Sarah Djebali

Sarah Djebali

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Sarah Djebali

Sarah Djebali

Publications by authors named "Sarah Djebali"

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Analysis of pig transcriptomes suggests a global regulation mechanism enabling temporary bursts of circular RNAs.

RNA Biol 2019 09 3;16(9):1190-1204. Epub 2019 Jun 3.

b Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN) , Dummerstorf , Germany.

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http://dx.doi.org/10.1080/15476286.2019.1621621DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6693536PMC
September 2019

Bioinformatics Pipeline for Transcriptome Sequencing Analysis.

Methods Mol Biol 2017 ;1468:201-19

CNRS UMR6290 Dog Genetic Team, 2 av du Pr. Léon Bernard, Rennes, 35043, France.

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http://dx.doi.org/10.1007/978-1-4939-4035-6_14DOI Listing
January 2018

Erratum to: Bioinformatics Pipeline for Transcriptome Sequencing Analysis.

Methods Mol Biol 2017 ;1468:E1

CNRS UMR6290 Dog Genetic Team, 2 av du Pr. Léon Bernard, Rennes, 35043, France.

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http://dx.doi.org/10.1007/978-1-4939-4035-6_17DOI Listing
January 2017

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

BMC Genomics 2017 01 3;18(1). Epub 2017 Jan 3.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

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http://dx.doi.org/10.1186/s12864-016-3404-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209911PMC
January 2017

Erratum to: A benchmark for RNA-seq quantification pipelines.

Genome Biol 2016 09 30;17(1):203. Epub 2016 Sep 30.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1186/s13059-016-1060-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045616PMC
September 2016

Gene-specific patterns of expression variation across organs and species.

Genome Biol 2016 07 8;17(1):151. Epub 2016 Jul 8.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

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http://dx.doi.org/10.1186/s13059-016-1008-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937605PMC
July 2016

Erratum to: A benchmark for RNA-seq quantification pipelines.

Genome Biol 2016 May 23;17(1):107. Epub 2016 May 23.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1186/s13059-016-0986-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877800PMC
May 2016

A benchmark for RNA-seq quantification pipelines.

Genome Biol 2016 Apr 23;17:74. Epub 2016 Apr 23.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1186/s13059-016-0940-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4842274PMC
April 2016

Human genomics. The human transcriptome across tissues and individuals.

Science 2015 May;348(6235):660-5

Center for Genomic Regulation (CRG), Barcelona, Catalonia, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain. Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Catalonia, Spain. Joint CRG-Barcelona Super Computing Center (BSC)-Institut de Recerca Biomedica (IRB) Program in Computational Biology, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1126/science.aaa0355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547472PMC
May 2015

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

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

Nucleic Acids Res 2013 Aug 12;41(15):7220-30. Epub 2013 Jun 12.

Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Joint IRB-BSC Research Program on Computational Biology, Barcelona 08028, Spain, Bioinformatics and Genomics Group, Center for Genomic Regulation and Universitat Pompeu Fabra, Barcelona 08003, Spain, Barcelona Supercomputing Center, Barcelona 08034, Spain and Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona 08028, Spain.

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http://dx.doi.org/10.1093/nar/gkt511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753636PMC
August 2013

Landscape of transcription in human cells.

Nature 2012 Sep;489(7414):101-8

Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1038/nature11233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276PMC
September 2012

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 2012

Modeling gene expression using chromatin features in various cellular contexts.

Genome Biol 2012 Jun 13;13(9):R53. Epub 2012 Jun 13.

Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1186/gb-2012-13-9-r53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491397PMC
June 2012

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

Genome Biol 2006 7;7 Suppl 1:S7.1-10. Epub 2006 Aug 7.

Dyogen Lab, CNRS UMR8541, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France.

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http://dx.doi.org/10.1186/gb-2006-7-s1-s7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810556PMC
September 2006