Creating reference gene annotation for the mouse C57BL6/J genome assembly

por Mudge, Jonathan M., Harrow, Jennifer
Publicado 2015

Functional transcriptomics in the post-ENCODE era

por Mudge, Jonathan M., Frankish, Adam, Harrow, Jennifer
Publicado 2013

The importance of identifying alternative splicing in vertebrate genome annotation

por Frankish, Adam, Mudge, Jonathan M., Thomas, Mark, Harrow, Jennifer
Publicado 2012

Functional signatures of evolutionarily young CTCF binding sites

por Azazi, Dhoyazan, Mudge, Jonathan M., Odom, Duncan T., Flicek, Paul
Publicado 2020

Flexible Data Analysis Pipeline for High-Confidence Proteogenomics

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

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

por Fedorova, Alla D., Kiniry, Stephen J., Andreev, Dmitry E., Mudge, Jonathan M., Baranov, Pavel V.
Publicado 2022

SCN1A: bioinformatically informed revised boundaries for promoter and enhancer regions

por Pagni, Susanna, Custodio, Helena Martins, Frankish, Adam, Mudge, Jonathan M, Mills, James D, Sisodiya, Sanjay M
Publicado 2023

Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation

por Martinez-Gomez, Laura, Abascal, Federico, Jungreis, Irwin, Pozo, Fernando, Kellis, Manolis, Mudge, Jonathan M, Tress, Michael L
Publicado 2019

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

Ribosome Decision Graphs for the Representation of Eukaryotic RNA Translation Complexity

por Tierney, Jack A. S., Świrski, Michał, Tjeldnes, Håkon, Mudge, Jonathan M., Kufel, Joanna, Whiffin, Nicola, Valen, Eivind, Baranov, Pavel V.
Publicado 2023

The Origins, Evolution, and Functional Potential of Alternative Splicing in Vertebrates

por Mudge, Jonathan M., Frankish, Adam, Fernandez-Banet, Julio, Alioto, Tyler, Derrien, Thomas, Howald, Cédric, Reymond, Alexandre, Guigó, Roderic, Hubbard, Tim, Harrow, Jennifer
Publicado 2011

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

por Frankish, Adam, Uszczynska, Barbara, Ritchie, Graham RS, Gonzalez, Jose M, Pervouchine, Dmitri, Petryszak, Robert, Mudge, Jonathan M, Fonseca, Nuno, Brazma, Alvis, Guigo, Roderic, Harrow, Jennifer
Publicado 2015

Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice

por Mudge, Jonathan M, Armstrong, Stuart D, McLaren, Karen, Beynon, Robert J, Hurst, Jane L, Nicholson, Christine, Robertson, Duncan H, Wilming, Laurens G, Harrow, Jennifer L
Publicado 2008

Molecular complexity of the major urinary protein system of the Norway rat, Rattus norvegicus

por Gómez-Baena, Guadalupe, Armstrong, Stuart D., Halstead, Josiah O., Prescott, Mark, Roberts, Sarah A., McLean, Lynn, Mudge, Jonathan M., Hurst, Jane L., Beynon, Robert J.
Publicado 2019

What can Ribo-seq and proteomics tell us about the non-canonical proteome?

por Prensner, John R., Abelin, Jennifer G., Kok, Leron W., Clauser, Karl R., Mudge, Jonathan M., Ruiz-Orera, Jorge, Bassani-Sternberg, Michal, Deutsch, Eric W., van Heesch, Sebastiaan
Publicado 2023

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

por Prensner, John R., Abelin, Jennifer G., Kok, Leron W., Clauser, Karl R., Mudge, Jonathan M., Ruiz-Orera, Jorge, Bassani-Sternberg, Michal, Moritz, Robert L., Deutsch, Eric W., van Heesch, Sebastiaan
Publicado 2023

Genome‐wide association study: Exploring the genetic basis for responsiveness to ketogenic dietary therapies for drug‐resistant epilepsy

por Schoeler, Natasha E., Leu, Costin, Balestrini, Simona, Mudge, Jonathan M., Steward, Charles A., Frankish, Adam, Leung, Mary‐Anne, Mackay, Mark, Scheffer, Ingrid, Williams, Ruth, Sander, Josemir W., Cross, J. Helen, Sisodiya, Sanjay M.
Publicado 2018

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

Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq)

por Lagarde, Julien, Uszczynska-Ratajczak, Barbara, Santoyo-Lopez, Javier, Gonzalez, Jose Manuel, Tapanari, Electra, Mudge, Jonathan M., Steward, Charles A., Wilming, Laurens, Tanzer, Andrea, Howald, Cédric, Chrast, Jacqueline, Vela-Boza, Alicia, Rueda, Antonio, Lopez-Domingo, Francisco J., Dopazo, Joaquin, Reymond, Alexandre, Guigó, Roderic, Harrow, Jennifer
Publicado 2016

Transcript expression-aware annotation improves rare variant interpretation

por Cummings, Beryl B., Karczewski, Konrad J., Kosmicki, Jack A., Seaby, Eleanor G., Watts, Nicholas A., Singer-Berk, Moriel, Mudge, Jonathan M., Karjalainen, Juha, Satterstrom, F. Kyle, O’Donnell-Luria, Anne H., Poterba, Timothy, Seed, Cotton, Solomonson, Matthew, Alföldi, Jessica, Daly, Mark J., MacArthur, Daniel G.
Publicado 2020