RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing

Autor: Ivan de la Rubia, Akanksha Srivastava, Wenjing Xue, Joel A. Indi, Silvia Carbonell-Sala, Julien Lagarde, M. Mar Albà, Eduardo Eyras

Publikováno v: Genome Biology, Vol 23, Iss 1, Pp 1-21 (2022)

Abstract Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes. Current methods for transcript identification and quantification rely on mapping reads to a reference genome, which precludes the study of species with a p

Externí odkaz: https://doaj.org/article/2aea7a73013a4bcfa785023e73ad47b8

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Autor: Hazuki Takahashi, Christopher Vollmers, Stefan Goetz, Margaret E. Hunter, Gabriela Balderrama-Gutierrez, David Moraga, Maite De María, Mark Diekhans, Francisco Jose Pardo-Palacios, Piero Carninci, Jonathan M. Mudge, Roderic Guigó, Gloria M. Sheynkman, Ingrid Youngworth, Kin Fai Au, Matthew Adams, Muhammed Hasan Çelik, Haoran Li, Alison D. Tang, Ana Conesa, Silvia Carbonell-Sala, Barbara J. Wold, Angela N. Brooks, Brian Williams, Julien Lagarde, Cindy Liang, Fairlie Reese, Ali Mortazavi, Andrey D. Prjibelski, Natàlia Garcia-Reyero, Jane E. Loveland, Nancy D. Denslow, Dingjie Wang, Amit Behera, Adam Frankish, Hagen Tilgner, Carlos Menor

With increased usage of long-read sequencing technologies to perform transcriptome analyses, there becomes a greater need to evaluate different methodologies including library preparation, sequencing platform, and computational analysis tools. Here,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::493797105c71ddbcbb569d8057a59b05
https://doi.org/10.21203/rs.3.rs-777702/v1

GENCODE reference annotation for the human and mouse genomes

Autor: Rory Johnson, Fernando Pozo, Andrew D. Yates, Magali Ruffier, Alexandra Bignell, Anne Parker, Adam Frankish, Osagie G. Izuogu, If Barnes, Jose Manuel Gonzalez, Tomás Di Domenico, Irwin Jungreis, Cristina Sisu, Fergal J. Martin, Anne-Maud Ferreira, Paul R. Muir, Benedict Paten, Matthew P. Hardy, Manolis Kellis, Jacqueline Chrast, Jane E. Loveland, Yan Zhang, Michael L. Tress, Fabio C. P. Navarro, Barbara Uszczynska-Ratajczak, Jonathan M. Mudge, Mark Diekhans, Shamika Mohanan, James C. Wright, Fiona Cunningham, Toby Hunt, Baikang Pei, Jinuri Xu, Tim Hubbard, Julien Lagarde, Roderic Guigó, Alexandre Reymond, Silvia Carbonell Sala, Bianca M. Schmitt, Sarah Donaldson, Mark Gerstein, Jyoti S. Choudhary, Eloise Stapleton, Bronwen Aken, Laura Martinez, Tiago Grego, Ian T. Fiddes, Joel Armstrong, Carlos García Girón, Marie-Marthe Suner, Paul Flicek, Andrew Berry, Irina Sycheva, Thibaut Hourlier, Daniel R. Zerbino

Publikováno v: Frankish, Adam; Diekhans, Mark; Ferreira, Anne-Maud; Johnson, Rory Baldwin; Jungreis, Irwin; Loveland, Jane; Mudge, Jonathan M; Sisu, Cristina; Wright, James; Armstrong, Joel; Barnes, If; Berry, Andrew; Bignell, Alexandra; Carbonell Sala, Silvia; Chrast, Jacqueline; Cunningham, Fiona; Di Domenico, Tomás; Donaldson, Sarah; Fiddes, Ian T; García Girón, Carlos; ... (2019). GENCODE reference annotation for the human and mouse genomes. Nucleic acids research, 47(D1), D766-D773. Oxford University Press 10.1093/nar/gky955
Repisalud
Instituto de Salud Carlos III (ISCIII)
Recercat. Dipósit de la Recerca de Catalunya
instname
Nucleic Acids Research
Nucleic acids research, vol. 47, no. D1, pp. D766-D773

The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e181df58a8de4f0403a4a267189a4855
https://doi.org/10.1093/nar/gky955

LRP5 gene polymorphism and cortical bone

Autor: Fulvio Lauretani, Stefania Bandinelli, Gina Paolo Ceda, Annalisa Tanini, Francesca Marini, Anna Maria Corsi, Luigi Ferrucci, Antonio Cherubini, Silvia Carbonell-Sala, Alessia Gozzini, Francesca Del Monte, Laura Masi, Alberto Falchetti, Chiara Cepollaro, Maria Luisa Brandi

Publikováno v: Scopus-Elsevier

Background and aims: There is evidence that distinct genetic polymorphisms of LRP5 are associated with low Bone Mineral Density (BMD) and the risk of fracture. However, relationships between LRP5 polymorphisms and micro- and macroarchitectural bone c

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9228c1d56b0e946315057105673b73c8
https://doi.org/10.1007/bf03324935

Osteogenic Differentiation of Human Adipose Tissue-Derived Stem Cells Is Modulated by the miR-26a Targeting of the SMAD1 Transcription Factor

Autor: Isabella Tognarini, Ettore Luzi, Francesca Marini, Gianna Galli, Maria Luisa Brandi, Silvia Carbonell Sala

Publikováno v: Journal of Bone and Mineral Research. 23:287-295

The molecular mechanisms that regulate hADSC differentiation toward osteogenic precursors and subsequent bone-forming osteoblasts is unknown. Using osteoblast precursors obtained from subcutaneous human adipose tissue, we observed that microRNA-26a m

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::04fa2311a3276f38bf183d24f91a9283
https://doi.org/10.1359/jbmr.071011