Systematic evaluation of spliced alignment programs for RNA-seq data

Autor: Engström, Pg, Steijger, T, Sipos, B, Grant, Gr, Kahles, A, Alioto, T, Behr, J, Bertone, P, Bohnert, R, Campagna, Davide, Davis, Ca, Dobin, A, Gingeras, Tr, Goldman, N, Guigó, R, Harrow, J, Hubbard, Tj, Jean, G, Kosarev, P, Li, S, Liu, J, Mason, Ce, Molodtsov, V, Ning, Z, Ponstingl, H, Prins, Jf, Rätsch, G, Ribeca, P, Seledtsov, I, Solovyev, V, Valle, Giorgio, Vitulo, Nicola, Wang, K, Wu, Td, Zeller, G, Rgasp, Consortium

Publikováno v: Nature methods
Nature Methods
Nature Methods, Nature Publishing Group, 2013, epub ahead of print. ⟨10.1038/nmeth.2722⟩
Recercat. Dipósit de la Recerca de Catalunya
instname

LINA-COMBI; International audience; : High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6385fd1559cfdc01d937b50d88596646
http://europepmc.org/articles/PMC4018468

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The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells

Autor: Castelo-Branco, G, Amaral, P, Engström, PG, Robson, S, Marques, SC, Bertone, P, Kouzarides, T

BACKGROUND: Pluripotency is characterized by a unique transcriptional state, in which lineage-specification genes are poised for transcription upon exposure to appropriate stimuli, via a bivalency mechanism involving the simultaneous presence of acti

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::5af4d1d57ed2f4540df21302033e8861

Novel loss-of-function variant in DENND5A impedes melanosomal cargo transport and predisposes to familial cutaneous melanoma.

Autor: Yang M; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden., Johnsson P; Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Ludwig Institute for Cancer Research, Stockholm, Sweden., Bräutigam L; Comparative Medicine, Karolinska Institutet, Stockholm, Sweden., Yang XR; Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD., Thrane K; Department of Gene Technology, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden., Gao J; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden., Tobin NP; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden., Zhou Y; Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden., Yu R; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden., Nagy N; Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden., Engström PG; Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, SciLifeLab, Stockholm University, Stockholm, Sweden., Tuominen R; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden., Eriksson H; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden., Lundeberg J; Department of Gene Technology, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden., Tucker MA; Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD., Goldstein AM; Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD., Egyhazi-Brage S; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden., Zhao J; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden. Electronic address: jian.zhao@ki.se., Cao Y; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden., Höiom V; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden. Electronic address: veronica.hoiom@ki.se.

Publikováno v: Genetics in medicine : official journal of the American College of Medical Genetics [Genet Med] 2022 Jan; Vol. 24 (1), pp. 157-169. Date of Electronic Publication: 2021 Nov 30.