, AA, Gelfand, MS, Pervouchine, DD (2009) . Modulation of alternative splicing by longrange RNA structures in Drosophila. Nucleic Acids Res. , 37, 14:453344.

12. Pervouchine, DD, Netoff, TI, Rotstein, HG, White, JA, Cunningham, MO, Whittington, MA, Kopell, NJ (2006) . Lowdimensional maps encoding dynamics in entorhinal cortex and hippocampus. Neural Comput , 18, 11:261750.

13. Danilova, LV, Pervouchine, DD, Favorov, AV, Mironov, AA (2006) . RNAKinetics: a web server that models secondary structure kinetics of an elongating RNA. J Bioinform Comput Biol , 4, 2:58996.

14. Cunningham, MO, Pervouchine, DD, Racca, C, Kopell, NJ, Davies, CH, Jones, RS, Traub, RD, Whittington, MA (2006) . Neuronal metabolism governs cortical network response state. Proc. Natl. Acad. Sci. U.S.A. , 103, 14:5597601.

15. Rotstein, HG, Pervouchine, DD, Acker, CD, Gillies, MJ, White, JA, Buhl, EH, Whittington, MA, Kopell, N (2005) . Slow and fast inhibition and an Hcurrent interact to create a theta rhythm in a model of CA1 interneuron network. J. Neurophysiol. , 94, 2:150918.

16. Pervouchine, DD (2004) . IRIS: intermolecular RNA interaction search. Genome Inform ,15, 2:92101.

17. Isaacs, FJ, Dwyer, DJ, Ding, C, Pervouchine, DD, Cantor, CR, Collins, JJ (2004). Engineered riboregulators enable posttranscriptional control of gene expression. Nat. Biotechnol. , 22, 7:8417.

18. DD Pervouchine, "Hierarchy of closures of matrix pencils", Journal of Lie theory 14(2):443479 (2004 )

19. Pervouchine, DD, Graber, JH, Kasif, S (2003) . On the normalization of RNA equilibrium free energy to the length of the sequence. Nucleic Acids Res. , 31, 9:e49.

20. Stitziel, NO, Tseng, YY, Pervouchine, D, Goddeau, D, Kasif, S, Liang, J (2003). Structural location of diseaseassociated singlenucleotide polymorphisms. J. Mol. Biol. , 327, 5:102130.

21. DD Pervouchine, "On the closures of orbits of fourth order matrix pencils", Izv. Math. , 2002 , 66(5), 10471055.

22. DD Pervouchine, "Invariants and orbits of the standard (SL 4 (C)×SL 4 (C)×SL 2 (C))module", Izv. Math. , 2000 , 64(5), 10031015.

PUGF Presidential University Graduate Fellowship, Boston University, 2000.

Soros Foundation Fellowship, Moscow State University, 1998.

Russian Foundation for Fundamental Research, 1995-1997.

2003-2004 Department of Mathematics and Statistics, Boston University

Courses: Calculus, Discrete Mathematics for Engeneers

1996-2000 Department of Economics, Moscow State University

Courses: Calculus, Probability and Statistics, Discrete Mathematics