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Items: 1 to 50 of 75

1.

Identification of novel GLI1 target genes and regulatory circuits in human cancer cells.

Diao Y, Rahman MF, Vyatkin Y, Azatyan A, St Laurent G, Kapranov P, Zaphiropoulos PG.

Mol Oncol. 2018 Oct;12(10):1718-1734. doi: 10.1002/1878-0261.12366. Epub 2018 Aug 30.

2.

Strategies to Annotate and Characterize Long Noncoding RNAs: Advantages and Pitfalls.

Cao H, Wahlestedt C, Kapranov P.

Trends Genet. 2018 Sep;34(9):704-721. doi: 10.1016/j.tig.2018.06.002. Epub 2018 Jul 17. Review.

PMID:
30017313
3.

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

St Laurent G, Vyatkin Y, Antonets D, Ri M, Qi Y, Saik O, Shtokalo D, de Hoon MJ, Kawaji H, Itoh M, Lassmann T, Arner E, Forrest AR; FANTOM consortium, Nicolas E, McCaffrey TA, Carninci P, Hayashizaki Y, Wahlestedt C, Kapranov P.

Nucleic Acids Res. 2016 Apr 20;44(7):3233-52. doi: 10.1093/nar/gkw162. Epub 2016 Mar 21.

4.

The Bromodomain protein BRD4 controls HOTAIR, a long noncoding RNA essential for glioblastoma proliferation.

Pastori C, Kapranov P, Penas C, Peschansky V, Volmar CH, Sarkaria JN, Bregy A, Komotar R, St Laurent G, Ayad NG, Wahlestedt C.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):8326-31. doi: 10.1073/pnas.1424220112. Epub 2015 Jun 25.

5.

The Landscape of long noncoding RNA classification.

St Laurent G, Wahlestedt C, Kapranov P.

Trends Genet. 2015 May;31(5):239-51. doi: 10.1016/j.tig.2015.03.007. Epub 2015 Apr 10. Review.

6.

Erratum: A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus.

Lazorthes S, Vallot C, Briois S, Aguirrebengoa M, Thuret JY, St Laurent G, Rougeulle C, Kapranov P, Mann C, Trouche D, Nicolas E.

Nat Commun. 2015 Apr 8;6:6918. doi: 10.1038/ncomms7918. No abstract available.

7.

A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus.

Lazorthes S, Vallot C, Briois S, Aguirrebengoa M, Thuret JY, St Laurent G, Rougeulle C, Kapranov P, Mann C, Trouche D, Nicolas E.

Nat Commun. 2015 Jan 20;6:5971. doi: 10.1038/ncomms6971. Erratum in: Nat Commun. 2015;6:6918.

8.

Efficient production of dual recombinant adeno-associated viral vectors for factor VIII delivery.

Wang Q, Dong B, Firrman J, Roberts S, Moore AR, Cao W, Diao Y, Kapranov P, Xu R, Xiao W.

Hum Gene Ther Methods. 2014 Aug;25(4):261-8. doi: 10.1089/hgtb.2014.093.

9.

Dark matter RNA illuminates the puzzle of genome-wide association studies.

St Laurent G, Vyatkin Y, Kapranov P.

BMC Med. 2014 Jun 12;12:97. doi: 10.1186/1741-7015-12-97.

10.

Identification of novel non-coding RNA-based negative feedback regulating the expression of the oncogenic transcription factor GLI1.

Villegas VE, Rahman MF, Fernandez-Barrena MG, Diao Y, Liapi E, Sonkoly E, Ståhle M, Pivarcsi A, Annaratone L, Sapino A, Ramírez Clavijo S, Bürglin TR, Shimokawa T, Ramachandran S, Kapranov P, Fernandez-Zapico ME, Zaphiropoulos PG.

Mol Oncol. 2014 Jul;8(5):912-26. doi: 10.1016/j.molonc.2014.03.009. Epub 2014 Mar 22.

11.

Proteomics analysis of co-purifying cellular proteins associated with rAAV vectors.

Dong B, Duan X, Chow HY, Chen L, Lu H, Wu W, Hauck B, Wright F, Kapranov P, Xiao W.

PLoS One. 2014 Feb 3;9(2):e86453. doi: 10.1371/journal.pone.0086453. eCollection 2014.

12.

RNA editing regulates transposon-mediated heterochromatic gene silencing.

Savva YA, Jepson JE, Chang YJ, Whitaker R, Jones BC, St Laurent G, Tackett MR, Kapranov P, Jiang N, Du G, Helfand SL, Reenan RA.

Nat Commun. 2013;4:2745. doi: 10.1038/ncomms3745.

13.

Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila.

St Laurent G, Tackett MR, Nechkin S, Shtokalo D, Antonets D, Savva YA, Maloney R, Kapranov P, Lawrence CE, Reenan RA.

Nat Struct Mol Biol. 2013 Nov;20(11):1333-9. doi: 10.1038/nsmb.2675. Epub 2013 Sep 29.

PMID:
24077224
14.

VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer.

St Laurent G, Shtokalo D, Dong B, Tackett MR, Fan X, Lazorthes S, Nicolas E, Sang N, Triche TJ, McCaffrey TA, Xiao W, Kapranov P.

Genome Biol. 2013 Jul 22;14(7):R73. doi: 10.1186/gb-2013-14-7-r73.

15.

A concept of eliminating nonhomologous recombination for scalable and safe AAV vector generation for human gene therapy.

Dong B, Moore AR, Dai J, Roberts S, Chu K, Kapranov P, Moss B, Xiao W.

Nucleic Acids Res. 2013 Jul;41(13):6609-17. doi: 10.1093/nar/gkt404. Epub 2013 May 15.

16.

On the importance of small changes in RNA expression.

St Laurent G, Shtokalo D, Tackett MR, Yang Z, Vyatkin Y, Milos PM, Seilheimer B, McCaffrey TA, Kapranov P.

Methods. 2013 Sep 1;63(1):18-24. doi: 10.1016/j.ymeth.2013.03.027. Epub 2013 Apr 4.

PMID:
23563143
17.

Genomics in the assessment of a multi-component, multi-target medication in soft tissue disorders.

St Laurent G, Kapranov P.

Curr Med Res Opin. 2013;29 Suppl 2:11-4. doi: 10.1185/03007995.2013.779879. No abstract available.

PMID:
23517420
18.

Inflammation in soft tissue disorders: the evidence and potential role for a natural multi-target medication.

Wolfarth B, de Vega CG, Kapranov P, St Laurent G, Speed C.

Curr Med Res Opin. 2013;29 Suppl 2:1-2. doi: 10.1185/03007995.2013.779874. No abstract available.

PMID:
23517417
19.

In vitro and In vivo Model Systems for Hemophilia A Gene Therapy.

Mao J, Xi X, Kapranov P, Dong B, Firrman J, Xu R, Xiao W.

J Genet Syndr Gene Ther. 2013 Jan 17;Suppl 1. pii: 10911.

20.

Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells.

St Laurent G, Shtokalo D, Tackett MR, Yang Z, Eremina T, Wahlestedt C, Urcuqui-Inchima S, Seilheimer B, McCaffrey TA, Kapranov P.

BMC Genomics. 2012 Sep 24;13:504. doi: 10.1186/1471-2164-13-504.

21.

5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary.

Khare T, Pai S, Koncevicius K, Pal M, Kriukiene E, Liutkeviciute Z, Irimia M, Jia P, Ptak C, Xia M, Tice R, Tochigi M, Moréra S, Nazarians A, Belsham D, Wong AH, Blencowe BJ, Wang SC, Kapranov P, Kustra R, Labrie V, Klimasauskas S, Petronis A.

Nat Struct Mol Biol. 2012 Oct;19(10):1037-43. doi: 10.1038/nsmb.2372. Epub 2012 Sep 9.

22.

Landscape of transcription in human cells.

Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR.

Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233.

23.

Genomic "dark matter": implications for understanding human disease mechanisms, diagnostics, and cures.

Kapranov P, St Laurent G.

Front Genet. 2012 May 29;3:95. doi: 10.3389/fgene.2012.00095. eCollection 2012. No abstract available.

24.

Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape.

St Laurent G, Savva YA, Kapranov P.

Front Genet. 2012 Apr 26;3:57. doi: 10.3389/fgene.2012.00057. eCollection 2012.

25.

Dark Matter RNA: Existence, Function, and Controversy.

Kapranov P, St Laurent G.

Front Genet. 2012 Apr 23;3:60. doi: 10.3389/fgene.2012.00060. eCollection 2012.

26.

Evidence for transcript networks composed of chimeric RNAs in human cells.

Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpí JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR.

PLoS One. 2012;7(1):e28213. doi: 10.1371/journal.pone.0028213. Epub 2012 Jan 4.

27.

Profiling of short RNAs using Helicos single-molecule sequencing.

Kapranov P, Ozsolak F, Milos PM.

Methods Mol Biol. 2012;822:219-32. doi: 10.1007/978-1-61779-427-8_15.

28.

Native molecular state of adeno-associated viral vectors revealed by single-molecule sequencing.

Kapranov P, Chen L, Dederich D, Dong B, He J, Steinmann KE, Moore AR, Thompson JF, Milos PM, Xiao W.

Hum Gene Ther. 2012 Jan;23(1):46-55. doi: 10.1089/hum.2011.160. Epub 2011 Oct 4.

29.

True single-molecule DNA sequencing of a pleistocene horse bone.

Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, Steinmann KE, Kapranov P, Thompson JF, Zazula G, Froese D, Moltke I, Shapiro B, Hofreiter M, Al-Rasheid KA, Gilbert MT, Willerslev E.

Genome Res. 2011 Oct;21(10):1705-19. doi: 10.1101/gr.122747.111. Epub 2011 Jul 29.

30.

Single-step capture and sequencing of natural DNA for detection of BRCA1 mutations.

Thompson JF, Reifenberger JG, Giladi E, Kerouac K, Gill J, Hansen E, Kahvejian A, Kapranov P, Knope T, Lipson D, Steinmann KE, Milos PM.

Genome Res. 2012 Feb;22(2):340-5. doi: 10.1101/gr.122192.111. Epub 2011 Jul 15.

31.

Protocol dependence of sequencing-based gene expression measurements.

Raz T, Kapranov P, Lipson D, Letovsky S, Milos PM, Thompson JF.

PLoS One. 2011 May 6;6(5):e19287. doi: 10.1371/journal.pone.0019287.

32.

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells.

Pastor WA, Pape UJ, Huang Y, Henderson HR, Lister R, Ko M, McLoughlin EM, Brudno Y, Mahapatra S, Kapranov P, Tahiliani M, Daley GQ, Liu XS, Ecker JR, Milos PM, Agarwal S, Rao A.

Nature. 2011 May 19;473(7347):394-7. doi: 10.1038/nature10102. Epub 2011 May 8.

33.

The developmental transcriptome of Drosophila melanogaster.

Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE.

Nature. 2011 Mar 24;471(7339):473-9. doi: 10.1038/nature09715. Epub 2010 Dec 22.

34.

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M.

Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.

35.

The transcriptional diversity of 25 Drosophila cell lines.

Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, Samsonova A, Choi JH, Roberts J, Davis CA, Tang H, van Baren MJ, Ghosh S, Dobin A, Bell K, Lin W, Langton L, Duff MO, Tenney AE, Zaleski C, Brent MR, Hoskins RA, Kaufman TC, Andrews J, Graveley BR, Perrimon N, Celniker SE, Gingeras TR, Cherbas P.

Genome Res. 2011 Feb;21(2):301-14. doi: 10.1101/gr.112961.110. Epub 2010 Dec 22.

36.

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA.

Kapranov P, St Laurent G, Raz T, Ozsolak F, Reynolds CP, Sorensen PH, Reaman G, Milos P, Arceci RJ, Thompson JF, Triche TJ.

BMC Biol. 2010 Dec 21;8:149. doi: 10.1186/1741-7007-8-149. Erratum in: BMC Biol. 2011;9:86.

37.

Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation.

Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan AP, John B, Milos PM.

Cell. 2010 Dec 10;143(6):1018-29. doi: 10.1016/j.cell.2010.11.020.

38.

Error tolerant indexing and alignment of short reads with covering template families.

Giladi E, Healy J, Myers G, Hart C, Kapranov P, Lipson D, Roels S, Thayer E, Letovsky S.

J Comput Biol. 2010 Oct;17(10):1397-1411. doi: 10.1089/cmb.2010.0005.

PMID:
20937014
39.

New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism.

Kapranov P, Ozsolak F, Kim SW, Foissac S, Lipson D, Hart C, Roels S, Borel C, Antonarakis SE, Monaghan AP, John B, Milos PM.

Nature. 2010 Jul 29;466(7306):642-6. doi: 10.1038/nature09190.

40.

Genome-wide mapping indicates that p73 and p63 co-occupy target sites and have similar dna-binding profiles in vivo.

Yang A, Zhu Z, Kettenbach A, Kapranov P, McKeon F, Gingeras TR, Struhl K.

PLoS One. 2010 Jul 14;5(7):e11572. doi: 10.1371/journal.pone.0011572.

41.

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.

Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, Lassmann T, Vitezic M, Severin J, Olivarius S, Lazarevic D, Hornig N, Orlando V, Bell I, Gao H, Dumais J, Kapranov P, Wang H, Davis CA, Gingeras TR, Kawai J, Daub CO, Hayashizaki Y, Gustincich S, Carninci P.

Nat Methods. 2010 Jul;7(7):528-34. doi: 10.1038/nmeth.1470. Epub 2010 Jun 13.

42.

High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans.

Ramani AK, Nelson AC, Kapranov P, Bell I, Gingeras TR, Fraser AG.

Genome Biol. 2009;10(9):R101. doi: 10.1186/gb-2009-10-9-r101. Epub 2009 Sep 24.

43.

Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls.

Makrythanasis P, Kapranov P, Bartoloni L, Reymond A, Deutsch S, Guigó R, Denoeud F, Drenkow J, Rossier C, Ariani F, Capra V, Excoffier L, Renieri A, Gingeras TR, Antonarakis SE.

Hum Mutat. 2009 Sep;30(9):E866-79. doi: 10.1002/humu.21073.

44.

Studying chromosome-wide transcriptional networks: new insights into disease?

Kapranov P.

Genome Med. 2009 May 11;1(5):50. doi: 10.1186/gm50.

45.

From transcription start site to cell biology.

Kapranov P.

Genome Biol. 2009;10(4):217. doi: 10.1186/gb-2009-10-4-217. Epub 2009 Apr 20. Review.

46.

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster.

Zhang X, Lian Z, Padden C, Gerstein MB, Rozowsky J, Snyder M, Gingeras TR, Kapranov P, Weissman SM, Newburger PE.

Blood. 2009 Mar 12;113(11):2526-34. doi: 10.1182/blood-2008-06-162164. Epub 2009 Jan 14.

47.

Efficient targeted transcript discovery via array-based normalization of RACE libraries.

Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR, Lin C, Szeto D, Denoeud F, Calvo M, Frankish A, Harrow J, Makrythanasis P, Vidal M, Salehi-Ashtiani K, Antonarakis SE, Gingeras TR, Guigó R.

Nat Methods. 2008 Jul;5(7):629-35. doi: 10.1038/nmeth.1216. Epub 2008 May 25.

48.

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS.

Genome Res. 2008 Mar;18(3):393-403. doi: 10.1101/gr.7080508. Epub 2008 Feb 7.

49.

Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders.

Rada-Iglesias A, Ameur A, Kapranov P, Enroth S, Komorowski J, Gingeras TR, Wadelius C.

Genome Res. 2008 Mar;18(3):380-92. doi: 10.1101/gr.6880908. Epub 2008 Jan 29.

50.

Differential analysis for high density tiling microarray data.

Ghosh S, Hirsch HA, Sekinger EA, Kapranov P, Struhl K, Gingeras TR.

BMC Bioinformatics. 2007 Sep 24;8:359.

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