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Items: 1 to 20 of 27

1.

Within-Host Recombination in the Foot-and-Mouth Disease Virus Genome.

Ferretti L, Di Nardo A, Singer B, Lasecka-Dykes L, Logan G, Wright CF, Pérez-Martín E, King DP, Tuthill TJ, Ribeca P.

Viruses. 2018 Apr 25;10(5). pii: E221. doi: 10.3390/v10050221.

2.

A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0).

Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes IT, Armstrong J, Laayouni H, Gordon D, Huddleston J, Garcia Perez R, Povolotskaya I, Serres Armero A, Gómez Garrido J, Ho D, Ribeca P, Alioto T, Green RE, Paten B, Navarro A, Betranpetit J, Herrero J, Eichler EE, Sharp AJ, Feuk L, Warren WC, Marques-Bonet T.

Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix098.

3.

ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data.

Rodríguez-Martín B, Palumbo E, Marco-Sola S, Griebel T, Ribeca P, Alonso G, Rastrojo A, Aguado B, Guigó R, Djebali S.

BMC Genomics. 2017 Jan 3;18(1):7. doi: 10.1186/s12864-016-3404-9.

4.

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.

Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, Ribeca P, Capella-Gutiérrez S, Rodríguez JM, Câmara F, Lowy E, Cozzuto L, Erb I, Tress ML, Rodriguez-Ales JL, Ruiz-Orera J, Reverter F, Casas-Marce M, Soriano L, Arango JR, Derdak S, Galán B, Blanc J, Gut M, Lorente-Galdos B, Andrés-Nieto M, López-Otín C, Valencia A, Gut I, García JL, Guigó R, Murphy WJ, Ruiz-Herrera A, Marques-Bonet T, Roma G, Notredame C, Mailund T, Albà MM, Gabaldón T, Alioto T, Godoy JA.

Genome Biol. 2016 Dec 14;17(1):251.

5.

Genome sequence of the olive tree, Olea europaea.

Cruz F, Julca I, Gómez-Garrido J, Loska D, Marcet-Houben M, Cano E, Galán B, Frias L, Ribeca P, Derdak S, Gut M, Sánchez-Fernández M, García JL, Gut IG, Vargas P, Alioto TS, Gabaldón T.

Gigascience. 2016 Jun 27;5:29. doi: 10.1186/s13742-016-0134-5.

6.

CARGO: effective format-free compressed storage of genomic information.

Roguski Ł, Ribeca P.

Nucleic Acids Res. 2016 Jul 8;44(12):e114. doi: 10.1093/nar/gkw318. Epub 2016 Apr 29.

7.

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier AS, Patch AM, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Gröbner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Giner FC, Beltran S, Raineri E, Dabad M, Heath SC, Gut M, Denroche RE, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch AG, Anderson CL, Waddell N, Pearson JV, Grimmond SM, Peto M, Spellman P, He M, Kandoth C, Lee S, Zhang J, Létourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, López-Otín C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones DT, Gut IG.

Nat Commun. 2015 Dec 9;6:10001. doi: 10.1038/ncomms10001.

8.

Boosting the FM-Index on the GPU: Effective Techniques to Mitigate Random Memory Access.

Chacón A, Marco-Sola S, Espinosa A, Ribeca P, Moure JC.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Sep-Oct;12(5):1048-59. doi: 10.1109/TCBB.2014.2377716.

PMID:
26451818
9.

Efficient Alignment of Illumina-Like High-Throughput Sequencing Reads with the GEnomic Multi-tool (GEM) Mapper.

Marco-Sola S, Ribeca P.

Curr Protoc Bioinformatics. 2015 Jun 19;50:11.13.1-20. doi: 10.1002/0471250953.bi1113s50.

PMID:
26094690
10.

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.

Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J; GTEx Consortium; Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG.

Science. 2015 May 8;348(6235):666-9. doi: 10.1126/science.1261877.

11.

Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.

Greger L, Su J, Rung J, Ferreira PG; Geuvadis consortium, Lappalainen T, Dermitzakis ET, Brazma A.

PLoS One. 2014 Aug 18;9(8):e104567. doi: 10.1371/journal.pone.0104567. eCollection 2014.

12.

Assessment of transcript reconstruction methods for RNA-seq.

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

Nat Methods. 2013 Dec;10(12):1177-84. doi: 10.1038/nmeth.2714. Epub 2013 Nov 3.

13.

Systematic evaluation of spliced alignment programs for RNA-seq data.

Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P; RGASP Consortium.

Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3.

14.

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.

't Hoen PA, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, Karlberg O, Brännvall M; GEUVADIS Consortium, den Dunnen JT, van Ommen GJ, Gut IG, Guigó R, Estivill X, Syvänen AC, Dermitzakis ET, Lappalainen T.

Nat Biotechnol. 2013 Nov;31(11):1015-22. doi: 10.1038/nbt.2702. Epub 2013 Sep 15.

PMID:
24037425
15.

Transcriptome and genome sequencing uncovers functional variation in humans.

Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM; Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET.

Nature. 2013 Sep 26;501(7468):506-11. doi: 10.1038/nature12531. Epub 2013 Sep 15.

16.

The GEM mapper: fast, accurate and versatile alignment by filtration.

Marco-Sola S, Sammeth M, Guigó R, Ribeca P.

Nat Methods. 2012 Dec;9(12):1185-8. doi: 10.1038/nmeth.2221. Epub 2012 Oct 28.

PMID:
23103880
17.

Modelling and simulating generic RNA-Seq experiments with the flux simulator.

Griebel T, Zacher B, Ribeca P, Raineri E, Lacroix V, Guigó R, Sammeth M.

Nucleic Acids Res. 2012 Nov 1;40(20):10073-83. doi: 10.1093/nar/gks666. Epub 2012 Sep 7.

18.

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.

19.

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium.

Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.

20.

The tomato genome sequence provides insights into fleshy fruit evolution.

Tomato Genome Consortium.

Nature. 2012 May 30;485(7400):635-41. doi: 10.1038/nature11119.

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