Identifying individuals using proteomics: are we there yet?

por Fierro-Monti, Ivo, Wright, James C., Choudhary, Jyoti S., Vizcaíno, Juan Antonio
Publicado 2022

Flexible Data Analysis Pipeline for High-Confidence Proteogenomics

por Weisser, Hendrik, Wright, James C., Mudge, Jonathan M., Gutenbrunner, Petra, Choudhary, Jyoti S.
Publicado 2016

Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation()

por Collins, Mark O., Wright, James C., Jones, Matthew, Rayner, Julian C., Choudhary, Jyoti S.
Publicado 2014

Enhanced Peptide Identification by Electron Transfer Dissociation Using an Improved Mascot Percolator

por Wright, James C., Collins, Mark O., Yu, Lu, Käll, Lukas, Brosch, Markus, Choudhary, Jyoti S.
Publicado 2012

Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon

por Khan, Yousuf A., Jungreis, Irwin, Wright, James C., Mudge, Jonathan M., Choudhary, Jyoti S., Firth, Andrew E., Kellis, Manolis
Publicado 2020

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

por Wright, James C., Mudge, Jonathan, Weisser, Hendrik, Barzine, Mitra P., Gonzalez, Jose M., Brazma, Alvis, Choudhary, Jyoti S., Harrow, Jennifer
Publicado 2016

A Survey of Clinical Usage of Non-steroidal Intra-Articular Therapeutics by Equine Practitioners

por Velloso Alvarez, Ana, Boone, Lindsey H., Braim, Amy Poulin, Taintor, Jenifer S., Caldwell, Fred, Wright, James C., Wooldridge, Anne A.
Publicado 2020

Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

por Wright, James C, Sugden, Deana, Francis-McIntyre, Sue, Riba-Garcia, Isabel, Gaskell, Simon J, Grigoriev, Igor V, Baker, Scott E, Beynon, Robert J, Hubbard, Simon J
Publicado 2009

The Citrobacter rodentium type III secretion system effector EspO affects mucosal damage repair and antimicrobial responses

por Berger, Cedric N., Crepin, Valerie F., Roumeliotis, Theodoros I., Wright, James C., Serafini, Nicolas, Pevsner-Fischer, Meirav, Yu, Lu, Elinav, Eran, Di Santo, James P., Choudhary, Jyoti S., Frankel, Gad
Publicado 2018

Using Deep Learning to Extrapolate Protein Expression Measurements

por Barzine, Mitra Parissa, Freivalds, Karlis, Wright, James C., Opmanis, Mārtiņš, Rituma, Darta, Ghavidel, Fatemeh Zamanzad, Jarnuczak, Andrew F., Celms, Edgars, Čerāns, Kārlis, Jonassen, Inge, Lace, Lelde, Antonio Vizcaíno, Juan, Choudhary, Jyoti Sharma, Brazma, Alvis, Viksna, Juris
Publicado 2020

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

por Mudge, Jonathan M., Jungreis, Irwin, Hunt, Toby, Gonzalez, Jose Manuel, Wright, James C., Kay, Mike, Davidson, Claire, Fitzgerald, Stephen, Seal, Ruth, Tweedie, Susan, He, Liang, Waterhouse, Robert M., Li, Yue, Bruford, Elspeth, Choudhary, Jyoti S., Frankish, Adam, Kellis, Manolis
Publicado 2019

Citrobacter rodentium Subverts ATP Flux and Cholesterol Homeostasis in Intestinal Epithelial Cells In Vivo

por Berger, Cedric N., Crepin, Valerie F., Roumeliotis, Theodoros I., Wright, James C., Carson, Danielle, Pevsner-Fischer, Meirav, Furniss, R. Christopher D., Dougan, Gordon, Dori-Bachash, Mally, Yu, Lu, Clements, Abigail, Collins, James W., Elinav, Eran, Larrouy-Maumus, Gerald J., Choudhary, Jyoti S., Frankel, Gad
Publicado 2017

The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium

por Côté, Richard G., Griss, Johannes, Dianes, José A., Wang, Rui, Wright, James C., van den Toorn, Henk W.P., van Breukelen, Bas, Heck, Albert J. R., Hulstaert, Niels, Martens, Lennart, Reisinger, Florian, Csordas, Attila, Ovelleiro, David, Perez-Rivevol, Yasset, Barsnes, Harald, Hermjakob, Henning, Vizcaíno, Juan Antonio
Publicado 2012

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells

por Roumeliotis, Theodoros I., Williams, Steven P., Gonçalves, Emanuel, Alsinet, Clara, Del Castillo Velasco-Herrera, Martin, Aben, Nanne, Ghavidel, Fatemeh Zamanzad, Michaut, Magali, Schubert, Michael, Price, Stacey, Wright, James C., Yu, Lu, Yang, Mi, Dienstmann, Rodrigo, Guinney, Justin, Beltrao, Pedro, Brazma, Alvis, Pardo, Mercedes, Stegle, Oliver, Adams, David J., Wessels, Lodewyk, Saez-Rodriguez, Julio, McDermott, Ultan, Choudhary, Jyoti S.
Publicado 2017

Interferon-driven alterations of the host’s amino acid metabolism in the pathogenesis of typhoid fever

por Blohmke, Christoph J., Darton, Thomas C., Jones, Claire, Suarez, Nicolas M., Waddington, Claire S., Angus, Brian, Zhou, Liqing, Hill, Jennifer, Clare, Simon, Kane, Leanne, Mukhopadhyay, Subhankar, Schreiber, Fernanda, Duque-Correa, Maria A., Wright, James C., Roumeliotis, Theodoros I., Yu, Lu, Choudhary, Jyoti S., Mejias, Asuncion, Ramilo, Octavio, Shanyinde, Milensu, Sztein, Marcelo B., Kingsley, Robert A., Lockhart, Stephen, Levine, Myron M., Lynn, David J., Dougan, Gordon, Pollard, Andrew J.
Publicado 2016

GENCODE 2021

por Frankish, Adam, Diekhans, Mark, Jungreis, Irwin, Lagarde, Julien, Loveland, Jane E, Mudge, Jonathan M, Sisu, Cristina, Wright, James C, Armstrong, Joel, Barnes, If, Berry, Andrew, Bignell, Alexandra, Boix, Carles, Carbonell Sala, Silvia, Cunningham, Fiona, Di Domenico, Tomás, Donaldson, Sarah, Fiddes, Ian T, García Girón, Carlos, Gonzalez, Jose Manuel, Grego, Tiago, Hardy, Matthew, Hourlier, Thibaut, Howe, Kevin L, Hunt, Toby, Izuogu, Osagie G, Johnson, Rory, Martin, Fergal J, Martínez, Laura, Mohanan, Shamika, Muir, Paul, Navarro, Fabio C P, Parker, Anne, Pei, Baikang, Pozo, Fernando, Riera, Ferriol Calvet, Ruffier, Magali, Schmitt, Bianca M, Stapleton, Eloise, Suner, Marie-Marthe, Sycheva, Irina, Uszczynska-Ratajczak, Barbara, Wolf, Maxim Y, Xu, Jinuri, Yang, Yucheng T, Yates, Andrew, Zerbino, Daniel, Zhang, Yan, Choudhary, Jyoti S, Gerstein, Mark, Guigó, Roderic, Hubbard, Tim J P, Kellis, Manolis, Paten, Benedict, Tress, Michael L, Flicek, Paul
Publicado 2020

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

por Frankish, Adam, Carbonell-Sala, Sílvia, 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, Cerdán-Vélez, Daniel, Cunningham, Fiona, Davidson, Claire, Donaldson, Sarah, Dursun, Cagatay, Fatima, Reham, Giorgetti, Stefano, Giron, Carlos Garcıa, 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, Gómez, Laura Martínez, 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
Publicado 2022