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2. Immunity and other defenses in pea aphids, Acyrthosiphon pisum

Author

Gerardo, Nicole M, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M, de Vos, Martin, Duncan, Elizabeth J, Evans, Jay D, Gabaldón, Toni, Ghanim, Murad, Heddi, Adelaziz, Kaloshian, Isgouhi, Latorre, Amparo, Moya, Andres, Nakabachi, Atsushi, Parker, Benjamin J, Pérez-Brocal, Vincente, Pignatelli, Miguel, Rahbé, Yvan, Ramsey, John S, Spragg, Chelsea J, Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vincent-Monegat, Caroline, and Vilcinskas, Andreas

Abstract

Abstract Background Recent genomic analyses of arthropod defense mechanisms suggest conservation of key elements underlying responses to pathogens, parasites and stresses. At the center of pathogen-induced immune responses are signaling pathways triggered by the recognition of fungal, bacterial and viral signatures. These pathways result in the production of response molecules, such as antimicrobial peptides and lysozymes, which degrade or destroy invaders. Using the recently sequenced genome of the pea aphid (Acyrthosiphon pisum), we conducted the first extensive annotation of the immune and stress gene repertoire of a hemipterous insect, which is phylogenetically distantly related to previously characterized insects models. Results Strikingly, pea aphids appear to be missing genes present in insect genomes characterized to date and thought critical for recognition, signaling and killing of microbes. In line with results of gene annotation, experimental analyses designed to characterize immune response through the isolation of RNA transcripts and proteins from immune-challenged pea aphids uncovered few immune-related products. Gene expression studies, however, indicated some expression of immune and stress-related genes. Conclusions The absence of genes suspected to be essential for the insect immune response suggests that the traditional view of insect immunity may not be as broadly applicable as once thought. The limitations of the aphid immune system may be representative of a broad range of insects, or may be aphid specific. We suggest that several aspects of the aphid life style, such as their association with microbial symbionts, could facilitate survival without strong immune protection.

Published
2010

3. A comparative encyclopedia of DNA elements in the mouse genome

Author

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

Subjects
Man -- Genetic aspects, Genetic research, Human beings -- Genetic aspects, Genomes -- Comparative analysis, Mice -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases., Author(s): Feng Yue [1, 2]; Yong Cheng [3]; Alessandra Breschi [4]; Jeff Vierstra [5]; Weisheng Wu [6]; Tyrone Ryba [7]; Richard Sandstrom [5]; Zhihai Ma [3]; Carrie Davis [8]; Benjamin [...]

Published
2014
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4. Ensembl 2015

Author

Cunningham, Fiona, Amode, Ridwan M., Barrell, Daniel, Beal, Kathryn, Billis, Konstantinos, Brent, Simon, Carvalho-Silva, Denise, Clapham, Peter, Coates, Guy, Fitzgerald, Stephen, Gil, Laurent, Girón, Carlos García, Gordon, Leo, Hourlier, Thibaut, Hunt, Sarah E., Janacek, Sophie H., Johnson, Nathan, Juettemann, Thomas, Kähäri, Andreas K., Keenan, Stephen, Martin, Fergal J., Maurel, Thomas, McLaren, William, Murphy, Daniel N., Nag, Rishi, Overduin, Bert, Parker, Anne, Patricio, Mateus, Perry, Emily, Pignatelli, Miguel, Riat, Harpreet Singh, Sheppard, Daniel, Taylor, Kieron, Thormann, Anja, Vullo, Alessandro, Wilder, Steven P., Zadissa, Amonida, Aken, Bronwen L., Birney, Ewan, Harrow, Jennifer, Kinsella, Rhoda, Muffato, Matthieu, Ruffier, Magali, Searle, Stephen M.J., Spudich, Giulietta, Trevanion, Stephen J., Yates, Andy, Zerbino, Daniel R., and Flicek, Paul

Published
2015
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8. Ensembl 2014

Author

Flicek, Paul, Amode, Ridwan M., Barrell, Daniel, Beal, Kathryn, Billis, Konstantinos, Brent, Simon, Carvalho-Silva, Denise, Clapham, Peter, Coates, Guy, Fitzgerald, Stephen, Gil, Laurent, Girón, Carlos García, Gordon, Leo, Hourlier, Thibaut, Hunt, Sarah, Johnson, Nathan, Juettemann, Thomas, Kähäri, Andreas K., Keenan, Stephen, Kulesha, Eugene, Martin, Fergal J., Maurel, Thomas, McLaren, William M., Murphy, Daniel N., Nag, Rishi, Overduin, Bert, Pignatelli, Miguel, Pritchard, Bethan, Pritchard, Emily, Riat, Harpreet S., Ruffier, Magali, Sheppard, Daniel, Taylor, Kieron, Thormann, Anja, Trevanion, Stephen J., Vullo, Alessandro, Wilder, Steven P., Wilson, Mark, Zadissa, Amonida, Aken, Bronwen L., Birney, Ewan, Cunningham, Fiona, Harrow, Jennifer, Herrero, Javier, Hubbard, Tim J.P., Kinsella, Rhoda, Muffato, Matthieu, Parker, Anne, Spudich, Giulietta, Yates, Andy, Zerbino, Daniel R., and Searle, Stephen M.J.

Published
2014
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9. Open Targets Platform: supporting systematic drug–target identification and prioritisation

Author

Ochoa, David, primary, Hercules, Andrew, additional, Carmona, Miguel, additional, Suveges, Daniel, additional, Gonzalez-Uriarte, Asier, additional, Malangone, Cinzia, additional, Miranda, Alfredo, additional, Fumis, Luca, additional, Carvalho-Silva, Denise, additional, Spitzer, Michaela, additional, Baker, Jarrod, additional, Ferrer, Javier, additional, Raies, Arwa, additional, Razuvayevskaya, Olesya, additional, Faulconbridge, Adam, additional, Petsalaki, Eirini, additional, Mutowo, Prudence, additional, Machlitt-Northen, Sandra, additional, Peat, Gareth, additional, McAuley, Elaine, additional, Ong, Chuang Kee, additional, Mountjoy, Edward, additional, Ghoussaini, Maya, additional, Pierleoni, Andrea, additional, Papa, Eliseo, additional, Pignatelli, Miguel, additional, Koscielny, Gautier, additional, Karim, Mohd, additional, Schwartzentruber, Jeremy, additional, Hulcoop, David G, additional, Dunham, Ian, additional, and McDonagh, Ellen M, additional

Published
2020
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12. Ensembl 2013

Author

Flicek, Paul, Ahmed, Ikhlak, Amode, Ridwan M., Barrell, Daniel, Beal, Kathryn, Brent, Simon, Carvalho-Silva, Denise, Clapham, Peter, Coates, Guy, Fairley, Susan, Fitzgerald, Stephen, Gil, Laurent, García-Girón, Carlos, Gordon, Leo, Hourlier, Thibaut, Hunt, Sarah, Juettemann, Thomas, Kähäri, Andreas K., Keenan, Stephen, Komorowska, Monika, Kulesha, Eugene, Longden, Ian, Maurel, Thomas, McLaren, William M., Muffato, Matthieu, Nag, Rishi, Overduin, Bert, Pignatelli, Miguel, Pritchard, Bethan, Pritchard, Emily, Riat, Harpreet Singh, Ritchie, Graham R. S., Ruffier, Magali, Schuster, Michael, Sheppard, Daniel, Sobral, Daniel, Taylor, Kieron, Thormann, Anja, Trevanion, Stephen, White, Simon, Wilder, Steven P., Aken, Bronwen L., Birney, Ewan, Cunningham, Fiona, Dunham, Ian, Harrow, Jennifer, Herrero, Javier, Hubbard, Tim J. P., Johnson, Nathan, Kinsella, Rhoda, Parker, Anne, Spudich, Giulietta, Yates, Andy, Zadissa, Amonida, and Searle, Stephen M. J.

Published
2013
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13. Ensembl 2012

Author

Flicek, Paul, Amode, M. Ridwan, Barrell, Daniel, Beal, Kathryn, Brent, Simon, Carvalho-Silva, Denise, Clapham, Peter, Coates, Guy, Fairley, Susan, Fitzgerald, Stephen, Gil, Laurent, Gordon, Leo, Hendrix, Maurice, Hourlier, Thibaut, Johnson, Nathan, Kähäri, Andreas K., Keefe, Damian, Keenan, Stephen, Kinsella, Rhoda, Komorowska, Monika, Koscielny, Gautier, Kulesha, Eugene, Larsson, Pontus, Longden, Ian, McLaren, William, Muffato, Matthieu, Overduin, Bert, Pignatelli, Miguel, Pritchard, Bethan, Riat, Harpreet Singh, Ritchie, Graham R. S., Ruffier, Magali, Schuster, Michael, Sobral, Daniel, Tang, Y. Amy, Taylor, Kieron, Trevanion, Stephen, Vandrovcova, Jana, White, Simon, Wilson, Mark, Wilder, Steven P., Aken, Bronwen L., Birney, Ewan, Cunningham, Fiona, Dunham, Ian, Durbin, Richard, Fernández-Suarez, Xosé M., Harrow, Jennifer, Herrero, Javier, Hubbard, Tim J. P., Parker, Anne, Proctor, Glenn, Spudich, Giulietta, Vogel, Jan, Yates, Andy, Zadissa, Amonida, and Searle, Stephen M. J.

Published
2012
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19. Open Targets Platform: new developments and updates two years on

Author

Carvalho-Silva, Denise, primary, Pierleoni, Andrea, additional, Pignatelli, Miguel, additional, Ong, ChuangKee, additional, Fumis, Luca, additional, Karamanis, Nikiforos, additional, Carmona, Miguel, additional, Faulconbridge, Adam, additional, Hercules, Andrew, additional, McAuley, Elaine, additional, Miranda, Alfredo, additional, Peat, Gareth, additional, Spitzer, Michaela, additional, Barrett, Jeffrey, additional, Hulcoop, David G, additional, Papa, Eliseo, additional, Koscielny, Gautier, additional, and Dunham, Ian, additional

Published
2018
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20. Environmental distribution of prokaryotic taxa

Author

Camacho Antonio, Pignatelli Miguel, Abellán Juan, Tamames Javier, and Moya Andrés

Subjects
Microbiology, QR1-502
Abstract

Abstract Background The increasing availability of gene sequences of prokaryotic species in samples extracted from all kind of locations allows addressing the study of the influence of environmental patterns in prokaryotic biodiversity. We present a comprehensive study to address the potential existence of environmental preferences of prokaryotic taxa and the commonness of the specialist and generalist strategies. We also assessed the most significant environmental factors shaping the environmental distribution of taxa. Results We used 16S rDNA sequences from 3,502 sampling experiments in natural and artificial sources. These sequences were taxonomically assigned, and the corresponding samples were also classified into a hierarchical classification of environments. We used several statistical methods to analyze the environmental distribution of taxa. Our results indicate that environmental specificity is not very common at the higher taxonomic levels (phylum to family), but emerges at lower taxonomic levels (genus and species). The most selective environmental characteristics are those of animal tissues and thermal locations. Salinity is another very important factor for constraining prokaryotic diversity. On the other hand, soil and freshwater habitats are the less restrictive environments, harboring the largest number of prokaryotic taxa. All information on taxa, samples and environments is provided at the envDB online database, http://metagenomics.uv.es/envDB. Conclusions This is, as far as we know, the most comprehensive assessment of the distribution and diversity of prokaryotic taxa and their associations with different environments. Our data indicate that we are still far from characterizing prokaryotic diversity in any environment, except, perhaps, for human tissues such as the oral cavity and the vagina.

Published
2010
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21. Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer

Author

Garcia-Alonso, Luz, primary, Iorio, Francesco, additional, Matchan, Angela, additional, Fonseca, Nuno, additional, Jaaks, Patricia, additional, Peat, Gareth, additional, Pignatelli, Miguel, additional, Falcone, Fiammetta, additional, Benes, Cyril H., additional, Dunham, Ian, additional, Bignell, Graham, additional, McDade, Simon S., additional, Garnett, Mathew J., additional, and Saez-Rodriguez, Julio, additional

Published
2018
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22. Designing an intuitive web application for drug discovery scientists

Author

Karamanis, Nikiforos, primary, Carvalho-Silva, Denise, additional, Cham, Jennifer A., additional, Fumis, Luca, additional, Hasan, Samiul, additional, Hulcoop, David, additional, Koscielny, Gautier, additional, Maguire, Michael, additional, Newell, William, additional, Ong, ChuangKee, additional, Papa, Eliseo, additional, Pierleoni, Andrea, additional, Pignatelli, Miguel, additional, Pundir, Sangya, additional, Rowland, Francis, additional, Vamathevan, Jessica, additional, Watkins, Xavier, additional, Barrett, Jeffrey C., additional, and Dunham, Ian, additional

Published
2017
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23. Open Targets: a platform for therapeutic target identification and validation

Author

Koscielny, Gautier, primary, An, Peter, additional, Carvalho-Silva, Denise, additional, Cham, Jennifer A., additional, Fumis, Luca, additional, Gasparyan, Rippa, additional, Hasan, Samiul, additional, Karamanis, Nikiforos, additional, Maguire, Michael, additional, Papa, Eliseo, additional, Pierleoni, Andrea, additional, Pignatelli, Miguel, additional, Platt, Theo, additional, Rowland, Francis, additional, Wankar, Priyanka, additional, Bento, A. Patrícia, additional, Burdett, Tony, additional, Fabregat, Antonio, additional, Forbes, Simon, additional, Gaulton, Anna, additional, Gonzalez, Cristina Yenyxe, additional, Hermjakob, Henning, additional, Hersey, Anne, additional, Jupe, Steven, additional, Kafkas, Şenay, additional, Keays, Maria, additional, Leroy, Catherine, additional, Lopez, Francisco-Javier, additional, Magarinos, Maria Paula, additional, Malone, James, additional, McEntyre, Johanna, additional, Munoz-Pomer Fuentes, Alfonso, additional, O'Donovan, Claire, additional, Papatheodorou, Irene, additional, Parkinson, Helen, additional, Palka, Barbara, additional, Paschall, Justin, additional, Petryszak, Robert, additional, Pratanwanich, Naruemon, additional, Sarntivijal, Sirarat, additional, Saunders, Gary, additional, Sidiropoulos, Konstantinos, additional, Smith, Thomas, additional, Sondka, Zbyslaw, additional, Stegle, Oliver, additional, Tang, Y. Amy, additional, Turner, Edward, additional, Vaughan, Brendan, additional, Vrousgou, Olga, additional, Watkins, Xavier, additional, Martin, Maria-Jesus, additional, Sanseau, Philippe, additional, Vamathevan, Jessica, additional, Birney, Ewan, additional, Barrett, Jeffrey, additional, and Dunham, Ian, additional

Published
2016
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24. Enhancer evolution across 20 mammalian species

Author

Villar, Diego, Berthelot, Camille, Aldridge, Sarah, Rayner, Tim F, Lukk, Margus, Pignatelli, Miguel, Park, Thomas J, Deaville, Robert, Erichsen, Jonathan T, Jasinska, Anna J, Turner, James MA, Bertelsen, Mads F, Murchison, Elizabeth P, Flicek, Paul, Odom, Duncan T, Murchison, Elizabeth [0000-0001-7462-8907], Odom, Duncan [0000-0001-6201-5599], and Apollo - University of Cambridge Repository

Subjects
Evolution, Molecular, Histone Code, Mammals, Enhancer Elements, Genetic, Liver, Biochemistry, Genetics and Molecular Biology(all), Animals, Humans, RE, Promoter Regions, Genetic, Transcription Factors
Abstract

SummaryThe mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals. Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation. We report that rapid evolution of enhancers is a universal feature of mammalian genomes. Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements. In contrast, almost all liver promoters are partially or fully conserved across these species. Our data further reveal that recently evolved enhancers can be associated with genes under positive selection, demonstrating the power of this approach for annotating regulatory adaptations in genomic sequences. These results provide important insight into the functional genetics underpinning mammalian regulatory evolution.

Published
2015

25. Open Targets Platform: new developments and updates two years on.

Author

Carvalho-Silva, Denise, Pierleoni, Andrea, Pignatelli, Miguel, Ong, ChuangKee, Fumis, Luca, Karamanis, Nikiforos, Carmona, Miguel, Faulconbridge, Adam, Hercules, Andrew, McAuley, Elaine, Miranda, Alfredo, Peat, Gareth, Spitzer, Michaela, Barrett, Jeffrey, Hulcoop, David G, Papa, Eliseo, Koscielny, Gautier, and Dunham, Ian

Published
2019
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27. Ensembl comparative genomics resources

Author

Herrero, Javier, primary, Muffato, Matthieu, additional, Beal, Kathryn, additional, Fitzgerald, Stephen, additional, Gordon, Leo, additional, Pignatelli, Miguel, additional, Vilella, Albert J., additional, Searle, Stephen M. J., additional, Amode, Ridwan, additional, Brent, Simon, additional, Spooner, William, additional, Kulesha, Eugene, additional, Yates, Andrew, additional, and Flicek, Paul, additional

Published
2016
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28. ncRNA orthologies in the vertebrate lineage

Author

Pignatelli, Miguel, primary, Vilella, Albert J., additional, Muffato, Matthieu, additional, Gordon, Leo, additional, White, Simon, additional, Flicek, Paul, additional, and Herrero, Javier, additional

Published
2016
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29. Ensembl 2016

Author

Yates, Andrew, primary, Akanni, Wasiu, additional, Amode, M. Ridwan, additional, Barrell, Daniel, additional, Billis, Konstantinos, additional, Carvalho-Silva, Denise, additional, Cummins, Carla, additional, Clapham, Peter, additional, Fitzgerald, Stephen, additional, Gil, Laurent, additional, Girón, Carlos García, additional, Gordon, Leo, additional, Hourlier, Thibaut, additional, Hunt, Sarah E., additional, Janacek, Sophie H., additional, Johnson, Nathan, additional, Juettemann, Thomas, additional, Keenan, Stephen, additional, Lavidas, Ilias, additional, Martin, Fergal J., additional, Maurel, Thomas, additional, McLaren, William, additional, Murphy, Daniel N., additional, Nag, Rishi, additional, Nuhn, Michael, additional, Parker, Anne, additional, Patricio, Mateus, additional, Pignatelli, Miguel, additional, Rahtz, Matthew, additional, Riat, Harpreet Singh, additional, Sheppard, Daniel, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Vullo, Alessandro, additional, Wilder, Steven P., additional, Zadissa, Amonida, additional, Birney, Ewan, additional, Harrow, Jennifer, additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Spudich, Giulietta, additional, Trevanion, Stephen J., additional, Cunningham, Fiona, additional, Aken, Bronwen L., additional, Zerbino, Daniel R., additional, and Flicek, Paul, additional

Published
2015
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30. Ensembl 2015

Author

Cunningham, Fiona, primary, Amode, M. Ridwan, additional, Barrell, Daniel, additional, Beal, Kathryn, additional, Billis, Konstantinos, additional, Brent, Simon, additional, Carvalho-Silva, Denise, additional, Clapham, Peter, additional, Coates, Guy, additional, Fitzgerald, Stephen, additional, Gil, Laurent, additional, Girón, Carlos García, additional, Gordon, Leo, additional, Hourlier, Thibaut, additional, Hunt, Sarah E., additional, Janacek, Sophie H., additional, Johnson, Nathan, additional, Juettemann, Thomas, additional, Kähäri, Andreas K., additional, Keenan, Stephen, additional, Martin, Fergal J., additional, Maurel, Thomas, additional, McLaren, William, additional, Murphy, Daniel N., additional, Nag, Rishi, additional, Overduin, Bert, additional, Parker, Anne, additional, Patricio, Mateus, additional, Perry, Emily, additional, Pignatelli, Miguel, additional, Riat, Harpreet Singh, additional, Sheppard, Daniel, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Vullo, Alessandro, additional, Wilder, Steven P., additional, Zadissa, Amonida, additional, Aken, Bronwen L., additional, Birney, Ewan, additional, Harrow, Jennifer, additional, Kinsella, Rhoda, additional, Muffato, Matthieu, additional, Ruffier, Magali, additional, Searle, Stephen M.J., additional, Spudich, Giulietta, additional, Trevanion, Stephen J., additional, Yates, Andy, additional, Zerbino, Daniel R., additional, and Flicek, Paul, additional

Published
2014
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31. The Ensembl REST API: Ensembl Data for Any Language

Author

Yates, Andrew, primary, Beal, Kathryn, additional, Keenan, Stephen, additional, McLaren, William, additional, Pignatelli, Miguel, additional, Ritchie, Graham R. S., additional, Ruffier, Magali, additional, Taylor, Kieron, additional, Vullo, Alessandro, additional, and Flicek, Paul, additional

Published
2014
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32. Uncovering the limitation of the aphid immune response

Author

Gerardo, Nicole M, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M, De Vos, Martin, Evans, Jay D, Gabaldón, Toni, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Latorre, Amparo, Monégat, C., Moya, Andrès, Nakabachi, Atsushi, Parker, Benjamin J, Perez-Brocal, Vincente, Pignatelli, Miguel, Rahbé, Yvan, Ramsey, J., Spragg, Chelsea, Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, ProdInra, Migration, O. Wayne Rollins Research Center (WRRC), Emory University [Atlanta, GA], Institute of Phytopathology and Applied Zoology (IPAZ), Justus-Liebig-Universität Gießen (JLU), Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València (UV), Environmental Molecular Biology Laboratory (RIKEN), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Institute for Phytopathology and Applied Zoology, Partenaires INRAE, Centro de Regulación Genómica (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), RIKEN Plant Science Center, and Laboratoire Bf2i, Insa

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], aphid, [SDV.OT] Life Sciences [q-bio]/Other [q-bio.OT], limitation, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS, immune response, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience

Published
2009

33. Open Targets: a platform for therapeutic target identification and validation.

Author

Koscielny, Gautier, An, Peter, Carvalho-Silva, Denise, Cham, Jennifer A., Fumis, Luca, Gasparyan, Rippa, Hasan, Samiul, Karamanis, Nikiforos, Maguire, Michael, Papa, Eliseo, Pierleoni, Andrea, Pignatelli, Miguel, Platt, Theo, Rowland, Francis, Wankar, Priyanka, Bento, A. Patrícia, Burdett, Tony, Fabregat, Antonio, Forbes, Simon, and Gaulton, Anna

Published
2017
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34. iHam and pyHam: visualizing and processing hierarchical orthologous groups.

Author

Train, Clément-Marie, Pignatelli, Miguel, Altenhoff, Adrian, and Dessimoz, Christophe

Subjects
*JAVASCRIPT programming language, *LIBRARY technical services, *COMPARATIVE genomics, *GENE families, *SWINE, *CHROMOSOME duplication, *PYTHON programming language
Abstract

Summary The evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of genomes simultaneously considered in contemporary comparative genomic analyses. As provided by several orthology databases, hierarchical orthologous groups (HOGs) are sets of genes that are inferred to have descended from a common ancestral gene within a species clade. This implies that the set of HOGs defined for a particular clade correspond to the ancestral genes found in its last common ancestor. Furthermore, by keeping track of HOG composition along the species tree, it is possible to infer the emergence, duplications and losses of genes within a gene family of interest. However, the lack of tools to manipulate and analyse HOGs has made it difficult to extract, display and interpret this type of information. To address this, we introduce i nteractive H OG a nalysis m ethod, an interactive JavaScript widget to visualize and explore gene family history encoded in HOGs and py thon H OG a nalysis m ethod, a python library for programmatic processing of genes families. These complementary open source tools greatly ease adoption of HOGs as a scalable and interpretable concept to relate genes across multiple species. Availability and implementation iHam's code is available at https://github.com/DessimozLab/iHam or can be loaded dynamically. pyHam's code is available at https://github.com/DessimozLab/pyHam and or via the pip package 'pyham'. [ABSTRACT FROM AUTHOR]

Published
2019
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35. Erratum: Corrigendum: The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

Author

Wang, Zhuo, primary, Pascual-Anaya, Juan, additional, Zadissa, Amonida, additional, Li, Wenqi, additional, Niimura, Yoshihito, additional, Huang, Zhiyong, additional, Li, Chunyi, additional, White, Simon, additional, Xiong, Zhiqiang, additional, Fang, Dongming, additional, Wang, Bo, additional, Ming, Yao, additional, Chen, Yan, additional, Zheng, Yuan, additional, Kuraku, Shigehiro, additional, Pignatelli, Miguel, additional, Herrero, Javier, additional, Beal, Kathryn, additional, Nozawa, Masafumi, additional, Li, Qiye, additional, Wang, Juan, additional, Zhang, Hongyan, additional, Yu, Lili, additional, Shigenobu, Shuji, additional, Wang, Junyi, additional, Liu, Jiannan, additional, Flicek, Paul, additional, Searle, Steve, additional, Wang, Jun, additional, Kuratani, Shigeru, additional, Yin, Ye, additional, Aken, Bronwen, additional, Zhang, Guojie, additional, and Irie, Naoki, additional

Published
2014
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38. The peroxisome proliferator-activated receptor gamma is an inhibitor of ErbBs activity in human breast cancer cells

Author

Pignatelli, Miguel, Cortés-Canteli, Marta, Lai, Cary, Santos, Ángel, and Pérez Castillo, Ana

Subjects
Breast cancer, ErbBs, PPAR(gamma), Phosphorylation, Transformation
Abstract

10 pages, 8 figures.-- Research article., One of the most interesting recent developments in the nuclear receptor field has been the identification of natural and synthetic agonists of the peroxisome proliferator-activated receptor (PPAR) family, coupled with a growing recognition that the gamma isoform (PPARgamma) affects pathways important in a variety of human diseases. Here we show that the activation of PPARgamma through the 15-deoxy-Delta-12,14-prostaglandin J(2) (PG-J(2)) ligand causes a dramatic inhibition of ErbB-2 and ErbB-3 tyrosine phosphorylation caused by neuregulin 1 (NRG1) and neuregulin 2 (NRG2) in MCF-7 cells. This effect is accompanied by a very efficient blocking of ErbBs effects upon proliferation, differentiation and cell death in these cells. Preincubation of MCF-7 cells with PG-J(2) before addition of NRG1 and NRG2 had a dramatic growth-suppressive effect accompanied by accumulation of cells in the G0/G1 compartment of the cell cycle, and a marked increase in apoptosis. NRG1 and NRG2 induce G1 progression, which was associated with stimulation of the phosphatidylinositol-3 kinase (PI 3-K) pathway, whereas survival was dependent on ERK1/ERK2 activation. Both pathways were inhibited by PG-J(2). Furthermore, PG-J(2) can abolish the NRG1 and NRG2-induced increase in anchorage-independent growth of these cells. PG-J(2) also blocks phosphorylation of other receptor tyrosine kinases, such as IGF-IR, in MCF-7 cells, and suppress proliferation of other breast cancer cell lines. In summary, our data show a specific inhibitory action of PG-J(2) on the activity of the ErbB receptors in breast cancer cells., This work has been supported by Grants from the Dirección General de Enseñanza Superior e Investigación Científica, Grants PM97-0063 (A.P.-C.) and PM96-0051 (A.S.) and by the Comunidad de Madrid, Grant 08.5/0003/1997 (A.P.-C. and A.S.). M.P. is a fellow of the Fondo de Investigaciones Sanitarias de la Seguridad Social. M.C.-C. has a fellowship from the Comunidad de Madrid.

Published
2001

39. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

Author

Wang, Zhuo, primary, Pascual-Anaya, Juan, additional, Zadissa, Amonida, additional, Li, Wenqi, additional, Niimura, Yoshihito, additional, Huang, Zhiyong, additional, Li, Chunyi, additional, White, Simon, additional, Xiong, Zhiqiang, additional, Fang, Dongming, additional, Wang, Bo, additional, Ming, Yao, additional, Chen, Yan, additional, Zheng, Yuan, additional, Kuraku, Shigehiro, additional, Pignatelli, Miguel, additional, Herrero, Javier, additional, Beal, Kathryn, additional, Nozawa, Masafumi, additional, Li, Qiye, additional, Wang, Juan, additional, Zhang, Hongyan, additional, Yu, Lili, additional, Shigenobu, Shuji, additional, Wang, Junyi, additional, Liu, Jiannan, additional, Flicek, Paul, additional, Searle, Steve, additional, Wang, Jun, additional, Kuratani, Shigeru, additional, Yin, Ye, additional, Aken, Bronwen, additional, Zhang, Guojie, additional, and Irie, Naoki, additional

Published
2013
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40. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

Author

Smith, Jeramiah J, primary, Kuraku, Shigehiro, additional, Holt, Carson, additional, Sauka-Spengler, Tatjana, additional, Jiang, Ning, additional, Campbell, Michael S, additional, Yandell, Mark D, additional, Manousaki, Tereza, additional, Meyer, Axel, additional, Bloom, Ona E, additional, Morgan, Jennifer R, additional, Buxbaum, Joseph D, additional, Sachidanandam, Ravi, additional, Sims, Carrie, additional, Garruss, Alexander S, additional, Cook, Malcolm, additional, Krumlauf, Robb, additional, Wiedemann, Leanne M, additional, Sower, Stacia A, additional, Decatur, Wayne A, additional, Hall, Jeffrey A, additional, Amemiya, Chris T, additional, Saha, Nil R, additional, Buckley, Katherine M, additional, Rast, Jonathan P, additional, Das, Sabyasachi, additional, Hirano, Masayuki, additional, McCurley, Nathanael, additional, Guo, Peng, additional, Rohner, Nicolas, additional, Tabin, Clifford J, additional, Piccinelli, Paul, additional, Elgar, Greg, additional, Ruffier, Magali, additional, Aken, Bronwen L, additional, Searle, Stephen M J, additional, Muffato, Matthieu, additional, Pignatelli, Miguel, additional, Herrero, Javier, additional, Jones, Matthew, additional, Brown, C Titus, additional, Chung-Davidson, Yu-Wen, additional, Nanlohy, Kaben G, additional, Libants, Scot V, additional, Yeh, Chu-Yin, additional, McCauley, David W, additional, Langeland, James A, additional, Pancer, Zeev, additional, Fritzsch, Bernd, additional, de Jong, Pieter J, additional, Zhu, Baoli, additional, Fulton, Lucinda L, additional, Theising, Brenda, additional, Flicek, Paul, additional, Bronner, Marianne E, additional, Warren, Wesley C, additional, Clifton, Sandra W, additional, Wilson, Richard K, additional, and Li, Weiming, additional

Published
2013
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41. The oral metagenome in health and disease

Author

Belda-Ferre, Pedro, primary, Alcaraz, Luis David, additional, Cabrera-Rubio, Raúl, additional, Romero, Héctor, additional, Simón-Soro, Aurea, additional, Pignatelli, Miguel, additional, and Mira, Alex, additional

Published
2011
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47. Hnf1α (MODY3) Controls Tissue-Specific Transcriptional Programs and Exerts Opposed Effects on Cell Growth in Pancreatic Islets and Liver

Author

Servitja, Joan-Marc, primary, Pignatelli, Miguel, additional, Maestro, Miguel Ángel, additional, Cardalda, Carina, additional, Boj, Sylvia F., additional, Lozano, Juanjo, additional, Blanco, Enrique, additional, Lafuente, Amàlia, additional, McCarthy, Mark I., additional, Sumoy, Lauro, additional, Guigó, Roderic, additional, and Ferrer, Jorge, additional

Published
2009
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