Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA

por Djebali, Sarah, Delaplace, Franck, Crollius, Hugues Roest
Publicado 2006

TAGADA: a scalable pipeline to improve genome annotations with RNA-seq data

por Kurylo, Cyril, Guyomar, Cervin, Foissac, Sylvain, Djebali, Sarah
Publicado 2023

Correlation Networks Provide New Insights into the Architecture of Testicular Steroid Pathways in Pigs

por Robic, Annie, Faraut, Thomas, Feve, Katia, Djebali, Sarah, Prunier, Armelle, Larzul, Catherine, Liaubet, Laurence
Publicado 2021

Enhancer/gene relationships: Need for more reliable genome-wide reference sets

por Hoellinger, Tristan, Mestre, Camille, Aschard, Hugues, Le Goff, Wilfried, Foissac, Sylvain, Faraut, Thomas, Djebali, Sarah
Publicado 2023

Gene-specific patterns of expression variation across organs and species

por Breschi, Alessandra, Djebali, Sarah, Gillis, Jesse, Pervouchine, Dmitri D., Dobin, Alex, Davis, Carrie A., Gingeras, Thomas R., Guigó, Roderic
Publicado 2016

Unravelling the hidden DNA structural/physical code provides novel insights on promoter location

por Durán, Elisa, Djebali, Sarah, González, Santi, Flores, Oscar, Mercader, Josep Maria, Guigó, Roderic, Torrents, David, Soler-López, Montserrat, Orozco, Modesto
Publicado 2013

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

por Rodríguez-Martín, Bernardo, Palumbo, Emilio, Marco-Sola, Santiago, Griebel, Thasso, Ribeca, Paolo, Alonso, Graciela, Rastrojo, Alberto, Aguado, Begoña, Guigó, Roderic, Djebali, Sarah
Publicado 2017

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

por Tilgner, Hagen, Knowles, David G., Johnson, Rory, Davis, Carrie A., Chakrabortty, Sudipto, Djebali, Sarah, Curado, João, Snyder, Michael, Gingeras, Thomas R., Guigó, Roderic
Publicado 2012

Modeling gene expression using chromatin features in various cellular contexts

por Dong, Xianjun, Greven, Melissa C, Kundaje, Anshul, Djebali, Sarah, Brown, James B, Cheng, Chao, Gingeras, Thomas R, Gerstein, Mark, Guigó, Roderic, Birney, Ewan, Weng, Zhiping
Publicado 2012

Long noncoding RNA repertoire in chicken liver and adipose tissue

por Muret, Kévin, Klopp, Christophe, Wucher, Valentin, Esquerré, Diane, Legeai, Fabrice, Lecerf, Frédéric, Désert, Colette, Boutin, Morgane, Jehl, Frédéric, Acloque, Hervé, Giuffra, Elisabetta, Djebali, Sarah, Foissac, Sylvain, Derrien, Thomas, Lagarrigue, Sandrine
Publicado 2017

A benchmark for RNA-seq quantification pipelines

por Teng, Mingxiang, Love, Michael I., Davis, Carrie A., Djebali, Sarah, Dobin, Alexander, Graveley, Brenton R., Li, Sheng, Mason, Christopher E., Olson, Sara, Pervouchine, Dmitri, Sloan, Cricket A., Wei, Xintao, Zhan, Lijun, Irizarry, Rafael A.
Publicado 2016

Erratum to: A benchmark for RNA-seq quantification pipelines

por Teng, Mingxiang, Love, Michael I., Davis, Carrie A., Djebali, Sarah, Dobin, Alexander, Graveley, Brenton R., Li, Sheng, Mason, Christopher E., Olson, Sara, Pervouchine, Dmitri, Sloan, Cricket A., Wei, Xintao, Zhan, Lijun, Irizarry, Rafael A.
Publicado 2016

Erratum to: A benchmark for RNA-seq quantification pipelines

por Teng, Mingxiang, Love, Michael I., Davis, Carrie A., Djebali, Sarah, Dobin, Alexander, Graveley, Brenton R., Li, Sheng, Mason, Christopher E., Olson, Sara, Pervouchine, Dmitri, Sloan, Cricket A., Wei, Xintao, Zhan, Lijun, Irizarry, Rafael A.
Publicado 2016

An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues

por Jehl, Frédéric, Muret, Kévin, Bernard, Maria, Boutin, Morgane, Lagoutte, Laetitia, Désert, Colette, Dehais, Patrice, Esquerré, Diane, Acloque, Hervé, Giuffra, Elisabetta, Djebali, Sarah, Foissac, Sylvain, Derrien, Thomas, Pitel, Frédérique, Zerjal, Tatiana, Klopp, Christophe, Lagarrigue, Sandrine
Publicado 2020

Author Correction: An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues

por Jehl, Frédéric, Muret, Kévin, Bernard, Maria, Boutin, Morgane, Lagoutte, Laetitia, Désert, Colette, Dehais, Patrice, Esquerré, Diane, Acloque, Hervé, Giuffra, Elisabetta, Djebali, Sarah, Foissac, Sylvain, Derrien, Thomas, Pitel, Frédérique, Zerjal, Tatiana, Klopp, Christophe, Lagarrigue, Sandrine
Publicado 2021

A Bos taurus sequencing methods benchmark for assembly, haplotyping, and variant calling

por Eché, Camille, Iampietro, Carole, Birbes, Clément, Dréau, Andreea, Kuchly, Claire, Di Franco, Arnaud, Klopp, Christophe, Faraut, Thomas, Djebali, Sarah, Castinel, Adrien, Zytnicki, Matthias, Denis, Erwan, Boussaha, Mekki, Grohs, Cécile, Boichard, Didier, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile
Publicado 2023

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

por Cheng, Chao, Alexander, Roger, Min, Renqiang, Leng, Jing, Yip, Kevin Y., Rozowsky, Joel, Yan, Koon-Kiu, Dong, Xianjun, Djebali, Sarah, Ruan, Yijun, Davis, Carrie A., Carninci, Piero, Lassman, Timo, Gingeras, Thomas R., Guigó, Roderic, Birney, Ewan, Weng, Zhiping, Snyder, Michael, Gerstein, Mark
Publicado 2012

A limited set of transcriptional programs define major cell types

por Breschi, Alessandra, Muñoz-Aguirre, Manuel, Wucher, Valentin, Davis, Carrie A., Garrido-Martín, Diego, Djebali, Sarah, Gillis, Jesse, Pervouchine, Dmitri D., Vlasova, Anna, Dobin, Alexander, Zaleski, Chris, Drenkow, Jorg, Danyko, Cassidy, Scavelli, Alexandra, Reverter, Ferran, Snyder, Michael P., Gingeras, Thomas R., Guigó, Roderic
Publicado 2020

Efficient targeted transcript discovery via array-based normalization of RACE libraries

por Djebali, Sarah, Kapranov, Philipp, Foissac, Sylvain, Lagarde, Julien, Reymond, Alexandre, Ucla, Catherine, Wyss, Carine, Drenkow, Jorg, Dumais, Erica, Murray, Ryan R., Lin, Chenwei, Szeto, David, Denoeud, France, Calvo, Miquel, Frankish, Adam, Harrow, Jennifer, Makrythanasis, Periklis, Vidal, Marc, Salehi-Ashtiani, Kourosh, Antonarakis, Stylianos E., Gingeras, Thomas R., Guigó, Roderic
Publicado 2008

RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Sp...

por Jehl, Frédéric, Degalez, Fabien, Bernard, Maria, Lecerf, Frédéric, Lagoutte, Laetitia, Désert, Colette, Coulée, Manon, Bouchez, Olivier, Leroux, Sophie, Abasht, Behnam, Tixier-Boichard, Michèle, Bed’hom, Bertrand, Burlot, Thierry, Gourichon, David, Bardou, Philippe, Acloque, Hervé, Foissac, Sylvain, Djebali, Sarah, Giuffra, Elisabetta, Zerjal, Tatiana, Pitel, Frédérique, Klopp, Christophe, Lagarrigue, Sandrine
Publicado 2021