Publications

Anäis Prouteau, Jérôme Alexandre Denis, Pauline De Fornel, Edouard Cadieu, Thomas Derrien, Camille Kergal, Nadine Botherel, Ronan Ulvé, Mélanie Rault, Amira Bouzidi, Romain François, Laetitia Dorso, Alexandra Lespagnol, Patrick Devauchelle, Jérôme Abadie, Catherine André, Benoît Hédan (2021). Circulating tumor DNA is detectable in canine histiocytic sarcoma, oral malignant melanoma, and multicentric lymphoma. Scientific Reports.

Benoît Hédan, Édouard Cadieu, Maud Rimbault, Amaury Vaysse, Caroline Dufaure de Citres, Patrick Devauchelle, Nadine Botherel, Jérôme Abadie, Pascale Quignon, Thomas Derrien, Catherine André (2021). Identification of common predisposing loci to hematopoietic cancers in four dog breeds. PLoS genetics.

Julia V. Halo, Amanda L. Pendleton, Feichen Shen, Aurélien J. Doucet, Thomas Derrien, Christophe Hitte, Laura E. Kirby, Bridget Myers, Elzbieta Sliwerska, Sarah Emery, John V. Moran, Adam R. Boyko, Jeffrey M. Kidd (2021). Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes. Proceedings of the National Academy of Sciences.

Benoit Hédan, Mélanie Rault, Jérôme Abadie, Ronan Ulvé, Nadine Botherel, Patrick Devauchelle, Christiane Copie‐Bergman, Edouard Cadieu, Marie Parrens, Julia Alten, Emmanuelle L. Zalcman, Gunnar Cario, Gandhi Damaj, Karima Mokhtari, Francois Le Loarer, Aurore Coulomb‐Lhermine, Thomas Derrien, Christophe Hitte, Laura Bachelot, Matthew Breen, David Gilot, Jean Y. Blay, Jean Donadieu, Catherine André (2020). PTPN11 mutations in canine and human disseminated histiocytic sarcoma. International Journal of Cancer.

Sylvain Foissac, Sarah Djebali, Kylie Munyard, Nathalie Vialaneix, Andrea Rau, Kevin Muret, Diane Esquerre, Matthias Zytnicki, Thomas Derrien, Philippe Bardou, Fany Blanc, Cedric Cabau, Elisa Crisci, Sophie Dhorne-Pollet, Francoise Drouet, Thomas Faraut, Ignacio Gonzalez, Adeline Goubil, Sonia Lacroix-Lamande, Fabrice Laurent, Sylvain Marthey, Maria Marti-Marimon, Raphaelle Momal-Leisenring, Florence Mompart, Pascale Quere, David Robelin, Magali San Cristobal, Gwenola Tosser-Klopp, Silvia Vincent-Naulleau, Stephane Fabre, Marie-Helene Pinard-Van der Laan, Christophe Klopp, Michele Tixier-Boichard, Herve Acloque, Sandrine Lagarrigue, Elisabetta Giuffra (2019). Multi-species annotation of transcriptome and chromatin structure in domesticated animals.. BMC biology.

Camille Sessegolo, Corinne Cruaud, Corinne Da Silva, Audric Cologne, Marion Dubarry, Thomas Derrien, Vincent Lacroix, Jean-Marc Aury (2019). Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules.. Scientific reports.

Anais Prouteau, Florian Chocteau, Clotilde Brito, Edouard Cadieu, Aline Primot, Nadine Botherel, Frédérique Degorce, Laurence Cornevin, Marie A. Lagadic, Florian Cabillic, Pauline Fornel‐Thibaud, Patrick Devauchelle, Thomas Derrien, Jerome Abadie, Catherine André, Benoît Hédan (2019). Prognostic value of somatic focal amplifications on chromosome 30 in canine oral melanoma. Veterinary and Comparative Oncology.

Christophe Hitte, Céline Le Béguec, Edouard Cadieu, Valentin Wucher, Aline Primot, Anäis Prouteau, Nadine Botherel, Benoît Hédan, Kerstin Lindblad-Toh, Catherine André, Thomas Derrien (2019). Genome-Wide Analysis of Long Non-Coding RNA Profiles in Canine Oral Melanomas. Genes.

Benoit Hedan, Edouard Cadieu, Nadine Botherel, Caroline Dufaure de Citres, Anna Letko, Maud Rimbault, Cord Drogemuller, Vidhya Jagannathan, Thomas Derrien, Sheila Schmutz, Tosso Leeb, Catherine Andre (2019). Identification of a Missense Variant in MFSD12 Involved in Dilution of Phaeomelanin Leading to White or Cream Coat Color in Dogs.. Genes.

Céline Le Béguec, Valentin Wucher, Lætitia Lagoutte, Edouard Cadieu, Nadine Botherel, Benoît Hédan, Clotilde De Brito, Anne-Sophie Guillory, Catherine André, Thomas Derrien, Christophe Hitte (2018). Characterisation and functional predictions of canine long non-coding RNAs.. Scientific reports.

Ronan Ulve, Melanie Rault, Mathieu Bahin, Laetitia Lagoutte, Jerome Abadie, Clotilde De Brito, Jean-Michel Coindre, Nadine Botherel, Audrey Rousseau, Valentin Wucher, Edouard Cadieu, Catherine Thieblemont, Christophe Hitte, Laurence Cornevin, Florian Cabillic, Laura Bachelot, David Gilot, Benoit Hennuy, Thierry Guillaudeux, Arnaud Le Goff, Thomas Derrien, Benoit Hedan, Catherine Andre (2017). Discovery of Human-Similar Gene Fusions in Canine Cancers.. Cancer research.

Bart J G Broeckx, Thomas Derrien, Stéphanie Mottier, Valentin Wucher, Edouard Cadieu, Benoît Hédan, Céline Le Béguec, Nadine Botherel, Kerstin Lindblad-Toh, Jimmy H Saunders, Dieter Deforce, Catherine André, Luc Peelman, Christophe Hitte (2017). An exome sequencing based approach for genome-wide association studies in the dog.. Scientific reports.

Thomas C Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T Mugford, Patrice Baa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamas Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldon, Anna Jordan, Irene Julca, Graeme J Kettles, Krissana Kowitwanich, Dominique Lavenier, Paolo Lenzi, Sara Lopez-Gomollon, Damian Loska, Daniel Mapleson, Florian Maumus, Simon Moxon, Daniel R G Price, Akiko Sugio, Manuella van Munster, Marilyne Uzest, Darren Waite, Georg Jander, Denis Tagu, Alex C C Wilson, Cock van Oosterhout, David Swarbreck, Saskia A Hogenhout (2017). Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.. Genome biology.

Kevin Muret, Christophe Klopp, Valentin Wucher, Diane Esquerre, Fabrice Legeai, Frederic Lecerf, Colette Desert, Morgane Boutin, Frederic Jehl, Herve Acloque, Elisabetta Giuffra, Sarah Djebali, Sylvain Foissac, Thomas Derrien, Sandrine Lagarrigue (2017). Long noncoding RNA repertoire in chicken liver and adipose tissue.. Genetics, selection, evolution : GSE.

Valentin Wucher, Fabrice Legeai, Benoît Hédan, Guillaume Rizk, Laetitia Lagoutte, Tosso Leeb, Vidhya Jagannathan, Edouard Cadieu, Audrey David, Hannes Lohi, Susanna Cirera, Merete Fredholm, Nadine Botherel, Peter A.J. Leegwater, Céline Le Béguec, Hille Fieten, Jeremy Johnson, Jessica Alföldi, Catherine André, Kerstin Lindblad-Toh, Christophe Hitte, Thomas Derrien (2017). FEELnc: A tool for long non-coding RNA annotation and its application to the dog transcriptome. Nucleic Acids Research.

Sarah Djebali, Valentin Wucher, Sylvain Foissac, Christophe Hitte, Erwan Corre, Thomas Derrien (2017). Bioinformatics Pipeline for Transcriptome Sequencing Analysis.. Methods in molecular biology (Clifton, N.J.).

Jocelyn Plassais, Laetitia Lagoutte, Solenne Correard, Manon Paradis, Eric Guaguere, Benoit Hedan, Alix Pommier, Nadine Botherel, Marie-Christine Cadiergues, Philippe Pilorge, David Silversides, Maud Bizot, Mark Samuels, Carme Arnan, Rory Johnson, Christophe Hitte, Gilles Salbert, Agnes Mereau, Pascale Quignon, Thomas Derrien, Catherine Andre (2016). A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory Neuropathies.. PLoS genetics.

Bart J G Broeckx, Christophe Hitte, Frank Coopman, Geert E C Verhoeven, Sarah De Keulenaer, Ellen De Meester, Thomas Derrien, Jessica Alfoldi, Kerstin Lindblad-Toh, Tim Bosmans, Ingrid Gielen, Henri Van Bree, Bernadette Van Ryssen, Jimmy H Saunders, Filip Van Nieuwerburgh, Dieter Deforce (2015). Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes.. Scientific reports.

Michael Schmid, Jacqueline Smith, David W Burt, Bronwen L Aken, Parker B Antin, Alan L Archibald, Chris Ashwell, Perry J Blackshear, Clarissa Boschiero, C Titus Brown, Shane C Burgess, Hans H Cheng, William Chow, Derrick J Coble, Amanda Cooksey, Richard P M A Crooijmans, Joana Damas, Richard V N Davis, Dirk-Jan de Koning, Mary E Delany, Thomas Derrien, Takele T Desta, Ian C Dunn, Matthew Dunn, Hans Ellegren, Lel Eory, Ionas Erb, Marta Farre, Mario Fasold, Damarius Fleming, Paul Flicek, Katie E Fowler, Laure Fresard, David P Froman, Valerie Garceau, Paul P Gardner, Almas A Gheyas, Darren K Griffin, Martien A M Groenen, Thomas Haaf, Olivier Hanotte, Alan Hart, Julien Hasler, S Blair Hedges, Jana Hertel, Kerstin Howe, Allen Hubbard, David A Hume, Pete Kaiser, Darek Kedra, Stephen J Kemp, Christophe Klopp, Kalmia E Kniel, Richard Kuo, Sandrine Lagarrigue, Susan J Lamont, Denis M Larkin, Raman A Lawal, Sarah M Markland, Fiona McCarthy, Heather A McCormack, Marla C McPherson, Akira Motegi, Stefan A Muljo, Andrea Munsterberg, Rishi Nag, Indrajit Nanda, Michael Neuberger, Anne Nitsche, Cedric Notredame, Harry Noyes, Rebecca O'Connor, Elizabeth A O'Hare, Andrew J Oler, Sheila C Ommeh, Helio Pais, Michael Persia, Frederique Pitel, Likit Preeyanon, Pablo Prieto Barja, Elizabeth M Pritchett, Douglas D Rhoads, Charmaine M Robinson, Michael N Romanov, Max Rothschild, Pierre-Francois Roux, Carl J Schmidt, Alisa-Sophia Schneider, Matthew G Schwartz, Steve M Searle, Michael A Skinner, Craig A Smith, Peter F Stadler, Tammy E Steeves, Claus Steinlein, Liang Sun, Minoru Takata, Igor Ulitsky, Qing Wang, Ying Wang, Wesley C Warren, Jonathan M D Wood, David Wragg, Huaijun Zhou (2015). Third Report on Chicken Genes and Chromosomes 2015.. Cytogenetic and genome research.

Tamara Steijger, Josep F. Abril, Pär G. Engström, Felix Kokocinski, Martin Akerman, Tyler Alioto, Giovanna Ambrosini, Stylianos E. Antonarakis, Jonas Behr, Paul Bertone, Regina Bohnert, Philipp Bucher, Nicole Cloonan, Thomas Derrien, Sarah Djebali, Jiang Du, Sandrine Dudoit, Mark Gerstein, Thomas R. Gingeras, David Gonzalez, Sean M. Grimmond, Roderic Guigó, Lukas Habegger, Jennifer Harrow, Tim J. Hubbard, Christian Iseli, Géraldine Jean, André Kahles, Julien Lagarde, Jing Leng, Gregory Lefebvre, Suzanna Lewis, Ali Mortazavi, Peter Niermann, Gunnar Rätsch, Alexandre Reymond, Paolo Ribeca, Hugues Richard, Jacques Rougemont, Joel Rozowsky, Michael Sammeth, Andrea Sboner, Marcel H. Schulz, Steven M.J. Searle, Naryttza Diaz Solorzano, Victor Solovyev, Mario Stanke, Brian J. Stevenson, Heinz Stockinger, Armand Valsesia, David Weese, Simon White, Barbara J. Wold, Jie Wu, Thomas D. Wu, Georg Zeller, Daniel Zerbino, Michael Q. Zhang (2013). Assessment of transcript reconstruction methods for RNA-seq. Nature Methods.

Thomas Derrien, Rory Johnson, Giovanni Bussotti, Andrea Tanzer, Sarah Djebali, Hagen Tilgner, Gregory Guernec, David Martin, Angelika Merkel, David G Knowles, Julien Lagarde, Lavanya Veeravalli, Xiaoan Ruan, Yijun Ruan, Timo Lassmann, Piero Carninci, James B Brown, Leonard Lipovich, Jose M Gonzalez, Mark Thomas, Carrie A Davis, Ramin Shiekhattar, Thomas R Gingeras, Tim J Hubbard, Cedric Notredame, Jennifer Harrow, Roderic Guigo (2012). The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.. Genome research.

Sarah Djebali, Carrie A Davis, Angelika Merkel, Alex Dobin, Timo Lassmann, Ali Mortazavi, Andrea Tanzer, Julien Lagarde, Wei Lin, Felix Schlesinger, Chenghai Xue, Georgi K Marinov, Jainab Khatun, Brian A Williams, Chris Zaleski, Joel Rozowsky, Maik Roder, Felix Kokocinski, Rehab F Abdelhamid, Tyler Alioto, Igor Antoshechkin, Michael T Baer, Nadav S Bar, Philippe Batut, Kimberly Bell, Ian Bell, Sudipto Chakrabortty, Xian Chen, Jacqueline Chrast, Joao Curado, Thomas Derrien, Jorg Drenkow, Erica Dumais, Jacqueline Dumais, Radha Duttagupta, Emilie Falconnet, Meagan Fastuca, Kata Fejes-Toth, Pedro Ferreira, Sylvain Foissac, Melissa J Fullwood, Hui Gao, David Gonzalez, Assaf Gordon, Harsha Gunawardena, Cedric Howald, Sonali Jha, Rory Johnson, Philipp Kapranov, Brandon King, Colin Kingswood, Oscar J Luo, Eddie Park, Kimberly Persaud, Jonathan B Preall, Paolo Ribeca, Brian Risk, Daniel Robyr, Michael Sammeth, Lorian Schaffer, Lei-Hoon See, Atif Shahab, Jorgen Skancke, Ana Maria Suzuki, Hazuki Takahashi, Hagen Tilgner, Diane Trout, Nathalie Walters, Huaien Wang, John Wrobel, Yanbao Yu, Xiaoan Ruan, Yoshihide Hayashizaki, Jennifer Harrow, Mark Gerstein, Tim Hubbard, Alexandre Reymond, Stylianos E Antonarakis, Gregory Hannon, Morgan C Giddings, Yijun Ruan, Barbara Wold, Piero Carninci, Roderic Guigo, Thomas R Gingeras (2012). Landscape of transcription in human cells.. Nature.

Cedric Howald, Andrea Tanzer, Jacqueline Chrast, Felix Kokocinski, Thomas Derrien, Nathalie Walters, Jose M Gonzalez, Adam Frankish, Bronwen L Aken, Thibaut Hourlier, Jan-Hinnerk Vogel, Simon White, Stephen Searle, Jennifer Harrow, Tim J Hubbard, Roderic Guigo, Alexandre Reymond (2012). Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.. Genome research.

Thomas Derrien, Amaury Vaysse, Catherine Andre, Christophe Hitte (2012). Annotation of the domestic dog genome sequence: finding the missing genes.. Mammalian genome : official journal of the International Mammalian Genome Society.

Thomas Derrien, Jordi Estelle, Santiago Marco Sola, David G Knowles, Emanuele Raineri, Roderic Guigo, Paolo Ribeca (2012). Fast computation and applications of genome mappability.. PloS one.

Jonathan M Mudge, Adam Frankish, Julio Fernandez-Banet, Tyler Alioto, Thomas Derrien, Cedric Howald, Alexandre Reymond, Roderic Guigo, Tim Hubbard, Jennifer Harrow (2011). The origins, evolution, and functional potential of alternative splicing in vertebrates.. Molecular biology and evolution.

Amaury Vaysse, Abhirami Ratnakumar, Thomas Derrien, Erik Axelsson, Gerli Rosengren Pielberg, Snaevar Sigurdsson, Tove Fall, Eija H Seppala, Mark S T Hansen, Cindy T Lawley, Elinor K Karlsson, Danika Bannasch, Carles Vila, Hannes Lohi, Francis Galibert, Merete Fredholm, Jens Haggstrom, Ake Hedhammar, Catherine Andre, Kerstin Lindblad-Toh, Christophe Hitte, Matthew T Webster (2011). Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping.. PLoS genetics.

Thomas Derrien, Roderic Guigo (2011). [Long non-coding RNAs with enhancer-like function in human cells].. Medecine sciences : M/S.

Thomas Derrien, Roderic Guigo, Rory Johnson (2011). The Long Non-Coding RNAs: A New (P)layer in the \"Dark Matter\".. Frontiers in genetics.

Ulf Andersson Orom, Thomas Derrien, Malte Beringer, Kiranmai Gumireddy, Alessandro Gardini, Giovanni Bussotti, Fan Lai, Matthias Zytnicki, Cedric Notredame, Qihong Huang, Roderic Guigo, Ramin Shiekhattar (2010). Long noncoding RNAs with enhancer-like function in human cells.. Cell.

U A Orom, T Derrien, R Guigo, R Shiekhattar (2010). Long noncoding RNAs as enhancers of gene expression.. Cold Spring Harbor symposia on quantitative biology.

Thomas Derrien, Julien Theze, Amaury Vaysse, Catherine Andre, Elaine A Ostrander, Francis Galibert, Christophe Hitte (2009). Revisiting the missing protein-coding gene catalog of the domestic dog.. BMC genomics.

Thomas Derrien, Catherine Andre, Francis Galibert, Christophe Hitte (2007). AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps.. Bioinformatics (Oxford, England).

Thomas Derrien, Catherine Andre, Francis Galibert, Christophe Hitte (2007). Analysis of the unassembled part of the dog genome sequence: chromosomal localization of 115 genes inferred from multispecies comparative genomics.. The Journal of heredity.

T Faraut, S de Givry, P Chabrier, T Derrien, F Galibert, C Hitte, T Schiex (2007). A comparative genome approach to marker ordering.. Bioinformatics (Oxford, England).

Benoit Hedan, Sebastien Corre, Christophe Hitte, Stephane Dreano, Thierry Vilboux, Thomas Derrien, Bernard Denis, Francis Galibert, Marie-Dominique Galibert, Catherine Andre (2006). Coat colour in dogs: identification of the merle locus in the Australian shepherd breed.. BMC veterinary research.

Christophe Hitte, Jennifer Madeoy, Ewen F Kirkness, Catherine Priat, Travis D Lorentzen, Fabrice Senger, Dan Thomas, Thomas Derrien, Christina Ramirez, Carol Scott, Gwenaelle Evanno, Barbara Pullar, Edouard Cadieu, Vinay Oza, Kristelle Lourgant, David B Jaffe, Sandrine Tacher, Stephane Dreano, Nadia Berkova, Catherine Andre, Panagiotis Deloukas, Claire Fraser, Kerstin Lindblad-Toh, Elaine A Ostrander, Francis Galibert (2005). Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping.. Nature reviews. Genetics.

Christophe Hitte, Thomas Derrien, Catherine Andre, Elaine A Ostrander, Francis Galibert (2004). CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome.. Bioinformatics (Oxford, England).