Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications
Acera Mateos, P, J Sethi, A, Ravindran, A, Srivastava, A, Woodward, K, Mahmud, S, Kanchi, M, Guarnacci, M, Xu, J, W S Yuen, Z, Zhou, Y, Sneddon, A, Hamilton, W, Gao, J, M Starrs, L, Hayashi, R, Wickramasinghe, V, Zarnack, K, Preiss, T, Burgio, G, Dehorter, N, E Shirokikh, N, Eyras, E
Published in Nature communications (09.05.2024)
Published in Nature communications (09.05.2024)
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The Ensembl genome database project
Hubbard, T, Barker, D, Birney, E, Cameron, G, Chen, Y, Clark, L, Cox, T, Cuff, J, Curwen, V, Down, T, Durbin, R, Eyras, E, Gilbert, J, Hammond, M, Huminiecki, L, Kasprzyk, A, Lehvaslaiho, H, Lijnzaad, P, Melsopp, C, Mongin, E, Pettett, R, Pocock, M, Potter, S, Rust, A, Schmidt, E, Searle, S, Slater, G, Smith, J, Spooner, W, Stabenau, A, Stalker, J, Stupka, E, Ureta-Vidal, A, Vastrik, I, Clamp, M
Published in Nucleic acids research (01.01.2002)
Published in Nucleic acids research (01.01.2002)
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Ensembl 2002: accommodating comparative genomics
Clamp, M., Andrews, D., Barker, D., Bevan, P., Cameron, G., Chen, Y., Clark, L., Cox, T., Cuff, J., Curwen, V., Down, T., Durbin, R., Eyras, E., Gilbert, J., Hammond, M., Hubbard, T., Kasprzyk, A., Keefe, D., Lehvaslaiho, H., Iyer, V., Melsopp, C., Mongin, E., Pettett, R., Potter, S., Rust, A., Schmidt, E., Searle, S., Slater, G., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Stupka, E., Ureta-Vidal, A., Vastrik, I., Birney, E.
Published in Nucleic acids research (01.01.2003)
Published in Nucleic acids research (01.01.2003)
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Ensembl 2004
Birney, E., Andrews, D., Bevan, P., Caccamo, M., Cameron, G., Chen, Y., Clarke, L., Coates, G., Cox, T., Cuff, J., Curwen, V., Cutts, T., Down, T., Durbin, R., Eyras, E., Fernandez‐Suarez, X. M., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H., Iyer, V., Kahari, A., Jekosch, K., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta‐Vidal, A., Woodwark, C., Clamp, M., Hubbard, T.
Published in Nucleic acids research (01.01.2004)
Published in Nucleic acids research (01.01.2004)
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Journal Article
Chromatin and alternative splicing
Alló, M, Schor, I E, Muñoz, M J, de la Mata, M, Agirre, E, Valcárcel, J, Eyras, E, Kornblihtt, A R
Published in Cold Spring Harbor Symposia on Quantitative Biology (2010)
Published in Cold Spring Harbor Symposia on Quantitative Biology (2010)
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Intersections involving monopoles and waves in eleven dimensions
Bergshoeff, E, Roo, M de, Eyras, E, Janssen, B, Schaar, J P van der
Published in Classical and quantum gravity (01.10.1997)
Published in Classical and quantum gravity (01.10.1997)
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Multiple intersections of D-branes and M-branes
Bergshoeff, E., de Roo, M., Eyras, E., Janssen, B., van der Schaar, J.P.
Published in Nuclear physics. B (09.06.1997)
Published in Nuclear physics. B (09.06.1997)
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Space-time-filling branes and strings with sixteen supercharges
Bergshoeff, E., Eyras, E., Halbersma, R., van der Schaar, J.P., Hull, C.M., Lozano, Y.
Published in Nuclear physics. B (03.01.2000)
Published in Nuclear physics. B (03.01.2000)
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The BioMart community portal: an innovative alternative to large, centralized data repositories
Smedley, Damian, Haider, Syed, Durinck, Steffen, Pandini, Luca, Provero, Paolo, Allen, James, Arnaiz, Olivier, Awedh, Mohammad Hamza, Baldock, Richard, Barbiera, Giulia, Bardou, Philippe, Beck, Tim, Blake, Andrew, Bonierbale, Merideth, Brookes, Anthony J, Bucci, Gabriele, Buetti, Iwan, Burge, Sarah, Cabau, Cédric, Carlson, Joseph W, Chelala, Claude, Chrysostomou, Charalambos, Cittaro, Davide, Collin, Olivier, Cordova, Raul, Cutts, Rosalind J, Dassi, Erik, Di Genova, Alex, Djari, Anis, Esposito, Anthony, Estrella, Heather, Eyras, Eduardo, Fernandez-Banet, Julio, Forbes, Simon, Free, Robert C, Fujisawa, Takatomo, Gadaleta, Emanuela, Garcia-Manteiga, Jose M, Goodstein, David, Gray, Kristian, Guerra-Assunção, José Afonso, Haggarty, Bernard, Han, Dong-Jin, Han, Byung Woo, Harris, Todd, Harshbarger, Jayson, Hastings, Robert K, Hayes, Richard D, Hoede, Claire, Hu, Shen, Hu, Zhi-Liang, Hutchins, Lucie, Kan, Zhengyan, Kawaji, Hideya, Keliet, Aminah, Kerhornou, Arnaud, Kim, Sunghoon, Kinsella, Rhoda, Klopp, Christophe, Kong, Lei, Lawson, Daniel, Lazarevic, Dejan, Lee, Ji-Hyun, Letellier, Thomas, Li, Chuan-Yun, Lio, Pietro, Liu, Chu-Jun, Luo, Jie, Maass, Alejandro, Mariette, Jerome, Maurel, Thomas, Merella, Stefania, Mohamed, Azza Mostafa, Moreews, Francois, Nabihoudine, Ibounyamine, Ndegwa, Nelson, Noirot, Céline, Perez-Llamas, Cristian, Primig, Michael, Quattrone, Alessandro, Quesneville, Hadi, Rambaldi, Davide, Reecy, James, Riba, Michela, Rosanoff, Steven, Saddiq, Amna Ali, Salas, Elisa, Sallou, Olivier, Shepherd, Rebecca, Simon, Reinhard, Sperling, Linda, Spooner, William, Staines, Daniel M, Steinbach, Delphine, Stone, Kevin, Stupka, Elia, Teague, Jon W, Dayem Ullah, Abu Z, Wang, Jun, Ware, Doreen
Published in Nucleic acids research (01.07.2015)
Published in Nucleic acids research (01.07.2015)
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IRFinder: assessing the impact of intron retention on mammalian gene expression
Middleton, Robert, Gao, Dadi, Thomas, Aubin, Singh, Babita, Au, Amy, Wong, Justin J-L, Bomane, Alexandra, Cosson, Bertrand, Eyras, Eduardo, Rasko, John E J, Ritchie, William
Published in Genome Biology (15.03.2017)
Published in Genome Biology (15.03.2017)
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The ENCODE (ENCyclopedia of DNA Elements) Project
Feingold, E A, Good, P J, Guyer, M S, Kamholz, S
Published in Science (American Association for the Advancement of Science) (22.10.2004)
Published in Science (American Association for the Advancement of Science) (22.10.2004)
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Journal Article
Initial sequencing and comparative analysis of the mouse genome
Waterston, Robert H, Lindblad-Toh, Kerstin, Birney, Ewan, Rogers, Jane, Abril, Josep F, Agarwal, Pankaj, Agarwala, Richa, Ainscough, Rachel, Alexandersson, Marina, An, Peter, Antonarakis, Stylianos E, Attwood, John, Baertsch, Robert, Bailey, Jonathon, Barlow, Karen, Beck, Stephan, Berry, Eric, Birren, Bruce, Bloom, Toby, Bork, Peer, Botcherby, Marc, Bray, Nicolas, Brent, Michael R, Brown, Daniel G, Brown, Stephen D, Bult, Carol, Burton, John, Butler, Jonathan, Campbell, Robert D, Carninci, Piero, Cawley, Simon, Chiaromonte, Francesca, Chinwalla, Asif T, Church, Deanna M, Clamp, Michele, Clee, Christopher, Collins, Francis S, Cook, Lisa L, Copley, Richard R, Coulson, Alan, Couronne, Olivier, Cuff, James, Curwen, Val, Cutts, Tim, Daly, Mark, David, Robert, Davies, Joy, Delehaunty, Kimberly D, Deri, Justin, Dermitzakis, Emmanouil T, Dewey, Colin, Dickens, Nicholas J, Diekhans, Mark, Dodge, Sheila, Dubchak, Inna, Dunn, Diane M, Eddy, Sean R, Elnitski, Laura, Emes, Richard D, Eswara, Pallavi, Eyras, Eduardo, Felsenfeld, Adam, Fewell, Ginger A, Flicek, Paul, Foley, Karen, Frankel, Wayne N, Fulton, Lucinda A, Fulton, Robert S, Furey, Terrence S, Gage, Diane, Gibbs, Richard A, Glusman, Gustavo, Gnerre, Sante, Goldman, Nick, Goodstadt, Leo, Grafham, Darren, Graves, Tina A, Green, Eric D, Gregory, Simon, Guigó, Roderic, Guyer, Mark, Hardison, Ross C, Haussler, David, Hayashizaki, Yoshihide, Hillier, LaDeana W, Hinrichs, Angela, Hlavina, Wratko, Holzer, Timothy, Hsu, Fan, Hua, Axin, Hubbard, Tim, Hunt, Adrienne, Jackson, Ian, Jaffe, David B, Johnson, L Steven, Jones, Matthew, Jones, Thomas A, Joy, Ann, Kamal, Michael, Karlsson, Elinor K
Published in Nature (London) (05.12.2002)
Published in Nature (London) (05.12.2002)
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The Ensembl automatic gene annotation system
Curwen, Val, Eyras, Eduardo, Andrews, T Daniel, Clarke, Laura, Mongin, Emmanuel, Searle, Steven M J, Clamp, Michele
Published in Genome research (01.05.2004)
Published in Genome research (01.05.2004)
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Journal Article
An overview of Ensembl
Birney, Ewan, Andrews, T Daniel, Bevan, Paul, Caccamo, Mario, Chen, Yuan, Clarke, Laura, Coates, Guy, Cuff, James, Curwen, Val, Cutts, Tim, Down, Thomas, Eyras, Eduardo, Fernandez-Suarez, Xose M, Gane, Paul, Gibbins, Brian, Gilbert, James, Hammond, Martin, Hotz, Hans-Rudolf, Iyer, Vivek, Jekosch, Kerstin, Kahari, Andreas, Kasprzyk, Arek, Keefe, Damian, Keenan, Stephen, Lehvaslaiho, Heikki, McVicker, Graham, Melsopp, Craig, Meidl, Patrick, Mongin, Emmanuel, Pettett, Roger, Potter, Simon, Proctor, Glenn, Rae, Mark, Searle, Steve, Slater, Guy, Smedley, Damian, Smith, James, Spooner, Will, Stabenau, Arne, Stalker, James, Storey, Roy, Ureta-Vidal, Abel, Woodwark, K Cara, Cameron, Graham, Durbin, Richard, Cox, Anthony, Hubbard, Tim, Clamp, Michele
Published in Genome research (01.05.2004)
Published in Genome research (01.05.2004)
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Journal Article
T-duality and actions for non-BPS D-branes
Bergshoeff, Eric A, Roo, Mees de, Wit, Tim C. de, Eyras, Eduardo, Panda, Sudhakar
Published in The journal of high energy physics (01.05.2000)
Published in The journal of high energy physics (01.05.2000)
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Journal Article
Integrative annotation of 21,037 human genes validated by full-length cDNA clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, Barrero, Roberto A, Tamura, Takuro, Yamaguchi-Kabata, Yumi, Tanino, Motohiko, Yura, Kei, Miyazaki, Satoru, Ikeo, Kazuho, Homma, Keiichi, Kasprzyk, Arek, Nishikawa, Tetsuo, Hirakawa, Mika, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Ashurst, Jennifer, Jia, Libin, Nakao, Mitsuteru, Thomas, Michael A, Mulder, Nicola, Karavidopoulou, Youla, Jin, Lihua, Kim, Sangsoo, Yasuda, Tomohiro, Lenhard, Boris, Eveno, Eric, Suzuki, Yoshiyuki, Yamasaki, Chisato, Takeda, Jun-ichi, Gough, Craig, Hilton, Phillip, Fujii, Yasuyuki, Sakai, Hiroaki, Tanaka, Susumu, Amid, Clara, Bellgard, Matthew, Bonaldo, Maria de Fatima, Bono, Hidemasa, Bromberg, Susan K, Brookes, Anthony J, Bruford, Elspeth, Carninci, Piero, Chelala, Claude, Couillault, Christine, de Souza, Sandro J, Debily, Marie-Anne, Devignes, Marie-Dominique, Dubchak, Inna, Endo, Toshinori, Estreicher, Anne, Eyras, Eduardo, Fukami-Kobayashi, Kaoru, Gopinath, Gopal R, Graudens, Esther, Hahn, Yoonsoo, Han, Michael, Han, Ze-Guang, Hanada, Kousuke, Hanaoka, Hideki, Harada, Erimi, Hashimoto, Katsuyuki, Hinz, Ursula, Hirai, Momoki, Hishiki, Teruyoshi, Hopkinson, Ian, Imbeaud, Sandrine, Inoko, Hidetoshi, Kanapin, Alexander, Kaneko, Yayoi, Kasukawa, Takeya, Kelso, Janet, Kersey, Paul, Kikuno, Reiko, Kimura, Kouichi, Korn, Bernhard, Kuryshev, Vladimir, Makalowska, Izabela, Makino, Takashi, Mano, Shuhei, Mariage-Samson, Regine, Mashima, Jun, Matsuda, Hideo, Mewes, Hans-Werner, Minoshima, Shinsei, Nagai, Keiichi, Nagasaki, Hideki, Nagata, Naoki, Nigam, Rajni, Ogasawara, Osamu, Ohara, Osamu, Ohtsubo, Masafumi, Okada, Norihiro, Okido, Toshihisa, Oota, Satoshi, Ota, Motonori, Ota, Toshio
Published in PLoS biology (01.06.2004)
Published in PLoS biology (01.06.2004)
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ASTD: The Alternative Splicing and Transcript Diversity database
Koscielny, Gautier, Texier, Vincent Le, Gopalakrishnan, Chellappa, Kumanduri, Vasudev, Riethoven, Jean-Jack, Nardone, Francesco, Stanley, Eleanor, Fallsehr, Christine, Hofmann, Oliver, Kull, Meelis, Harrington, Eoghan, Boué, Stéphanie, Eyras, Eduardo, Plass, Mireya, Lopez, Fabrice, Ritchie, William, Moucadel, Virginie, Ara, Takeshi, Pospisil, Heike, Herrmann, Alexander, G. Reich, Jens, Guigó, Roderic, Bork, Peer, Doeberitz, Magnus von Knebel, Vilo, Jaak, Hide, Winston, Apweiler, Rolf, Thanaraj, Thangavel Alphonse, Gautheret, Daniel
Published in Genomics (San Diego, Calif.) (01.03.2009)
Published in Genomics (San Diego, Calif.) (01.03.2009)
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