Tim Hubbard

Tim Hubbard

Professor

 https://orcid.org/0000-0002-1767-9318
  • 104156
    Citations

Search results

  • 2022

    GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements

    NIHR BioResource & Genomics England Research Consortium Collaborators, Dec 2022, In: Nature Communications. 13, 1, 4840.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    21 Citations (Scopus)
  • 2021

    GENCODE 2021

    Frankish, A., Diekhans, M., Jungreis, I., Lagarde, J., Loveland, J. E., Mudge, J. M., Sisu, C., Wright, J. C., Armstrong, J., Barnes, I., Berry, A., Bignell, A., Boix, C., Sala, S. C., Cunningham, F., Domenico, T. D., Donaldson, S., Fiddes, I. T., Girón, C. G. & Gonzalez, J. M. & 36 others, Grego, T., Hardy, M., Hourlier, T., Howe, K. L., Hunt, T., Izuogu, O. G., Johnson, R., Martin, F. J., Martínez, L., Mohanan, S., Muir, P., Navarro, F. C. P., Parker, A., Pei, B., Pozo, F., Riera, F. C., Ruffier, M., Schmitt, B. M., Stapleton, E., Suner, M. M., Sycheva, I., Uszczynska-Ratajczak, B., Wolf, M. Y., Xu, J., Yang, Y. T., Yates, A., Zerbino, D., Zhang, Y., Choudhary, J. S., Gerstein, M., Guigó, R., Hubbard, T. J. P., Kellis, M., Paten, B., Tress, M. L. & Flicek, P., 8 Jan 2021, In: Nucleic Acids Research. 49, D1, p. D916-D923

    Research output: Contribution to journal › Article › peer-review

    Open Access
    600 Citations (Scopus)

  • Pharmacogenomic testing in paediatrics: Clinical implementation strategies

    Barker, C. I. S., Groeneweg, G., Maitland‐van der Zee, A. H., Rieder, M. J., Hawcutt, D. B., Hubbard, T. J., Swen, J. J. & Carleton, B. C., 15 Dec 2021, (E-pub ahead of print) In: British Journal of Clinical Pharmacology.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    15 Citations (Scopus)

  • Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in cutaneous T-cell lymphoma

    Genomics England Research Consortium, Dec 2021, In: Scientific Reports. 11, 1, 3962.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    36 Citations (Scopus)
  • 2020

    Low-frequency variation in TP53 has large effects on head circumference and intracranial volume

    UK10K Consortium & Breen, G., 21 Jan 2020, In: Nature Communications. 10, 1, 357.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    25 Citations (Scopus)

  • Mining Social Media Data to Study the Consequences of Dementia Diagnosis on Caregivers and Relatives

    Gkotsis, G., Mueller, C., Dobson, R., Hubbard, T. & Dutta, R., Nov 2020, In: Dementia and Geriatric Cognitive Disorders. 49, 3, p. 295-302 8 p.

    Research output: Contribution to journal › Article › peer-review

    File
    15 Citations (Scopus)
    150 Downloads (Pure)

  • Transcriptional activity and strain-specific history of mouse pseudogenes

    Sisu, C., Muir, P., Frankish, A., Fiddes, I., Diekhans, M., Thybert, D., Odom, D. T., Flicek, P., Keane, T. M., Hubbard, T., Harrow, J. & Gerstein, M., 1 Dec 2020, In: Nature Communications. 11, 1, 3695.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    17 Citations (Scopus)
  • 2019

    Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia

    Deciphering Developmental Disorders Study, UK10K Consortium, NIHR BioResource, Simpson, M. A., Prigmore, E., Jones, P., Armstrong, R., Bennett, C., Berg, J., Bernhard, B., Cooper, N., Cox, H., Flinter, F., Fry, A., Gill, H., Gray, E., Harrison, V., Irving, M., Josifova, D. & Langman, C. & 44 others, Mohammed, S., Moore, D., Murphy, H., Roberts, J., Tischkowitz, M., Wright, M., Bolton, P., Breen, G., Clement, G., Collier, D., Curran, S., Ellis, P., Evans, D., Hart, D., Hubbard, T., Hysi, P., Jamshidi, Y., Lachance, G., Lopes, M., McGuffin, P., Metrustry, S., Moayyeri, A., Onoufriadis, A., Parr, J. R., Quaye, L., Sharp, S. I., Small, K., Spasic-Boskovic, O., Stevens, E., Valdes, A., Walters, J. T. R., Wang, Y., Bennett, D., Bradley, J. R., Davis, J., Koziell, A., Machado, R., Richards, M., Smith, K., Southgate, L., Thomas, E., Trembath, R., Williamson, C. & Yong, P., 2 May 2019, In: American Journal of Human Genetics. 104, 5, p. 948-956 9 p.

    Research output: Contribution to journal › Article › peer-review

    47 Citations (Scopus)

  • GENCODE reference annotation for the human and mouse genomes

    Frankish, A., Diekhans, M., Ferreira, A. M., Johnson, R., Jungreis, I., Loveland, J., Mudge, J. M., Sisu, C., Wright, J., Armstrong, J., Barnes, I., Berry, A., Bignell, A., Carbonell Sala, S., Chrast, J., Cunningham, F., Di Domenico, T., Donaldson, S., Fiddes, I. T. & García Girón, C. & 35 others, Gonzalez, J. M., Grego, T., Hardy, M., Hourlier, T., Hunt, T., Izuogu, O. G., Lagarde, J., Martin, F. J., Martínez, L., Mohanan, S., Muir, P., Navarro, F. C. P., Parker, A., Pei, B., Pozo, F., Ruffier, M., Schmitt, B. M., Stapleton, E., Suner, M. M., Sycheva, I., Uszczynska-Ratajczak, B., Xu, J., Yates, A., Zerbino, D., Zhang, Y., Aken, B., Choudhary, J. S., Gerstein, M., Guigó, R., Hubbard, T. J. P., Kellis, M., Paten, B., Reymond, A., Tress, M. L. & Flicek, P., 8 Jan 2019, In: Nucleic Acids Research. 47, D1, p. D766-D773

    Research output: Contribution to journal › Article › peer-review

    Open Access
    1815 Citations (Scopus)
  • 2018

    Scientists on the Spot: Sequencing the human genome to influence patient healthcare

    Schmidt, C. & Hubbard, T., 15 Jul 2018, In: Cardiovascular Research. 114, 9, p. E66-E67

    Research output: Contribution to journal › Comment/debate › peer-review

  • The 100 000 Genomes Project: bringing whole genome sequencing to the NHS

    100 000 Genomes Project, Turnbull, C., Scott, R. H., Thomas, E., Jones, L., Murugaesu, N., Pretty, F. B., Halai, D., Baple, E., Craig, C., Hamblin, A., Henderson, S., Patch, C., O'Neill, A., Devereaux, A., Smith, K., Martin, A. R., Sosinsky, A., McDonagh, E. M. & Sultana, R. & 10 others, Mueller, M., Smedley, D., Toms, A., Dinh, L., Fowler, T., Bale, M., Hubbard, T., Rendon, A., Hill, S. & Caulfield, M. J., 24 Apr 2018, In: BMJ. 361, 0, 7 p., k1687.

    Research output: Contribution to journal › Article › peer-review

    301 Citations (Scopus)
    15 Downloads (Pure)
  • 2017

    Analysis of diagnoses extracted from Electronic health records in a large mental health Case Register

    Kovalchuk, Y., Stewart, R., Broadbent, M., Hubbard, T. J. P. & Dobson, R. J. B., 2017, In: PL o S One . 12, 2, p. 1-12 e0171526.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    8 Citations (Scopus)
    244 Downloads (Pure)

  • Automated PDF highlights to support faster curation of literature on Parkinson’s and Alzheimer’s disease

    Wu, H., Oellrich, A., Girges, C., de Bono, B., Hubbard, T. J. P. & Dobson, R. J. B., 2017, In: Database: The Journal of Biological Databases and Curation. 2017, 1, p. 1-14 bax027.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    2 Citations (Scopus)
    322 Downloads (Pure)

  • Characterisation of mental health conditions in social media using Informed Deep Learning

    Gkotsis, G., Oellrich, A., Velupillai, S., Liakata, M., Hubbard, T. J. P., Dobson, R. J. B. & Dutta, R., 22 Mar 2017, In: Scientific Reports. 7, 45141.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    159 Citations (Scopus)
    398 Downloads (Pure)

  • Corrigendum: Characterisation of mental health conditions in social media using Informed Deep Learning

    Gkotsis, G., Oellrich, A., Velupillai, S., Liakata, M., Hubbard, T. J. P., Dobson, R. J. B. & Dutta, R., 16 May 2017, In: Scientific Reports. 7, p. 46813

    Research output: Contribution to journal › Article › peer-review

    Open Access

  • Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

    Schneider, V. A., Graves-Lindsay, T., Howe, K., Bouk, N., Chen, H.-C., Kitts, P. A., Murphy, T. D., Pruitt, K. D., Thibaud-Nissen, F., Albracht, D., Fulton, R. S., Kremitzki, M., Magrini, V., Markovic, C., McGrath, S., Steinberg, K. M., Auger, K., Chow, W., Collins, J. & Harden, G. & 18 others, Hubbard, T., Pelan, S., Simpson, J. T., Threadgold, G., Torrance, J., Wood, J. M., Clarke, L., Koren, S., Boitano, M., Peluso, P., Li, H., Chin, C.-S., Phillippy, A. M., Durbin, R., Wilson, R. K., Flicek, P., Eichler, E. E. & Church, D. M., May 2017, In: Genome Research. 27, 5, p. 849-864 16 p.

    Research output: Contribution to journal › Article › peer-review

    574 Citations (Scopus)
  • 2016

    Challenges and opportunities for system biology standards and tools in medical research

    König, M., Oellrich, A., Waltemath, D., Dobson, R. J. B., Hubbard, T. J. P. & Wolkenhauer, O., 29 Sept 2016, Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences, organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences. CEUR-WS, Vol. 1692.

    Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review

    Open Access
    File
    1 Citation (Scopus)
    166 Downloads (Pure)

  • Erratum to: Making sense of big data in health research: Towards an EU action plan [Genome Med., 8 (2016) (71)]

    Auffray, C., Balling, R., Barroso, I., Bencze, L., Benson, M., Bergeron, J., Bernal-Delgado, E., Blomberg, N., Bock, C., Conesa, A., Del Signore, S., Delogne, C., Devilee, P., Di Meglio, A., Eijkemans, M., Flicek, P., Graf, N., Grimm, V., Guchelaar, H. J. & Guo, Y. K. & 37 others, Gut, I. G., Hanbury, A., Hanif, S., Hilgers, R. D., Honrado, Á., Hose, D. R., Houwing-Duistermaat, J., Hubbard, T., Janacek, S. H., Karanikas, H., Kievits, T., Kohler, M., Kremer, A., Lanfear, J., Lengauer, T., Maes, E., Meert, T., Müller, W., Nickel, D., Oledzki, P., Pedersen, B., Petkovic, M., Pliakos, K., Rattray, M., i Màs, J. R., Schneider, R., Sengstag, T., Serra-Picamal, X., Spek, W., Vaas, L. A. I., van Batenburg, O., Vandelaer, M., Varnai, P., Villoslada, P., Vizcaíno, J. A., Wubbe, J. P. M. & Zanetti, G., 7 Nov 2016, In: Genome medicine. 8, 1, 2 p., 118.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    4 Citations (Scopus)
    182 Downloads (Pure)

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

    Auffray, C., Balling, R., Barroso, I., Bencze, L., Benson, M., Bergeron, J., Bernal-Delgado, E., Blomberg, N., Bock, C., Conesa, A., Del Signore, S., Delogne, C., Devilee, P., Di Meglio, A., Eijkemans, M., Flicek, P., Graf, N., Grimm, V., Guchelaar, H. J. & Guo, Y. K. & 37 others, Gut, I. G., Hanbury, A., Hanif, S., Hilgers, R. D., Honrado, Á., Hose, D. R., Houwing-Duistermaat, J., Hubbard, T., Janacek, S. H., Karanikas, H., Kievits, T., Kohler, M., Kremer, A., Lanfear, J., Lengauer, T., Maes, E., Meert, T., Müller, W., Nickel, D., Oledzki, P., Pedersen, B., Petkovic, M., Pliakos, K., Rattray, M., i Màs, J. R., Schneider, R., Sengstag, T., Serra-Picamal, X., Spek, W., Vaas, L. A. I., van Batenburg, O., Vandelaer, M., Varnai, P., Villoslada, P., Vizcaíno, J. A., Wubbe, J. P. M. & Zanetti, G., 23 Jun 2016, In: Genome medicine. 8, 1, 71.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    217 Citations (Scopus)
    260 Downloads (Pure)

  • The language of mental health problems in social media

    Gkotsis, G., Oellrich, A., Hubbard, T., Dobson, R. J., Liakata, M., Velupillai, S. & Dutta, R., 16 Jun 2016, The Third Computational Linguistics and Clinical Psychology Workshop (CLPsych). p. 63-73

    Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review

    Open Access
    File
    84 Citations (Scopus)
    476 Downloads (Pure)
  • 2015

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

    Geihs, M., Yan, Y., Walter, K., Huang, J., Memari, Y., Min, J. L., Mead, D., UK10 Consortium, Hubbard, T. J., Timpson, N. J., Down, T. A. & Soranzo, N., Dec 2015, In: BIOINFORMATICS. 31, 24, p. 4029-4031 3 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    9 Citations (Scopus)
    176 Downloads (Pure)

  • Global implementation of genomic medicine: We are not alone

    Manolio, T. A., Abramowicz, M., Al-Mulla, F., Anderson, W., Balling, R., Berger, A. C., Bleyl, S., Chakravarti, A., Chantratita, W., Chisholm, R. L., Dissanayake, V. H. W., Dunn, M., Dzau, V. J., Han, B. G., Hubbard, T., Kolbe, A., Korf, B., Kubo, M., Lasko, P. & Leego, E. & 24 others, Mahasirimongkol, S., Majumdar, P. P., Matthijs, G., McLeod, H. L., Metspalu, A., Meulien, P., Miyano, S., Naparstek, Y., O'Rourke, P. P., Patrinos, G. P., Rehm, H. L., Relling, M. V., Rennert, G., Rodriguez, L. L., Roden, D. M., Shuldiner, A. R., Sinha, S., Tan, P., Ulfendahl, M., Ward, R., Williams, M. S., Wong, J. E. L., Green, E. D. & Ginsburg, G. S., 3 Jun 2015, In: Science Translational Medicine. 7, 290, 290ps13.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    154 Citations (Scopus)
    289 Downloads (Pure)

  • The UK10K project identifies rare variants in health and disease

    UK10K Consortium, Perry, J. R. B., Brent Richards, J., Clement, G., Hart, D., Hysi, P., Metrustry, S., Hubbard, T., Lachance, G., Small, K. S. & Breen, G., 1 Oct 2015, In: NATURE. 526, p. 82-90 8 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    753 Citations (Scopus)
    233 Downloads (Pure)
  • 2014

    A Comparison of Peak Callers Used for DNase-Seq Data

    Koohy, H., Down, T. A., Spivakov, M. & Hubbard, T., 8 May 2014, In: PLoS ONE. 9, 5, 11 p., e96303.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    54 Citations (Scopus)
    83 Downloads (Pure)

  • Characterizing genetic variants for clinical action

    Ramos, E. M., Din-Lovinescu, C., Berg, J. S., Brooks, L. D., Duncanson, A., Dunn, M., Good, P., Hubbard, T. J. P., Jarvik, G. P., O'Donnell, C., Sherry, S. T., Aronson, N., Biesecker, L. G., Blumberg, B., Calonge, N., Colhoun, H. M., Epstein, R. S., Flicek, P., Gordon, E. S. & Green, E. D. & 15 others, Green, R. C., Hurles, M., Kawamoto, K., Knaus, W., Ledbetter, D. H., Levy, H. P., Lyon, E., Maglott, D., Mcleod, H. L., Rahman, N., Randhawa, G., Wicklund, C., Manolio, T. A., Chisholm, R. L. & Williams, M. S., 18 Mar 2014, In: American Journal of Medical Genetics. Part C: Seminars in Medical Genetics. 166, 1, p. 93-104 12 p.

    Research output: Contribution to journal › Article › peer-review

    49 Citations (Scopus)

  • Comparative analysis of pseudogenes across three phyla

    Sisu, C., Pei, B., Leng, J., Frankish, A., Zhang, Y., Balasubramanian, S., Harte, R., Wang, D., Rutenberg-Schoenberg, M., Clark, W., Diekhans, M., Rozowsky, J., Hubbard, T., Harrow, J. & Gerstein, M. B., 16 Sept 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 37, p. 13361-13366 6 p.

    Research output: Contribution to journal › Article › peer-review

    61 Citations (Scopus)

  • Comparative analysis of the transcriptome across distant species

    Gerstein, M. B., Rozowsky, J., Yan, K.-K., Wang, D., Cheng, C., Brown, J. B., Davis, C. A., Hillier, L., Sisu, C., Li, J. J., Pei, B., Harmanci, A. O., Duff, M. O., Djebali, S., Alexander, R. P., Alver, B. H., Auerbach, R., Bell, K., Bickel, P. J. & Boeck, M. E. & 76 others, Boley, N. P., Booth, B. W., Cherbas, L., Cherbas, P., Di, C., Dobins, A., Drenkows, J., Ewing, B., Fang, G., Fastucas, M., Feingold, E. A., Frankish, A., Gao, G., Good, P. J., Guigo, R., Hammonds, A., Harrow, J., Hoskins, R. A., Howald, C., Hu, L., Huang, H., Hubbard, T. J. P., Huynh, C., Jhas, S., Kasper, D., Kato, M., Kaufman, T. C., Kitchen, R. R., Ladewig, E., Lagarde, J., Lai, E., Leng, L., Lu, Z., MacCoss, M., May, G., McWhirter, R., Merrihew, G., Miller, D. M., Mortazavi, A., Murad, R., Oliver, B., Olson, S., Park, P. J., Pazin, M. J., Perrimon, N., Pervouchine, D., Reinke, V., Reymond, A., Robinson, G., Samsonova, A., Saunders, G. I., Schlesingers, F., Sethi, A., Slack, F. J., Spencer, W. C., Stoiber, M. H., Strasbourger, P., Tanzer, A., Thompson, O. A., Wan, K. H., Wang, G., Wang, H., Watkins, K. L., Wen, J., Wen, K., Xue, C., Yang, L., Yip, K., Zaleskis, C., Zhang, Y., Zheng, H., Brenner, S. E., Graveley, B. R., Ceniker, S. E., Gingeras, T. R. & Waterston, R., 28 Aug 2014, In: NATURE. 512, 7515, p. 445-448 4 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    223 Citations (Scopus)

  • Current status and new features of the Consensus Coding Sequence database

    Farrell, C. M., O'Leary, N. A., Harte, R. A., Loveland, J. E., Wilming, L. G., Wallin, C., Diekhans, M., Barrell, D., Searle, S. M. J., Aken, B., Hiatt, S. M., Frankish, A., Suner, M.-M., Rajput, B., Steward, C. A., Brown, G. R., Bennett, R., Murphy, M., Wu, W. & Kay, M. P. & 23 others, Hart, J., Rajan, J., Weber, J., Snow, C., Riddick, L. D., Hunt, T., Webb, D., Thomas, M., Tamez, P., Rangwala, S. H., McGarvey, K. M., Pujar, S., Shkeda, A., Mudge, J. M., Gonzalez, J. M., Gilbert, J. G. R., Trevanion, S. J., Baertsch, R., Harrow, J. L., Hubbard, T., Ostell, J. M., Haussler, D. & Pruitt, K. D., 1 Jan 2014, In: Nucleic Acids Research. 42, D1, p. D865-D872 8 p., N/A.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    123 Citations (Scopus)

  • Defining functional DNA elements in the human genome

    Kellis, M., Wold, B., Snyder, M. P., Bernstein, B. E., Kundaje, A., Marinov, G. K., Ward, L. D., Birney, E., Crawford, G. E., Dekker, J., Dunham, I., Elnitski, L. L., Farnham, P. J., Feingold, E. A., Gerstein, M., Giddings, M. C., Gilbert, D. M., Gingeras, T. R., Green, E. D. & Guigo, R. & 10 others, Hubbard, T., Kent, J., Lieb, J. D., Myers, R. M., Pazin, M. J., Ren, B., Stamatoyannopoulos, J. A., Weng, Z., White, K. P. & Hardison, R. C., 29 Apr 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 17, p. 6131-6138 8 p., N/A.

    Research output: Contribution to journal › Article › peer-review

    516 Citations (Scopus)

  • Ensembl 2014

    Flicek, P., Amode, M. R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S., Gil, L., Girón, C. G., Gordon, L., Hourlier, T., Hunt, S., Johnson, N., Juettemann, T., Kähäri, A. K., Keenan, S. & Kulesha, E. & 32 others, Martin, F. J., Maurel, T., McLaren, W. M., Murphy, D. N., Nag, R., Overduin, B., Pignatelli, M., Pritchard, B., Pritchard, E., Riat, H. S., Ruffier, M., Sheppard, D., Taylor, K., Thormann, A., Trevanion, S. J., Vullo, A., Wilder, S. P., Wilson, M., Zadissa, A., Aken, B. L., Birney, E., Cunningham, F., Harrow, J., Herrero, J., Hubbard, T. J. P., Kinsella, R., Muffato, M., Parker, A., Spudich, G., Yates, A., Zerbino, D. R. & Searle, S. M. J., 1 Jan 2014, In: Nucleic Acids Research. 42, D1, p. D749-D755 7 p., N/A.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    1093 Citations (Scopus)

  • Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

    Kellis, M., Wold, B., Snyder, M. P., Bernstein, B. E., Kundaje, A., Marinov, G. K., Ward, L. D., Birney, E., Crawford, G. E., Dekker, J., Dunham, I., Elnitski, L. L., Farnham, P. J., Feingold, E. A., Gerstein, M., Giddings, M. C., Gilbert, D. M., Gingeras, T. R., Green, E. D. & Guigo, R. & 10 others, Hubbard, T., Kent, J., Lieb, J. D., Myers, R. M., Pazin, M. J., Ren, B., Stamatoyannopoulos, J., Weng, Z., White, K. P. & Hardison, R. C., 19 Aug 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 33, E3366.

    Research output: Contribution to journal › Comment/debate › peer-review

    12 Citations (Scopus)
  • 2013

    Assessment of transcript reconstruction methods for RNA-seq

    Steijger, T., Abril, J. F., Engström, P. G., Kokocinski, F., Abril, J. F., Akerman, M., Alioto, T., Ambrosini, G., Antonarakis, S. E., Behr, J., Bertone, P., Bohnert, R., Bucher, P., Cloonan, N., Derrien, T., Djebali, S., Du, J., Dudoit, S., Engström, P. G. & Gerstein, M. & 31 others, Gingeras, T. R., Gonzalez, D., Grimmond, S. M., Guigó, R., Habegger, L., Harrow, J., Iseli, C., Jean, G., Kahles, A., Kokocinski, F., Lagarde, J., Leng, J., Lefebvre, G., Lewis, S., Mortazavi, A., Niermann, P., Rätsch, G., Reymond, A., Ribeca, P., Richard, H., Rougemont, J., Rozowsky, J., Sammeth, M., Sboner, A., Schulz, M. H., Searle, S. M. J., Solorzano, N. D., Solovyev, V., Stanke, M., Hubbard, T. J. & RGASP Consortium, Dec 2013, In: NATURE METHODS. 10, 12, p. 1177-1184 8 p., N/A.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    521 Citations (Scopus)

  • Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme

    Koohy, H., Down, T. A. & Hubbard, T. J., 26 Jul 2013, In: PLoS ONE. 8, 7, p. N/A 9 p., e69853.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    51 Citations (Scopus)

  • Ensembl 2013

    Flicek, P., Ahmed, I., Amode, M. R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gil, L., García-Girón, C., Gordon, L., Hourlier, T., Hunt, S., Juettemann, T., Kähäri, A. K., Keenan, S. & Komorowska, M. & 35 others, Kulesha, E., Longden, I., Maurel, T., McLaren, W. M., Muffato, M., Nag, R., Overduin, B., Pignatelli, M., Pritchard, B., Pritchard, E., Riat, H. S., Ritchie, G. R. S., Ruffier, M., Schuster, M., Sheppard, D., Sobral, D., Taylor, K., Thormann, A., Trevanion, S., White, S., Wilder, S. P., Aken, B. L., Birney, E., Cunningham, F., Dunham, I., Harrow, J., Herrero, J., Hubbard, T. J. P., Johnson, N., Kinsella, R., Parker, A., Spudich, G., Yates, A., Zadissa, A. & Searle, S. M. J., Jan 2013, In: Nucleic Acids Research. 41, D1, p. D48-D55 8 p., N/A.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    823 Citations (Scopus)

  • Systematic evaluation of spliced alignment programs for RNA-seq data

    Engström, P. G., Steijger, T., Sipos, B., Grant, G. R., Kahles, A., RGASP Consortium, Rätsch, G., Goldman, N., Hubbard, T. J., Harrow, J., Guigó, R. & Bertone, P., Dec 2013, In: NATURE METHODS. 10, 12, p. 1185-1191 7 p., N/A.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    372 Citations (Scopus)

  • The zebrafish reference genome sequence and its relationship to the human genome

    Howe, K., Clark, M. D., Torroja, C. F., Torrance, J., Berthelot, C., Muffato, M., Collins, J. E., Humphray, S., McLaren, K., Matthews, L., McLaren, S., Sealy, I., Caccamo, M., Churcher, C., Scott, C., Barrett, J. C., Koch, R., Rauch, G.-J., White, S. & Chow, W. & 152 others, Kilian, B., Quintais, L. T., Guerra-Assunção, J. A., Zhou, Y., Gu, Y., Yen, J., Vogel, J.-H., Eyre, T., Redmond, S., Banerjee, R., Chi, J., Fu, B., Langley, E., Maguire, S. F., Laird, G. K., Lloyd, D., Kenyon, E., Donaldson, S., Sehra, H., Almeida-King, J., Loveland, J., Trevanion, S., Jones, M., Quail, M., Willey, D., Hunt, A., Burton, J., Sims, S., McLay, K., Plumb, B., Davis, J., Clee, C., Oliver, K., Clark, R., Riddle, C., Eliott, D., Threadgold, G., Harden, G., Ware, D., Mortimer, B., Kerry, G., Heath, P., Phillimore, B., Tracey, A., Corby, N., Dunn, M., Johnson, C., Wood, J., Clark, S., Pelan, S., Griffiths, G., Smith, M., Glithero, R., Howden, P., Barker, N., Stevens, C., Harley, J., Holt, K., Panagiotidis, G., Lovell, J., Beasley, H., Henderson, C., Gordon, D., Auger, K., Wright, D., Collins, J., Raisen, C., Dyer, L., Leung, K., Robertson, L., Ambridge, K., Leongamornlert, D., McGuire, S., Gilderthorp, R., Griffiths, C., Manthravadi, D., Nichol, S., Barker, G., Whitehead, S., Kay, M., Brown, J., Murnane, C., Gray, E., Humphries, M., Sycamore, N., Barker, D., Saunders, D., Wallis, J., Babbage, A., Hammond, S., Mashreghi-Mohammadi, M., Barr, L., Martin, S., Wray, P., Ellington, A., Matthews, N., Ellwood, M., Woodmansey, R., Clark, G., Cooper, J., Tromans, A., Grafham, D., Skuce, C., Pandian, R., Andrews, R., Harrison, E., Kimberley, A., Garnett, J., Fosker, N., Hall, R., Garner, P., Kelly, D., Bird, C., Palmer, S., Gehring, I., Berger, A., Dooley, C. M., Ersan-Ürün, Z., Eser, C., Geiger, H., Geisler, M., Karotki, L., Kirn, A., Konantz, J., Konantz, M., Oberländer, M., Rudolph-Geiger, S., Teucke, M., Osoegawa, K., Zhu, B., Rapp, A., Widaa, S., Langford, C., Yang, F., Carter, N. P., Harrow, J., Ning, Z., Herrero, J., Searle, S. M. J., Enright, A., Geisler, R., Plasterk, R. H. A., Lee, C., Westerfield, M., de Jong, P. J., Zon, L. I., Postlethwait, J. H., Nüsslein-Volhard, C., Hubbard, T. J. P., Roest Crollius, H., Rogers, J. & Stemple, D. L., 25 Apr 2013, In: NATURE. 496, 7446, p. 498-503 6 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    3650 Citations (Scopus)
  • 2012

    An integrated encyclopedia of DNA elements in the human genome

    Bernstein, B. E., Birney, E., Dunham, I., Green, E. D., Gunter, C., Snyder, M., ENCODE Project Consortium & Hubbard, T., 5 Sept 2012, In: NATURE. 489, 7414, p. 57-74 18 p., N/A.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    12780 Citations (Scopus)

  • Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome

    Howald, C., Tanzer, A., Chrast, J., Kokocinski, F., Derrien, T., Walters, N., Gonzalez, J. M., Frankish, A., Aken, B. L., Hourlier, T., Vogel, J.-H., White, S., Searle, S., Harrow, J., Hubbard, T. J., Guigó, R. & Reymond, A., Sept 2012, In: Genome Research. 22, 9, p. 1698-1710 13 p., N/A.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    48 Citations (Scopus)

  • Ensembl 2012

    Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gil, L., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kähäri, A. K., Keefe, D., Keenan, S., Kinsella, R. & Komorowska, M. & 37 others, Koscielny, G., Kulesha, E., Larsson, P., Longden, I., McLaren, W., Muffato, M., Overduin, B., Pignatelli, M., Pritchard, B., Riat, H. S., Ritchie, G. R. S., Ruffier, M., Schuster, M., Sobral, D., Tang, Y. A., Taylor, K., Trevanion, S., Vandrovcova, J., White, S., Wilson, M., Wilder, S. P., Aken, B. L., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernández-Suarez, X. M., Harrow, J., Herrero, J., Hubbard, T. J. P., Parker, A., Proctor, G., Spudich, G., Vogel, J., Yates, A., Zadissa, A. & Searle, S. M. J., Jan 2012, In: Nucleic Acids Research. 40, D1 (Database Issue), p. D84-D90 7 p., N/A.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    783 Citations (Scopus)

  • Evidence for transcript networks composed of chimeric RNAs in human cells

    Djebali, S., Lagarde, J., Kapranov, P., Lacroix, V., Borel, C., Mudge, J. M., Howald, C., Foissac, S., Ucla, C., Chrast, J., Ribeca, P., Martin, D., Murray, R. R., Yang, X., Ghamsari, L., Lin, C., Bell, I., Dumais, E., Drenkow, J. & Tress, M. L. & 18 others, Gelpí, J. L., Orozco, M., Valencia, A., van Berkum, N. L., Lajoie, B. R., Vidal, M., Stamatoyannopoulos, J., Batut, P., Dobin, A., Harrow, J., Hubbard, T., Dekker, J., Frankish, A., Salehi-Ashtiani, K., Reymond, A., Antonarakis, S. E., Guigó, R. & Gingeras, T. R., 4 Jan 2012, In: PLoS ONE. 7, 1, p. N/A 22 p., e28213.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    55 Citations (Scopus)

  • GENCODE: the reference human genome annotation for The ENCODE Project

    Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., Barnes, I., Bignell, A., Boychenko, V., Hunt, T., Kay, M., Mukherjee, G., Rajan, J., Despacio-Reyes, G., Saunders, G. & Steward, C. & 21 others, Harte, R., Lin, M., Howald, C., Tanzer, A., Derrien, T., Chrast, J., Walters, N., Balasubramanian, S., Pei, B., Tress, M., Rodriguez, J. M., Ezkurdia, I., van Baren, J., Brent, M., Haussler, D., Kellis, M., Valencia, A., Reymond, A., Gerstein, M., Guigó, R. & Hubbard, T. J., Sept 2012, In: Genome Research. 22, 9, p. 1760-1774 15 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    3401 Citations (Scopus)

  • Landscape of transcription in human cells

    Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., Xue, C., Marinov, G. K., Khatun, J., Williams, B. A., Zaleski, C., Rozowsky, J., Röder, M., Kokocinski, F., Abdelhamid, R. F. & Alioto, T. & 65 others, Antoshechkin, I., Baer, M. T., Bar, N. S., Batut, P., Bell, K., Bell, I., Chakrabortty, S., Chen, X., Chrast, J., Curado, J., Derrien, T., Drenkow, J., Dumais, E., Dumais, J., Duttagupta, R., Falconnet, E., Fastuca, M., Fejes-Toth, K., Ferreira, P., Foissac, S., Fullwood, M. J., Gao, H., Gonzalez, D., Gordon, A., Gunawardena, H., Howald, C., Jha, S., Johnson, R., Kapranov, P., King, B., Kingswood, C., Luo, O. J., Park, E., Persaud, K., Preall, J. B., Ribeca, P., Risk, B., Robyr, D., Sammeth, M., Schaffer, L., See, L.-H., Shahab, A., Skancke, J., Suzuki, A. M., Takahashi, H., Tilgner, H., Trout, D., Walters, N., Wang, H., Wrobel, J., Yu, Y., Ruan, X., Hayashizaki, Y., Harrow, J., Gerstein, M., Hubbard, T., Reymond, A., Antonarakis, S. E., Hannon, G., Giddings, M. C., Ruan, Y., Wold, B., Carninci, P., Guigó, R. & Gingeras, T. R., 6 Sept 2012, In: NATURE. 489, 7414, p. 101-108 8 p., N/A.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    4163 Citations (Scopus)

  • The GENCODE pseudogene resource

    Pei, B., Sisu, C., Frankish, A., Howald, C., Habegger, L., Mu, X. J., Harte, R., Balasubramanian, S., Tanzer, A., Diekhans, M., Reymond, A., Hubbard, T. J., Harrow, J. & Gerstein, M. B., 9 Sept 2012, In: GENOME BIOLOGY. 13, 9, p. N/A 26 p., R51.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    260 Citations (Scopus)

  • The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

    Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., Lagarde, J., Veeravalli, L., Ruan, X., Ruan, Y., Lassmann, T., Carninci, P., Lipovich, L., Gonzalez, J. M., Davis, C. A. & Shiekhattar, R. & 5 others, Gingeras, T. R., Hubbard, T. J., Notredame, C., Harrow, J. & Guigó, R., Sept 2012, In: Genome Research. 22, 9, p. 1775-1789 15 p., N/A.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    4169 Citations (Scopus)
  • 2011

    A user's guide to the encyclopedia of DNA elements (ENCODE)

    ENCODE Project Consortium & Hubbard, T., 19 Apr 2011, In: PL o S Biology. 9, 4, p. N/A 21 p., e1001046.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    1187 Citations (Scopus)

  • Dalliance: interactive genome viewing on the web

    Down, T. A., Piipari, M. & Hubbard, T. J. P., 15 Mar 2011, In: Bioinformatics (Oxford, England). 27, 6, p. 889-890 2 p., N/A.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    71 Citations (Scopus)

  • Developing and implementing an institute-wide data sharing policy

    Dyke, S. O. & Hubbard, T. J., 28 Sept 2011, In: Genome medicine. 3, 9, p. N/A 8 p., 60.

    Research output: Contribution to journal › Article › peer-review

    31 Citations (Scopus)

  • Ensembl 2011

    Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kähäri, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F. & Kulesha, E. & 32 others, Larsson, P., Longden, I., McLaren, W., Overduin, B., Pritchard, B., Riat, H. S., Rios, D., Ritchie, G. R. S., Ruffier, M., Schuster, M., Sobral, D., Spudich, G., Tang, Y. A., Trevanion, S., Vandrovcova, J., Vilella, A. J., White, S., Wilder, S. P., Zadissa, A., Zamora, J., Aken, B. L., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernández-Suarez, X. M., Herrero, J., Hubbard, T. J. P., Parker, A., Proctor, G., Vogel, J. & Searle, S. M. J., Jan 2011, In: Nucleic Acids Research. 39, Suppl 1 (Database issue), p. D800-D806 7 p., N/A.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    597 Citations (Scopus)

  • ITFoM - The IT future of medicine

    Lehrach, H., Subrak, R., Boyle, P., Pasterk, M., Zatloukal, K., Müller, H., Hubbard, T., Brand, A., Girolami, M., Jameson, D., Bruggeman, F. J. & Westerhoff, H. V., 22 Dec 2011, Procedia Computer Science. Vol. 7. p. 26-29 4 p.

    Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review

    Open Access
    File
    14 Citations (Scopus)
    134 Downloads (Pure)

  • Modernizing reference genome assemblies

    Church, D. M., Schneider, V. A., Graves, T., Auger, K., Cunningham, F., Bouk, N., Chen, H.-C., Agarwala, R., McLaren, W. M., Ritchie, G. R. S., Albracht, D., Kremitzki, M., Rock, S., Kotkiewicz, H., Kremitzki, C., Wollam, A., Trani, L., Fulton, L., Fulton, R. & Matthews, L. & 19 others, Whitehead, S., Chow, W., Torrance, J., Dunn, M., Harden, G., Threadgold, G., Wood, J., Collins, J., Heath, P., Griffiths, G., Pelan, S., Grafham, D., Eichler, E. E., Weinstock, G., Mardis, E. R., Wilson, R. K., Howe, K., Flicek, P. & Hubbard, T., 5 Jul 2011, In: PL o S Biology. 9, 7, e1001091.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    371 Citations (Scopus)
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