What can we learn from noncoding regions of similarity between genomes?

by Hubbard Tim JP, Down Thomas A
Published 2004-09-01

AnnoTrack - a tracking system for genome annotation

by Hubbard Tim, Harrow Jennifer, Kokocinski Felix
Published 2010-10-01

A machine learning strategy to identify candidate binding sites in human protein-coding sequence

by Leong Bernard, Down Thomas, Hubbard Tim JP
Published 2006-09-01

Metamotifs - a generative model for building families of nucleotide position weight matrices

by Down Thomas A, Piipari Matias, Hubbard Tim JP
Published 2010-06-01

NestedMICA as an ab initio protein motif discovery tool

by Down Thomas A, Doğruel Mutlu, Hubbard Tim JP
Published 2008-01-01

Integrating sequence and structural biology with DAS

by Finn Robert D, Kulesha Eugene, Down Thomas A, Prlić Andreas, Kähäri Andreas, Hubbard Tim JP
Published 2007-09-01

Integrating biological data – the Distributed Annotation System

by Jones Philip, Jimenez Rafael C, Hubbard Tim JP, Hermjakob Henning, Finn Robert D, Down Thomas, Blankenburg Hagen, Birney Ewan, Albrecht Mario, Jenkinson Andrew M, Kähäri Andreas, Kulesha Eugene, Macías José R, Reeves Gabrielle A, Prlić Andreas
Published 2008-07-01

Assessment of transcript reconstruction methods for RNA-seq.

by Steijger, Tamara, Abril, Josep F, Engström, Pär G, Kokocinski, Felix, RGASP Consortium, Hubbard, Tim J, Guigó, Roderic, Harrow, Jennifer, Bertone, Paul
Published 2013

An interactive genome browser of association results from the UK10K cohorts project.

by Geihs, Matthias, Yan, Ying, Walter, Klaudia, Huang, Jie, Memari, Yasin, Min, Josine L, Mead, Daniel, UK10K Consortium, Hubbard, Tim J, Timpson, Nicholas J, Down, Thomas A, Soranzo, Nicole
Published 2018

Transcriptional activity and strain-specific history of mouse pseudogenes

by Sisu, Cristina, Muir, Paul, Frankish, Adam, Fiddes, Ian, Diekhans, Mark, Thybert, David, Odom, Duncan T., Flicek, Paul, Keane, Thomas M., Hubbard, Tim, Harrow, Jennifer, Gerstein, Mark
Published 2021

Transcriptional activity and strain-specific history of mouse pseudogenes.

by Sisu, Cristina, Muir, Paul, Frankish, Adam, Fiddes, Ian, Diekhans, Mark, Thybert, David, Odom, Duncan T, Flicek, Paul, Keane, Thomas M, Hubbard, Tim, Harrow, Jennifer, Gerstein, Mark
Published 2020

Transcriptional activity and strain-specific history of mouse pseudogenes

by Sisu, Cristina, Muir, Paul, Frankish, Adam, Fiddes, Ian, Diekhans, Mark, Thybert, David, Odom, Duncan T., Flicek, Paul, Keane, Thomas M., Hubbard, Tim, Harrow, Jennifer, Gerstein, Mark
Published 2020

Integrating sequence and structural biology with DAS.

by Prlić, Andreas, Down, Thomas A, Kulesha, Eugene, Finn, Robert D, Kähäri, Andreas, Hubbard, Tim JP
Published 2011

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

by Djebali, Sarah, Lagarde, Julien, Kapranov, Philipp, Lacroix, Vincent, Borel, Christelle, Mudge, Jonathan M., Howald, Cédric, Foissac, Sylvain, Ucla, Catherine, Chrast, Jacqueline, Ribeca, Paolo, Murray, Ryan R., Lin, Chenwei, Bell, Ian, Dumais, Erica, Drenkow, Jorg, Tress, Michael L., Gelpí, Josep Lluís, Orozco, Modesto, Valencia, Alfonso, van Berkum, Nynke L., Lajoie, Bryan R., Stamatoyannopoulos, John, Batut, Philippe, Dobin, Alex, Harrow, Jennifer, Hubbard, Tim, Dekker, Job, Frankish, Adam, Salehi-Ashtiani, Kourosh, Reymond, Alexandre, Antonarakis, Stylianos E., Guigó, Roderic, Gingeras, Thomas R., Martin, David, Yang, Xinping, Ghamsari, Lila, Vidal, Marc
Published 2012

NestedMICA as an ab initio protein motif discovery tool.

by Doğruel, Mutlu, Down, Thomas A, Hubbard, Tim Jp
Published 2011

iMotifs: an integrated sequence motif visualization and analysis environment.

by Piipari, Matias, Down, Thomas A, Saini, Harpreet, Enright, Anton, Hubbard, Tim JP
Published 2017

Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin.

by Boles, Melissa K, Wilkinson, Bonney M, Wilming, Laurens G, Liu, Bin, Probst, Frank J, Harrow, Jennifer, Grafham, Darren, Hentges, Kathryn E, Woodward, Lanette P, Maxwell, Andrea, Mitchell, Karen, Risley, Michael D, Johnson, Randy, Hirschi, Karen, Lupski, James R, Funato, Yosuke, Miki, Hiroaki, Marin-Garcia, Pablo, Matthews, Lucy, Coffey, Alison J, Parker, Anne, Hubbard, Tim J, Rogers, Jane, Bradley, Allan, Adams, David J, Justice, Monica J
Published 2020

Comparative Analysis of the Transcriptome across Distant Species

by Gerstein, Mark B., Rozowsky, Joel, Yan, Koon-Kiu, Wang, Daifeng, Cheng, Chao, Brown, James B., Davis, Carrie A, Hillier, LaDeana, Sisu, Cristina, Li, Jingyi Jessica, Pei, Baikang, Harmanci, Arif O., Duff, Michael O., Djebali, Sarah, Alexander, Roger P., Alver, Burak H., Auerbach, Raymond, Bell, Kimberly, Bickel, Peter J., Boeck, Max E., Boley, Nathan P., Booth, Benjamin W., Cherbas, Lucy, Cherbas, Peter, Di, Chao, Dobin, Alex, Drenkow, Jorg, Ewing, Brent, Fang, Gang, Fastuca, Megan, Feingold, Elise A., Frankish, Adam, Gao, Guanjun, Good, Peter J., Guigó, Roderic, Hammonds, Ann, Harrow, Jen, Hoskins, Roger A., Howald, Cédric, Hu, Long, Huang, Haiyan, Hubbard, Tim J. P., Huynh, Chau, Jha, Sonali, Kasper, Dionna, Kato, Masaomi, Kaufman, Thomas C., Kitchen, Robert R., Ladewig, Erik, Lagarde, Julien, Lai, Eric, Leng, Jing, Lu, Zhi, MacCoss, Michael, May, Gemma, McWhirter, Rebecca, Merrihew, Gennifer, Miller, David M., Mortazavi, Ali, Murad, Rabi, Oliver, Brian, Olson, Sara, Park, Peter J., Pazin, Michael J., Perrimon, Norbert, Pervouchine, Dmitri, Reinke, Valerie, Reymond, Alexandre, Robinson, Garrett, Samsonova, Anastasia, Saunders, Gary I., Schlesinger, Felix, Sethi, Anurag, Slack, Frank J., Spencer, William C., Stoiber, Marcus H., Strasbourger, Pnina, Tanzer, Andrea, Thompson, Owen A., Wan, Kenneth H., Wang, Guilin, Wang, Huaien, Watkins, Kathie L., Wen, Jiayu, Wen, Kejia, Xue, Chenghai, Yang, Li, Yip, Kevin, Zaleski, Chris, Zhang, Yan, Zheng, Henry, Brenner, Steven E., Graveley, Brenton R., Celniker, Susan E., Gingeras, Thomas R, Waterston, Robert
Published 2015

GENCODE reference annotation for the human and mouse genomes

by Frankish, Adam, Diekhans, Mark, Ferreira, Anne-Maud, Johnson, Rory, Jungreis, Irwin, Loveland, Jane, Mudge, Jonathan M, Sisu, Cristina, Wright, James, Armstrong, Joel, Barnes, If, Berry, Andrew, Bignell, Alexandra, Carbonell Sala, Silvia, Chrast, Jacqueline, Cunningham, Fiona, Di Domenico, Tomás, Donaldson, Sarah, Fiddes, Ian T, García Girón, Carlos, Gonzalez, Jose Manuel, Grego, Tiago, Hardy, Matthew, Hourlier, Thibaut, Hunt, Toby, Izuogu, Osagie G, Lagarde, Julien, Martin, Fergal J, Martínez, Laura, Mohanan, Shamika, Muir, Paul, Navarro, Fabio C P, Parker, Anne, Pei, Baikang, Pozo, Fernando, Ruffier, Magali, Schmitt, Bianca M, Stapleton, Eloise, Suner, Marie-Marthe, Sycheva, Irina, Uszczynska-Ratajczak, Barbara, Xu, Jinuri, Yates, Andrew, Zerbino, Daniel, Zhang, Yan, Aken, Bronwen, Choudhary, Jyoti S, Gerstein, Mark, Guigó, Roderic, Hubbard, Tim J P, Kellis, Manolis, Paten, Benedict, Reymond, Alexandre, Tress, Michael L, Flicek, Paul
Published 2022

Making sense of big data in health research: Towards an EU action plan.

by Auffray, Charles, Balling, Rudi, Barroso, Inês, Bencze, László, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk-Jan, Guo, Yi-Ke, Gut, Ivo Glynne, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf-Dieter, Honrado, Ángel, Hose, D Rod, Houwing-Duistermaat, Jeanine, Hubbard, Tim, Janacek, Sophie Helen, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Müller, Werner, Nickel, Dörthe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, I Màs, Josep Redón, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea AI, van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Vizcaíno, Juan Antonio, Wubbe, John Peter Mary, Zanetti, Gianluigi
Published 2019