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Items: 36

1.

Is it time to change the reference genome?

Ballouz S, Dobin A, Gillis JA.

Genome Biol. 2019 Aug 9;20(1):159. doi: 10.1186/s13059-019-1774-4.

2.

The long noncoding RNA ROCKI regulates inflammatory gene expression.

Zhang Q, Chao TC, Patil VS, Qin Y, Tiwari SK, Chiou J, Dobin A, Tsai CM, Li Z, Dang J, Gupta S, Urdahl K, Nizet V, Gingeras TR, Gaulton KJ, Rana TM.

EMBO J. 2019 Apr 15;38(8). pii: e100041. doi: 10.15252/embj.2018100041. Epub 2019 Mar 27.

3.

The fractured landscape of RNA-seq alignment: the default in our STARs.

Ballouz S, Dobin A, Gingeras TR, Gillis J.

Nucleic Acids Res. 2018 Jun 1;46(10):5125-5138. doi: 10.1093/nar/gky325.

4.

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.

5.

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.

6.

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.

7.

Optimizing RNA-Seq Mapping with STAR.

Dobin A, Gingeras TR.

Methods Mol Biol. 2016;1415:245-62. doi: 10.1007/978-1-4939-3572-7_13.

PMID:
27115637
8.

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.

9.

Mapping RNA-seq Reads with STAR.

Dobin A, Gingeras TR.

Curr Protoc Bioinformatics. 2015 Sep 3;51:11.14.1-19. doi: 10.1002/0471250953.bi1114s51. Review.

10.

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.

11.

Comparison of the transcriptional landscapes between human and mouse tissues.

Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17224-9. doi: 10.1073/pnas.1413624111. Epub 2014 Nov 20.

12.

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.

13.

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.

14.

STAR: ultrafast universal RNA-seq aligner.

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR.

Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.

15.

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.

16.

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.

Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR.

Genome Res. 2013 Jan;23(1):169-80. doi: 10.1101/gr.139618.112. Epub 2012 Aug 30.

17.

An encyclopedia of mouse DNA elements (Mouse ENCODE).

Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB.

Genome Biol. 2012 Aug 13;13(8):418. doi: 10.1186/gb-2012-13-8-418.

18.

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.

19.

Genome-wide antisense transcription drives mRNA processing in bacteria.

Lasa I, Toledo-Arana A, Dobin A, Villanueva M, de los Mozos IR, Vergara-Irigaray M, Segura V, Fagegaltier D, Penadés JR, Valle J, Solano C, Gingeras TR.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20172-7. doi: 10.1073/pnas.1113521108. Epub 2011 Nov 28.

20.

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.

21.

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.

22.

Dissipation of spin angular momentum in magnetic switching.

Stamm C, Tudosa I, Siegmann HC, Stöhr J, Dobin AY, Woltersdorf G, Heinrich B, Vaterlaus A.

Phys Rev Lett. 2005 May 20;94(19):197603. Epub 2005 May 19.

PMID:
16090212
23.

Surface roughness induced extrinsic damping in thin magnetic films.

Dobin AY, Victora RH.

Phys Rev Lett. 2004 Jun 25;92(25 Pt 1):257204. Epub 2004 Jun 25.

PMID:
15245059
24.

Intrinsic nonlinear ferromagnetic relaxation in thin metallic films.

Dobin AY, Victora RH.

Phys Rev Lett. 2003 Apr 25;90(16):167203. Epub 2003 Apr 22.

PMID:
12732001
25.

Exchange field induced magnetoresistance in colossal magnetoresistance manganites.

Krivorotov IN, Nikolaev KR, Dobin AY, Goldman AM, Dahlberg ED.

Phys Rev Lett. 2001 Jun 18;86(25):5779-82.

PMID:
11415356
26.

Oscillatory exchange coupling and positive magnetoresistance in epitaxial oxide heterostructures

Nikolaev KR, Dobin AY, Krivorotov IN, Cooley WK, Bhattacharya A, Kobrinskii AL, Glazman LI, Wentzovitch RM, Dahlberg ED, Goldman AM.

Phys Rev Lett. 2000 Oct 23;85(17):3728-31.

PMID:
11030992
27.

Genetic heterogeneity of Usher syndrome type II in a Dutch population.

Pieke-Dahl S, van Aarem A, Dobin A, Cremers CW, Kimberling WJ.

J Med Genet. 1996 Sep;33(9):753-7.

28.

Sexual dimorphism of renal alpha2-adrenergic receptor regulation in Dahl rats.

Gong G, Dobin A, Johnson ML, Pettinger WA.

Hypertens Res. 1996 Jun;19(2):83-9.

29.

Cardiovascular abnormalities in children with autosomal dominant polycystic kidney disease.

Ivy DD, Shaffer EM, Johnson AM, Kimberling WJ, Dobin A, Gabow PA.

J Am Soc Nephrol. 1995 Jun;5(12):2032-6.

30.

Genetic contamination of inbred Dahl rats from Harlan Sprague Dawley.

Gong G, Dobin A, Johnson ML, Pettinger WA.

Hypertension. 1995 Apr;25(4 Pt 1):660. No abstract available.

PMID:
7721412
31.

Sex influence on renal alpha 2-adrenergic receptor density in the spontaneously hypertensive rat.

Gong G, Dobin A, McArdle S, Sun L, Johnson ML, Pettinger WA.

Hypertension. 1994 May;23(5):607-12.

PMID:
8175169
32.

Segregation analysis of autosomal dominant polycystic kidney disease.

Dobin A, Kimberling WJ, Pettinger W, Bailey-Wilson JE, Shugart YY, Gabow P.

Genet Epidemiol. 1993;10(3):189-200.

PMID:
8349100
33.

AIDS in pregnancy.

Loveman A, Colburn V, Dobin A.

J Obstet Gynecol Neonatal Nurs. 1986 Mar-Apr;15(2):91-3.

PMID:
3634799
34.

Prevention of endomyometritis by local application of antibiotic solution during cesarean section.

Jensen LP, Dobin AJ, O'Sullivan MJ, Hilsenbeck CE.

Am J Obstet Gynecol. 1985 Jul 1;152(5):565-8.

PMID:
4014348
35.

Left ventricular ejection times during exercise testing with scintigraphy. Their use in the detection of ischemic heart disease.

Rubler S, Fisher VJ, Schreiber SS, Rothschild MA, Dobin AS.

Arch Intern Med. 1984 Jul;144(7):1386-91.

PMID:
6732400

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