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Items: 1 to 20 of 30

1.

Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing.

Hjelmsø MH, Hellmér M, Fernandez-Cassi X, Timoneda N, Lukjancenko O, Seidel M, Elsässer D, Aarestrup FM, Löfström C, Bofill-Mas S, Abril JF, Girones R, Schultz AC.

PLoS One. 2017 Jan 18;12(1):e0170199. doi: 10.1371/journal.pone.0170199.

2.

The coelomic epithelium transcriptome from a clonal sea star, Coscinasterias muricata.

Gabre JL, Martinez P, Nilsson Sköld H, Ortega-Martinez O, Abril JF.

Mar Genomics. 2015 Dec;24 Pt 3:245-8. doi: 10.1016/j.margen.2015.07.010.

PMID:
26321383
3.

Distilling a Visual Network of Retinitis Pigmentosa Gene-Protein Interactions to Uncover New Disease Candidates.

Boloc D, Castillo-Lara S, Marfany G, Gonzàlez-Duarte R, Abril JF.

PLoS One. 2015 Aug 12;10(8):e0135307. doi: 10.1371/journal.pone.0135307.

4.

Evidence of viral dissemination and seasonality in a Mediterranean river catchment: Implications for water pollution management.

Rusiñol M, Fernandez-Cassi X, Timoneda N, Carratalà A, Abril JF, Silvera C, Figueras MJ, Gelati E, Rodó X, Kay D, Wyn-Jones P, Bofill-Mas S, Girones R.

J Environ Manage. 2015 Aug 15;159:58-67. doi: 10.1016/j.jenvman.2015.05.019.

PMID:
26046988
5.

Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.

Rodríguez-Esteban G, González-Sastre A, Rojo-Laguna JI, Saló E, Abril JF.

BMC Genomics. 2015 May 8;16:361. doi: 10.1186/s12864-015-1533-1.

6.

The nervous system of Xenacoelomorpha: a genomic perspective.

Perea-Atienza E, Gavilán B, Chiodin M, Abril JF, Hoff KJ, Poustka AJ, Martinez P.

J Exp Biol. 2015 Feb 15;218(Pt 4):618-28. doi: 10.1242/jeb.110379.

7.

Assessment of transcript reconstruction methods for RNA-seq.

Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P; RGASP Consortium..

Nat Methods. 2013 Dec;10(12):1177-84. doi: 10.1038/nmeth.2714.

8.

Planarians as a model to assess in vivo the role of matrix metalloproteinase genes during homeostasis and regeneration.

Isolani ME, Abril JF, Saló E, Deri P, Bianucci AM, Batistoni R.

PLoS One. 2013;8(2):e55649. doi: 10.1371/journal.pone.0055649.

9.

High transcriptional complexity of the retinitis pigmentosa CERKL gene in human and mouse.

Garanto A, Riera M, Pomares E, Permanyer J, de Castro-Miró M, Sava F, Abril JF, Marfany G, Gonzàlez-Duarte R.

Invest Ophthalmol Vis Sci. 2011 Jul 13;52(8):5202-14. doi: 10.1167/iovs.10-7101.

PMID:
21508105
10.

A proteomics approach to decipher the molecular nature of planarian stem cells.

Fernández-Taboada E, Rodríguez-Esteban G, Saló E, Abril JF.

BMC Genomics. 2011 Feb 28;12:133. doi: 10.1186/1471-2164-12-133.

11.

Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea.

Abril JF, Cebrià F, Rodríguez-Esteban G, Horn T, Fraguas S, Calvo B, Bartscherer K, Saló E.

BMC Genomics. 2010 Dec 31;11:731. doi: 10.1186/1471-2164-11-731.

12.

Complex selection on 5' splice sites in intron-rich organisms.

Irimia M, Roy SW, Neafsey DE, Abril JF, Garcia-Fernandez J, Koonin EV.

Genome Res. 2009 Nov;19(11):2021-7. doi: 10.1101/gr.089276.108.

13.

Computational gene annotation in new genome assemblies using GeneID.

Blanco E, Abril JF.

Methods Mol Biol. 2009;537:243-61. doi: 10.1007/978-1-59745-251-9_12.

PMID:
19378148
14.

Planarian regeneration: achievements and future directions after 20 years of research.

Saló E, Abril JF, Adell T, Cebrià F, Eckelt K, Fernandez-Taboada E, Handberg-Thorsager M, Iglesias M, Molina MD, Rodríguez-Esteban G.

Int J Dev Biol. 2009;53(8-10):1317-27. doi: 10.1387/ijdb.072414es. Review.

15.

The diploid genome sequence of an individual human.

Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Borman J, Rogers YH, Frazier ME, Scherer SW, Strausberg RL, Venter JC.

PLoS Biol. 2007 Sep 4;5(10):e254.

16.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium., Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program.; Baylor College of Medicine Human Genome Sequencing Center.; Washington University Genome Sequencing Center.; Broad Institute.; Children's Hospital Oakland Research Institute., Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

17.

EGASP: the human ENCODE Genome Annotation Assessment Project.

Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG.

Genome Biol. 2006;7 Suppl 1:S2.1-31. Review.

18.

Comparison of splice sites in mammals and chicken.

Abril JF, Castelo R, Guigó R.

Genome Res. 2005 Jan;15(1):111-9.

19.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F; Rat Genome Sequencing Project Consortium..

Nature. 2004 Apr 1;428(6982):493-521.

PMID:
15057822
20.

gff2aplot: Plotting sequence comparisons.

Abril JF, Guigó R, Wiehe T.

Bioinformatics. 2003 Dec 12;19(18):2477-9.

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