Robust inference of expression state in bulk and single-cell RNA-Seq using curated intergenic regions

Autor: Sara S. Fonseca Costa, Marta Rosikiewicz, Julien Roux, Julien Wollbrett, Frederic B. Bastian, Marc Robinson-Rechavi

RNA-Seq is a powerful technique to provide quantitative information on gene expression. While many applications focus on estimated expression levels, it is also important to determine which genes are actively transcribed, and which are not. The probl

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::0b4b1488c76a94201505cf0fbe0aed4f
https://doi.org/10.1101/2022.03.31.486555

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

Autor: Julien Roux, Sara S. Fonseca Costa, Philippe Moret, Julien Wollbrett, Sébastien Moretti, Frederic B. Bastian, Anne Niknejad, Komal Sanjeev, Valentine Rech de Laval, Yohan Jarosz, Marc Robinson-Rechavi, Amina Echchiki, Mar Gonzales-Porta, Angelique Escoriza, Emilie Person, Balazs Laurenczy, Aurélie Comte, Marta Rosikiewicz, Gilles Parmentier, Walid H. Gharib, Mathieu Seppey, Tarcisio Mendes de Farias, Patrick Roelli

Publikováno v: Nucleic acids research, vol. 49, no. D1, pp. D831-D847
Nucleic Acids Research

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-ty

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::18c02da2c43d54ed381b35fef7cfc28b
https://doi.org/10.1093/nar/gkaa793

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations

Autor: Suzanna E. Lewis, Gemma L. Holliday, Frederic B. Bastian, Sylvain Poux, Sandra Orchard, Nives Škunca, Pascale Gaudet, Michelle G. Giglio, Anne Niknejad, Marc Robinson-Rechavi, Marcus C. Chibucos, Hong Huang

Publikováno v: Database, vol. 2015, pp. bav043
Database: The Journal of Biological Databases and Curation
Database, Vol. 2015 (2015) P. bav043
Database, 2015

Biocuration has become a cornerstone for analyses in biology, and to meet needs, the amount of annotations has considerably grown in recent years. However, the reliability of these annotations varies; it has thus become necessary to be able to assess

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cf19dde32c1b743930bf52c2aa68f5c8
https://serval.unil.ch/resource/serval:BIB_60CACFAC405E.P001/REF.pdf

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests

Autor: Andrea Komljenovic, Julien Roux, Marc Robinson-Rechavi, Frederic B. Bastian

Publikováno v: F1000Research. 5:2748

BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and reprocessed expression data available in the Bgee database. This includes data from thousands of wild-type healthy samples of multiple animal species, generated

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::292270b08d48c6a9914209fedb9870a0
https://doi.org/10.12688/f1000research.9973.1

vHOG, a multispecies vertebrate ontology of homologous organs groups

Autor: Julien Roux, Aurélie Comte, Anne Niknejad, Gilles Parmentier, Frederic B. Bastian, Marc Robinson-Rechavi

Publikováno v: Bioinformatics
Bioinformatics, vol. 28, no. 7, pp. 1017-1020
Bioinformatics (Oxford England)

Motivation: Most anatomical ontologies are species-specific, whereas a framework for comparative studies is needed. We describe the vertebrate Homologous Organs Groups ontology, vHOG, used to compare expression patterns between species. Results: vHOG

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::22aa01021e54cded2fac39cbb855c4a5
https://pubmed.ncbi.nlm.nih.gov/22285560