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ORCIDJonathan M. Mudge
- > Home > Persons > Jonathan M. Mudge
Publications
- 2023
[j14]Fergal J. Martin
, M. Ridwan Amode, Alisha Aneja, Olanrewaju Austine-Orimoloye, Andrey G. Azov, If Barnes, Arne Becker, Ruth Bennett, Andrew E. Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Alexandra Bignell, Sanjay Boddu, Paulo R. B. Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Mehrnaz Charkhchi, Alexander Cockburn, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Jayantilal Dodiya, Sarah M. Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos García-Girón, Thiago Augusto Lopes Genez, Gurpreet S. Ghattaoraya, Jose Gonzalez Martinez, Cristi Guijarro, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike P. Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Diego Marques-Coelho, José Carlos Marugán, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N. Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Pilizota, Irina Prosovetskaia, José G. Pérez-Silva, Ahamed Imran Abdul Salam, Nuno Saraiva-Agostinho, Helen Schuilenburg, Dan Sheppard, Swati Sinha, Botond Sipos, William Stark, Emily Steed, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Michal Szpak, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A. Walsh, Brandon Walts, Elizabeth Wass, Natalie L. Willhoft, Jamie Allen, Jorge Álvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jane E. Loveland, Benjamin Moore, Jonathan M. Mudge, John G. Tate, David Thybert, Stephen J. Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E. Hunt, Magali Ruffier, Fiona Cunningham, Sarah Dyer, Robert D. Finn, Kevin L. Howe, Peter W. Harrison, Andrew D. Yates, Paul Flicek:
Ensembl 2023. Nucleic Acids Res. 51(D1): 933-941 (2023)- [j13]Adam Frankish, Silvia Carbonell Sala, Mark Diekhans, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Carme Arnan, If Barnes, Abhimanyu Banerjee, Ruth Bennett, Andrew E. Berry, Alexandra Bignell, Carles Boix, Ferriol Calvet Riera, Daniel Cerdán-Vélez, Fiona Cunningham, Claire Davidson, Sarah M. Donaldson, Cagatay Dursun, Reham Fatima, Stefano Giorgetti, Carlos García-Girón, Jose M. Gonzalez, Matthew Hardy, Peter W. Harrison, Thibaut Hourlier, Zoe Hollis, Toby Hunt, Benjamin James, Yunzhe Jiang, Rory Johnson, Mike P. Kay, Julien Lagarde, Fergal J. Martin, Laura Martínez Gómez, Surag Nair, Pengyu Ni, Fernando Pozo, Vivek Ramalingam, Magali Ruffier, Bianca M. Schmitt, Jacob M. Schreiber, Emily Steed, Marie-Marthe Suner, Dulika Sumathipala, Irina Sycheva, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T. Yang, Andrew D. Yates, Zahoor Zafrulla, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L. Tress, Paul Flicek:
GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 51(D1): 942-949 (2023) - 2022
- [j12]Fiona Cunningham, James E. Allen, Jamie Allen, Jorge Álvarez-Jarreta, M. Ridwan Amode, Irina M. Armean, Olanrewaju Austine-Orimoloye, Andrey G. Azov, If Barnes, Ruth Bennett, Andrew E. Berry, Jyothish Bhai, Alexandra Bignell, Konstantinos Billis, Sanjay Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla A. Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Jayantilal Dodiya, Sarah M. Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos García-Girón, Thiago A. L. Genez, Jose Gonzalez Martinez, Cristina Guijarro-Clarke, Arthur Gymer, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Thomas Juettemann, Vinay Kaikala, Mike P. Kay, Ilias Lavidas, Tuan Le, Diana Lemos, José Carlos Marugán, Shamika Mohanan, Aleena Mushtaq, Marc Naven, Denye N. Oheh, Anne Parker, Andrew Parton, Malcolm Perry, Ivana Pilizota, Irina Prosovetskaia, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Dan Sheppard, José G. Pérez-Silva, William Stark, Emily Steed, Kyösti Sutinen, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Michal Szpak, Anja Thormann, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A. Walsh, Brandon Walts, Natalie L. Willhoft, Andrea Winterbottom, Elizabeth Wass, Marc Chakiachvili, Bethany Flint, Adam Frankish, Stefano Giorgetti, Leanne Haggerty, Sarah E. Hunt, Garth IIsley, Jane E. Loveland, Fergal J. Martin, Benjamin Moore, Jonathan M. Mudge, Matthieu Muffato, Emily Perry, Magali Ruffier, John G. Tate, David Thybert, Stephen J. Trevanion, Sarah Dyer, Peter W. Harrison, Kevin L. Howe, Andrew D. Yates, Daniel R. Zerbino, Paul Flicek:
Ensembl 2022. Nucleic Acids Res. 50(D1): 988-995 (2022) - 2021
- [j11]Blake A. Sweeney, Anton I. Petrov, Carlos Eduardo Ribas, Robert D. Finn, Alex Bateman, Maciej Szymanski, Wojciech M. Karlowski, Stefan E. Seemann, Jan Gorodkin, Jamie J. Cannone, Robin Ray Gutell, Simon Kay, Steven J. Marygold, Gilberto dos Santos, Adam Frankish, Jonathan M. Mudge, Ruth Barshir, Simon Fishilevich, Patricia P. Chan, Todd M. Lowe, Ruth L. Seal, Elspeth A. Bruford, Simona Panni, Pablo Porras, Dimitra Karagkouni, Artemis G. Hatzigeorgiou, Lina Ma, Zhang Zhang, Pieter-Jan Volders, Pieter Mestdagh, Sam Griffiths-Jones, Bastian Fromm, Kevin J. Peterson, Ioanna Kalvari, Eric P. Nawrocki, Anton S. Petrov, Shuai Weng, Philia Bouchard-Bourelle, Michelle S. Scott, Lauren M. Lui, David Hoksza, Ruth C. Lovering, Barbara Kramarz, Prita Mani, Sridhar Ramachandran, Zasha Weinberg:
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res. 49(Database-Issue): D212-D220 (2021) - [j10]Kevin L. Howe, Premanand Achuthan, James E. Allen, Jamie Allen, Jorge Álvarez-Jarreta, M. Ridwan Amode, Irina M. Armean, Andrey G. Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Mehrnaz Charkhchi, Carla A. Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Jayantilal Dodiya, Bilal El Houdaigui, Reham Fatima, Astrid Gall, Carlos García-Girón, Tiago Grego, Cristina Guijarro-Clarke, Leanne Haggerty, Anmol Hemrom, Thibaut Hourlier, Osagie G. Izuogu, Thomas Juettemann, Vinay Kaikala, Mike P. Kay, Ilias Lavidas, Tuan Le, Diana Lemos, Jose Gonzalez Martinez, José Carlos Marugán, Thomas Maurel, Aoife C. McMahon, Shamika Mohanan, Benjamin Moore, Matthieu Muffato, Denye N. Oheh, Dimitrios Paraschas, Anne Parker, Andrew Parton, Irina Prosovetskaia, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Dan Sheppard, Emily Steed, Michal Szpak, Marek Szuba, Kieron R. Taylor, Anja Thormann, Glen Threadgold, Brandon Walts, Andrea Winterbottom, Marc Chakiachvili, Ameya Chaubal, Nishadi De Silva, Bethany Flint, Adam Frankish, Sarah E. Hunt, Garth IIsley, Nick Langridge, Jane E. Loveland, Fergal J. Martin, Jonathan M. Mudge, Joannella Morales, Emily Perry, Magali Ruffier, John G. Tate, David Thybert, Stephen J. Trevanion, Fiona Cunningham, Andrew D. Yates, Daniel R. Zerbino, Paul Flicek:
Ensembl 2021. Nucleic Acids Res. 49(Database-Issue): D884-D891 (2021) - [j9]Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew E. Berry, Alexandra Bignell, Carles Boix, Silvia Carbonell Sala, Fiona Cunningham, Tomás Di Domenico, Sarah M. Donaldson, Ian T. Fiddes, Carlos García-Girón, Jose M. Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Kevin L. Howe, Toby Hunt, Osagie G. Izuogu, Rory Johnson, Fergal J. Martin, Laura Martínez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Ferriol Calvet Riera, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Maxim Y. Wolf, Jinrui Xu, Yucheng T. Yang, Andrew D. Yates, Daniel R. Zerbino, Yan Zhang, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Michael L. Tress, Paul Flicek:
GENCODE 2021. Nucleic Acids Res. 49(Database-Issue): D916-D923 (2021) - 2020
- [j8]Andrew D. Yates, Premanand Achuthan, Wasiu A. Akanni, James E. Allen, Jamie Allen, Jorge Álvarez-Jarreta, M. Ridwan Amode, Irina M. Armean, Andrey G. Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, José Carlos Marugán, Carla A. Cummins, Claire Davidson, Kamalkumar Jayantilal Dodiya, Reham Fatima, Astrid Gall, Carlos García-Girón, Laurent Gil, Tiago Grego, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G. Izuogu, Sophie H. Janacek, Thomas Juettemann, Mike P. Kay, Ilias Lavidas, Tuan Le, Diana Lemos, Jose Gonzalez Martinez, Thomas Maurel, Mark D. McDowall, Aoife McMahon, Shamika Mohanan, Benjamin Moore, Michael Nuhn, Denye N. Oheh, Anne Parker, Andrew Parton, Mateus Patricio, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Dan Sheppard, Mira Sycheva, Marek Szuba, Kieron R. Taylor, Anja Thormann, Glen Threadgold, Alessandro Vullo, Brandon Walts, Andrea Winterbottom, Amonida Zadissa, Marc Chakiachvili, Bethany Flint, Adam Frankish, Sarah E. Hunt, Garth IIsley, Myrto Kostadima, Nick Langridge, Jane E. Loveland, Fergal J. Martin, Joannella Morales, Jonathan M. Mudge, Matthieu Muffato, Emily Perry, Magali Ruffier, Stephen J. Trevanion, Fiona Cunningham, Kevin L. Howe, Daniel R. Zerbino, Paul Flicek:
Ensembl 2020. Nucleic Acids Res. 48(Database-Issue): D682-D688 (2020) - 2019
- [j7]Fiona Cunningham, Premanand Achuthan, Wasiu A. Akanni, James E. Allen, M. Ridwan Amode, Irina M. Armean, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Carla A. Cummins, Claire Davidson, Kamalkumar Jayantilal Dodiya, Astrid Gall, Carlos García-Girón, Laurent Gil, Tiago Grego, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G. Izuogu, Sophie H. Janacek, Thomas Juettemann, Mike P. Kay, Matthew R. Laird, Ilias Lavidas, Zhicheng Liu, Jane E. Loveland, José Carlos Marugán, Thomas Maurel, Aoife C. McMahon, Benjamin Moore, Joannella Morales, Jonathan M. Mudge, Michael Nuhn, Denye N. Ogeh, Anne Parker, Andrew Parton, Mateus Patricio, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Daniel Sheppard, Helen Sparrow, Eloise Stapleton, Marek Szuba, Kieron R. Taylor, Glen Threadgold, Anja Thormann, Alessandro Vullo, Brandon Walts, Andrea Winterbottom, Amonida Zadissa, Marc Chakiachvili, Adam Frankish, Sarah E. Hunt, Myrto Kostadima, Nick Langridge, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Daniel M. Staines, Stephen J. Trevanion, Bronwen L. Aken, Andrew D. Yates, Daniel R. Zerbino, Paul Flicek:
Ensembl 2019. Nucleic Acids Res. 47(Database-Issue): D745-D751 (2019) - [j6]Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew E. Berry, Alexandra Bignell, Silvia Carbonell Sala, Jacqueline Chrast, Fiona Cunningham, Tomás Di Domenico, Sarah M. Donaldson, Ian T. Fiddes, Carlos García-Girón, Jose M. Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Toby Hunt, Osagie G. Izuogu, Julien Lagarde, Fergal J. Martin, Laura Martínez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Jinrui Xu, Andrew D. Yates, Daniel R. Zerbino, Yan Zhang, Bronwen L. Aken, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Alexandre Reymond, Michael L. Tress, Paul Flicek:
GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 47(Database-Issue): D766-D773 (2019) - 2018
- [j5]Shashikant Pujar, Nuala A. O'Leary, Catherine M. Farrell, Jane E. Loveland, Jonathan M. Mudge, Craig Wallin, Carlos García-Girón, Mark Diekhans, If Barnes, Ruth Bennett, Andrew E. Berry, Eric Cox, Claire Davidson, Tamara Goldfarb, Jose M. Gonzalez, Toby Hunt, John Jackson, Vinita S. Joardar, Mike P. Kay, Vamsi K. Kodali, Fergal J. Martin, Monica McAndrews, Kelly M. McGarvey, Michael R. Murphy, Bhanu Rajput, Sanjida H. Rangwala, Lillian D. Riddick, Ruth L. Seal, Marie-Marthe Suner, David Webb, Yunxia Sophia Zhu, Bronwen L. Aken, Elspeth A. Bruford, Carol J. Bult, Adam Frankish, Terence D. Murphy, Kim D. Pruitt:
Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation. Nucleic Acids Res. 46(Database-Issue): D221-D228 (2018) - [j4]Daniel R. Zerbino, Premanand Achuthan, Wasiu A. Akanni, M. Ridwan Amode, Daniel Barrell, Jyothish Bhai, Konstantinos Billis, Carla A. Cummins, Astrid Gall, Carlos García-Girón, Laurent Gil, Leo Gordon, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G. Izuogu, Sophie H. Janacek, Thomas Juettemann, Jimmy Kiang To, Matthew R. Laird, Ilias Lavidas, Zhicheng Liu, Jane E. Loveland, Thomas Maurel, William M. McLaren, Benjamin Moore, Jonathan M. Mudge, Daniel N. Murphy, Victoria Newman, Michael Nuhn, Denye N. Ogeh, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Helen Schuilenburg, Daniel Sheppard, Helen Sparrow, Kieron R. Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Amonida Zadissa, Adam Frankish, Sarah E. Hunt, Myrto Kostadima, Nicholas Langridge, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Daniel M. Staines, Stephen J. Trevanion, Bronwen L. Aken, Fiona Cunningham, Andrew D. Yates, Paul Flicek:
Ensembl 2018. Nucleic Acids Res. 46(Database-Issue): D754-D761 (2018) - 2014
- [j3]Jennifer L. Harrow, Charles A. Steward, Adam Frankish, James G. R. Gilbert, Jose M. Gonzalez, Jane E. Loveland, Jonathan M. Mudge, Daniel Sheppard, Mark Thomas, Stephen J. Trevanion, Laurens G. Wilming:
NAR Breakthrough Article: The Vertebrate Genome Annotation browser 10 years on. Nucleic Acids Res. 42(Database-Issue): 771-779 (2014) - [j2]Catherine M. Farrell, Nuala A. O'Leary, Rachel A. Harte, Jane E. Loveland, Laurens G. Wilming, Craig Wallin, Mark Diekhans, Daniel Barrell, Stephen M. J. Searle, Bronwen L. Aken, Susan M. Hiatt, Adam Frankish, Marie-Marthe Suner, Bhanu Rajput, Charles A. Steward, Garth R. Brown, Ruth Bennett, Michael R. Murphy, Wendy Wu, Mike P. Kay, Jennifer Hart, Jeena Rajan, Janet Weber, Catherine Snow, Lillian D. Riddick, Toby Hunt, David Webb, Mark Thomas, Pamela Tamez, Sanjida H. Rangwala, Kelly M. McGarvey, Shashikant Pujar, Andrei Shkeda, Jonathan M. Mudge, Jose M. Gonzalez, James G. R. Gilbert, Stephen J. Trevanion, Robert Baertsch, Jennifer L. Harrow, Tim J. P. Hubbard, James M. Ostell, David Haussler, Kim D. Pruitt:
Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res. 42(Database-Issue): 865-872 (2014) - 2012
- [j1]Adam Frankish, Jonathan M. Mudge, Mark Thomas, Jennifer L. Harrow:
The importance of identifying alternative splicing in vertebrate genome annotation. Database J. Biol. Databases Curation 2012 (2012)
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