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Items: 28

1.

Circular exonic RNAs: When RNA structure meets topology.

Pervouchine DD.

Biochim Biophys Acta Gene Regul Mech. 2019 May 15:194384. doi: 10.1016/j.bbagrm.2019.05.002. [Epub ahead of print] Review.

PMID:
31102674
2.

Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay.

Pervouchine D, Popov Y, Berry A, Borsari B, Frankish A, Guigó R.

Nucleic Acids Res. 2019 Jun 4;47(10):5293-5306. doi: 10.1093/nar/gkz193.

3.

An Evolutionary Mechanism for the Generation of Competing RNA Structures Associated with Mutually Exclusive Exons.

Ivanov TM, Pervouchine DD.

Genes (Basel). 2018 Jul 17;9(7). pii: E356. doi: 10.3390/genes9070356.

4.

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes.

Pervouchine DD.

Genes (Basel). 2018 Jun 15;9(6). pii: E302. doi: 10.3390/genes9060302. Review.

5.

The effects of death and post-mortem cold ischemia on human tissue transcriptomes.

Ferreira PG, Muñoz-Aguirre M, Reverter F, Sá Godinho CP, Sousa A, Amadoz A, Sodaei R, Hidalgo MR, Pervouchine D, Carbonell-Caballero J, Nurtdinov R, Breschi A, Amador R, Oliveira P, Çubuk C, Curado J, Aguet F, Oliveira C, Dopazo J, Sammeth M, Ardlie KG, Guigó R.

Nat Commun. 2018 Feb 13;9(1):490. doi: 10.1038/s41467-017-02772-x.

6.

Hypoxic renal injury in newborns with abdominal compartment syndrome (clinical and experimental study).

Morozov D, Morozova O, Pervouchine D, Severgina L, Tsyplakov A, Zakharova N, Sushentsev N, Maltseva L, Budnik I.

Pediatr Res. 2018 Feb;83(2):520-526. doi: 10.1038/pr.2017.263. Epub 2017 Nov 15.

PMID:
29053704
7.

Erratum to: A benchmark for RNA-seq quantification pipelines.

Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA.

Genome Biol. 2016 Sep 30;17(1):203. No abstract available.

8.

Gene-specific patterns of expression variation across organs and species.

Breschi A, Djebali S, Gillis J, Pervouchine DD, Dobin A, Davis CA, Gingeras TR, Guigó R.

Genome Biol. 2016 Jul 8;17(1):151. doi: 10.1186/s13059-016-1008-y.

9.

Erratum to: A benchmark for RNA-seq quantification pipelines.

Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA.

Genome Biol. 2016 May 23;17(1):107. No abstract available.

10.

A benchmark for RNA-seq quantification pipelines.

Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA.

Genome Biol. 2016 Apr 23;17:74. doi: 10.1186/s13059-016-0940-1. Erratum in: Genome Biol. 2016;17(1):107. Genome Biol. 2016 Sep 30;17 (1):203.

11.

Urinary cytokines as markers of latent inflammation in children with chronic pyelonephritis and anorectal malformations.

Morozov D, Morozova O, Budnik I, Pervouchine D, Pimenova E, Zakharova N.

J Pediatr Urol. 2016 Jun;12(3):153.e1-6. doi: 10.1016/j.jpurol.2016.01.013. Epub 2016 Feb 16.

PMID:
26936433
12.

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.

Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J.

BMC Genomics. 2015;16 Suppl 8:S2. doi: 10.1186/1471-2164-16-S8-S2. Epub 2015 Jun 18.

13.

Human genomics. The human transcriptome across tissues and individuals.

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.

Science. 2015 May 8;348(6235):660-5. doi: 10.1126/science.aaa0355.

14.

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.

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.

Nat Commun. 2015 Jan 13;6:5903. doi: 10.1038/ncomms6903.

15.

A comparative encyclopedia of DNA elements in the mouse genome.

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.

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

16.

Comparative analysis of the transcriptome across distant species.

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.

Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424.

17.

IRBIS: a systematic search for conserved complementarity.

Pervouchine DD.

RNA. 2014 Oct;20(10):1519-31. doi: 10.1261/rna.045088.114. Epub 2014 Aug 20.

18.

Intron-centric estimation of alternative splicing from RNA-seq data.

Pervouchine DD, Knowles DG, Guigó R.

Bioinformatics. 2013 Jan 15;29(2):273-4. doi: 10.1093/bioinformatics/bts678. Epub 2012 Nov 21.

19.

Evidence for widespread association of mammalian splicing and conserved long-range RNA structures.

Pervouchine DD, Khrameeva EE, Pichugina MY, Nikolaienko OV, Gelfand MS, Rubtsov PM, Mironov AA.

RNA. 2012 Jan;18(1):1-15. doi: 10.1261/rna.029249.111. Epub 2011 Nov 29.

20.

Modulation of alternative splicing by long-range RNA structures in Drosophila.

Raker VA, Mironov AA, Gelfand MS, Pervouchine DD.

Nucleic Acids Res. 2009 Aug;37(14):4533-44. doi: 10.1093/nar/gkp407. Epub 2009 May 22.

21.

Low-dimensional maps encoding dynamics in entorhinal cortex and hippocampus.

Pervouchine DD, Netoff TI, Rotstein HG, White JA, Cunningham MO, Whittington MA, Kopell NJ.

Neural Comput. 2006 Nov;18(11):2617-50. Erratum in: Neural Comput. 2007 Jan;19(1):302.

PMID:
16999573
22.

RNAKinetics: a web server that models secondary structure kinetics of an elongating RNA.

Danilova LV, Pervouchine DD, Favorov AV, Mironov AA.

J Bioinform Comput Biol. 2006 Apr;4(2):589-96.

PMID:
16819804
23.

Neuronal metabolism governs cortical network response state.

Cunningham MO, Pervouchine DD, Racca C, Kopell NJ, Davies CH, Jones RS, Traub RD, Whittington MA.

Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5597-601. Epub 2006 Mar 24.

24.

Slow and fast inhibition and an H-current interact to create a theta rhythm in a model of CA1 interneuron network.

Rotstein HG, Pervouchine DD, Acker CD, Gillies MJ, White JA, Buhl EH, Whittington MA, Kopell N.

J Neurophysiol. 2005 Aug;94(2):1509-18. Epub 2005 Apr 27.

25.

IRIS: intermolecular RNA interaction search.

Pervouchine DD.

Genome Inform. 2004;15(2):92-101.

PMID:
15706495
26.

Engineered riboregulators enable post-transcriptional control of gene expression.

Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ.

Nat Biotechnol. 2004 Jul;22(7):841-7. Epub 2004 Jun 20.

PMID:
15208640
27.

On the normalization of RNA equilibrium free energy to the length of the sequence.

Pervouchine DD, Graber JH, Kasif S.

Nucleic Acids Res. 2003 May 1;31(9):e49.

28.

Structural location of disease-associated single-nucleotide polymorphisms.

Stitziel NO, Tseng YY, Pervouchine D, Goddeau D, Kasif S, Liang J.

J Mol Biol. 2003 Apr 11;327(5):1021-30.

PMID:
12662927

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