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1. Haplosaurus computes protein haplotypes for use in precision drug design

Author

William Spooner, William McLaren, Timothy Slidel, Donna K. Finch, Robin Butler, Jamie Campbell, Laura Eghobamien, David Rider, Christine Mione Kiefer, Matthew J. Robinson, Colin Hardman, Fiona Cunningham, Tristan Vaughan, Paul Flicek, and Catherine Chaillan Huntington

Subjects
Science
Abstract

Proteoforms arise as protein isoforms or as protein haplotypes, which are the result of genetic variation. Here, the authors develop Haplosaurus, a database that computes protein haplotypes genome-wide from existing genotype data and analyse protein haplotype variability in the 1000 Genomes dataset.

Published
2018
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2. PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants.

Author

Charles Chen, Genevieve DeClerck, Feng Tian, William Spooner, Susan McCouch, and Edward Buckler

Subjects
Medicine, Science
Abstract

PICARA is an analytical pipeline designed to systematically summarize observed SNP/trait associations identified by genome wide association studies (GWAS) and to identify candidate genes involved in the regulation of complex trait variation. The pipeline provides probabilistic inference about a priori candidate genes using integrated information derived from genome-wide association signals, gene homology, and curated gene sets embedded in pathway descriptions. In this paper, we demonstrate the performance of PICARA using data for flowering time variation in maize - a key trait for geographical and seasonal adaption of plants. Among 406 curated flowering time-related genes from Arabidopsis, we identify 61 orthologs in maize that are significantly enriched for GWAS SNP signals, including key regulators such as FT (Flowering Locus T) and GI (GIGANTEA), and genes centered in the Arabidopsis circadian pathway, including TOC1 (Timing of CAB Expression 1) and LHY (Late Elongated Hypocotyl). In addition, we discover a regulatory feature that is characteristic of these a priori flowering time candidates in maize. This new probabilistic analytical pipeline helps researchers infer the functional significance of candidate genes associated with complex traits and helps guide future experiments by providing statistical support for gene candidates based on the integration of heterogeneous biological information.

Published
2012
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4. The BioMart community portal: an innovative alternative to large, centralized data repositories.

Author

Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, James E. Allen, Olivier Arnaiz, Mohammad Hamza Awedh, Richard A. Baldock, Giulia Barbiera, Philippe Bardou, Tim Beck, Andrew Blake 0003, Merideth Bonierbale, Anthony J. Brookes, Gabriele Bucci, Iwan Buetti, Sarah W. Burge, Cédric Cabau, Joseph W. Carlson, Claude Chelala, Charalambos Chrysostomou, Davide Cittaro, Olivier Collin, Raul Cordova, Rosalind J. Cutts, Erik Dassi, Alex Di Génova, Anis Djari, Anthony Esposito, Heather Estrella, Eduardo Eyras, Julio Fernandez-Banet, Simon A. Forbes, Robert C. Free, Takatomo Fujisawa, Emanuela Gadaleta, Jose M. Garcia-Manteiga, David M. Goodstein, Kristian A. Gray, José Afonso Guerra-Assunção, Bernard Haggarty, Dongjin Han, Byungwoo Han, Todd W. Harris, Jayson Harshbarger, Robert K. Hastings, Richard D. Hayes, Claire Hoede, Shen Hu, Zhi-Liang Hu, Lucie N. Hutchins, Zhengyan Kan, Hideya Kawaji, Aminah-Olivia Keliet, Arnaud Kerhornou, Sunghoon Kim 0001, Rhoda Kinsella, Christophe Klopp, Lei Kong, Daniel Lawson, Dejan Lazarevic, Ji-Hyun Lee, Thomas Letellier, Chuan-Yun Li, Pietro Liò, Chu-Jun Liu, Jie Luo, Alejandro Maass, Jérôme Mariette, Thomas Maurel, Stefania Merella, Azza Mostafa Mohamed, François Moreews, Nabihoudine Ibouniyamine, Nelson Ndegwa, Céline Noirot, Christian Perez-Llamas, Michael Primig, Alessandro Quattrone, Hadi Quesneville, Davide Rambaldi, James M. Reecy, Michela Riba, Steven Rosanoff, Amna Ali Saddiq, Elisa Salas, Olivier Sallou, Rebecca Shepherd, Reinhard Simon, Linda Sperling, William Spooner, Daniel M. Staines, Delphine Steinbach, Kevin R. Stone, Elia Stupka, Jon W. Teague, Abu Z. Dayem Ullah, Jun Wang 0060, Doreen Ware, Marie Wong-Erasmus, Ken Youens-Clark, Amonida Zadissa, Shi-Jian Zhang, and Arek Kasprzyk

Published
2015
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5. Gramene database in 2010: updates and extensions.

Author

Ken Youens-Clark, Edward S. Buckler, Terry M. Casstevens, Charles Chen, Genevieve DeClerck, Paul S. Derwent, Palitha Dharmawardhana, Pankaj Jaiswal, Paul J. Kersey, A. S. Karthikeyan, Jerry Lu, Susan McCouch, Liya Ren, William Spooner, Joshua C. Stein, Jim Thomason, Sharon Wei, and Doreen Ware

Published
2011
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6. Ensembl 2009.

Author

Tim J. P. Hubbard, Bronwen L. Aken, Sarah C. Ayling, Benoît Ballester, Kathryn Beal, Eugene Bragin, Simon Brent, Yuan Chen 0007, Peter Clapham, Laura Clarke, Guy Coates, Susan Fairley, Stephen Fitzgerald, Julio Fernandez-Banet, Leo Gordon, Stefan Gräf, Syed Haider, Martin Hammond, Richard C. G. Holland, Kevin L. Howe, Andrew M. Jenkinson, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, Ian Longden, Karine Megy, Patrick Meidl, Bert Overduin, Anne Parker, Bethan Pritchard, Daniel Rios, Michael Schuster, Guy Slater, Damian Smedley, William Spooner, Giulietta Spudich, Stephen J. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, Steven P. Wilder, Arek Zadissa, Ewan Birney, Fiona Cunningham, Val Curwen, Richard Durbin, Xosé M. Fernández-Suárez, Javier Herrero, Arek Kasprzyk, Glenn Proctor, James A. Smith, Stephen M. J. Searle, and Paul Flicek

Published
2009
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7. Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study

Author

Kristina Ibañez, James Polke, R Tanner Hagelstrom, Egor Dolzhenko, Dorota Pasko, Ellen Rachel Amy Thomas, Louise C Daugherty, Dalia Kasperaviciute, Katherine R Smith, Zandra C Deans, Sue Hill, Tom Fowler, Richard H Scott, John Hardy, Patrick F Chinnery, Henry Houlden, Augusto Rendon, Mark J Caulfield, Michael A Eberle, Ryan J Taft, Arianna Tucci, Ellen M McDonagh, Antonio Rueda, Dimitris Polychronopoulos, Georgia Chan, Heather Angus-Leppan, Kailash P Bhatia, James E Davison, Richard Festenstein, Pietro Fratta, Paola Giunti, Robin Howard, Laxmi Venkata, Matilde Laurá, Meriel McEntagart, Lara Menzies, Huw Morris, Mary M Reilly, Robert Robinson, Elisabeth Rosser, Francesca Faravelli, Anette Schrag, Jonathan M Schott, Thomas T Warner, Nicholas W Wood, David Bourn, Kelly Eggleton, Robyn Labrum, Philip Twiss, Stephen Abbs, Liana Santos, Ghareesa Almheiri, Isabella Sheikh, Jana Vandrovcova, Christine Patch, Ana Lisa Taylor Tavares, Zerin Hyder, Anna Need, Helen Brittain, Emma Baple, Loukas Moutsianas, Viraj Deshpande, Denise L Perry, Subramanian S. Ajay, Aditi Chawla, Vani Rajan, Kathryn Oprych, Angela Douglas, Gill Wilson, Sian Ellard, I Karen Temple, Andrew Mumford, Dom McMullan, Kikkeri Naresh, Frances A Flinter, Jenny C Taylor, Lynn Greenhalgh, William Newman, Paul Brennan, John A Sayer, F Lucy Raymond, Lyn S Chitty, John C. Ambrose, Prabhu Arumugam, Marta Bleda, Freya Boardman-Pretty, Jeanne M. Boissiere, Christopher R. Boustred, Clare E.H. Craig, Anna de Burca, Andrew Devereau, Greg Elgar, Rebecca E. Foulger, Pedro Furió-Tarí, Joanne Hackett, Dina Halai, Angela Hamblin, Shirley Henderson, James Holman, Tim J.P. Hubbard, Rob Jackson, Louise J. Jones, Melis Kayikci, Lea Lahnstein, Kay Lawson, Sarah E.A. Leigh, Ivonne U.S. Leong, Javier F. Lopez, Fiona Maleady-Crowe, Joanne Mason, Michael Mueller, Nirupa Murugaesu, Chris A. Odhams, Daniel Perez-Gil, John Pullinger, Tahrima Rahim, Pablo Riesgo-Ferreiro, Tim Rogers, Mina Ryten, Kevin Savage, Kushmita Sawant, Afshan Siddiq, Alexander Sieghart, Damian Smedley, Alona Sosinsky, William Spooner, Helen E. Stevens, Alexander Stuckey, Razvan Sultana, Simon R. Thompson, Carolyn Tregidgo, Emma Walsh, Sarah A. Watters, Matthew J. Welland, Eleanor Williams, Katarzyna Witkowska, Suzanne M. Wood, and Magdalena Zarowiecki

Subjects
Fragile X Mental Retardation Protein, DNA Repeat Expansion, Whole Genome Sequencing, Whole Genome Sequencing/methods, Humans, Neurology (clinical), Prospective Studies, Child, Fragile X Mental Retardation Protein/genetics, State Medicine, United Kingdom, Retrospective Studies
Abstract

BACKGROUND: Repeat expansion disorders affect about 1 in 3000 individuals and are clinically heterogeneous diseases caused by expansions of short tandem DNA repeats. Genetic testing is often locus-specific, resulting in underdiagnosis of people who have atypical clinical presentations, especially in paediatric patients without a previous positive family history. Whole genome sequencing is increasingly used as a first-line test for other rare genetic disorders, and we aimed to assess its performance in the diagnosis of patients with neurological repeat expansion disorders.METHODS: We retrospectively assessed the diagnostic accuracy of whole genome sequencing to detect the most common repeat expansion loci associated with neurological outcomes (AR, ATN1, ATXN1, ATXN2, ATXN3, ATXN7, C9orf72, CACNA1A, DMPK, FMR1, FXN, HTT, and TBP) using samples obtained within the National Health Service in England from patients who were suspected of having neurological disorders; previous PCR test results were used as the reference standard. The clinical accuracy of whole genome sequencing to detect repeat expansions was prospectively examined in previously genetically tested and undiagnosed patients recruited in 2013-17 to the 100 000 Genomes Project in the UK, who were suspected of having a genetic neurological disorder (familial or early-onset forms of ataxia, neuropathy, spastic paraplegia, dementia, motor neuron disease, parkinsonian movement disorders, intellectual disability, or neuromuscular disorders). If a repeat expansion call was made using whole genome sequencing, PCR was used to confirm the result.FINDINGS: The diagnostic accuracy of whole genome sequencing to detect repeat expansions was evaluated against 793 PCR tests previously performed within the NHS from 404 patients. Whole genome sequencing correctly classified 215 of 221 expanded alleles and 1316 of 1321 non-expanded alleles, showing 97·3% sensitivity (95% CI 94·2-99·0) and 99·6% specificity (99·1-99·9) across the 13 disease-associated loci when compared with PCR test results. In samples from 11 631 patients in the 100 000 Genomes Project, whole genome sequencing identified 81 repeat expansions, which were also tested by PCR: 68 were confirmed as repeat expansions in the full pathogenic range, 11 were non-pathogenic intermediate expansions or premutations, and two were non-expanded repeats (16% false discovery rate).INTERPRETATION: In our study, whole genome sequencing for the detection of repeat expansions showed high sensitivity and specificity, and it led to identification of neurological repeat expansion disorders in previously undiagnosed patients. These findings support implementation of whole genome sequencing in clinical laboratories for diagnosis of patients who have a neurological presentation consistent with a repeat expansion disorder.FUNDING: Medical Research Council, Department of Health and Social Care, National Health Service England, National Institute for Health Research, and Illumina.

Published
2022
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8. WormBase 2007.

Author

Anthony Rogers, Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Carol Bastiani, Payan Canaran, Juancarlos Chan, Wen J. Chen, Paul Davis 0001, Jolene Fernandes, Tristan J. Fiedler, Michael Han 0001, Todd W. Harris, Ranjana Kishore, Raymond Y. N. Lee, Sheldon J. McKay, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Gary Schindelman, Erich M. Schwarz, William Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang 0001, Xiaodong Wang 0008, Gary Williams, Karen Yook, Richard Durbin, Lincoln D. Stein, John Spieth, and Paul W. Sternberg

Published
2008
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9. Gramene: a growing plant comparative genomics resource.

Author

Chengzhi Liang, Pankaj Jaiswal, Claire Hebbard, Shuly Avraham, Edward S. Buckler, Terry M. Casstevens, Bonnie L. Hurwitz, Susan McCouch, Junjian Ni, Anuradha Pujar, Dean Ravenscroft, Liya Ren, William Spooner, Isaak Y. Tecle, Jim Thomason, Chih-Wei Tung, Xuehong Wei, Immanuel Yap, Ken Youens-Clark, Doreen Ware, and Lincoln Stein

Published
2008
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10. Ensembl comparative genomics resources.

Author

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

Published
2016
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11. WormBase: new content and better access.

Author

Tamberlyn Bieri, Darin Blasiar, Philip Ozersky, Igor Antoshechkin, Carol Bastiani, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen, Paul Davis 0001, Tristan J. Fiedler, Lisa R. Girard, Michael Han 0001, Todd W. Harris, Ranjana Kishore, Raymond Y. N. Lee, Sheldon J. McKay, Hans-Michael Müller, Cecilia Nakamura, Andrei Petcherski, Arun Rangarajan, Anthony Rogers, Gary Schindelman, Erich M. Schwarz, William Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang 0001, Xiaodong Wang 0008, Gary Williams, Richard Durbin, Lincoln D. Stein, Paul W. Sternberg, and John Spieth

Published
2007
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12. WormBase: better software, richer content.

Author

Erich M. Schwarz, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen, Paul Davis 0001, Tristan J. Fiedler, Lisa R. Girard, Todd W. Harris, Eimear Kenny, Ranjana Kishore, Daniel Lawson, Raymond Y. N. Lee, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Anthony Rogers, William Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang 0001, Richard Durbin, John Spieth, Lincoln D. Stein, and Paul W. Sternberg

Published
2006
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13. Gramene: a bird's eye view of cereal genomes.

Author

Pankaj Jaiswal, Junjian Ni, Immanuel Yap, Doreen Ware, William Spooner, Ken Youens-Clark, Liya Ren, Chengzhi Liang, Wei Zhao 0005, Kiran Ratnapu, Benjamin Faga, Payan Canaran, Molly Fogleman, Claire Hebbard, Shuly Avraham, Steven Schmidt, Terry M. Casstevens, Edward S. Buckler, Lincoln Stein, and Susan McCouch

Published
2006
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14. Ensembl 2005.

Author

Tim J. P. Hubbard, D. Andrews, Mario Cáccamo, Graham Cameron, Yuan Chen 0007, Michele E. Clamp, Laura Clarke, Guy Coates, Tony Cox 0001, Fiona Cunningham, Val Curwen, Tim Cutts, Thomas A. Down, Richard Durbin, Xosé M. Fernández-Suárez, James G. R. Gilbert, Martin Hammond, Javier Herrero, H. Hotz, Kevin L. Howe, Vivek Iyer, Kerstin Jekosch, Andreas Kähäri, Arek Kasprzyk, Damian Keefe, Stephen Keenan, Felix Kokocinski, D. London, Ian Longden, Graham P. McVicker, Craig Melsopp, Patrick Meidl, Simon C. Potter, Glenn Proctor, Mark Rae, Daniel Rios, Michael Schuster, Stephen M. J. Searle, Jessica Severin, Guy Slater, Damian Smedley, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, R. Storey, Stephen J. Trevanion, Abel Ureta-Vidal, Jan Vogel, Simon White, Cara Woodwark, and Ewan Birney

Published
2005
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15. Ensembl 2002: accommodating comparative genomics.

Author

Michele E. Clamp, T. Daniel Andrews, Daniel Barker, Paul Bevan 0001, Graham Cameron, Yuan Chen 0007, Laura Clarke, Tony Cox 0001, James A. Cuff, Val Curwen, Thomas A. Down, Richard Durbin, Eduardo Eyras, James G. R. Gilbert, Martin Hammond, Tim J. P. Hubbard, Arek Kasprzyk, Damian Keefe, Heikki Lehväslaiho, Vivek Iyer, Craig Melsopp, Emmanuel Mongin, Roger Pettett, Simon C. Potter, Alistair G. Rust, Esther Schmidt, Stephen M. J. Searle, Guy Slater, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, Elia Stupka, Abel Ureta-Vidal, Imre Vastrik, and Ewan Birney

Published
2003
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16. The Ensembl genome database project.

Author

Tim J. P. Hubbard, Daniel Barker, Ewan Birney, Graham Cameron, Yuan Chen 0007, Laura Clarke, Tony Cox 0001, James A. Cuff, Val Curwen, Thomas A. Down, Richard Durbin, Eduardo Eyras, James G. R. Gilbert, Martin Hammond, Lukasz Huminiecki, Arek Kasprzyk, Heikki Lehväslaiho, Philip Lijnzaad, Craig Melsopp, Emmanuel Mongin, Roger Pettett, Matthew R. Pocock, Simon C. Potter, Alistair G. Rust, Esther Schmidt, Stephen M. J. Searle, Guy Slater, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, Elia Stupka, Abel Ureta-Vidal, Imre Vastrik, and Michele E. Clamp

Published
2002
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17. Ensembl 2004.

Author

Ewan Birney, T. Daniel Andrews, Paul Bevan 0001, Mario Cáccamo, Graham Cameron, Yuan Chen 0007, Laura Clarke, Guy Coates, Tony Cox 0001, James A. Cuff, Val Curwen, Tim Cutts, Thomas A. Down, Richard Durbin, Eduardo Eyras, Xosé M. Fernández-Suárez, Paul J. Gane, B. Gibbins, James G. R. Gilbert, Martin Hammond, H. Hotz, Vivek Iyer, Andreas Kähäri, Kerstin Jekosch, Arek Kasprzyk, Damian Keefe, Stephen Keenan, Heikki Lehväslaiho, Graham P. McVicker, Craig Melsopp, Patrick Meidl, Emmanuel Mongin, Roger Pettett, Simon C. Potter, Glenn Proctor, Mark Rae, Stephen M. J. Searle, Guy Slater, Damian Smedley, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, R. Storey, Abel Ureta-Vidal, Cara Woodwark, Michele E. Clamp, and Tim J. P. Hubbard

Published
2004
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19. BioMart Central Portal: an open database network for the biological community.

Author

Jonathan M. Guberman, Jiye Ai, Olivier Arnaiz, Joachim Baran, Andrew Blake 0003, Richard A. Baldock, Claude Chelala, David Croft 0001, Anthony Cros, Rosalind J. Cutts, Alex Di Génova, Simon A. Forbes, Takatomo Fujisawa, Emanuela Gadaleta, David M. Goodstein, Gunes Gundem, Bernard Haggarty, Syed Haider, Matthew Hall, Todd W. Harris, Robin Haw, Shen Hu, Simon J. Hubbard, Jack Hsu, Vivek Iyer, Philip Jones, Toshiaki Katayama, Rhoda Kinsella, Lei Kong, Daniel Lawson, Yong Liang 0004, Núria López-Bigas, Jie Luo, Michael J. Lush, Jeremy C. Mason, François Moreews, Nelson Ndegwa, Darren J. Oakley, Christian Perez-Llamas, Michael Primig, Elena Rivkin, Steven Rosanoff, Rebecca Shepherd, Reinhard Simon, William C. Skarnes, Damian Smedley, Linda Sperling, William Spooner, Peter Stevenson, Kevin R. Stone, Jon W. Teague, Jun Wang 0060, Jianxin Wang, Brett Whitty, David Tai Wai Wong, Marie Wong-Erasmus, Long Yao, Ken Youens-Clark, Christina K. Yung, Junjun Zhang, and Arek Kasprzyk

Published
2011
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21. Pathogenic huntingtin repeat expansions in patients with frontotemporal dementia and amyotrophic lateral sclerosis

Author

Ramita Dewan, Ruth Chia, Jinhui Ding, Richard A. Hickman, Thor D. Stein, Yevgeniya Abramzon, Sarah Ahmed, Marya S. Sabir, Makayla K. Portley, Arianna Tucci, Kristina Ibáñez, F.N.U. Shankaracharya, Pamela Keagle, Giacomina Rossi, Paola Caroppo, Fabrizio Tagliavini, Maria L. Waldo, Per M. Johansson, Christer F. Nilsson, James B. Rowe, Luisa Benussi, Giuliano Binetti, Roberta Ghidoni, Edwin Jabbari, Coralie Viollet, Jonathan D. Glass, Andrew B. Singleton, Vincenzo Silani, Owen A. Ross, Mina Ryten, Ali Torkamani, Toshiko Tanaka, Luigi Ferrucci, Susan M. Resnick, Stuart Pickering-Brown, Christopher B. Brady, Neil Kowal, John A. Hardy, Vivianna Van Deerlin, Jean Paul Vonsattel, Matthew B. Harms, Huw R. Morris, Raffaele Ferrari, John E. Landers, Adriano Chiò, J. Raphael Gibbs, Clifton L. Dalgard, Sonja W. Scholz, Bryan J. Traynor, Adelani Adeleye, Camille Alba, Dagmar Bacikova, Daniel N. Hupalo, Elisa McGrath Martinez, Harvey B. Pollard, Gauthaman Sukumar, Anthony R. Soltis, Meila Tuck, Xijun Zhang, Matthew D. Wilkerson, Bradley N. Smith, Nicola Ticozzi, Claudia Fallini, Athina Soragia Gkazi, Simon D. Topp, Jason Kost, Emma L. Scotter, Kevin P. Kenna, Jack W. Miller, Cinzia Tiloca, Caroline Vance, Eric W. Danielson, Claire Troakes, Claudia Colombrita, Safa Al-Sarraj, Elizabeth A. Lewis, Andrew King, Daniela Calini, Viviana Pensato, Barbara Castellotti, Jacqueline de Belleroche, Frank Baas, Anneloor L.M.A. ten Asbroek, Peter C. Sapp, Diane McKenna-Yasek, Russell L. McLaughlin, Meraida Polak, Seneshaw Asress, Jesús Esteban-Pérez, José Luis Muñoz-Blanco, Zorica Stevic, Sandra D’Alfonso, Letizia Mazzini, Giacomo P. Comi, Roberto Del Bo, Mauro Ceroni, Stella Gagliardi, Giorgia Querin, Cinzia Bertolin, Wouter van Rheenen, Frank P. Diekstra, Rosa Rademakers, Marka van Blitterswijk, Kevin B. Boylan, Giuseppe Lauria, Stefano Duga, Stefania Corti, Cristina Cereda, Lucia Corrado, Gianni Sorarù, Kelly L. Williams, Garth A. Nicholson, Ian P. Blair, Claire Leblond-Manry, Guy A. Rouleau, Orla Hardiman, Karen E. Morrison, Jan H. Veldink, Leonard H. van den Berg, Ammar Al-Chalabi, Hardev Pall, Pamela J. Shaw, Martin R. Turner, Kevin Talbot, Franco Taroni, Alberto García-Redondo, Zheyang Wu, Cinzia Gellera, Antonia Ratti, Robert H. Brown, Christopher E. Shaw, John C. Ambrose, Prabhu Arumugam, Emma L. Baple, Marta Bleda, Freya Boardman-Pretty, Jeanne M. Boissiere, Christopher R. Boustred, H. Brittain, Mark J. Caulfield, Georgia C. Chan, Clare E.H. Craig, Louise C. Daugherty, Anna de Burca, Andrew Devereau, Greg Elgar, Rebecca E. Foulger, Tom Fowler, Pedro Furió-Tarí, Joanne M. Hackett, Dina Halai, Angela Hamblin, Shirley Henderson, James E. Holman, Tim J.P. Hubbard, Rob Jackson, Louise J. Jones, Dalia Kasperaviciute, Melis Kayikci, Lea Lahnstein, Kay Lawson, Sarah E.A. Leigh, Ivonne U.S. Leong, Javier F. Lopez, Fiona Maleady-Crowe, Joanne Mason, Ellen M. McDonagh, Loukas Moutsianas, Michael Mueller, Nirupa Murugaesu, Anna C. Need, Chris A. Odhams, Christine Patch, Daniel Perez-Gil, Dimitris Polychronopoulos, John Pullinger, Tahrima Rahim, Augusto Rendon, Pablo Riesgo-Ferreiro, Tim Rogers, Kevin Savage, Kushmita Sawant, Richard H. Scott, Afshan Siddiq, Alexander Sieghart, Damian Smedley, Katherine R. Smith, Alona Sosinsky, William Spooner, Helen E. Stevens, Alexander Stuckey, Razvan Sultana, Ellen R.A. Thomas, Simon R. Thompson, Carolyn Tregidgo, Emma Walsh, Sarah A. Watters, Matthew J. Welland, Eleanor Williams, Katarzyna Witkowska, Suzanne M. Wood, Magdalena Zarowiecki, Sampath Arepalli, Pavan Auluck, Robert H. Baloh, Robert Bowser, Alexis Brice, James Broach, William Camu, John Cooper-Knock, Philippe Corcia, Carsten Drepper, Vivian E. Drory, Travis L. Dunckley, Faraz Faghri, Jennifer Farren, Eva Feldman, Mary Kay Floeter, Pietro Fratta, Glenn Gerhard, Summer B. Gibson, Stephen A. Goutman, Terry D. Heiman-Patterson, Dena G. Hernandez, Ben Hoover, Lilja Jansson, Freya Kamel, Janine Kirby, Neil W. Kowall, Hannu Laaksovirta, Francesco Landi, Isabelle Le Ber, Serge Lumbroso, Daniel JL. MacGowan, Nicholas J. Maragakis, Gabriele Mora, Kevin Mouzat, Liisa Myllykangas, Mike A. Nalls, Richard W. Orrell, Lyle W. Ostrow, Roger Pamphlett, Erik Pioro, Stefan M. Pulst, John M. Ravits, Alan E. Renton, Wim Robberecht, Ian Robey, Ekaterina Rogaeva, Jeffrey D. Rothstein, Michael Sendtner, Katie C. Sidle, Zachary Simmons, David J. Stone, Pentti J. Tienari, John Q. Trojanowski, Juan C. Troncoso, Miko Valori, Philip Van Damme, Ludo Van Den Bosch, Lorne Zinman, Diego Albani, Barbara Borroni, Alessandro Padovani, Amalia Bruni, Jordi Clarimon, Oriol Dols-Icardo, Ignacio Illán-Gala, Alberto Lleó, Adrian Danek, Daniela Galimberti, Elio Scarpini, Maria Serpente, Caroline Graff, Huei-Hsin Chiang, Behzad Khoshnood, Linn Öijerstedt, Christopher M. Morris, Benedetta Nacmias, Sandro Sorbi, Jorgen E. Nielsen, Lynne E. Hjermind, Valeria Novelli, Annibale A. Puca, Pau Pastor, Ignacio Alvarez, Monica Diez-Fairen, Miquel Aguilar, Robert Perneczky, Janine Diehl-Schimd, Mina Rossi, Agustin Ruiz, Mercè Boada, Isabel Hernández, Sonia Moreno-Grau, Johannes C. Schlachetzki, Dag Aarsland, Marilyn S. Albert, Johannes Attems, Matthew J. Barrett, Thomas G. Beach, Lynn M. Bekris, David A. Bennett, Lilah M. Besser, Eileen H. Bigio, Sandra E. Black, Bradley F. Boeve, Ryan C. Bohannan, Francesca Brett, Maura Brunetti, Chad A. Caraway, Jose-Alberto Palma, Andrea Calvo, Antonio Canosa, Dennis Dickson, Charles Duyckaerts, Kelley Faber, Tanis Ferman, Margaret E. Flanagan, Gianluca Floris, Tatiana M. Foroud, Juan Fortea, Ziv Gan-Or, Steve Gentleman, Bernardino Ghetti, Jesse Raphael Gibbs, Alison Goate, David Goldstein, Isabel González-Aramburu, Neill R. Graff-Radford, Angela K. Hodges, Heng-Chen Hu, Daniel Hupalo, Jon Infante, Alex Iranzo, Scott M. Kaiser, Horacio Kaufmann, Julia Keith, Ronald C. Kim, Gregory Klein, Rejko Krüger, Walter Kukull, Amanda Kuzma, Carmen Lage, Suzanne Lesage, James B. Leverenz, Giancarlo Logroscino, Grisel Lopez, Seth Love, Qinwen Mao, Maria Jose Marti, Elisa Martinez-McGrath, Mario Masellis, Eliezer Masliah, Patrick May, Ian McKeith, Marek-Marsel Mesulam, Edwin S. Monuki, Kathy L. Newell, Lucy Norcliffe-Kaufmann, Laura Palmer, Matthew Perkins, Olga Pletnikova, Laura Molina-Porcel, Regina H. Reynolds, Eloy Rodríguez-Rodríguez, Jonathan D. Rohrer, Pascual Sanchez-Juan, Clemens R. Scherzer, Geidy E. Serrano, Vikram Shakkottai, Ellen Sidransky, Nahid Tayebi, Alan J. Thomas, Bension S. Tilley, Ronald L. Walton, Randy Woltjer, Zbigniew K. Wszolek, Georgia Xiromerisiou, Chiara Zecca, Hemali Phatnani, Justin Kwan, Dhruv Sareen, James R. Broach, Ximena Arcila-Londono, Edward B. Lee, Neil A. Shneider, Ernest Fraenkel, Noah Zaitlen, James D. Berry, Andrea Malaspina, Gregory A. Cox, Leslie M. Thompson, Steve Finkbeiner, Efthimios Dardiotis, Timothy M. Miller, Siddharthan Chandran, Suvankar Pal, Eran Hornstein, Daniel J. MacGowan, Terry Heiman-Patterson, Molly G. Hammell, Nikolaos.A. Patsopoulos, Oleg Butovsky, Joshua Dubnau, Avindra Nath, Matt Harms, Eleonora Aronica, Mary Poss, Jennifer Phillips-Cremins, John Crary, Nazem Atassi, Dale J. Lange, Darius J. Adams, Leonidas Stefanis, Marc Gotkine, Suma Babu, Towfique Raj, Sabrina Paganoni, Ophir Shalem, Colin Smith, Bin Zhang, Brent Harris, Iris Broce, Vivian Drory, John Ravits, Corey McMillan, Vilas Menon, Lani Wu, Steven Altschuler, Khaled Amar, Neil Archibald, Oliver Bandmann, Erica Capps, Alistair Church, Jan Coebergh, Alyssa Costantini, Peter Critchley, Boyd CP. Ghosh, Michele T.M. Hu, Christopher Kobylecki, P. Nigel Leigh, Carl Mann, Luke A. Massey, Uma Nath, Nicola Pavese, Dominic Paviour, Jagdish Sharma, Jenny Vaughan, HUS Neurocenter, Neurologian yksikkö, Department of Neurosciences, Clinicum, Pentti Tienari / Principal Investigator, Parkinson's UK, Human Genetics, ARD - Amsterdam Reproduction and Development, ANS - Complex Trait Genetics, Pathology, ANS - Cellular & Molecular Mechanisms, AII - Inflammatory diseases, Universidad de Cantabria, Rowe, James [0000-0001-7216-8679], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Huntington's Disease, Pathology, amyotrophic lateral sclerosis, Huntingtin, Neurology, 1702 Cognitive Sciences, International ALS/FTD Genomics Consortium, Neurodegenerative, frontotemporal dementia, 3124 Neurology and psychiatry, 0302 clinical medicine, Medicine, 2.1 Biological and endogenous factors, Psychology, Amyotrophic lateral sclerosis, Aetiology, Alzheimer's Disease Related Dementias (ADRD), NYGC ALS Consortium, Huntingtin Protein, DNA Repeat Expansion, General Neuroscience, Frontotemporal Dementia (FTD), International FTD Genetics Consortium, whole-genome sequencing, Frontotemporal Dementia, Neurological, Cognitive Sciences, Lewy body dementia, huntingtin, repeat expansions, Amyotrophic Lateral Sclerosis, Humans, Mutation, Whole Genome Sequencing, Frontotemporal dementia, Huntington’s disease, medicine.medical_specialty, congenital, hereditary, and neonatal diseases and abnormalities, FALS Sequencing Consortium, Article, 03 medical and health sciences, Atrophy, Rare Diseases, American Genome Center, Clinical Research, mental disorders, Genetics, Acquired Cognitive Impairment, Dementia, PROSPECT Consortium, Neurology & Neurosurgery, Lewy body, business.industry, International LBD Genomics Consortium, Neurosciences, 3112 Neurosciences, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), nutritional and metabolic diseases, medicine.disease, Brain Disorders, nervous system diseases, 030104 developmental biology, Genomics England Research Consortium, 1701 Psychology, ALS, business, 1109 Neurosciences, 030217 neurology & neurosurgery
Abstract

Hannu Laaksovirta konsortion jäsenenä. The Genomics England Research Consortium, The International ALS/FTD Genomics Consortium (iAFGC), The International FTD Genetics Consortium (IFGC), The International LBD Genomics Consortium (iLBDGC), The NYGC ALS Consortium, The PROSPECT Consortium,17 James B. Rowe,17 Luisa Benussi,18 Giuliano Binetti,18,19 Roberta Ghidoni,18 Edwin Jabbari,20,21 Coralie Viollet,22 Jonathan D. Glass,23 Andrew B. Singleton,24 Vincenzo Silani,25,26 Owen A. Ross,27 Mina Ryten,8,28,29 Ali Torkamani,30 Toshiko Tanaka,31 Luigi Ferrucci,31 Susan M. Resnick,32 We examined the role of repeat expansions in the pathogenesis of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) by analyzing whole-genome sequence data from 2,442 FTD/ALS patients, 2,599 Lewy body dementia (LBD) patients, and 3,158 neurologically healthy subjects. Pathogenic expansions (range, 40?64 CAG repeats) in the huntingtin (HTT) gene were found in three (0.12%) patients diagnosed with pure FTD/ALS syndromes but were not present in the LBD or healthy cohorts. We replicated our findings in an independent collection of 3,674 FTD/ALS patients. Postmortem evaluations of two patients revealed the classical TDP-43 pathology of FTD/ALS, as well as huntingtin-positive, ubiquitin-positive aggregates in the frontal cortex. The neostriatal atrophy that pathologically defines Huntington?s disease was absent in both cases. Our findings reveal an etiological relationship between HTT repeat expansions and FTD/ALS syndromes and indicate that genetic screening of FTD/ALS patients for HTT repeat expansions should be considered. We examined the role of repeat expansions in the pathogenesis of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) by analyzing whole-genome sequence data from 2,442 FTD/ALS patients, 2,599 Lewy body dementia (LBD) patients, and 3,158 neurologically healthy subjects. Pathogenic expansions (range, 40?64 CAG repeats) in the huntingtin (HTT) gene were found in three (0.12%) patients diagnosed with pure FTD/ALS syndromes but were not present in the LBD or healthy cohorts. We replicated our findings in an independent collection of 3,674 FTD/ALS patients. Postmortem evaluations of two patients revealed the classical TDP-43 pathology of FTD/ALS, as well as huntingtin-positive, ubiquitin-positive aggregates in the frontal cortex. The neostriatal atrophy that pathologically defines Huntington?s disease was absent in both cases. Our findings reveal an etiological relationship between HTT repeat expansions and FTD/ALS syndromes and indicate that genetic screening of FTD/ALS patients for HTT repeat expansions should be considered.

Published
2020
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22. De novo SOX6 variants cause a neurodevelopmental syndrome associated with ADHD, craniosynostosis, and osteochondromas

Author

M. Zarowiecki, A. Devereau, S.M. Wood, J. M. Boissiere, G. Elgar, Cara Forster, Liesbeth Keldermans, A. Sieghart, Allyn McConkie-Rosell, Augusto Rendon, S. R. Thompson, D. Polychronopoulos, Alexandre Arkader, Julien Thevenon, D. Kasperaviciute, Alma Kuechler, Bryan L. Krock, Dominique Martin-Coignard, Damian Smedley, T. Rahim, Barbara Mikat, Amber Begtrup, Priya Prasad, Lindsay B. Henderson, A. Stuckey, Mathilde Nizon, Tim Hubbard, I. U. S. Leong, M. Bleda, L. Lahnstein, C. E. H. Craig, Bertrand Isidor, Sarah Leigh, Joanne Mason, L. Moutsianas, T. Fowler, A. Siddiq, J. Pullinger, Marco Angelozzi, J. Ambrose, S. A. Watters, Saadet Mercimek-Andrews, K. Lawson, Claudia A. L. Ruivenkamp, Ian D. Krantz, J. E. Holman, Solveig Heide, Christel Depienne, Elizabeth T. DeChene, L. C. Daugherty, Alvaro Serrano Russi, Arianna Tucci, Mark J. Caulfield, Marie T. McDonald, Boris Keren, A. C. Need, Damara Ortiz, Nicola Foulds, William Spooner, Dara Tolchin, Eduardo Calpena, C. R. Boustred, Abdul Haseeb, Rudolf Gorazd, Charles Coutton, Alona Sosinsky, D. Perez-Gil, Sarah Stewart, J. M. Hackett, Giada Melistaccio, Andrew O.M. Wilkie, Radka Stoeva, Cédric Le Caignec, Pauline Le Tanno, Benjamin Cogné, Martina Mueller, Naghmeh Dorrani, Pedro Furió-Tarí, Gijs W. E. Santen, Hermann-Josef Lüdecke, Jessica P. Yeager, Julian A. Martinez-Agosto, Damien Haye, Kieran B. Pechter, Mohnish Suri, Livija Medne, M. J. Welland, Patrick Reed, K. Savage, G. C. Chan, Anne C.H. Tsai, F. Maleady-Crowe, A. de Burca, Ellen M. McDonagh, T. Rogers, F. Boardman-Pretty, Emily Lancaster, Katherine R. Smith, Christopher A. Odhams, Véronique Lefebvre, M. Ryten, Olivier Pichon, D. Halai, Aleš Maver, Christine Patch, R. E. Foulger, Frédéric Bilan, Helen Stevens, Hilde Van Esch, Eleanor Williams, Brigitte Gilbert-Dussardier, C. Tregidgo, K. Witkowska, F. J. Lopez, Gwenaël Le Guyader, Richard H Scott, M. Kayikci, Ellen Thomas, and E. Walsh

Subjects
0301 basic medicine, Male, Osteochondroma, Adolescent, Transcription, Genetic, media_common.quotation_subject, Nonsense, Medizin, Active Transport, Cell Nucleus, Mutation, Missense, Biology, Cell fate determination, Translocation, Genetic, Article, Craniosynostosis, 03 medical and health sciences, Craniosynostoses, 0302 clinical medicine, Intellectual disability, Genetics, medicine, Missense mutation, Humans, Computer Simulation, Amino Acid Sequence, RNA-Seq, Child, Gene, Genetics (clinical), media_common, Base Sequence, Brain, Infant, Syndrome, medicine.disease, 030104 developmental biology, Attention Deficit Disorder with Hyperactivity, Neurodevelopmental Disorders, Child, Preschool, Genomic Structural Variation, Autism, Female, Haploinsufficiency, Transcriptome, SOXD Transcription Factors, 030217 neurology & neurosurgery
Abstract

SOX6 belongs to a family of 20 SRY-related HMG-box-containing (SOX) genes that encode transcription factors controlling cell fate and differentiation in many developmental and adult processes. For SOX6, these processes include, but are not limited to, neurogenesis and skeletogenesis. Variants in half of the SOX genes have been shown to cause severe developmental and adult syndromes, referred to as SOXopathies. We here provide evidence that SOX6 variants also cause a SOXopathy. Using clinical and genetic data, we identify 19 individuals harboring various types of SOX6 alterations and exhibiting developmental delay and/or intellectual disability; the individuals are from 17 unrelated families. Additional, inconstant features include attention-deficit/hyperactivity disorder (ADHD), autism, mild facial dysmorphism, craniosynostosis, and multiple osteochondromas. All variants are heterozygous. Fourteen are de novo, one is inherited from a mosaic father, and four offspring from two families have a paternally inherited variant. Intragenic microdeletions, balanced structural rearrangements, frameshifts, and nonsense variants are predicted to inactivate the SOX6 variant allele. Four missense variants occur in residues and protein regions highly conserved evolutionarily. These variants are not detected in the gnomAD control cohort, and the amino acid substitutions are predicted to be damaging. Two of these variants are located in the HMG domain and abolish SOX6 transcriptional activity in vitro. No clear genotype-phenotype correlations are found. Taken together, these findings concur that SOX6 haploinsufficiency leads to a neurodevelopmental SOXopathy that often includes ADHD and abnormal skeletal and other features.

Published
2020

25. Community-driven development for computational biology at Sprints, Hackathons and Codefests.

Author

Steffen Möller, Enis Afgan, Michael Banck, Raoul Jean Pierre Bonnal, Timothy Booth, John Chilton, Peter J. A. Cock, Markus Gumbel, Nomi L. Harris, Richard C. G. Holland, Matús Kalas, László Kaján, Eri Kibukawa, David R. Powell, Pjotr Prins, Jacqueline Quinn, Olivier Sallou, Francesco Strozzi, Torsten Seemann, Clare Sloggett, Stian Soiland-Reyes, William Spooner, Sascha Steinbiss, Andreas Tille, Anthony J. Travis, Roman Guimera, Toshiaki Katayama, and Brad A. Chapman

Published
2014
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26. Ensembl comparative genomics resources

Author

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

Subjects
0301 basic medicine, Quality Control, DNA, Complementary, RNA, Untranslated, Genomics, Biology, Genome, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, Annotation, Consistency (database systems), 0302 clinical medicine, Ensembl Genomes, Databases, Genetic, Ensembl, Animals, Humans, Phylogeny, 030304 developmental biology, Synteny, Comparative genomics, Expressed Sequence Tags, 0303 health sciences, Information retrieval, Sequence Analysis, RNA, Computational Biology, 030104 developmental biology, Database Update, Erratum, General Agricultural and Biological Sciences, Sequence Alignment, 030217 neurology & neurosurgery, Algorithms, Software, Information Systems
Abstract

Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org.

Published
2016

27. Gramene database in 2010: updates and extensions

Author

Doreen Ware, William Spooner, Ken Youens-Clark, Sharon Wei, Liya Ren, Paul J. Kersey, Jerry Lu, Joshua C. Stein, Palitha Dharmawardhana, Pankaj Jaiswal, Terry M. Casstevens, A. S. Karthikeyan, Paul S. Derwent, Genevieve DeClerck, Charles Chen, Edward S. Buckler, James Thomason, and Susan R. McCouch

Subjects
0106 biological sciences, Quantitative Trait Loci, Genomics, Genome browser, computer.software_genre, Genes, Plant, 01 natural sciences, Genome, Synteny, 03 medical and health sciences, Annotation, Databases, Genetic, Genetics, Ensembl, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Database, biology, food and beverages, Chromosome Mapping, Genetic Variation, Articles, 15. Life on land, Plants, biology.organism_classification, Brachypodium, Web service, computer, Genome, Plant, Metabolic Networks and Pathways, 010606 plant biology & botany
Abstract

Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene began with the addition of an Ensembl genome browser and has expanded in the last decade to become a robust resource for plant genomics hosting a wide array of data sets including quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps from various published studies (genetic, physical, bin, etc.). In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data.

Published
2010

28. Comparison of different statistical approaches for urinary peptide biomarker detection in the context of coronary artery disease

Author

Joost P. Schanstra, Thomas Koeck, Esther Nkuipou-Kenfack, Eleanor Stanley, William Spooner, Harald Mischak, Walter Kolch, Eleni Ioanna Delatola, The Biodata Innovation Centre [Cambridge, U.K.], Eagle Genomics Ltd [Cambridge, U.K.], Systems Biology Ireland, University College Dublin [Dublin] (UCD), Mosaiques Diagnostics GmbH [Hannover, Germany], Mosaiques Diagnostics and Therapeutics AG [Hannover, Germany], Conway Institute of Biomolecular and Biomedical Research [Dublin, Irlande], School of Medicine and Medical Science [Dublin, Irlande], Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Institute of Cardiovascular and Medical Sciences [Glasgow], University of Glasgow, and BMC, BMC

Subjects
Adult, Male, Proteomics, 0301 basic medicine, Wilcoxon signed-rank test, [SDV]Life Sciences [q-bio], Coronary Artery Disease, Computational biology, Biomarker detection, 030204 cardiovascular system & hematology, Bioinformatics, Biochemistry, Statistical power, Coronary artery disease, 03 medical and health sciences, 0302 clinical medicine, Structural Biology, Classifier modelling, Humans, Medicine, Biomarker discovery, Molecular Biology, Statistical proteome analysis, business.industry, Applied Mathematics, Discriminant Analysis, Middle Aged, Prognosis, Linear discriminant analysis, medicine.disease, Random forest, Computer Science Applications, Support vector machine, [SDV] Life Sciences [q-bio], 030104 developmental biology, Biomarker (medicine), Female, Peptides, business, Biomarkers, Research Article
Abstract

Background When combined with a clinical outcome variable, the size, complexity and nature of mass-spectrometry proteomics data impose great statistical challenges in the discovery of potential disease-associated biomarkers. The purpose of this study was thus to evaluate the effectiveness of different statistical methods applied for urinary proteomic biomarker discovery and different methods of classifier modelling in respect of the diagnosis of coronary artery disease in 197 study subjects and the prognostication of acute coronary syndromes in 368 study subjects. Results Computing the discovery sub-cohorts comprising \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {\scriptscriptstyle \raisebox{1ex}{$2$}\!\left/ \!\raisebox{-1ex}{$3$}\right.} $$\end{document}23 of the study subjects based on the Wilcoxon rank sum test, t-score, cat-score, binary discriminant analysis and random forests provided largely different numbers (ranging from 2 to 398) of potential peptide biomarkers. Moreover, these biomarker patterns showed very little overlap limited to fragments of type I and III collagens as the common denominator. However, these differences in biomarker patterns did mostly not translate into significant differently performing diagnostic or prognostic classifiers modelled by support vector machine, diagonal discriminant analysis, linear discriminant analysis, binary discriminant analysis and random forest. This was even true when different biomarker patterns were combined into master-patterns. Conclusion In conclusion, our study revealed a very considerable dependence of peptide biomarker discovery on statistical computing of urinary peptide profiles while the observed diagnostic and/or prognostic reliability of classifiers was widely independent of the modelling approach. This may however be due to the limited statistical power in classifier testing. Nonetheless, our study showed that urinary proteome analysis has the potential to provide valuable biomarkers for coronary artery disease mirroring especially alterations in the extracellular matrix. It further showed that for a comprehensive discovery of biomarkers and thus of pathological information, the results of different statistical methods may best be combined into a master pattern that then can be used for classifier modelling. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1390-1) contains supplementary material, which is available to authorized users.

Published
2016
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29. The Ensembl Web Site: Mechanics of a Genome Browser

Author

James Stalker, Brian Gibbins, Patrick Meidl, Antony V. Cox, James Smith, Hans-Rudolf Hotz, and William Spooner

Subjects
Gigabyte, Genome browser, Biology, computer.software_genre, Bioinformatics, World Wide Web, Mice, Relational database management system, Databases, Genetic, Genetics, Animals, Humans, Ensembl, Genetics (clinical), computer.programming_language, Internet, business.industry, Computational Biology, Disparate system, ENSEMBL Special, The Internet, User interface, Perl, business, computer, Software
Abstract

The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (∼2.5 million hits) per week, providing access to >80 GB (gigabyte) of data to users in more than 80 countries. Built atop an open-source platform comprising Apache/mod_perl and the MySQL relational database management system, it is modular, extensible, and freely available. It is being actively reused and extended in several different projects, and has been downloaded and installed in companies and academic institutions worldwide. Here, we describe some of the technical features of the site, with particular reference to its dynamic configuration that enables it to handle disparate data from multiple species.

Published
2004
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30. EnsMart: A Generic System for Fast and Flexible Access to Biological Data

Author

Ewan Birney, Craig Melsopp, Philippe Rocca-Serra, Damian Smedley, William Spooner, Martin Hammond, Arek Kasprzyk, Tony Cox, Damian Keefe, and Darin London

Subjects
Java, Molecular Sequence Data, Biology, Bioinformatics, Computer graphics, Mice, User-Computer Interface, Annotation, Software, Databases, Genetic, Computer Graphics, Genetics, Animals, Humans, Ensembl, Genetics (clinical), computer.programming_language, Biological data, Information retrieval, Base Sequence, business.industry, Suite, Computational Biology, Resources, Data warehouse, Rats, Genes, Database Management Systems, business, computer
Abstract

The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools. The system consists of a query-optimized database and interactive, user-friendly interfaces. EnsMart has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval of customized data sets. A wide variety of complex queries, on various types of annotations, for numerous species are supported. These can be applied to many research problems, ranging from SNP selection for candidate gene screening, through cross-species evolutionary comparisons, to microarray annotation. Users can group and refine biological data according to many criteria, including cross-species analyses, disease links, sequence variations, and expression patterns. Both tabulated list data and biological sequence output can be generated dynamically, in HTML, text, Microsoft Excel, and compressed formats. A wide range of sequence types, such as cDNA, peptides, coding regions, UTRs, and exons, with additional upstream and downstream regions, can be retrieved. The EnsMart database can be accessed via a public Web site, or through a Java application suite. Both implementations and the database are freely available for local installation, and can be extended or adapted to `non-Ensembl' data sets.

Published
2004
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31. The BioMart community portal: an innovative alternative to large, centralized data repositories

Author

Byung Woo Han, Jose Manuel Garcia-Manteiga, Alejandro Maass, Jayson Harshbarger, Daniel M. Staines, Zhengyan Kan, Davide Rambaldi, Dong Jin Han, Richard Baldock, Ji Hyun Lee, Merideth Bonierbale, Hadi Quesneville, Anthony Esposito, Thomas Letellier, Jun Wang, Steven Rosanoff, Céline Noirot, Richard D. Hayes, Sarah W. Burge, Anthony J. Brookes, Gabriele Bucci, Giulia Barbiera, Elia Stupka, Olivier Arnaiz, Thomas Maurel, Shen Hu, Olivier Sallou, Emanuela Gadaleta, Jérôme Mariette, Rosalind J. Cutts, Joseph W. Carlson, Damian Smedley, Robert C. Free, James E. Allen, Simon A. Forbes, Kevin R. Stone, Jie Luo, Andrew Blake, Chu Jun Liu, Takatomo Fujisawa, Jon W. Teague, Cristian Perez-Llamas, Rebecca Shepherd, Julio Fernandez-Banet, Raul Cordova, David Goodstein, Shi Jian Zhang, Ken Youens-Clark, Cédric Cabau, José Afonso Guerra-Assunção, Iwan Buetti, Stefania Merella, Delphine Steinbach, Linda Sperling, Robert K. Hastings, Abu Z. Dayem Ullah, Claude Chelala, Erik Dassi, Eduardo Eyras, Sunghoon Kim, Kristian Gray, Dejan Lazarevic, Luca Pandini, Azza M. Mohamed, Doreen Ware, William Spooner, Alex Di Genova, Daniel Lawson, Alessandro Quattrone, Davide Cittaro, Heather Estrella, Rhoda Kinsella, Chuan-Yun Li, Christophe Klopp, Aminah Keliet, Michela Riba, Zhi-Liang Hu, Hideya Kawaji, Arnaud Kerhornou, James M. Reecy, Tim Beck, Charalambos Chrysostomou, François Moreews, Nelson Ndegwa, Arek Kasprzyk, Michael Primig, Claire Hoede, Ibounyamine Nabihoudine, Amonida Zadissa, Paolo Provero, Reinhard Simon, Todd W. Harris, Bernard Haggarty, Lucie N. Hutchins, Marie Wong-Erasmus, Philippe Bardou, Elisa Salas, Lei Kong, Anis Djari, Syed Haider, Steffen Durinck, Mohammad Awedh, Pietro Liò, Amna A. Saddiq, Olivier Collin, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Computer Laboratory [Cambridge], University of Cambridge [UK] (CAM), Genentech, Inc., Genentech, Inc. [San Francisco], San Raffaele Scientific Institute, Vita-Salute San Raffaele University and Center for Translational Genomics and Bioinformatics, Genetics, Biology and Biochemistry, Molecular Biotechnology Centre, Centre de génétique moléculaire (CGM), Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), King Abdulaziz University, MRC Human Genetics Unit, University of Edinburgh-Western General Hospital, Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Department of Genetics [Leicester], University of Leicester, Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Medical Research Counc, International Potato Center, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Centre for Molecular Oncology and Imaging, Centre for Molecular Oncology and Imaging, Barts Cancer Institute, Plateforme bioinformatique GenOuest [Rennes], Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Plateforme Génomique Santé Biogenouest®-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec, University of Trento [Trento], University of Chile [Santiago], Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Pfizer Oncology, Institució Catalana de Recerca i Estudis Avançats (ICREA), Cancer Genome Project, The Wellcome Trust Sanger Institute [Cambridge], Kasuza DNA Research Institute, Seoul National University [Seoul] (SNU), Cold Spring Harbor Laboratory (CSHL), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), School of Dentistry and Dental Research Institute [UCLA], University of California [Los Angeles] (UCLA), University of California-University of California, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University (ISU), Mouse Genomic Informatics Group (MGI), The Jackson Laboratory, Unité de Recherche Génomique Info (URGI), Center for Bioinformatics [Pekin], Peking University [Beijing], Division of Industrial Ecology (KTH), Royal Institute of Technology [Stockholm] (KTH ), Institute of Molecular Medicine, Universidad de Santiago de Chile [Santiago] (USACH), Centro de Regulación Génica (CRG), Pontificia Universidad Católica de Chile (UC)-Universidad Andrés Bello [Santiago] (UNAB)-Universidad de Santiago de Chile [Santiago] (USACH), Centre de Modélisation Mathématique / Centro de Modelamiento Matemático (CMM), Centre National de la Recherche Scientifique (CNRS), Unité Mathématiques et Informatique Appliquées de Toulouse (MIAT), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Mathématiques et Informatique Appliquées Toulouse, Universitat Pompeu Fabra [Barcelona], Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Department of Animal Science, Eagle Genomics Ltd, Eagle Genomics, State Key Laboratory of Lithospheric Evolution (SKL), Institute of Geology and Geophysics [Beijing] (IGG), Chinese Academy of Sciences [Beijing] (CAS)-Chinese Academy of Sciences [Beijing] (CAS), University of the Chinese Academy of Sciences, Ontario Institute for Cancer Research [Canada] (OICR), Ontario Institute for Cancer Research, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, International Potato Center [Lima] (CIP), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Universidad de Chile = University of Chile [Santiago] (UCHILE), The Jackson Laboratory [Bar Harbor] (JAX), Center for Bioinformatics [Peking], Pontificia Universidad Católica de Chile (UC)-Universidad Andrés Bello [Santiago] (UNAB), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Universitat Pompeu Fabra [Barcelona] (UPF), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Santé et de la Recherche Médicale (INSERM)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université d'Angers (UA), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), University of California (UC)-University of California (UC), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Jonchère, Laurent, CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Lio, Pietro [0000-0002-0540-5053], and Apollo - University of Cambridge Repository

Subjects
Proteomics, Interface (Java), Data management, [SDV]Life Sciences [q-bio], génomique fonctionnelle, Biology, Ontology (information science), computer.software_genre, World Wide Web, Genomics, Humans, Internet, Neoplasms, Database Management Systems, Genetics, cancer, Web Server issue, protéomique, ontologie, ComputingMilieux_MISCELLANEOUS, base de données, business.industry, Toolbox, [SDV] Life Sciences [q-bio], espèce modèle, Scalability, The Internet, Web service, business, Host (network), computer
Abstract

International audience; The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.

Published
2015
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32. PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants

Author

Feng Tian, William Spooner, Charles Chen, Edward S. Buckler, Genevieve DeClerck, and Susan R. McCouch

Subjects
0106 biological sciences, Candidate gene, Heredity, TOC1, Quantitative Trait Loci, Arabidopsis, Cereals, lcsh:Medicine, Locus (genetics), Genome-wide association study, Crops, Computational biology, Plant Science, Quantitative trait locus, Genes, Plant, Plant Genetics, 01 natural sciences, Polymorphism, Single Nucleotide, 03 medical and health sciences, Gene Expression Regulation, Plant, Genome Analysis Tools, Genetics, Genome-Wide Association Studies, Trait Locus Analysis, lcsh:Science, Gene, Biology, 030304 developmental biology, Probability, 2. Zero hunger, 0303 health sciences, Multidisciplinary, biology, Models, Genetic, Quantitative Traits, Arabidopsis Proteins, lcsh:R, Gigantea, Computational Biology, Agriculture, Genomics, biology.organism_classification, Maize, lcsh:Q, 010606 plant biology & botany, Research Article
Abstract

PICARA is an analytical pipeline designed to systematically summarize observed SNP/trait associations identified by genome wide association studies (GWAS) and to identify candidate genes involved in the regulation of complex trait variation. The pipeline provides probabilistic inference about a priori candidate genes using integrated information derived from genome-wide association signals, gene homology, and curated gene sets embedded in pathway descriptions. In this paper, we demonstrate the performance of PICARA using data for flowering time variation in maize - a key trait for geographical and seasonal adaption of plants. Among 406 curated flowering time-related genes from Arabidopsis, we identify 61 orthologs in maize that are significantly enriched for GWAS SNP signals, including key regulators such as FT (Flowering Locus T) and GI (GIGANTEA), and genes centered in the Arabidopsis circadian pathway, including TOC1 (Timing of CAB Expression 1) and LHY (Late Elongated Hypocotyl). In addition, we discover a regulatory feature that is characteristic of these a priori flowering time candidates in maize. This new probabilistic analytical pipeline helps researchers infer the functional significance of candidate genes associated with complex traits and helps guide future experiments by providing statistical support for gene candidates based on the integration of heterogeneous biological information.

Published
2012

33. BioMart Central Portal: An open database network for the biological community

Author

Brett R Whitty, Marie Wong-Erasmus, Richard Baldock, Michael Lush, François Moreews, Jun Wang, Ken Youens-Clark, Philip Jones, Gunes Gundem, Nuria Lopez-Bigas, Junjun Zhang, Nelson Ndegwa, Toshiaki Katayama, L. Yao, Arek Kasprzyk, S. Rosanoff, Jianxin Wang, Michael Primig, Anthony Cros, Claude Chelala, Jack Hsu, Emanuela Gadaleta, Lei Kong, J. Ai, Shen Hu, Robin Haw, Vivek Iyer, Rosalind J. Cutts, Reinhard Simon, William Spooner, Rebecca Shepherd, Takatomo Fujisawa, Christina K. Yung, Jeremy Mason, Linda Sperling, Simon J. Hubbard, Bernard Haggarty, B. Skarnes, Todd W. Harris, Joachim Baran, Damian Smedley, Simon A. Forbes, Yong Liang, Syed Haider, Kevin R. Stone, Christian Perez-Llamas, Matthew Hall, Elena Rivkin, Daniel Lawson, Peter Stevenson, Darren J. Oakley, D. T. Wong, Jie Luo, Andrew Blake, A. Di Génova, Olivier Arnaiz, Rhoda Kinsella, Jon W. Teague, Jonathan M. Guberman, David Goodstein, David Croft, Ontario Institute for Cancer Research [Canada] (OICR), Ontario Institute for Cancer Research, School of Dentistry and Dental Research Institute [UCLA], University of California [Los Angeles] (UCLA), University of California-University of California, Centre de génétique moléculaire (CGM), Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Medical Research Coucil Harwell [Oxford, UK] (MRC Harwell), MRC Harwell, MRC Human Genetics Unit, University of Edinburgh-Western General Hospital, Centre for Molecular Oncology and Imaging, Centre for Molecular Oncology and Imaging, Barts Cancer Institute, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Center for Mathematical Modeling (CMM), Universidad de Santiago de Chile [Santiago] (USACH), Cancer Genome Project, The Wellcome Trust Sanger Institute [Cambridge], Kasuza DNA Research Institute, DOE Joint Genome Institute [Walnut Creek], Genomics Division [LBNL Berkeley], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Research Unit on Biomedical Informatics (GRIB), Universitat Pompeu Fabra [Barcelona], Computer Laboratory [Cambridge], University of Cambridge [UK] (CAM), Mouse Genomic Informatics Group (MGI), The Jackson Laboratory, Cold Spring Harbor Laboratory (CSHL), Faculty of Life Sciences [Manchester], University of Manchester [Manchester], The University of Tokyo, Center for Bioinformatics [Pekin], Peking University [Beijing], Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de la Recherche Agronomique (INRA), Groupe d'Etude de la Reproduction Chez l'Homme et les Mammiferes (GERHM), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-IFR140-Institut National de la Santé et de la Recherche Médicale (INSERM), International Potato Center, Eagle Genomics Ltd, Eagle Genomics, the Ontario Institute for Cancer Research, the Ontario Ministry for Research and Innovation, University of California (UC)-University of California (UC), Universidad de Chile = University of Chile [Santiago] (UCHILE), Universitat Pompeu Fabra [Barcelona] (UPF), The Jackson Laboratory [Bar Harbor] (JAX), The University of Tokyo (UTokyo), Center for Bioinformatics [Peking], Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), International Potato Center [Lima] (CIP), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Biomedical Research, Databases, Factual, Interface (Java), Computer science, Data management, International Cooperation, Biological database, Ontology (information science), computer.software_genre, IDENTIFICATIONS, User-Computer Interface, 0302 clinical medicine, Resource (project management), Medicine(all), 0303 health sciences, Biological data, Genome, Database, Agricultural and Biological Sciences(all), [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 030220 oncology & carcinogenesis, KEGG, Viruses, Original Article, The Internet, General Agricultural and Biological Sciences, GENOMICS, Information Systems, General Biochemistry, Genetics and Molecular Biology, World Wide Web, 03 medical and health sciences, Databases, Library and Information Studies, Animals, Humans, Bases de dades -- Gestió, Factual, 030304 developmental biology, Structure (mathematical logic), Internet, Information retrieval, Bacteria, business.industry, Biochemistry, Genetics and Molecular Biology(all), Fungi, Data Format, Database Management Systems, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer
Abstract

International audience; BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities. Database URL: http://central.biomart.org.

Published
2011
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34. Evidence for Network Evolution in an Arabidopsis Interactome Map

Author

Viviana Romero, Jeffery L. Dangl, Jyotika Mirchandani, M. Shahid Mukhtar, Eric Olivares, Samuel J. Pevzner, Gopalakrishna Ramaswamy, Jonathan D. Chesnut, Geetha M. Swamilingiah, Thomas Rolland, Doreen Ware, William Spooner, Tijana Milenkovic, Edward A. Rietman, Huaming Chen, Rosa Cheuk Kim, Pascal Braun, Frederick P. Roth, Lantian Gai, Matthew M. Poulin, Gourab Ghoshal, Robert J. Schmitz, Balaji Santhanam, Stacy Wu, Murat Tasan, Paul Shinn, Michael E. Cusick, Danielle Byrdsong, Marc Vidal, Andrew MacWilliams, Selma Waaijers, Chris de los Reyes, Jonathan D. Moore, Uday Matrubutham, Fana Gebreab, Patrick Reichert, Claire Lurin, Dario Monachello, Changyu Fan, Jean Vandenhaute, Padmavathi Balumuri, Matija Dreze, Vanessa Bautista, Yong-Yeol Ahn, Albert-László Barabási, Natasa Przulj, Benoit Charloteaux, Joshua C. Stein, Tong Hao, Mary Galli, Joseph R. Ecker, Junshi Yazaki, Amélie Dricot, Suswapna Patnaik, Melissa Duarte, Sabrina Rabello, Evan M. Weiner, Anne-Ruxandra Carvunis, Christopher Kim, Rosa Quan, Patrick Gilles, Bryan J. Gutierrez, David E. Hill, Stanley Tam, Harvard Medical School [Boston] (HMS), Department of Genetics [Boston], Faculté de Médecine, Université de Liège, Faculté Universitaire Notre Dame de la Paix, Partenaires INRAE, Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, department of biological chemistry and molecular pharmacology, Life Technologies, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Department of Biology, Northern Arizona University [Flagstaff], Northeastern University [Boston], University of Notre Dame [Indiana] (UND), University of Warwick, Boston University [Boston] (BU), Department of Computing, Imperial College London, Cold Spring Harbor Laboratory (CSHL), Eagle Genomics Ltd, Eagle Genomics, and University of Warwick [Coventry]

Subjects
0106 biological sciences, binding, [SDV]Life Sciences [q-bio], plant, Computational biology, Biology, 01 natural sciences, Interactome, 03 medical and health sciences, Arabidopsis, Botany, expression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, genome, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Multidisciplinary, evolve, fungi, food and beverages, 15. Life on land, biology.organism_classification, duplicated gene, protein interaction network, fate, plasticity, divergence, 010606 plant biology & botany
Abstract

International audience; Plants have unique features that evolved in response to their environments and ecosystems. A full account of the complex cellular networks that underlie plant-specific functions is still missing. We describe a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing about 6200 highly reliable interactions between about 2700 proteins. A global organization of plant biological processes emerges from community analyses of the resulting network, together with large numbers of novel hypothetical functional links between proteins and pathways. We observe a dynamic rewiring of interactions following gene duplication events, providing evidence for a model of evolution acting upon interactome networks. This and future plant interactome maps should facilitate systems approaches to better understand plant biology and improve crops.

Published
2011
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35. The B73 maize genome: complexity, diversity, and dynamics

Author

Kristi Collura, Nay Thane, Sanzhen Liu, Sharon Wei, Joshua C. Stein, Jason Waligorski, Shanmugam Rajasekar, Robert A. Martienssen, Patrick S. Schnable, Marc Cotton, Georgina Lopez, R. Kelly Dawe, Jennifer Sgro, Krista Delaney, Linda McMahan, Krishna L. Kanchi, Qi Sun, Jeffrey L. Bennetzen, Asif T. Chinwalla, Zhijie Liu, Gernot G. Presting, Jennifer S. Hodges, Jianwei Zhang, Doreen Ware, William Spooner, Melissa Kramer, Stephanie Muller, Kelly Mead, Jeffrey A. Jeddeloh, Peter Van Buren, W. Richard McCombie, Thomas J. Wang, Stephanie M. Jackson, Beth Miller, Ananth Kalyanaraman, Wolfgang Golser, Rene Lomeli, Aswathy Sebastian, Ara Ko, Alan M. Myers, Carol Soderlund, Kai Ying, Thomas K. Wolfgruber, Lixing Yang, Sunita Kumari, Yujun Han, Jayson Talag, John D. Nguyen, Shawn Leonard, Shiran Pasternak, Chad Tomlinson, Barbara Gillam, Angelina Angelova, Weizu Chen, Bryan W. Penning, Catrina Fronick, Apurva Narechania, Zeljko Dujmic, Matt Cordes, Tina Graves, Cheng Ting Yeh, Jennifer Currie, Michael S. Waterman, Seunghee Lee, Amy Denise Reily, Sandra W. Clifton, Jean-Marc Deragon, Matthew W. Vaughn, Jessica Ruppert, Chengzhi Liang, Dan Nettleton, Maureen C. McCann, Michele Braidotti, Scott Kruchowski, Shiguo Zhou, Ning Jiang, Feiyu Du, Cindy Strong, Thomas P. Brutnell, Scott J. Emrich, Nicholas C. Carpita, Michael J. Levy, Srinivas Aluru, Yi Jia, Liya Ren, Laura Courtney, Teri Mueller, Ruifeng He, Marco Cardenas, Fusheng Wei, Brandon Delgado, Lalit Ponnala, Robert S. Fulton, Elizabeth Applebaum, Jinke Lin, Kevin L. Schneider, Le Yan, Kelsi Rotter, Ben Faga, Susan M. Rock, Elizabeth Ingenthron, Adam Scimone, Andrea Zuccolo, Cristian Chaparro, Neha Shah, Qihui Zhu, Hye-Ran Lee, Richard P. Westerman, Chuanzhu Fan, Dave Kudrna, Rachel Abbott, Lidia Nascimento, Jer Ming Chia, Kerri Ochoa, Lindsey Phelps, Elizabeth Ashley, Damon Lisch, Lucinda Fulton, Gabriel Scara, Bill Courtney, Lori Spiegel, Kim D. Delehaunty, Anupma Sharma, Andrew Levy, Hyeran Kim, Richard K. Wilson, Patrick Minx, Rod A. Wing, Phillip SanMiguel, An-Ping Hsia, Yan Fu, Kyung Kim, Nathan M. Springer, Regina S. Baucom, Woojin Kim, Jason Falcone, Pinghua Li, David C. Schwartz, W. Brad Barbazuk, Jamey Higginbotham, Susan R. Wessler, T. K. Thane, Jessica Henke, Hao Wang, Jiming Jiang, Yeisoo Yu, Sara Kohlberg, Claude Ambroise, Kevin Crouse, Theresa Zutavern, Pamela Marchetto, David Campos, Lifang Zhang, James C. Estill, Dawn H. Nagel, Marina Wissotski, Eddie Belter, Center for Plant Genomics, Iowa State University (ISU), Cold Spring Harbor Laboratory (CSHL), Department of Genetics [Saint-Louis], Washington University in Saint Louis (WUSTL), Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, Department of Genetics, Development, and Cell Biology, Department of Electrical and Computer Engineering [Iowa], University of Iowa [Iowa City], University of Florida [Gainesville] (UF), Department of Genetics, University of Georgia [USA], Cornell University [New York], Department of Botany and Plant Pathology, Purdue University [West Lafayette], Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Department of Agronomy, NimbleGen, Department of Horticulture, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Biological Sciences [West Lafayette], and Department of plant Biology

Subjects
0106 biological sciences, MESH: Genome, Plant, MESH: Sequence Analysis, DNA, MESH: Zea mays, MESH: Base Sequence, MESH: RNA, Plant, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Genome, Divergence, MESH: Ploidies, MESH: DNA Methylation, MESH: Genes, Plant, Nested association mapping, Copy-number variation, MESH: Genetic Variation, MESH: Chromosomes, Plant, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Arabidopsis-Thaliana, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Retrotransposons, MESH: DNA Transposable Elements, Helitron, MESH: Centromere, MESH: Recombination, Genetic, MESH: DNA Copy Number Variations, Ploidy, Transposable element, Genome evolution, Evolution, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Methylation, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, MESH: Retroelements, MESH: Inbreeding, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Zea-Mays, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], MESH: DNA, Plant, Gene, 030304 developmental biology, MESH: Molecular Sequence Data, Transposable Elements, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Plant, 15. Life on land, MESH: Crops, Agricultural, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Genes, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Chromosome Mapping, MESH: MicroRNAs, 010606 plant biology & botany
Abstract

A-Maize-ing Maize is one of our oldest and most important crops, having been domesticated approximately 9000 years ago in central Mexico. Schnable et al. (p. 1112 ; see the cover) present the results of sequencing the B73 inbred maize line. The findings elucidate how maize became diploid after an ancestral doubling of its chromosomes and reveals transposable element movement and activity and recombination. Vielle-Calzada et al. (p. 1078 ) have sequenced the Palomero Toluqueño ( Palomero ) landrace, a highland popcorn from Mexico, which, when compared to the B73 line, reveals multiple loci impacted by domestication. Swanson-Wagner et al. (p. 1118 ) exploit possession of the genome to analyze expression differences occurring between lines. The identification of single nucleotide polymorphisms and copy number variations among lines was used by Gore et al. (p. 1115 ) to generate a Haplotype map of maize. While chromosomal diversity in maize is high, it is likely that recombination is the major force affecting the levels of heterozygosity in maize. The availability of the maize genome will help to guide future agricultural and biofuel applications (see the Perspective by Feuillet and Eversole ).

Published
2009
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36. WormBase: better software, richer content

Author

Paul Davis, Juancarlos Chan, William Spooner, Erich M. Schwarz, Todd W. Harris, Tamberlyn Bieri, Raymond Lee, Nansheng Chen, Lincoln Stein, Carol Bastiani, Daniel Wang, Phil Ozersky, John Spieth, Hans-Michael Müller, Daniel Lawson, Tristan J. Fiedler, Richard Durbin, Andrei Petcherski, Mary Ann Tuli, Kimberly Van Auken, Paul W. Sternberg, Ranjana Kishore, Payan Canaran, Igor Antoshechkin, Lisa-Christine Girard, Anthony Rogers, Eimear E. Kenny, Wen J. Chen, Cecilia Nakamura, and Darin Blasiar

Subjects
DNA, Complementary, Genomics, Genome browser, Computational biology, Polymorphism, Single Nucleotide, Article, User-Computer Interface, 03 medical and health sciences, Software portability, 0302 clinical medicine, Databases, Genetic, Genetics, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Gene, 030304 developmental biology, Expressed Sequence Tags, Genome, Helminth, Internet, 0303 health sciences, Expressed sequence tag, biology, biology.organism_classification, Data structure, ComputingMethodologies_PATTERNRECOGNITION, RNA Interference, WormBase, Software, 030217 neurology & neurosurgery, Caltech Library Services
Abstract

WormBase (http://wormbase.org), the public database for genomics and biology of Caenorhabditis elegans, has been restructured for stronger performance and expanded for richer biological content. Performance was improved by accelerating the loading of central data pages such as the omnibus Gene page, by rationalizing internal data structures and software for greater portability, and by making the Genome Browser highly customizable in how it views and exports genomic subsequences. Arbitrarily complex, user-specified queries are now possible through Textpresso (for all available literature) and through WormMart (for most genomic data). Biological content was enriched by reconciling all available cDNA and expressed sequence tag data with gene predictions, clarifying single nucleotide polymorphism and RNAi sites, and summarizing known functions for most genes studied in this organism.

Published
2006

37. An overview of Ensembl

Author

Glenn Proctor, Mark Rae, James G. R. Gilbert, Roy Storey, Tim J.R. Cutts, Damian Keefe, Xosé M. Fernández-Suárez, Eduardo Eyras, William Spooner, Roger Pettett, Michele Clamp, Abel Ureta-Vidal, Martin Hammond, K. Cara Woodwark, Graham McVicker, Yuan Chen, Anthony J. Cox, Thomas A. Down, James Cuff, Simon C. Potter, Guy Coates, Vivek Iyer, Hans-Rudolf Hotz, Damian Smedley, Heikki Lehväslaiho, Paul Gane, Val Curwen, Arek Kasprzyk, Craig Melsopp, Andreas Kähäri, Richard Durbin, Patrick Meidl, Brian Gibbins, Graham Cameron, Steve Searle, Mario Caccamo, James Stalker, Kerstin Jekosch, James Smith, Arne Stabenau, Emmanuel Mongin, Stephen Keenan, Tim Hubbard, T. Daniel Andrews, Laura Clarke, Guy Slater, Ewan Birney, and Paul Bevan

Subjects
Biological data, Flat file database, Computational Biology, Computational biology, Biology, Bioinformatics, Genome, Set (abstract data type), Annotation, ComputingMethodologies_PATTERNRECOGNITION, Genetics, Code (cryptography), Ensembl, ENSEMBL Special, Genetics (clinical), Synteny
Abstract

Ensembl (http://www.ensembl.org/) is a bioinformatics project to organize biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of individual genomes, and of the synteny and orthology relationships between them. It is also a framework for integration of any biological data that can be mapped onto features derived from the genomic sequence. Ensembl is available as an interactive Web site, a set of flat files, and as a complete, portable open source software system for handling genomes. All data are provided without restriction, and code is freely available. Ensembl's aims are to continue to “widen” this biological integration to include other model organisms relevant to understanding human biology as they become available; to “deepen” this integration to provide an ever more seamless linkage between equivalent components in different species; and to provide further classification of functional elements in the genome that have been previously elusive.

Published
2004

39. The Ensembl genome database project

Author

Louise Clark, Tim Hubbard, Craig Melsopp, Matthew Pocock, Graham Cameron, William Spooner, Simon C. Potter, Martin Hammond, Eduardo Eyras, Roger Pettett, Abel Ureta-Vidal, Tony Cox, Arek Kasprzyk, Yuan Chen, James G. R. Gilbert, Lukasz Huminiecki, Ewan Birney, Val Curwen, Elia Stupka, Michele Clamp, Emmanuel Mongin, Arne Stabenau, Imre Vastrik, James Smith, Stephen M. J. Searle, Guy Slater, Philip Lijnzaad, Thomas A. Down, Alistair G. Rust, Jim Stalker, Daniel Barker, Richard Durbin, Esther Schmidt, James Cuff, and Heikki Lehväslaiho

Subjects
Internet, business.industry, Flat file database, Genome, Human, Computational Biology, Information Storage and Retrieval, Sequence Analysis, DNA, Vertebrate and Genome Annotation Project, Biology, Bioinformatics, Genome, Article, World Wide Web, Systems Integration, Annotation, Software, ComputingMethodologies_PATTERNRECOGNITION, Databases, Genetic, Genetics, Ensembl, Database Management Systems, Humans, The Internet, Human genome, business
Abstract

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

Published
2002

40. Eagle

Author

Richard Holland, Ivan Karabaliev, William Spooner, Richard Holland, Ivan Karabaliev, and William Spooner

Published
2013
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41. Gramene: a bird's eye view of cereal genomes

Author

Pankaj Jaiswal, Junjian Ni, Molly Fogleman, Chengzhi Liang, Edward S. Buckler, Shuly Avraham, Doreen Ware, William Spooner, Ken Youens-Clark, Liya Ren, Immanuel Yap, Wei Zhao, Lincoln Stein, Payan Canaran, Terry M. Casstevens, Susan R. McCouch, Claire Hebbard, Kiran Ratnapu, Benjamin P Faga, and Steven Schmidt

Subjects
0106 biological sciences, Genetic Markers, Quantitative Trait Loci, Arabidopsis, Genomics, Quantitative trait locus, Genes, Plant, 01 natural sciences, Genome, Zea mays, Article, Crop, 03 medical and health sciences, User-Computer Interface, Databases, Genetic, Genetics, Poaceae, 030304 developmental biology, Synteny, Plant Proteins, 2. Zero hunger, 0303 health sciences, Internet, Oryza sativa, biology, business.industry, Chromosome Mapping, Oryza, 15. Life on land, Sorghum, biology.organism_classification, Biotechnology, Agronomy, Vocabulary, Controlled, business, Edible Grain, Genome, Plant, 010606 plant biology & botany
Abstract

Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov). Continued improvement of Poaceae crops is necessary in order to continue to feed an ever-growing world population. However, of the major crop grasses, only rice (Oryza sativa), with a compact genome of approximately 400 Mbp, has been sequenced and annotated. The Gramene database (http://www.gramene.org) takes advantage of the known genetic colinearity (synteny) between rice and the major crop plant genomes to provide maize, sorghum, millet, wheat, oat and barley researchers with the benefits of an annotated genome years before their own species are sequenced. Gramene is a one stop portal for finding curated literature, genetic and genomic datasets related to maps, markers, genes, genomes and quantitative trait loci. The addition of several new tools to Gramene has greatly facilitated the potential for comparative analysis among the grasses and contributes to our understanding of the anatomy, development, environmental responses and the factors influencing agronomic performance of cereal crops. Since the last publication on Gramene database by D. H. Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant Physiol., 130, 1606-1613], the database has undergone extensive changes that are described in this publication.

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