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1. Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M., Formenti, Giulio, Mouton, Alice, De Panis, Diego, Marins, Luísa S., Leitão, Henrique G., Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, De Pooter, Tim, Joris, Geert, Strazisar, Mojca, Wood, Jonathan M. D., Herron, Katie E., Seehausen, Ole, Watts, Phillip C., Shaw, Felix, Davey, Robert P., Minotto, Alice, Fernández, José M., Böhne, Astrid, Alegria, Carla, Alioto, Tyler, Alves, Paulo C., Amorim, Isabel R., Aury, Jean-Marc, Backstrom, Niclas, Baldrian, Petr, Baltrunaite, Laima, Barta, Endre, BedHom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo A. V., Dias, Guilherme Borges, Bosse, Mirte, Brown, Tom, Bruggmann, Rémy, Buena-Atienza, Elena, Burgin, Josephine, Buzan, Elena, Cariani, Alessia, Casadei, Nicolas, Chiara, Matteo, Chozas, Sergio, Čiampor, Jr., Fedor, Crottini, Angelica, Cruaud, Corinne, Cruz, Fernando, Dalen, Love, De Biase, Alessio, del Campo, Javier, Delic, Teo, Dennis, Alice B., Derks, Martijn F. L., Diroma, Maria Angela, Djan, Mihajla, Duprat, Simone, Eleftheriadi, Klara, Feulner, Philine G. D., Flot, Jean-François, Forni, Giobbe, Fosso, Bruno, Fournier, Pascal, Fournier-Chambrillon, Christine, Gabaldon, Toni, Garg, Shilpa, Gissi, Carmela, Giupponi, Luca, Gomez-Garrido, Jessica, González, Josefa, Grilo, Miguel L., Grüning, Björn, Guerin, Thomas, Guiglielmoni, Nadege, Gut, Marta, Haesler, Marcel P., Hahn, Christoph, Halpern, Balint, Harrison, Peter W., Heintz, Julia, Hindrikson, Maris, Höglund, Jacob, Howe, Kerstin, Hughes, Graham M., Istace, Benjamin, Cock, Mark J., Janžekovič, Franc, Jonsson, Zophonias O., Joye-Dind, Sagane, Koskimäki, Janne J., Krystufek, Boris, Kubacka, Justyna, Kuhl, Heiner, Kusza, Szilvia, Labadie, Karine, Lähteenaro, Meri, Lantz, Henrik, Lavrinienko, Anton, Leclère, Lucas, Lopes, Ricardo Jorge, Madsen, Ole, Magdelenat, Ghislaine, Magoga, Giulia, Manousaki, Tereza, Mappes, Tapio, Marques, Joao Pedro, Redondo, Gemma I. Martinez, Maumus, Florian, McCarthy, Shane A., Megens, Hendrik-Jan, Melo-Ferreira, Jose, Mendes, Sofia L., Montagna, Matteo, Moreno, Joao, Mosbech, Mai-Britt, Moura, Mónica, Musilova, Zuzana, Myers, Eugene, Nash, Will J., Nater, Alexander, Nicholson, Pamela, Niell, Manuel, Nijland, Reindert, Noel, Benjamin, Noren, Karin, Oliveira, Pedro H., Olsen, Remi-Andre, Ometto, Lino, Oomen, Rebekah A., Ossowski, Stephan, Palinauskas, Vaidas, Palsson, Snaebjorn, Panibe, Jerome P., Pauperio, Joana, Pavlek, Martina, Payen, Emilie, Pawlowska, Julia, Pellicer, Jaume, Pesole, Graziano, Pimenta, Joao, Pippel, Martin, Pirttilä, Anna Maria, Poulakakis, Nikos, Rajan, Jeena, M.C. Rego, Rúben, Resendes, Roberto, Resl, Philipp, Riesgo, Ana, Rodin-Morch, Patrik, Soares, Andre E. R., Fernandes, Carlos Rodriguez, Romeiras, Maria M., Roxo, Guilherme, Rüber, Lukas, Ruiz-Lopez, Maria Jose, Saarma, Urmas, da Silva, Luis P., Sim-Sim, Manuela, Soler, Lucile, Sousa, Vitor C., Santos, Carla Sousa, Spada, Alberto, Stefanovic, Milomir, Steger, Viktor, Stiller, Josefin, Stöck, Matthias, Struck, Torsten H., Sudasinghe, Hiranya, Tapanainen, Riikka, Tellgren-Roth, Christian, Trindade, Helena, Tukalenko, Yevhen, Urso, Ilenia, Vacherie, Benoit, Van Belleghem, Steven M., Van Oers, Kees, Vargas-Chavez, Carlos, Velickovic, Nevena, Vella, Noel, Vella, Adriana, Vernesi, Cristiano, Vicente, Sara, Villa, Sara, Pettersson, Olga Vinnere, Volckaert, Filip A. M., Voros, Judit, Wincker, Patrick, Winkler, Sylke, Ciofi, Claudio, Waterhouse, Robert M., and Mazzoni, Camila J.

Published
2024
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2. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M., Formenti, Giulio, Mouton, Alice, De Panis, Diego, Marins, Luísa S., Leitão, Henrique G., Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, De Pooter, Tim, Joris, Geert, Strazisar, Mojca, Wood, Jonathan M. D., Herron, Katie E., Seehausen, Ole, Watts, Phillip C., Shaw, Felix, Davey, Robert P., Minotto, Alice, Fernández, José M., Böhne, Astrid, Alegria, Carla, Alioto, Tyler, Alves, Paulo C., Amorim, Isabel R., Aury, Jean-Marc, Backstrom, Niclas, Baldrian, Petr, Baltrunaite, Laima, Barta, Endre, BedHom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo A. V., Dias, Guilherme Borges, Bosse, Mirte, Brown, Tom, Bruggmann, Rémy, Buena-Atienza, Elena, Burgin, Josephine, Buzan, Elena, Cariani, Alessia, Casadei, Nicolas, Chiara, Matteo, Chozas, Sergio, Čiampor, Jr., Fedor, Crottini, Angelica, Cruaud, Corinne, Cruz, Fernando, Dalen, Love, De Biase, Alessio, del Campo, Javier, Delic, Teo, Dennis, Alice B., Derks, Martijn F. L., Diroma, Maria Angela, Djan, Mihajla, Duprat, Simone, Eleftheriadi, Klara, Feulner, Philine G. D., Flot, Jean-François, Forni, Giobbe, Fosso, Bruno, Fournier, Pascal, Fournier-Chambrillon, Christine, Gabaldon, Toni, Garg, Shilpa, Gissi, Carmela, Giupponi, Luca, Gomez-Garrido, Jessica, González, Josefa, Grilo, Miguel L., Grüning, Björn, Guerin, Thomas, Guiglielmoni, Nadege, Gut, Marta, Haesler, Marcel P., Hahn, Christoph, Halpern, Balint, Harrison, Peter W., Heintz, Julia, Hindrikson, Maris, Höglund, Jacob, Howe, Kerstin, Hughes, Graham M., Istace, Benjamin, Cock, Mark J., Janžekovič, Franc, Jonsson, Zophonias O., Joye-Dind, Sagane, Koskimäki, Janne J., Krystufek, Boris, Kubacka, Justyna, Kuhl, Heiner, Kusza, Szilvia, Labadie, Karine, Lähteenaro, Meri, Lantz, Henrik, Lavrinienko, Anton, Leclère, Lucas, Lopes, Ricardo Jorge, Madsen, Ole, Magdelenat, Ghislaine, Magoga, Giulia, Manousaki, Tereza, Mappes, Tapio, Marques, Joao Pedro, Redondo, Gemma I. Martinez, Maumus, Florian, McCarthy, Shane A., Megens, Hendrik-Jan, Melo-Ferreira, Jose, Mendes, Sofia L., Montagna, Matteo, Moreno, Joao, Mosbech, Mai-Britt, Moura, Mónica, Musilova, Zuzana, Myers, Eugene, Nash, Will J., Nater, Alexander, Nicholson, Pamela, Niell, Manuel, Nijland, Reindert, Noel, Benjamin, Noren, Karin, Oliveira, Pedro H., Olsen, Remi-Andre, Ometto, Lino, Oomen, Rebekah A., Ossowski, Stephan, Palinauskas, Vaidas, Palsson, Snaebjorn, Panibe, Jerome P., Pauperio, Joana, Pavlek, Martina, Payen, Emilie, Pawlowska, Julia, Pellicer, Jaume, Pesole, Graziano, Pimenta, Joao, Pippel, Martin, Pirttilä, Anna Maria, Poulakakis, Nikos, Rajan, Jeena, M.C. Rego, Rúben, Resendes, Roberto, Resl, Philipp, Riesgo, Ana, Rodin-Morch, Patrik, Soares, Andre E. R., Fernandes, Carlos Rodriguez, Romeiras, Maria M., Roxo, Guilherme, Rüber, Lukas, Ruiz-Lopez, Maria Jose, Saarma, Urmas, da Silva, Luis P., Sim-Sim, Manuela, Soler, Lucile, Sousa, Vitor C., Santos, Carla Sousa, Spada, Alberto, Stefanovic, Milomir, Steger, Viktor, Stiller, Josefin, Stöck, Matthias, Struck, Torsten H., Sudasinghe, Hiranya, Tapanainen, Riikka, Tellgren-Roth, Christian, Trindade, Helena, Tukalenko, Yevhen, Urso, Ilenia, Vacherie, Benoit, Van Belleghem, Steven M., Van Oers, Kees, Vargas-Chavez, Carlos, Velickovic, Nevena, Vella, Noel, Vella, Adriana, Vernesi, Cristiano, Vicente, Sara, Villa, Sara, Pettersson, Olga Vinnere, Volckaert, Filip A. M., Voros, Judit, Wincker, Patrick, Winkler, Sylke, Ciofi, Claudio, Waterhouse, Robert M., and Mazzoni, Camila J.

Published
2024
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4. The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the Tree of Life

Author

McKenna, Victoria, primary, Archibald, John M., additional, Beinart, Roxanne, additional, Dawson, Michael N., additional, Hentschel, Ute, additional, Keeling, Patrick J., additional, Lopez, Jose V., additional, Martín-Durán, José M., additional, Petersen, Jillian M., additional, Sigwart, Julia D., additional, Simakov, Oleg, additional, Sutherland, Kelly R., additional, Sweet, Michael, additional, Talbot, Nick, additional, Thompson, Anne W., additional, Bender, Sara, additional, Harrison, Peter W., additional, Rajan, Jeena, additional, Cochrane, Guy, additional, Berriman, Matthew, additional, Lawniczak, Mara K.N., additional, and Blaxter, Mark, additional

Published
2024
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5. Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

Author

Rahman, Nadim, O'cathail, Colman, Zyoud, Ahmad, Sokolov, Alexey, Munnink, Bas Oude, Grüning, Björn, Cummins, Carla, Amid, Clara, Nieuwenhuijse, David F., Visontai, Dávid, Yuan, David Yu, Gupta, Dipayan, Prasad, Divyae K., Gulyás, Gábor Máté, Rinck, Gabriele, McKinnon, Jasmine, Rajan, Jeena, Knaggs, Jeff, Skiby, Jeffrey Edward, Stéger, József, Szarvas, Judit, Gueye, Khadim, Papp, Krisztián, Hoek, Maarten, Kumar, Manish, Ventouratou, Marianna A., Bouquieaux, Marie Catherine, Koliba, Martin, Mansurova, Milena, Haseeb, Muhammad, Worp, Nathalie, Harrison, Peter W., Leinonen, Rasko, Thorne, Ross, Selvakumar, Sandeep, Hunt, Sarah, Venkataraman, Sundar, Jayathilaka, Suran, Cezard, Timothée, Maier, Wolfgang, Waheed, Zahra, Iqbal, Zamin, Aarestrup, Frank Møller, Csabai, Istvan, Koopmans, Marion, Burdett, Tony, Cochrane, Guy, Rahman, Nadim, O'cathail, Colman, Zyoud, Ahmad, Sokolov, Alexey, Munnink, Bas Oude, Grüning, Björn, Cummins, Carla, Amid, Clara, Nieuwenhuijse, David F., Visontai, Dávid, Yuan, David Yu, Gupta, Dipayan, Prasad, Divyae K., Gulyás, Gábor Máté, Rinck, Gabriele, McKinnon, Jasmine, Rajan, Jeena, Knaggs, Jeff, Skiby, Jeffrey Edward, Stéger, József, Szarvas, Judit, Gueye, Khadim, Papp, Krisztián, Hoek, Maarten, Kumar, Manish, Ventouratou, Marianna A., Bouquieaux, Marie Catherine, Koliba, Martin, Mansurova, Milena, Haseeb, Muhammad, Worp, Nathalie, Harrison, Peter W., Leinonen, Rasko, Thorne, Ross, Selvakumar, Sandeep, Hunt, Sarah, Venkataraman, Sundar, Jayathilaka, Suran, Cezard, Timothée, Maier, Wolfgang, Waheed, Zahra, Iqbal, Zamin, Aarestrup, Frank Møller, Csabai, Istvan, Koopmans, Marion, Burdett, Tony, and Cochrane, Guy

Abstract

The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and vari-ants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. In this paper we describe (1) open data sharing, (2) tools for submission, analysis, visualisation and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learnt. This paper describes a component of the Platform, the SARS-CoV-2 Data Hubs, which enable the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.

Published
2024

7. Data Reuse in Agricultural Genomics Research: Present Challenges and Future Solutions

Author

Hafner, Alenka, primary, DeLeo, Victoria, additional, Deng, Cecilia, additional, Elsik, Christine G., additional, Fleming, Damarius, additional, Harrison, Peter W., additional, Kalbfleisch, Theodore S., additional, Petry, Bruna, additional, Pucker, Boas, additional, Quezada-Rodríguez, Elsa H., additional, Tuggle, Christopher K., additional, and Koltes, James, additional

Published
2024
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10. Ensembl 2024

Author

Harrison, Peter W, primary, Amode, M Ridwan, additional, Austine-Orimoloye, Olanrewaju, additional, Azov, Andrey G, additional, Barba, Matthieu, additional, Barnes, If, additional, Becker, Arne, additional, Bennett, Ruth, additional, Berry, Andrew, additional, Bhai, Jyothish, additional, Bhurji, Simarpreet Kaur, additional, Boddu, Sanjay, additional, Branco Lins, Paulo R, additional, Brooks, Lucy, additional, Ramaraju, Shashank Budhanuru, additional, Campbell, Lahcen I, additional, Martinez, Manuel Carbajo, additional, Charkhchi, Mehrnaz, additional, Chougule, Kapeel, additional, Cockburn, Alexander, additional, Davidson, Claire, additional, De Silva, Nishadi H, additional, Dodiya, Kamalkumar, additional, Donaldson, Sarah, additional, El Houdaigui, Bilal, additional, Naboulsi, Tamara El, additional, Fatima, Reham, additional, Giron, Carlos Garcia, additional, Genez, Thiago, additional, Grigoriadis, Dionysios, additional, Ghattaoraya, Gurpreet S, additional, Martinez, Jose Gonzalez, additional, Gurbich, Tatiana A, additional, Hardy, Matthew, additional, Hollis, Zoe, additional, Hourlier, Thibaut, additional, Hunt, Toby, additional, Kay, Mike, additional, Kaykala, Vinay, additional, Le, Tuan, additional, Lemos, Diana, additional, Lodha, Disha, additional, Marques-Coelho, Diego, additional, Maslen, Gareth, additional, Merino, Gabriela Alejandra, additional, Mirabueno, Louisse Paola, additional, Mushtaq, Aleena, additional, Hossain, Syed Nakib, additional, Ogeh, Denye N, additional, Sakthivel, Manoj Pandian, additional, Parker, Anne, additional, Perry, Malcolm, additional, Piližota, Ivana, additional, Poppleton, Daniel, additional, Prosovetskaia, Irina, additional, Raj, Shriya, additional, Pérez-Silva, José G, additional, Salam, Ahamed Imran Abdul, additional, Saraf, Shradha, additional, Saraiva-Agostinho, Nuno, additional, Sheppard, Dan, additional, Sinha, Swati, additional, Sipos, Botond, additional, Sitnik, Vasily, additional, Stark, William, additional, Steed, Emily, additional, Suner, Marie-Marthe, additional, Surapaneni, Likhitha, additional, Sutinen, Kyösti, additional, Tricomi, Francesca Floriana, additional, Urbina-Gómez, David, additional, Veidenberg, Andres, additional, Walsh, Thomas A, additional, Ware, Doreen, additional, Wass, Elizabeth, additional, Willhoft, Natalie L, additional, Allen, Jamie, additional, Alvarez-Jarreta, Jorge, additional, Chakiachvili, Marc, additional, Flint, Bethany, additional, Giorgetti, Stefano, additional, Haggerty, Leanne, additional, Ilsley, Garth R, additional, Keatley, Jon, additional, Loveland, Jane E, additional, Moore, Benjamin, additional, Mudge, Jonathan M, additional, Naamati, Guy, additional, Tate, John, additional, Trevanion, Stephen J, additional, Winterbottom, Andrea, additional, Frankish, Adam, additional, Hunt, Sarah E, additional, Cunningham, Fiona, additional, Dyer, Sarah, additional, Finn, Robert D, additional, Martin, Fergal J, additional, and Yates, Andrew D, additional

Published
2023
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15. Ensembl 2024.

Author

Harrison, Peter W, Amode, M Ridwan, Austine-Orimoloye, Olanrewaju, Azov, Andrey G, Barba, Matthieu, Barnes, If, Becker, Arne, Bennett, Ruth, Berry, Andrew, Bhai, Jyothish, Bhurji, Simarpreet Kaur, Boddu, Sanjay, Branco Lins, Paulo R, Brooks, Lucy, Ramaraju, Shashank Budhanuru, Campbell, Lahcen I, Martinez, Manuel Carbajo, Charkhchi, Mehrnaz, Chougule, Kapeel, and Cockburn, Alexander

Published
2024
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16. Time Course of Neuromuscular, Hormonal, and Perceptual Responses Following Moderate- and High-Load Resistance Priming Exercise.

Author

Harrison, Peter W., James, Lachlan P., Jenkins, David G., McGuigan, Michael R., Schuster, Robert W., and Kelly, Vincent G.

Subjects
CONFIDENCE intervals, SALIVA, TESTOSTERONE, TIME, EXERCISE physiology, RANDOMIZED controlled trials, BODY movement, WEIGHT lifting, ATHLETIC ability, JUMPING, EMOTIONS, PSYCHOPHYSIOLOGY, BIOMECHANICS, EXERCISE therapy, HYDROCORTISONE
Abstract

Purpose: The aim of this study was to map responses over 32 hours following high-load (HL) and moderate-load (ML) half-squat priming. Methods: Fifteen participants completed control, HL (87% 1RM), and ML (65% 1RM) activities in randomized, counterbalanced order. Countermovement jump (CMJ), squat jump (SJ), saliva testosterone, saliva cortisol, and perceptual measures were assessed before and 5 minutes, 8 hours, 24 hours, and 32 hours after each activity. Results are presented as percentage change from baseline and 95% confidence interval (CI). Cliff delta was used to determine threshold for group changes. Results: SJ height increased by 4.5% (CI = 2.2–6.8, Cliff delta = 0.20) 8 hours following HL. CMJ and SJ improved by 6.1% (CI = 2.1–7.8, Cliff delta = 0.27) and 6.5% (CI = 1.2–11.8, Cliff delta = 0.30), respectively, 32 hours after ML. No clear diurnal changes in CMJ or SJ occurred 8 hours following control; however, increases of 3.9% (CI = 2.9–9.2, Cliff delta = 0.26) and 4.5% (CI = 0.9–8.1, Cliff delta = 0.24), respectively, were observed after 32 hours. Although diurnal changes in saliva hormone concentration occurred (Cliff delta = 0.37–0.92), the influence of priming was unclear. Perceived "physical feeling" was greater 8 hours following HL (Cliff delta = 0.36) and 32 hours after ML and control (Cliff delta = 0.17–0.34). Conclusions: HL priming in the morning may result in small improvements in jump output and psychophysiological state in the afternoon. Similar improvements were observed in the afternoon the day after ML priming. [ABSTRACT FROM AUTHOR]

Published
2021
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17. Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

Author

Rahman, Nadim, primary, O'Cathail, Colman, additional, Zyoud, Ahmad, additional, Sokolov, Alexey, additional, Oude Munnink, Bas, additional, Grüning, Björn Andreas, additional, Cummins, Carla, additional, Amid, Clara, additional, Nieuwenhuijse, David F, additional, Visontai, Dávid, additional, Yuan, David Yu, additional, Gupta, Dipayan, additional, Prasad, Divyae, additional, Gulyás, Gábor Máté, additional, Rinck, Gabriele, additional, McKinnon, Jasmine, additional, Knaggs, Jeff, additional, Skiby, Jeffrey Edward, additional, Stéger, József, additional, Szarvas, Judit, additional, Gueye, Khadim, additional, Papp, Krisztián, additional, Hoek, Maarten, additional, Kumar, Manish, additional, Ventouratou, Marianna A., additional, Bouquieaux, Marie-Catherine, additional, Koliba, Martin, additional, Mansurova, Milena, additional, Haseeb, Muhammad, additional, Worp, Nathalie, additional, Harrison, Peter W, additional, Leinonen, Rasko, additional, Thorne, Ross, additional, Selvakumar, Sandeep, additional, Hunt, Sarah, additional, Venkataraman, Sundar, additional, Jayathilaka, Suran, additional, Cezard, Timothée, additional, Maier, Wolfgang, additional, Waheed, Zahra, additional, Iqbal, Zamin, additional, Aarestrup, Frank M., additional, Csabai, Istvan, additional, Koopmans, Marion, additional, Burdett, Tony, additional, and Cochrane, Guy, additional

Published
2023
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18. GENCODE: reference annotation for the human and mouse genomes in 2023

Author

Frankish, Adam, primary, Carbonell-Sala, Sílvia, additional, Diekhans, Mark, additional, Jungreis, Irwin, additional, Loveland, Jane E, additional, Mudge, Jonathan M, additional, Sisu, Cristina, additional, Wright, James C, additional, Arnan, Carme, additional, Barnes, If, additional, Banerjee, Abhimanyu, additional, Bennett, Ruth, additional, Berry, Andrew, additional, Bignell, Alexandra, additional, Boix, Carles, additional, Calvet, Ferriol, additional, Cerdán-Vélez, Daniel, additional, Cunningham, Fiona, additional, Davidson, Claire, additional, Donaldson, Sarah, additional, Dursun, Cagatay, additional, Fatima, Reham, additional, Giorgetti, Stefano, additional, Giron, Carlos Garcıa, additional, Gonzalez, Jose Manuel, additional, Hardy, Matthew, additional, Harrison, Peter W, additional, Hourlier, Thibaut, additional, Hollis, Zoe, additional, Hunt, Toby, additional, James, Benjamin, additional, Jiang, Yunzhe, additional, Johnson, Rory, additional, Kay, Mike, additional, Lagarde, Julien, additional, Martin, Fergal J, additional, Gómez, Laura Martínez, additional, Nair, Surag, additional, Ni, Pengyu, additional, Pozo, Fernando, additional, Ramalingam, Vivek, additional, Ruffier, Magali, additional, Schmitt, Bianca M, additional, Schreiber, Jacob M, additional, Steed, Emily, additional, Suner, Marie-Marthe, additional, Sumathipala, Dulika, additional, Sycheva, Irina, additional, Uszczynska-Ratajczak, Barbara, additional, Wass, Elizabeth, additional, Yang, Yucheng T, additional, Yates, Andrew, additional, Zafrulla, Zahoor, additional, Choudhary, Jyoti S, additional, Gerstein, Mark, additional, Guigo, Roderic, additional, Hubbard, Tim J P, additional, Kellis, Manolis, additional, Kundaje, Anshul, additional, Paten, Benedict, additional, Tress, Michael L, additional, and Flicek, Paul, additional

Published
2022
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19. Ensembl 2023

Author

Martin, Fergal J, primary, Amode, M Ridwan, additional, Aneja, Alisha, additional, Austine-Orimoloye, Olanrewaju, additional, Azov, Andrey G, additional, Barnes, If, additional, Becker, Arne, additional, Bennett, Ruth, additional, Berry, Andrew, additional, Bhai, Jyothish, additional, Bhurji, Simarpreet Kaur, additional, Bignell, Alexandra, additional, Boddu, Sanjay, additional, Branco Lins, Paulo R, additional, Brooks, Lucy, additional, Ramaraju, Shashank Budhanuru, additional, Charkhchi, Mehrnaz, additional, Cockburn, Alexander, additional, Da Rin Fiorretto, Luca, additional, Davidson, Claire, additional, Dodiya, Kamalkumar, additional, Donaldson, Sarah, additional, El Houdaigui, Bilal, additional, El Naboulsi, Tamara, additional, Fatima, Reham, additional, Giron, Carlos Garcia, additional, Genez, Thiago, additional, Ghattaoraya, Gurpreet S, additional, Martinez, Jose Gonzalez, additional, Guijarro, Cristi, additional, Hardy, Matthew, additional, Hollis, Zoe, additional, Hourlier, Thibaut, additional, Hunt, Toby, additional, Kay, Mike, additional, Kaykala, Vinay, additional, Le, Tuan, additional, Lemos, Diana, additional, Marques-Coelho, Diego, additional, Marugán, José Carlos, additional, Merino, Gabriela Alejandra, additional, Mirabueno, Louisse Paola, additional, Mushtaq, Aleena, additional, Hossain, Syed Nakib, additional, Ogeh, Denye N, additional, Sakthivel, Manoj Pandian, additional, Parker, Anne, additional, Perry, Malcolm, additional, Piližota, Ivana, additional, Prosovetskaia, Irina, additional, Pérez-Silva, José G, additional, Salam, Ahamed Imran Abdul, additional, Saraiva-Agostinho, Nuno, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Sinha, Swati, additional, Sipos, Botond, additional, Stark, William, additional, Steed, Emily, additional, Sukumaran, Ranjit, additional, Sumathipala, Dulika, additional, Suner, Marie-Marthe, additional, Surapaneni, Likhitha, additional, Sutinen, Kyösti, additional, Szpak, Michal, additional, Tricomi, Francesca Floriana, additional, Urbina-Gómez, David, additional, Veidenberg, Andres, additional, Walsh, Thomas A, additional, Walts, Brandon, additional, Wass, Elizabeth, additional, Willhoft, Natalie, additional, Allen, Jamie, additional, Alvarez-Jarreta, Jorge, additional, Chakiachvili, Marc, additional, Flint, Bethany, additional, Giorgetti, Stefano, additional, Haggerty, Leanne, additional, Ilsley, Garth R, additional, Loveland, Jane E, additional, Moore, Benjamin, additional, Mudge, Jonathan M, additional, Tate, John, additional, Thybert, David, additional, Trevanion, Stephen J, additional, Winterbottom, Andrea, additional, Frankish, Adam, additional, Hunt, Sarah E, additional, Ruffier, Magali, additional, Cunningham, Fiona, additional, Dyer, Sarah, additional, Finn, Robert D, additional, Howe, Kevin L, additional, Harrison, Peter W, additional, Yates, Andrew D, additional, and Flicek, Paul, additional

Published
2022
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20. Common genetic variation drives molecular heterogeneity in human iPSCs

Author

Kilpinen, Helena, Goncalves, Angela, Leha, Andreas, Afzal, Vackar, Alasoo, Kaur, Ashford, Sofie, Bala, Sendu, Bensaddek, Dalila, Casale, Francesco Paolo, Culley, Oliver J., Danecek, Petr, Faulconbridge, Adam, Harrison, Peter W., Kathuria, Annie, McCarthy, Davis, McCarthy, Shane A., Meleckyte, Ruta, Memari, Yasin, Moens, Nathalie, Soares, Filipa, Mann, Alice, Streeter, Ian, Agu, Chukwuma A., Alderton, Alex, Nelson, Rachel, Harper, Sarah, Patel, Minal, White, Alistair, Patel, Sharad R., Clarke, Laura, Halai, Reena, Kirton, Christopher M., Kolb-Kokocinski, Anja, Beales, Philip, Birney, Ewan, Danovi, Davide, Lamond, Angus I., Ouwehand, Willem H., Vallier, Ludovic, Watt, Fiona M., Durbin, Richard, Stegle, Oliver, and Gaffney, Daniel J.

Subjects
Genetic variation -- Health aspects, Stem cells -- Genetic aspects -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterization of many existing iPS cell lines limits their potential use for research and therapy. Here we describe the systematic generation, genotyping and phenotyping of 711 iPS cell lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative. Our study outlines the major sources of genetic and phenotypic variation in iPS cells and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 546% of the variation in different iPS cell phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of genomic copy-number alterations that are repeatedly observed in iPS cells. In addition, we present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells., Author(s): Helena Kilpinen [1]; Angela Goncalves [2]; Andreas Leha [2]; Vackar Afzal [3]; Kaur Alasoo [2]; Sofie Ashford [4]; Sendu Bala [2]; Dalila Bensaddek [3]; Francesco Paolo Casale [1]; Oliver [...]

Published
2017
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26. Factors Modulating the Priming Response to Resistance and Stretch-Shortening Cycle Exercise Stimuli.

Author

Holmberg, Patrick M., Harrison, Peter W., Jenkins, David G., and Kelly, Vincent G.

Abstract

"Priming exercises" are gaining popularity as a precompetition strategy to improve subsequent performance. Although priming exercise has been shown to improve various neuromuscular performance measures within 48 hours, a number of studies have also found no change or significant decreases in performance following priming interventions. Inconsistencies in findings are likely due to the many different variables used in the research. In addition, evidence suggests that the potential performance response following a priming stimulus is likely to be influenced by individual characteristics. Therefore, the purpose of this review is to examine the available evidence and identify those variables that most strongly determine whether priming stimuli involving resistance and stretch-shortening cycle exercise tasks are likely to improve performance within 48 hours of that stimulus. In addition to making recommendations based on the evidence to date, directions for future research are also identified. [ABSTRACT FROM AUTHOR]

Published
2023
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27. The European Nucleotide Archive in 2021

Author

Cummins, Carla, primary, Ahamed, Alisha, additional, Aslam, Raheela, additional, Burgin, Josephine, additional, Devraj, Rajkumar, additional, Edbali, Ossama, additional, Gupta, Dipayan, additional, Harrison, Peter W, additional, Haseeb, Muhammad, additional, Holt, Sam, additional, Ibrahim, Talal, additional, Ivanov, Eugene, additional, Jayathilaka, Suran, additional, Kadhirvelu, Vishnukumar, additional, Kay, Simon, additional, Kumar, Manish, additional, Lathi, Ankur, additional, Leinonen, Rasko, additional, Madeira, Fabio, additional, Madhusoodanan, Nandana, additional, Mansurova, Milena, additional, O’Cathail, Colman, additional, Pearce, Matt, additional, Pesant, Stéphane, additional, Rahman, Nadim, additional, Rajan, Jeena, additional, Rinck, Gabriele, additional, Selvakumar, Sandeep, additional, Sokolov, Alexey, additional, Suman, Swati, additional, Thorne, Ross, additional, Totoo, Prabhat, additional, Vijayaraja, Senthilnathan, additional, Waheed, Zahra, additional, Zyoud, Ahmad, additional, Lopez, Rodrigo, additional, Burdett, Tony, additional, and Cochrane, Guy, additional

Published
2021
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28. Ensembl 2022

Author

Cunningham, Fiona, primary, Allen, James E, additional, Allen, Jamie, additional, Alvarez-Jarreta, Jorge, additional, Amode, M Ridwan, additional, Armean, Irina M, additional, Austine-Orimoloye, Olanrewaju, additional, Azov, Andrey G, additional, Barnes, If, additional, Bennett, Ruth, additional, Berry, Andrew, additional, Bhai, Jyothish, additional, Bignell, Alexandra, additional, Billis, Konstantinos, additional, Boddu, Sanjay, additional, Brooks, Lucy, additional, Charkhchi, Mehrnaz, additional, Cummins, Carla, additional, Da Rin Fioretto, Luca, additional, Davidson, Claire, additional, Dodiya, Kamalkumar, additional, Donaldson, Sarah, additional, El Houdaigui, Bilal, additional, El Naboulsi, Tamara, additional, Fatima, Reham, additional, Giron, Carlos Garcia, additional, Genez, Thiago, additional, Martinez, Jose Gonzalez, additional, Guijarro-Clarke, Cristina, additional, Gymer, Arthur, additional, Hardy, Matthew, additional, Hollis, Zoe, additional, Hourlier, Thibaut, additional, Hunt, Toby, additional, Juettemann, Thomas, additional, Kaikala, Vinay, additional, Kay, Mike, additional, Lavidas, Ilias, additional, Le, Tuan, additional, Lemos, Diana, additional, Marugán, José Carlos, additional, Mohanan, Shamika, additional, Mushtaq, Aleena, additional, Naven, Marc, additional, Ogeh, Denye N, additional, Parker, Anne, additional, Parton, Andrew, additional, Perry, Malcolm, additional, Piližota, Ivana, additional, Prosovetskaia, Irina, additional, Sakthivel, Manoj Pandian, additional, Salam, Ahamed Imran Abdul, additional, Schmitt, Bianca M, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Pérez-Silva, José G, additional, Stark, William, additional, Steed, Emily, additional, Sutinen, Kyösti, additional, Sukumaran, Ranjit, additional, Sumathipala, Dulika, additional, Suner, Marie-Marthe, additional, Szpak, Michal, additional, Thormann, Anja, additional, Tricomi, Francesca Floriana, additional, Urbina-Gómez, David, additional, Veidenberg, Andres, additional, Walsh, Thomas A, additional, Walts, Brandon, additional, Willhoft, Natalie, additional, Winterbottom, Andrea, additional, Wass, Elizabeth, additional, Chakiachvili, Marc, additional, Flint, Bethany, additional, Frankish, Adam, additional, Giorgetti, Stefano, additional, Haggerty, Leanne, additional, Hunt, Sarah E, additional, IIsley, Garth R, additional, Loveland, Jane E, additional, Martin, Fergal J, additional, Moore, Benjamin, additional, Mudge, Jonathan M, additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Tate, John, additional, Thybert, David, additional, Trevanion, Stephen J, additional, Dyer, Sarah, additional, Harrison, Peter W, additional, Howe, Kevin L, additional, Yates, Andrew D, additional, Zerbino, Daniel R, additional, and Flicek, Paul, additional

Published
2021
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29. The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life [version 1; peer review: 1 approved, 1 approved with reservations]

Author

McKenna, Victoria, Archibald, John M., Beinart, Roxanne, Dawson, Michael N., Hentschel, Ute, Keeling, Patrick J., Lopez, Jose V., Martín-Durán, José M., Petersen, Jillian M., Sigwart, Julia D., Simakov, Oleg, Sutherland, Kelly R., Sweet, Michael, Talbot, Nick, Thompson, Anne W., Bender, Sara, Harrison, Peter W., Rajan, Jeena, Cochrane, Guy, Berriman, Matthew, Lawniczak, Mara, and Blaxter, Mark

Abstract

We present the Aquatic Symbiosis Genomics Project, a global collaboration to generate high quality genome sequences for a wide range of eukaryotes and their microbial symbionts. Launched under the Symbiosis in Aquatic Systems Initiative of the Gordon and Betty Moore Foundation, the ASG Project brings together researchers from across the globe who hope to use these reference genomes to augment and extend their analyses of the dynamics, mechanisms and environmental importance of symbiosis. Applying large-scale, high-throughput sequencing and assembly technologies, the ASG collaboration will assemble and annotate the genomes of 500 symbiotic organisms – both the “hosts” and the microbial symbionts with which they associate. These data will be released openly to benefit all who work on symbiosis, from conservation geneticists to those interested in the origin of the eukaryotic cell.

Published
2021

31. The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life

Author

McKenna, Victoria, primary, Archibald, John M., additional, Beinart, Roxanne, additional, Dawson, Michael N., additional, Hentschel, Ute, additional, Keeling, Patrick J., additional, Lopez, Jose V., additional, Martín-Durán, José M., additional, Petersen, Jillian M., additional, Sigwart, Julia D., additional, Simakov, Oleg, additional, Sutherland, Kelly R., additional, Sweet, Michael, additional, Talbot, Nick, additional, Thompson, Anne W., additional, Bender, Sara, additional, Harrison, Peter W., additional, Rajan, Jeena, additional, Cochrane, Guy, additional, Berriman, Matthew, additional, Lawniczak, Mara K.N., additional, and Blaxter, Mark, additional

Published
2021
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32. Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap

Author

Giuffra, Elisabetta, Tuggle, Christopher K., Archibald, A.L., ACLOQUE, Hervé, Chamberlain, Amanda J., Cochrane, Guy, Daetwyler, Hans D., Djebali Quelen, Sarah, Eory, Lel, Foissac, Sylvain, Goddard, Michael E., Groenen, Martien A.M., Halstead, Michelle, Harrison, Peter W., Hayes, B.J., Kern, Colin, Khatib, Hassan, Kuo, Richard I., MacHugh, David E., MacLeod, I.M., Madsen, Ole, Reecy, Mark James, Ross, Pablo, J., Watson, Mick, Wells, Jerry M., Zhou, H.J., Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Iowa State University (ISU), University of Edinburgh, Dept Econ Dev Jobs Transport & Resources, European Molecular Biology Laboratory European Bioinformatics Institute, La Trobe University, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-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-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Melbourne, Wageningen University and Research Centre (WUR), University of California [Davis] (UC Davis), University of California, University of Queensland [Brisbane], University of Wisconsin-Madison, University College Dublin (UCD), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Epigenomics, 0301 basic medicine, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], domesticated animal, Genotype, Genomics, Computational biology, Animal Breeding and Genomics, Biology, Genome, genomic selection, 03 medical and health sciences, Annotation, Genome editing, functional genomic, Genetics, Animals, genome editing, Fokkerij en Genomica, Epigenetics, Gene Editing, 2. Zero hunger, epigenetics, General Veterinary, 0402 animal and dairy science, Molecular Sequence Annotation, 04 agricultural and veterinary sciences, genotype-to-phenotype, 040201 dairy & animal science, Chromatin, Phenotype, 030104 developmental biology, domesticated animals, Animals, Domestic, DNA methylation, WIAS, Animal Science and Zoology, functional genomics, Functional genomics, epigenetic, Biotechnology
Abstract

International audience; Functional annotation of genomes is a prerequisite for contemporary basic and applied genomic research, yet farmed animal genomics is deficient in such annotation. To address this, the FAANG (Functional Annotation of Animal Genomes) Consortium is producing genome-wide data sets on RNA expression, DNA methylation, and chromatin modification, as well as chromatin accessibility and interactions. In addition to informing our understanding of genome function, including comparative approaches to elucidate constrained sequence or epigenetic elements, these annotation maps will improve the precision and sensitivity of genomic selection for animal improvement. A scientific community-driven effort has already created a coordinated data collection and analysis enterprise crucial for the success of this global effort. Although it is early in this continuing process, functional data have already been produced and application to genetic improvement reported. The functional annotation delivered by the FAANG initiative will add value and utility to the greatly improved genome sequences being established for domesticated animal species.

Published
2019

35. The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing

Author

Harrison, Peter W, primary, Lopez, Rodrigo, additional, Rahman, Nadim, additional, Allen, Stefan Gutnick, additional, Aslam, Raheela, additional, Buso, Nicola, additional, Cummins, Carla, additional, Fathy, Yasmin, additional, Felix, Eloy, additional, Glont, Mihai, additional, Jayathilaka, Suran, additional, Kadam, Sandeep, additional, Kumar, Manish, additional, Lauer, Katharina B, additional, Malhotra, Geetika, additional, Mosaku, Abayomi, additional, Edbali, Ossama, additional, Park, Young Mi, additional, Parton, Andrew, additional, Pearce, Matt, additional, Estrada Pena, Jose Francisco, additional, Rossetto, Joseph, additional, Russell, Craig, additional, Selvakumar, Sandeep, additional, Sitjà, Xènia Pérez, additional, Sokolov, Alexey, additional, Thorne, Ross, additional, Ventouratou, Marianna, additional, Walter, Peter, additional, Yordanova, Galabina, additional, Zadissa, Amonida, additional, Cochrane, Guy, additional, Blomberg, Niklas, additional, and Apweiler, Rolf, additional

Published
2021
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36. Time Course of Neuromuscular, Hormonal, and Perceptual Responses Following Moderate- and High-Load Resistance Priming Exercise

Author

Harrison, Peter W, James, Lachlan P, Jenkins, David G, McGuigan, Michael R., Schuster, Robert W., Kelly, Vincent G, Harrison, Peter W, James, Lachlan P, Jenkins, David G, McGuigan, Michael R., Schuster, Robert W., and Kelly, Vincent G

Abstract

PURPOSE: The aim of this study was to map responses over 32 hours following high-load (HL) and moderate-load (ML) half-squat priming.METHODS: Fifteen participants completed control, HL (87% 1RM), and ML (65% 1RM) activities in randomized, counterbalanced order. Countermovement jump (CMJ), squat jump (SJ), saliva testosterone, saliva cortisol, and perceptual measures were assessed before and 5 minutes, 8 hours, 24 hours, and 32 hours after each activity. Results are presented as percentage change from baseline and 95% confidence interval (CI). Cliff delta was used to determine threshold for group changes.RESULTS: SJ height increased by 4.5% (CI = 2.2-6.8, Cliff delta = 0.20) 8 hours following HL. CMJ and SJ improved by 6.1% (CI = 2.1-7.8, Cliff delta = 0.27) and 6.5% (CI = 1.2-11.8, Cliff delta = 0.30), respectively, 32 hours after ML. No clear diurnal changes in CMJ or SJ occurred 8 hours following control; however, increases of 3.9% (CI = 2.9-9.2, Cliff delta = 0.26) and 4.5% (CI = 0.9-8.1, Cliff delta = 0.24), respectively, were observed after 32 hours. Although diurnal changes in saliva hormone concentration occurred (Cliff delta = 0.37-0.92), the influence of priming was unclear. Perceived "physical feeling" was greater 8 hours following HL (Cliff delta = 0.36) and 32 hours after ML and control (Cliff delta = 0.17-0.34).CONCLUSIONS: HL priming in the morning may result in small improvements in jump output and psychophysiological state in the afternoon. Similar improvements were observed in the afternoon the day after ML priming.

Published
2021

37. The European Nucleotide Archive in 2020

Author

Harrison, Peter W. and Cochrane, Guy

Subjects
DNA variation, database, data services
Abstract

This review highlights themajor developments to ENA services and contentin 2020, focussing in particular on the recently released updated ENA browser, modernisation of therelease process and thedata coordination collaborationswithspecific research communities.

Published
2020

40. Population-scale proteome variation in human induced pluripotent stem cells

Author

Mirauta, Bogdan Andrei, Seaton, Daniel D, Bensaddek, Dalila, Brenes, Alejandro, Bonder, Marc Jan, Kilpinen, Helena, Agu, Chukwuma A, Alderton, Alex, Danecek, Petr, Denton, Rachel, Durbin, Richard, Gaffney, Daniel J, Goncalves, Angela, Halai, Reena, Harper, Sarah, Kirton, Christopher M, Kolb-Kokocinski, Anja, Leha, Andreas, McCarthy, Shane A, Memari, Yasin, Patel, Minal, Birney, Ewan, Casale, Francesco Paolo, Clarke, Laura, Harrison, Peter W, Streeter, Ian, Denovi, Davide, Stegle, Oliver, Lamond, Angus I, Meleckyte, Ruta, Moens, Natalie, Watt, Fiona M, Ouwehand, Willem H, Beales, Philip, Mirauta, Bogdan Andrei [0000-0002-9733-292X], Bonder, Marc Jan [0000-0002-8431-3180], Kilpinen, Helena [0000-0001-6692-6154], Stegle, Oliver [0000-0002-8818-7193], Lamond, Angus I [0000-0001-6204-6045], Apollo - University of Cambridge Repository, and Helsinki Institute of Life Science HiLIFE

Subjects
Male, Proteomics, Proteome, Genome-wide association study, VARIANTS, Transcriptome, 0302 clinical medicine, SCHIZOPHRENIA, Human proteome project, genetics, Disease, Biology (General), Induced pluripotent stem cell, Child, GENE-EXPRESSION, 0303 health sciences, education.field_of_study, Drug discovery, General Neuroscience, General Medicine, Middle Aged, Phenotype, Child, Preschool, Medicine, ABUNDANCE, Female, Research Article, Adult, Adolescent, Genotype, QH301-705.5, induced pluripotent stem cells, Science, Population, Quantitative Trait Loci, deleterious variants, Genomics, Computational biology, Quantitative trait locus, Biology, General Biochemistry, Genetics and Molecular Biology, DIFFERENTIAL EXPRESSION, 03 medical and health sciences, Young Adult, RESOURCE, REVEALS, genomics, Humans, human, RNA, Messenger, education, 030304 developmental biology, Aged, IDENTIFICATION, General Immunology and Microbiology, Infant, Newborn, Genetic Variation, Infant, Genetics and Genomics, QUANTIFICATION, Genetics, Population, REGULATORY VARIATION, 3111 Biomedicine, 030217 neurology & neurosurgery
Abstract

Human disease phenotypes are driven primarily by alterations in protein expression and/or function. To date, relatively little is known about the variability of the human proteome in populations and how this relates to variability in mRNA expression and to disease loci. Here, we present the first comprehensive proteomic analysis of human induced pluripotent stem cells (iPSC), a key cell type for disease modelling, analysing 202 iPSC lines derived from 151 donors, with integrated transcriptome and genomic sequence data from the same lines. We characterised the major genetic and non-genetic determinants of proteome variation across iPSC lines and assessed key regulatory mechanisms affecting variation in protein abundance. We identified 654 protein quantitative trait loci (pQTLs) in iPSCs, including disease-linked variants in protein-coding sequences and variants with trans regulatory effects. These include pQTL linked to GWAS variants that cannot be detected at the mRNA level, highlighting the utility of dissecting pQTL at peptide level resolution.

Published
2020

41. Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

Author

Cuomo, Anna S. E., Seaton, Daniel D., McCarthy, Davis J., Martinez, Iker, Bonder, Marc Jan, Garcia-Bernardo, Jose, Amatya, Shradha, Madrigal, Pedro, Isaacson, Abigail, Buettner, Florian, Knights, Andrew, Natarajan, Kedar Nath, Vallier, Ludovic, Marioni, John C., Chhatriwala, Mariya, Stegle, Oliver, Agu, Chukwuma A., Alderton, Alex, Danecek, Petr, Denton, Rachel, Durbin, Richard, Gaffney, Daniel J., Goncalves, Angela, Halai, Reena, Harper, Sarah, Kirton, Christopher M., Kolb-Kokocinski, Anja, Leha, Andreas, McCarthy, Shane A., Memari, Yasin, Patel, Minal, Birney, Ewan, Casale, Francesco Paolo, Clarke, Laura, Harrison, Peter W., Kilpinen, Helena, Streeter, Ian, Denovi, Davide, Meleckyte, Ruta, Moens, Natalie, Watt, Fiona M., Ouwehand, Willem H., Lamond, Angus I., Bensaddek, Dalila, Beales, Philip, Seaton, Daniel D. [0000-0002-5222-3893], McCarthy, Davis J. [0000-0002-2218-6833], Madrigal, Pedro [0000-0003-1959-8199], Knights, Andrew [0000-0003-2107-4175], Natarajan, Kedar Nath [0000-0002-9264-1280], Vallier, Ludovic [0000-0002-3848-2602], Marioni, John C. [0000-0001-9092-0852], and Apollo - University of Cambridge Repository

Subjects
13/31, 45/91, 631/532/2064/2158, 631/208/729/743, 45/43, article, 631/208/191, 631/208/205, 45/100, 45/15, 38/91
Abstract

Recent developments in stem cell biology have enabled the study of cell fate decisions in early human development that are impossible to study in vivo. However, understanding how development varies across individuals and, in particular, the influence of common genetic variants during this process has not been characterised. Here, we exploit human iPS cell lines from 125 donors, a pooled experimental design, and single-cell RNA-sequencing to study population variation of endoderm differentiation. We identify molecular markers that are predictive of differentiation efficiency of individual lines, and utilise heterogeneity in the genetic background across individuals to map hundreds of expression quantitative trait loci that influence expression dynamically during differentiation and across cellular contexts.

Published
2020

42. Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs

Author

Kilpinen, Helena, Goncalves, Angela, Leha, Andreas, Afzal, Vackar, Alasoo, Kaur, Ashford, Sofie, Bala, Sendu, Bensaddek, Dalila, Casale, Francesco Paolo, Culley, Oliver J., Danecek, Petr, Faulconbridge, Adam, Harrison, Peter W., Kathuria, Annie, McCarthy, Davis, McCarthy, Shane A., Meleckyte, Ruta, Memari, Yasin, Moens, Nathalie, Soares, Filipa, Mann, Alice, Streeter, Ian, Agu, Chukwuma A., Alderton, Alex, Nelson, Rachel, Harper, Sarah, Patel, Minal, White, Alistair, Patel, Sharad R., Clarke, Laura, Halai, Reena, Kirton, Christopher M., Kolb-Kokocinski, Anja, Beales, Philip, Birney, Ewan, Danovi, Davide, Lamond, Angus I., Ouwehand, Willem H., Vallier, Ludovic, Watt, Fiona M., Durbin, Richard, Stegle, Oliver, and Gaffney, Daniel J.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Helena Kilpinen; Angela Goncalves; Andreas Leha; Vackar Afzal; Kaur Alasoo; Sofie Ashford; Sendu Bala; Dalila Bensaddek; Francesco Paolo Casale; Oliver J. Culley; Petr Danecek; Adam Faulconbridge; Peter W. Harrison; [...]

Published
2017
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43. The European Nucleotide Archive in 2020

Author

Harrison, Peter W, primary, Ahamed, Alisha, additional, Aslam, Raheela, additional, Alako, Blaise T F, additional, Burgin, Josephine, additional, Buso, Nicola, additional, Courtot, Mélanie, additional, Fan, Jun, additional, Gupta, Dipayan, additional, Haseeb, Muhammad, additional, Holt, Sam, additional, Ibrahim, Talal, additional, Ivanov, Eugene, additional, Jayathilaka, Suran, additional, Balavenkataraman Kadhirvelu, Vishnukumar, additional, Kumar, Manish, additional, Lopez, Rodrigo, additional, Kay, Simon, additional, Leinonen, Rasko, additional, Liu, Xin, additional, O’Cathail, Colman, additional, Pakseresht, Amir, additional, Park, Youngmi, additional, Pesant, Stephane, additional, Rahman, Nadim, additional, Rajan, Jeena, additional, Sokolov, Alexey, additional, Vijayaraja, Senthilnathan, additional, Waheed, Zahra, additional, Zyoud, Ahmad, additional, Burdett, Tony, additional, and Cochrane, Guy, additional

Published
2020
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44. From FAANG to Fork: Application of Highly Annotated Genomes to Improve Farmed Animal Production

Author

Clark, Emily L, primary, Archibald, Alan L, additional, Daetwyler, Hans D, additional, Groenen, Martien AM, additional, Harrison, Peter W, additional, Houston, Ross D, additional, Kuehn, Christa, additional, Lien, Sigbjorn, additional, Macqueen, Daniel J, additional, Reecy, James M, additional, Robledo, Diego, additional, Watson, Mick, additional, Tuggle, Christopher K, additional, and Giuffra, Elisabetta, additional

Published
2020
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45. The European Nucleotide Archive in 2019

Author

Amid, Clara, primary, Alako, Blaise T F, additional, Balavenkataraman Kadhirvelu, Vishnukumar, additional, Burdett, Tony, additional, Burgin, Josephine, additional, Fan, Jun, additional, Harrison, Peter W, additional, Holt, Sam, additional, Hussein, Abdulrahman, additional, Ivanov, Eugene, additional, Jayathilaka, Suran, additional, Kay, Simon, additional, Keane, Thomas, additional, Leinonen, Rasko, additional, Liu, Xin, additional, Martinez-Villacorta, Josue, additional, Milano, Annalisa, additional, Pakseresht, Amir, additional, Rahman, Nadim, additional, Rajan, Jeena, additional, Reddy, Kethi, additional, Richards, Edward, additional, Smirnov, Dmitriy, additional, Sokolov, Alexey, additional, Vijayaraja, Senthilnathan, additional, and Cochrane, Guy, additional

Published
2019
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46. European Nucleotide Archive in 2021.

Author

Cummins, Carla, Ahamed, Alisha, Aslam, Raheela, Burgin, Josephine, Devraj, Rajkumar, Edbali, Ossama, Gupta, Dipayan, Harrison, Peter W, Haseeb, Muhammad, Holt, Sam, Ibrahim, Talal, Ivanov, Eugene, Jayathilaka, Suran, Kadhirvelu, Vishnukumar, Kay, Simon, Kumar, Manish, Lathi, Ankur, Leinonen, Rasko, Madeira, Fabio, and Madhusoodanan, Nandana

Published
2022
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47. The COMPARE Data Hubs

Author

Amid, Clara, Pakseresht, Nima, Silvester, Nicole, Jayathilaka, Suran, Lund, Ole, Dynovski, Lukasz D., Pataki, Bálint, Visontai, Dávid, Xavier, Basil Britto, Alako, Blaise T.F., Belka, Ariane, Cisneros, Jose L.B., Cotten, Matthew, Haringhuizen, George B., Harrison, Peter W., Höper, Dirk, Holt, Sam, Hundahl, Camilla, Hussein, Abdulrahman, Kaas, Rolf Sommer, Liu, Xin, Leinonen, Rasko, Malhotra-Kumar, Surbhi, Nieuwenhuijse, David F., Rahman, Nadim, Dos S Ribeiro, Carolina, Skiby, Jeffrey Edward, Schmitz, Dennis, Stéger, József, Szalai-Gindl, János M., Thomsen, Martin Christen Frølund, Cacciò, Simone M., Csabai, István, Kroneman, Annelies, Koopmans, Marion, Aarestrup, Frank Møller, Cochrane, Guy, Amid, Clara, Pakseresht, Nima, Silvester, Nicole, Jayathilaka, Suran, Lund, Ole, Dynovski, Lukasz D., Pataki, Bálint, Visontai, Dávid, Xavier, Basil Britto, Alako, Blaise T.F., Belka, Ariane, Cisneros, Jose L.B., Cotten, Matthew, Haringhuizen, George B., Harrison, Peter W., Höper, Dirk, Holt, Sam, Hundahl, Camilla, Hussein, Abdulrahman, Kaas, Rolf Sommer, Liu, Xin, Leinonen, Rasko, Malhotra-Kumar, Surbhi, Nieuwenhuijse, David F., Rahman, Nadim, Dos S Ribeiro, Carolina, Skiby, Jeffrey Edward, Schmitz, Dennis, Stéger, József, Szalai-Gindl, János M., Thomsen, Martin Christen Frølund, Cacciò, Simone M., Csabai, István, Kroneman, Annelies, Koopmans, Marion, Aarestrup, Frank Møller, and Cochrane, Guy

Abstract

Data sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats, often lead to data not being shared or at most shared in form of supplementary materials in journal publications. Here, we describe an informatics platform that includes workflows for structured data storage, managing and pre-publication sharing of pathogen sequencing data and its analysis interpretations with relevant stakeholders.

Published
2019

48. A Report from a Workshop of the International Stem Cell Banking Initiative, Held in Collaboration of Global Alliance for iPSC Therapies and the Harvard Stem Cell Institute, Boston, 2017

Author

Kim, Jung-Hyun, primary, Alderton, Alex, additional, Crook, Jeremy M., additional, Benvenisty, Nissim, additional, Brandsten, Catharina, additional, Firpo, Meri, additional, Harrison, Peter W., additional, Kawamata, Shin, additional, Kawase, Eihachiro, additional, Kurtz, Andreas, additional, Loring, Jeanne F., additional, Ludwig, Tenneille, additional, Man, Jennifer, additional, Mountford, Joanne C., additional, Turner, Marc L., additional, Oh, Steve, additional, da Veiga Pereira, Lygia, additional, Pranke, Patricia, additional, Sheldon, Michael, additional, Steeg, Rachel, additional, Sullivan, Stephen, additional, Yaffe, Michael, additional, Zhou, Qi, additional, and Stacey, Glyn N., additional

Published
2019
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49. The COMPARE Data Hubs

Author

Amid, Clara, primary, Pakseresht, Nima, additional, Silvester, Nicole, additional, Jayathilaka, Suran, additional, Lund, Ole, additional, Dynovski, Lukasz D., additional, Pataki, Bálint Á., additional, Visontai, Dávid, additional, Cotten, Matthew, additional, Xavier, Basil Britto, additional, Alako, Blaise, additional, Belka, Ariane, additional, Cisneros, Jose J. L., additional, Haringhuizen, George B., additional, Harrison, Peter W., additional, Höper, Dirk, additional, Holt, Sam, additional, Hundahl, Camilla, additional, Hussein, Abdulrahman, additional, Kaas, Rolf S., additional, Malhotra-Kumar, Surbhi, additional, Leinonen, Rasko, additional, Nieuwenhuijse, David F., additional, Rahman, Nadim, additional, Ribeiro, Carolina dos S, additional, Skiby, Jeffrey E., additional, Stéger, József, additional, Szalai-Gindl, János M., additional, Thomsen, Martin C. F., additional, Csabai, István, additional, Koopmans, Marion, additional, Aarestrup, Frank, additional, and Cochrane, Guy, additional

Published
2019
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50. The European Nucleotide Archive in 2018

Author

Harrison, Peter W, primary, Alako, Blaise, additional, Amid, Clara, additional, Cerdeño-Tárraga, Ana, additional, Cleland, Iain, additional, Holt, Sam, additional, Hussein, Abdulrahman, additional, Jayathilaka, Suran, additional, Kay, Simon, additional, Keane, Thomas, additional, Leinonen, Rasko, additional, Liu, Xin, additional, Martínez-Villacorta, Josué, additional, Milano, Annalisa, additional, Pakseresht, Nima, additional, Rajan, Jeena, additional, Reddy, Kethi, additional, Richards, Edward, additional, Rosello, Marc, additional, Silvester, Nicole, additional, Smirnov, Dmitriy, additional, Toribio, Ana-Luisa, additional, Vijayaraja, Senthilnathan, additional, and Cochrane, Guy, additional

Published
2018
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