Jonathan M. Mudge - Publications, H-index & Citations

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Jonathan M. Mudge

hinxton

43H-index

107Paper Count

2.8WCitation Count

Published Papers 55

Publication Date

Author Correction: Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics

Nature Communications

IF15.7

2026-06-02

OAAI

Aaron Wacholder; Eric W. Deutsch; Leron W. Kok; Jip T. van Dinter; Jiwon Lee; James C. Wright; Sebastien Leblanc; Ayodya H. Jayatissa; Kevin Jiang; Ihor Arefiev; Kevin Cao; Francis Bourassa; Felix-Antoine Trifiro; Michal Bassani-Sternberg; Pavel V. Baranov; Annelies Bogaert; Sonia Chothani; Ivo Fierro-Monti; Daria Fijalkowska; Kris Gevaert; Norbert Hubner; Jonathan M. Mudge; Jorge Ruiz-Orera; Jana Schulz; Juan Antonio Vizcaíno; John R. Prensner; Marie A. Brunet; Thomas F. Martinez; Sarah A. Slavoff; Xavier Roucou; Jyoti S. Choudhary; Sebastiaan van Heesch; Robert L. Moritz; Anne-Ruxandra Carvunis

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Human SRD5A1 as a case of gene expression indel-resistance in triple-coding region

Genome Biology

IF9.4

2026-05-18

OAAI

Martina M. Yordanova; Jack A. S. Tierney; Kyle A. Meiklejohn; Conor Slattery; Michał I. Świrski; Mirriam Baranova-Gurvich; Manon Engels; Oscar Ting; Ananth Prakash; Håkon Tjeldnes; Jonathan M. Mudge; Gary Loughran; Juan Antonio Vizcaíno; Dmitry E. Andreev; Pavel V. Baranov

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Expanding the human proteome with microproteins and peptideins

Nature

IF48.5

2026-05-01

PREAI

Deutsch, Eric W.; Kok, Leron W.; Mudge, Jonathan M.; Valls, Cristian F.; Jungreis, Irwin; Ruiz-Orera, Jorge; Sun, Zhi; Kusebauch, Ulrike; Fierro-Monti, Ivo; Abelin, Jennifer G.; Alba, M. Mar; Aspden, Julie L.; Bandyopadhyay, Sreejan; Banerjee, Kaushik; Baranov, Pavel V.; Bazzini, Ariel A.; Bourassa, Francis; Bruford, Elspeth A.; Calviello, Lorenzo; Carr, Steven A.; Carvunis, Anne-Ruxandra; Chothani, Sonia; Clauwaert, Jim; Dean, Kellie; Faridi, Pouya; Frankish, Adam; Goodale, Amy; Green, Thomas; Hubner, Norbert; Ingolia, Nicholas T.; Kellis, Manolis; Magrane, Michele; Martin, Maria Jesus; Martinez, Thomas F.; Menschaert, Gerben; Ohler, Uwe; Orchard, Sandra; Potter, Alisa; Rackham, Owen J. L.; Rees, Matthew G.; Root, David E.; Roth, Jennifer A.; Roucou, Xavier; Sialana, Fernando J.; Slavoff, Sarah A.; Swirski, Michal I.; Tierney, Jack A. S.; Trifiro, Felix-Antoine; Valen, Eivind; Vasylieva, Valeriia; Wacholder, Aaron; Wang, Shengbo; Wang, Li; Weissman, Jonathan S.; Wu, Wei; Choudhary, Jyoti S.; Bassani-Sternberg, Michal; Vizcaino, Juan Antonio; Ternette, Nicola; Brunet, Marie A.; Moritz, Robert L.; Prensner, John R.; van Heesch, Sebastiaan

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An expanded reference catalog of translated open reading frames for biomedical research

Nucleic Acids Research

IF13.1

2026-04-13

PREAI

Chothani, Sonia; Ruiz-Orera, Jorge; Tierney, Jack A. S.; Swirski, Michal, I; Tjeldnes, Hakon; Kok, Leron W.; Clauwaert, Jim; Deutsch, Eric W.; Alba, M. Mar; Aspden, Julie L.; Baranov, Pavel, V; Bazzini, Ariel Alejandro; Bruford, Elspeth A.; Brunet, Marie A.; Cardon, Tristan; Carvunis, Anne-Ruxandra; Casola, Claudio; Choudhary, Jyoti Sharma; Dean, Kellie; Faridi, Pouya; Fierro-Monti, Ivo; Fournier, Isabelle; Frankish, Adam; Gerstein, Mark; Hubner, Norbert; Jiang, Yunzhe; Kellis, Manolis; Martinez, Thomas F.; Menschaert, Gerben; Ni, Pengyu; Orchard, Sandra; Roucou, Xavier; Rozowsky, Joel; Salzet, Michel; Siragusa, Mauro; Slavoff, Sarah; Ternette, Nicola; Vizcaino, Juan Antonio; Wacholder, Aaron; Wu, Wei; Xie, Zhi; Yang, Yucheng T.; Moritz, Robert L.; Valen, Eivind; Mudge, Jonathan; van Heesch, Sebastiaan; Prensner, John R.; Rackham, Owen J. L.

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Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics

Nature Communications

IF15.7

2026-01-21

OAAI

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The 2025 Report on the Human Proteome from the HUPO Human Proteome Project

Journal of Proteome Research

IF3.6

2026-01-05

PREAI

Eric W. Deutsch; Cecilia Lindskog; Bogdan Budnik; Claudia Ctortecka; Tiannan Guo; Charles Pineau; Gong Zhang; Marie Andken; Clarissa Zheng; Zhi Sun; Jonathan M. Mudge; Sandra Orchard; Christopher M. Overall; Nicolle H. Packer; Susan T. Weintraub; Michael H. A. Roehrl; Edouard Nice; Jennifer E. Van Eyk; Uwe Völker; Nuno Bandeira; Ruedi Aebersold; Robert L. Moritz; Gilbert S. Omenn

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Ensembl 2026

NUCLEIC ACIDS RESEARCH

IF13.1

2025-11-01

OAAI

Yates, Andrew D.; Austine-Orimoloye, Olanrewaju; Azov, Andrey G.; Barba, Matthieu; Barnes, If; Barrera-Enriquez, Vianey Paola; Becker, Arne; Bennett, Ruth; Berry, Andrew; Bhai, Jyothish; Bhurji, Simarpreet Kaur; Branco Lins, Paulo R.; Brooks, Lucy; Budhanuru Ramaraju, Shashank; Campbell, Lahcen, I; Carbajo Martinez, Manuel; Carpenter, Jack; Charkhchi, Mehrnaz; Cortes, Lucas A.; Davidson, Claire; Dickson, Suzanna; Dodiya, Kamalkumar; Donaldson, Sarah; El Houdaigui, Bilal; El Naboulsi, Tamara; Fairbrother-Browne, Aine; Falola, Oluwadamilare; Fatima, Reham; Gonzalez Martinez, Jose; Gurbich, Tatiana; Hall, Holly; Hardy, Matthew; Hollis, Zoe; Hunt, Toby; Kay, Mike; Kaikala, Vinay; Lazar, Anna; Lemos, Diana; Lodha, Disha; Mathlouthi, Nourhen; Merino, Gabriela A.; Merritt, Ryan; Mirabueno, Louisse Paola; Mushtaq, Aleena; Nakib Hossain, Syed; Perez-Silva, Jose G.; Pilizota, Ivana; Poppleton, Daniel; Prosovetskaia, Irina; Raj, Shriya; Salam, Ahamed Imran Abdul; Saraf, Shradha; Sinha, Swati; Sipos, Botond; Sitnik, Vasily; Suner, Marie-Marthe; Surapaneni, Likhitha; Tierney, Jack A. S.; Urbina-Gomez, David; Veidenberg, Andres; Walsh, Thomas A.; Allen, Jamie M.; Alvarez-Jarreta, Jorge; Cheema, Jitender; Batista da Rocha, Jorge; De silva, Nishadi H.; Tricomi, Francesca Floriana; Giorgetti, Stefano; Ilsley, Garth R.; Keatley, Jon; Loveland, Jane E.; Mudge, Jonathan M.; Naamati, Guy; Tate, John; Willhoft, Natalie L.; Winterbottom, Andrea; Flint, Bethany R.; Frankish, Adam; Haggerty, Leanne; Hunt, Sarah E.; Clark, Emily L.; Dyer, Sarah C.; Freeberg, Mallory A.; Martin, Fergal J.; Finn, Robert D.

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Programmed ribosomal frameshifting during PLEKHM2 mRNA decoding generates a constitutively active proteoform that supports myocardial function

Science Advances

IF12.5

2025-10-24

PREAI

Gary Loughran; Raffaella De Pace; Ningyu Ding; Jianchao Zhang; Irwin Jungreis; Gionmattia Carancini; Jonathan M. Mudge; Ji Wang; Manolis Kellis; John F. Atkins; Pavel V. Baranov; Andrew E. Firth; Xiaowei Li; Juan S. Bonifacino; Yousuf A. Khan

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Ensembl 2025

NUCLEIC ACIDS RESEARCH

IF13.1

2024-12-04

OAAI

Dyer, Sarah C.; Austine-Orimoloye, Olanrewaju; Azov, Andrey G.; Barba, Matthieu; Barnes, If; Barrera-Enriquez, Vianey Paola; Becker, Arne; Bennett, Ruth; Beracochea, Martin; Berry, Andrew; Bhai, Jyothish; Bhurji, Simarpreet Kaur; Boddu, Sanjay; Lins, Paulo R. Branco; Brooks, Lucy; Ramaraju, Shashank Budhanuru; Campbell, Lahcen, I; Martinez, Manuel Carbajo; Charkhchi, Mehrnaz; Cortes, Lucas A.; Davidson, Claire; Denni, Sukanya; Dodiya, Kamalkumar; Donaldson, Sarah; El Houdaigui, Bilal; El Naboulsi, Tamara; Falola, Oluwadamilare; Fatima, Reham; Genez, Thiago; Martinez, Jose Gonzalez; Gurbich, Tatiana; Hardy, Matthew; Hollis, Zoe; Hunt, Toby; Kay, Mike; Kaykala, Vinay; Lemos, Diana; Lodha, Disha; Mathlouthi, Nourhen; Merino, Gabriela Alejandra; Merritt, Ryan; Mirabueno, Louisse Paola; Mushtaq, Aleena; Hossain, Syed Nakib; Perez-Silva, Jose G.; Perry, Malcolm; Pilizota, Ivana; Poppleton, Daniel; Prosovetskaia, Irina; Raj, Shriya; Salam, Ahamed Imran Abdul; Saraf, Shradha; Saraiva-Agostinho, Nuno; Sinha, Swati; Sipos, Botond; Sitnik, Vasily; Steed, Emily; Suner, Marie-Marthe; Surapaneni, Likhitha; Sutinen, Kyosti; Tricomi, Francesca Floriana; Tsang, Ian; Urbina-Gomez, David; Veidenberg, Andres; Walsh, Thomas A.; Willhoft, Natalie L.; Allen, Jamie; Alvarez-Jarreta, Jorge; Chakiachvili, Marc; Cheema, Jitender; da Rocha, Jorge Batista; De Silva, Nishadi H.; Giorgetti, Stefano; Haggerty, Leanne; Ilsley, Garth R.; Keatley, Jon; Loveland, Jane E.; Moore, Benjamin; Mudge, Jonathan M.; Naamati, Guy; Tate, John; Trevanion, Stephen J.; Winterbottom, Andrea; Flint, Bethany; Frankish, Adam; Hunt, Sarah E.; Finn, Robert D.; Freeberg, Mallory A.; Harrison, Peter W.; Martin, Fergal J.; Yates, Andrew D.

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The 2024 Report on the Human Proteome from the HUPO Human Proteome Project

JOURNAL OF PROTEOME RESEARCH

IF3.6

2024-11-08

PREAI

Omenn, Gilbert S.; Orchard, Sandra; Lane, Lydie; Lindskog, Cecilia; Pineau, Charles; Overall, Christopher M.; Budnik, Bogdan; Mudge, Jonathan M.; Packer, Nicolle H.; Weintraub, Susan T.; Roehrl, Michael H. A.; Nice, Edouard; Guo, Tiannan; Van Eyk, Jennifer E.; Voelker, Uwe; Zhang, Gong; Bandeira, Nuno; Aebersold, Ruedi; Moritz, Robert L.; Deutsch, Eric W.

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Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

NATURE METHODS

IF32.1

2024-06-07

OAAI

Pardo-Palacios, Francisco J.; Wang, Dingjie; Reese, Fairlie; Diekhans, Mark; Carbonell-Sala, Silvia; Williams, Brian; Loveland, Jane E.; De Maria, Maite; Adams, Matthew S.; Balderrama-Gutierrez, Gabriela; Behera, Amit K.; Gonzalez Martinez, Jose M.; Hunt, Toby; Lagarde, Julien; Liang, Cindy E.; Li, Haoran; Meade, Marcus Jerryd; Moraga Amador, David A.; Prjibelski, Andrey D.; Birol, Inanc; Bostan, Hamed; Brooks, Ashley M.; Celik, Muhammed Hasan; Chen, Ying; Du, Mei R. M.; Felton, Colette; Goeke, Jonathan; Hafezqorani, Saber; Herwig, Ralf; Kawaji, Hideya; Lee, Joseph; Li, Jian-Liang; Lienhard, Matthias; Mikheenko, Alla; Mulligan, Dennis; Nip, Ka Ming; Pertea, Mihaela; Ritchie, Matthew E.; Sim, Andre D.; Tang, Alison D.; Wan, Yuk Kei; Wang, Changqing; Wong, Brandon Y.; Yang, Chen; Barnes, If; Berry, Andrew E.; Capella-Gutierrez, Salvador; Cousineau, Alyssa; Dhillon, Namrita; Fernandez-Gonzalez, Jose M.; Ferrandez-Peral, Luis; Garcia-Reyero, Natalia; Goetz, Stefan; Hernandez-Ferrer, Carles; Kondratova, Liudmyla; Liu, Tianyuan; Martinez-Martin, Alessandra; Menor, Carlos; Mestre-Tomas, Jorge; Mudge, Jonathan M.; Panayotova, Nedka G.; Paniagua, Alejandro; Repchevsky, Dmitry; Ren, Xingjie; Rouchka, Eric; Saint-John, Brandon; Sapena, Enrique; Sheynkman, Leon; Smith, Melissa Laird; Suner, Marie-Marthe; Takahashi, Hazuki; Youngworth, Ingrid A.; Carninci, Piero; Denslow, Nancy D.; Guigo, Roderic; Hunter, Margaret E.; Maehr, Rene; Shen, Yin; Tilgner, Hagen U.; Wold, Barbara J.; Vollmers, Christopher; Frankish, Adam; Au, Kin Fai; Sheynkman, Gloria M.; Mortazavi, Ali; Conesa, Ana; Brooks, Angela N.

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Ribosome decision graphs for the representation of eukaryotic RNA translation complexity

GENOME RESEARCH

IF5.5

2024-05-07

OAAI

Tierney, Jack A. S.; Swirski, Michal; Tjeldnes, Hakon; Mudge, Jonathan M.; Kufel, Joanna; Whiffin, Nicola; Valen, Eivind; Baranov, Pavel V.

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CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

GENOME BIOLOGY

IF9.4

2024-02-22

OAAI

Jain, Shantanu; Bakolitsa, Constantina; Brenner, Steven E.; Radivojac, Predrag; Moult, John; Repo, Susanna; Hoskins, Roger A.; Andreoletti, Gaia; Barsky, Daniel; Chellapan, Ajithavalli; Chu, Hoyin; Dabbiru, Navya; Kollipara, Naveen K.; Ly, Melissa; Neumann, Andrew J.; Pal, Lipika R.; Odell, Eric; Pandey, Gaurav; Peters-Petrulewicz, Robin C.; Srinivasan, Rajgopal; Yee, Stephen F.; Yeleswarapu, Sri Jyothsna; Zuhl, Maya; Adebali, Ogun; Patra, Ayoti; Beer, Michael A.; Hosur, Raghavendra; Peng, Jian; Bernard, Brady M.; Berry, Michael; Dong, Shengcheng; Boyle, Alan P.; Adhikari, Aashish; Chen, Jingqi; Hu, Zhiqiang; Wang, Robert; Wang, Yaqiong; Miller, Maximilian; Wang, Yanran; Bromberg, Yana; Turina, Paola; Capriotti, Emidio; Han, James J.; Ozturk, Kivilcim; Carter, Hannah; Babbi, Giulia; Bovo, Samuele; Di Lena, Pietro; Martelli, Pier Luigi; Savojardo, Castrense; Casadio, Rita; Cline, Melissa S.; De Baets, Greet; Bonache, Sandra; Diez, Orland; Gutierrez-Enriquez, Sara; Fernandez, Alejandro; Montalban, Gemma; Ootes, Lars; Ozkan, Selen; Padilla, Natalia; Riera, Casandra; De la Cruz, Xavier; Diekhans, Mark; Huwe, Peter J.; Wei, Qiong; Xu, Qifang; Dunbrack, Roland L.; Gotea, Valer; Elnitski, Laura; Margolin, Gennady; Fariselli, Piero; Kulakovskiy, Ivan V.; Makeev, Vsevolod J.; Penzar, Dmitry D.; Vorontsov, Ilya E.; Favorov, Alexander V.; Forman, Julia R.; Hasenahuer, Marcia; Fornasari, Maria S.; Parisi, Gustavo; Avsec, Ziga; Celik, Muhammed H.; Thi Yen Duong Nguyen; Gagneur, Julien; Shi, Fang-Yuan; Edwards, Matthew D.; Guo, Yuchun; Tian, Kevin; Zeng, Haoyang; Gifford, David K.; Goke, Jonathan; Zaucha, Jan; Gough, Julian; Ritchie, Graham R. S.; Frankish, Adam; Mudge, Jonathan M.; Harrow, Jennifer; Young, Erin L.; Yu, Yao; Huff, Chad D.; Murakami, Katsuhiko; Nagai, Yoko; Imanishi, Tadashi; Mungall, Christopher J.; Jacobsen, Julius O. B.; Kim, Dongsup; Jeong, Chan-Seok; Jones, David T.; Li, Mulin Jun; Guthrie, Violeta Beleva; Bhattacharya, Rohit; Chen, Yun-Ching; Douville, Christopher; Fan, Jean; Kim, Dewey; Masica, David; Niknafs, Noushin; Sengupta, Sohini; Tokheim, Collin; Turner, Tychele N.; Yeo, Hui Ting Grace; Karchin, Rachel; Shin, Sunyoung; Welch, Rene; Keles, Sunduz; Li, Yue; Kellis, Manolis; Corbi-Verge, Carles; Strokach, Alexey V.; Kim, Philip M.; Klein, Teri E.; Mohan, Rahul; Sinnott-Armstrong, Nicholas A.; Wainberg, Michael; Kundaje, Anshul; Gonzaludo, Nina; Mak, Angel C. Y.; Chhibber, Aparna; Lam, Hugo Y. K.; Dahary, Dvir; Fishilevich, Simon; Lancet, Doron; Lee, Insuk; Bachman, Benjamin; Katsonis, Panagiotis; Lua, Rhonald C.; Wilson, Stephen J.; Lichtarge, Olivier; Bhat, Rajendra R.; Sundaram, Laksshman; Viswanath, Vivek; Bellazzi, Riccardo; Nicora, Giovanna; Rizzo, Ettore; Limongelli, Ivan; Mezlini, Aziz M.; Chang, Ray; Kim, Serra; Lai, Carmen; O'Connor, Robert; Topper, Scott; van den Akker, Jeroen; Zhou, Alicia Y.; Zimmer, Anjali D.; Mishne, Gilad; Bergquist, Timothy R.; Breese, Marcus R.; Guerrero, Rafael F.; Jiang, Yuxiang; Kiga, Nikki; Li, Biao; Mort, Matthew; Pagel, Kymberleigh A.; Pejaver, Vikas; Stamboulian, Moses H.; Thusberg, Janita; Mooney, Sean D.; Teerakulkittipong, Nuttinee; Cao, Chen; Kundu, Kunal; Yin, Yizhou; Yu, Chen-Hsin; Kleyman, Michael; Lin, Chiao-Feng; Stackpole, Mary; Mount, Stephen M.; Eraslan, Gokcen; Mueller, Nikola S.; Naito, Tatsuhiko; Rao, Aliz R.; Azaria, Johnathan R.; Brodie, Aharon; Ofran, Yanay; Garg, Aditi; Pal, Debnath; Hawkins-Hooker, Alex; Kenlay, Henry; Reid, John; Mucaki, Eliseos J.; Rogan, Peter K.; Schwarz, Jana M.; Searls, David B.; Lee, Gyu Rie; Seok, Chaok; Kramer, Andreas; Shah, Sohela; Huang, ChengLai V.; Kirsch, Jack F.; Shatsky, Maxim; Cao, Yue; Chen, Haoran; Karimi, Mostafa; Moronfoye, Oluwaseyi; Sun, Yuanfei; Shen, Yang; Shigeta, Ron; Ford, Colby T.; Nodzak, Conor; Uppal, Aneeta; Shi, Xinghua; Joseph, Thomas; Kotte, Sujatha; Rana, Sadhna; Rao, Aditya; Saipradeep, V. G.; Sivadasan, Naveen; Sunderam, Uma; Stanke, Mario; Su, Andrew; Adzhubey, Ivan; Jordan, Daniel M.; Sunyaev, Shamil; Rousseau, Frederic; Schymkowitz, Joost; Van Durme, Joost; Tavtigian, Sean V.; Carraro, Marco; Giollo, Manuel; Tosatto, Silvio C. E.; Adato, Orit; Carmel, Liran; Cohen, Noa E.; Fenesh, Izila; Holtzer, Iamar; Juven-Gershon, Tamar; Unger, Ron; Niroula, Abhishek; Olatubosun, Ayodeji; Valiaho, Jouni; Yang, Yang; Vihinen, Mauno; Wahl, Mary E.; Chang, Billy; Chong, Ka Chun; Hu, Inchi; Sun, Rui; Wu, William Ka Kei; Xia, Xiaoxuan; Zee, Benny C.; Wang, Maggie H.; Wang, Meng; Wu, Chunlei; Lu, Yutong; Chen, Ken; Yang, Yuedong; Yates, Christopher M.; Kreimer, Anat; Yan, Zhongxia; Yosef, Nir; Zhao, Huying; Wei, Zhipeng; Yao, Zhaomin; Zhou, Fengfeng; Folkman, Lukas; Zhou, Yaoqi; Daneshjou, Roxana; Altman, Russ B.; Inoue, Fumitaka; Ahituv, Nadav; Arkin, Adam P.; Lovisa, Federica; Bonvini, Paolo; Bowdin, Sarah; Gianni, Stefano; Mantuano, Elide; Minicozzi, Velia; Novak, Leonore; Pasquo, Alessandra; Pastore, Annalisa; Petrosino, Maria; Puglisi, Rita; Toto, Angelo; Veneziano, Liana; Chiaraluce, Roberta; Ball, Mad P.; Bobe, Jason R.; Church, George M.; Consalvi, Valerio; Mort, Matthew; Cooper, David N.; Buckley, Bethany A.; Sheridan, Molly B.; Cutting, Garry R.; Scaini, Maria Chiara; Cygan, Kamil J.; Fredericks, Alger M.; Glidden, David T.; Neil, Christopher; Rhine, Christy L.; Fairbrother, William G.; Alontaga, Aileen Y.; Fenton, Aron W.; Matreyek, Kenneth A.; Starita, Lea M.; Fowler, Douglas M.; Loescher, Britt-Sabina; Franke, Andre; Adamson, Scott I.; Graveley, Brenton R.; Gray, Joe W.; Malloy, Mary J.; Kane, John P.; Kousi, Maria; Katsanis, Nicholas; Schubach, Max; Kircher, Martin; Tang, Paul L. F.; Kwok, Pui-Yan; Lathrop, Richard H.; Clark, Wyatt T.; Yu, Guoying K.; LeBowitz, Jonathan H.; Benedicenti, Francesco; Bettella, Elisa; Bigoni, Stefania; Cesca, Federica; Mammi, Isabella; Marino-Bus-Ije, Cristina; Milani, Donatella; Peron, Angela; Polli, Roberta; Sartori, Stefano; Stanzial, Franco; Ioldo, Irene; Turolla, Licia; Aspromonte, Maria C.; Bellini, Mariagrazia; Leonardi, Emanuela; Liu, Xiaoming; Marshall, Christian; McCombie, W. Richard; Elefanti, Lisa; Menin, Chiara; Meyn, M. Stephen; Murgia, Alessandra; Nadeau, Kari C. Y.; Neuhausen, Susan L.; Nussbaum, Robert L.; Pirooznia, Mehdi; Potash, James B.; Dimster-Denk, Dago F.; Rine, Jasper D.; Sanford, Jeremy R.; Snyder, Michael; Tavtigian, Sean V.; Cole, Alina G.; Sun, Song; Verby, Marta W.; Weile, Jochen; Roth, Frederick P.; Tewhey, Ryan; Sabeti, Pardis C.; Campagna, Joan; Refaat, Marwan M.; Wojciak, Julianne; Grubb, Soren; Schmitt, Nicole; Shendure, Jay; Spurdle, Amanda B.; Stavropoulos, Dimitri J.; Walton, Nephi A.; Zandi, Peter P.; Ziv, Elad; Burke, Wylie; Chen, Flavia; Carr, Lawrence R.; Martinez, Selena; Paik, Jodi; Harris-Wai, Julie; Yarborough, Mark; Fullerton, Stephanie M.; Koenig, Barbara A.; McInnes, Gregory; Shigaki, Dustin; Chandonia, John-Marc; Furutsuki, Mabel; Kasak, Laura; Yu, Changhua; Chen, Rui; Cline, Melissa S.; Pandey, Gaurav; Friedberg, Iddo; Getz, Gad A.; Cong, Qian; Kinch, Lisa N.; Zhang, Jing; Grishin, Nick V.; Voskanian, Alin; Kann, Maricel G.; Clark, Wyatt T.; Tran, Elizabeth; Ioannidis, Nilah M.; Hunter, Jesse M.; Udani, Rupa; Cai, Binghuang; Morgan, Alexander A.; Sokolov, Artem; Stuart, Joshua M.; Tavtigian, Sean V.; Minervini, Giovanni; Monzon, Alexander M.; Batzoglou, Serafim; Butte, Atul J.; Church, George M.; Greenblatt, Marc S.; Hart, Reece K.; Hernandez, Ryan; Hubbard, Tim J. P.; Kahn, Scott; O'Donnell-Luria, Anne; Ng, Pauline C.; Shon, John; Tavtigian, Sean V.; Veltman, Joris; Zook, Justin M.

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Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals (vol 15, 228, 2024)

NATURE COMMUNICATIONS

IF15.7

2024-01-03

OAAI

Fedorova, Alla D.; Kiniry, Stephen J.; Andreev, Dmitry E.; Mudge, Jonathan M.; Baranov, Pavel V.

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Ensembl 2024

NUCLEIC ACIDS RESEARCH

IF13.1

2023-11-11

OAAI

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

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What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?

MOLECULAR & CELLULAR PROTEOMICS

IF5.5

2023-09-01

OAAI

Prensner, John R.; Abelin, Jennifer G.; Kok, Leron W.; Clauser, Karl R.; Mudge, Jonathan M.; Ruiz-Orera, Jorge; -Sternberg, Michal Bassani; Moritz, Robert L.; Deutsch, Eric W.; van Heesch, Sebastiaan

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Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames

MOLECULAR CELL

IF16.6

2023-03-01

OAAI

Sandmann, Clara-L.; Schulz, Jana F.; Ruiz-Orera, Jorge; Kirchner, Marieluise; Ziehm, Matthias; Adami, Eleonora; Marczenke, Maike; Christ, Annabel; Liebe, Nina; Greiner, Johannes; Schoenenberger, Aaron; Muecke, Michael B.; Liang, Ning; Moritz, Robert L.; Sun, Zhi; Deutsch, Eric W.; Gotthardt, Michael; Mudge, Jonathan M.; Prensner, John R.; Willnow, Thomas E.; Mertins, Philipp; van Heesch, Sebastiaan; Hubner, Norbert

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SCN1A: bioinformatically informed revised boundaries for promoter and enhancer regions

HUMAN MOLECULAR GENETICS

IF3.2

2023-01-28

OAAI

Pagni, Susanna; Custodio, Helena Martins; Frankish, Adam; Mudge, Jonathan M.; Mills, James D.; Sisodiya, Sanjay M.

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Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals

NATURE COMMUNICATIONS

IF15.7

2022-12-23

OAAI

Fedorova, Alla D.; Kiniry, Stephen J.; Andreev, Dmitry E.; Mudge, Jonathan M.; Baranov, Pavel V.

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

NUCLEIC ACIDS RESEARCH

IF13.1

2022-11-24

OAAI

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

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Research Directions