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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. Steijger T, et al. Among authors: harrow j. Nat Methods. 2013 Dec;10(12):1177-84. doi: 10.1038/nmeth.2714. Epub 2013 Nov 3. Nat Methods. 2013. PMID: 24185837 Free PMC article.
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. Engström PG, et al. Among authors: harrow j. Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3. Nat Methods. 2013. PMID: 24185836 Free PMC article.
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. Djebali S, et al. Among authors: harrow j. Nat Methods. 2008 Jul;5(7):629-35. doi: 10.1038/nmeth.1216. Epub 2008 May 25. Nat Methods. 2008. PMID: 18500348 Free PMC article.
Identifying protein-coding genes in genomic sequences.
Harrow J, Nagy A, Reymond A, Alioto T, Patthy L, Antonarakis SE, Guigó R. Harrow J, et al. Genome Biol. 2009;10(1):201. doi: 10.1186/gb-2009-10-1-201. Epub 2009 Jan 30. Genome Biol. 2009. PMID: 19226436 Free PMC article. Review.
AnnoTrack--a tracking system for genome annotation.
Kokocinski F, Harrow J, Hubbard T. Kokocinski F, et al. Among authors: harrow j. BMC Genomics. 2010 Oct 5;11:538. doi: 10.1186/1471-2164-11-538. BMC Genomics. 2010. PMID: 20923551 Free PMC article.
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. Djebali S, et al. Among authors: harrow j. Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233. Nature. 2012. PMID: 22955620 Free PMC article.
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.
Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle S, Harrow J, Hubbard TJ, Guigó R, Reymond A. Howald C, et al. Among authors: harrow j. Genome Res. 2012 Sep;22(9):1698-710. doi: 10.1101/gr.134478.111. Genome Res. 2012. PMID: 22955982 Free PMC article.
Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).
Lagarde J, Uszczynska-Ratajczak B, Santoyo-Lopez J, Gonzalez JM, Tapanari E, Mudge JM, Steward CA, Wilming L, Tanzer A, Howald C, Chrast J, Vela-Boza A, Rueda A, Lopez-Domingo FJ, Dopazo J, Reymond A, Guigó R, Harrow J. Lagarde J, et al. Among authors: harrow j. Nat Commun. 2016 Aug 17;7:12339. doi: 10.1038/ncomms12339. Nat Commun. 2016. PMID: 27531712 Free PMC article.
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. Guigó R, et al. Among authors: harrow j. Genome Biol. 2006;7 Suppl 1(Suppl 1):S2.1-31. doi: 10.1186/gb-2006-7-s1-s2. Epub 2006 Aug 7. Genome Biol. 2006. PMID: 16925836 Free PMC article. Review.
149 results