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Michael Tress
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An integrated encyclopedia of DNA elements in the human genome
ENCODE Project Consortium
Nature 489 (7414), 57, 2012
124902012
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Management Group Liefer Laura A. 51 Wetterstrand Kris A. 51 Good Peter J. 51 ...
nature 447 (7146), 799-816, 2007
57702007
GENCODE: the reference human genome annotation for The ENCODE Project
J Harrow, A Frankish, JM Gonzalez, E Tapanari, M Diekhans, ...
Genome research 22 (9), 1760-1774, 2012
47352012
GENCODE reference annotation for the human and mouse genomes
A Frankish, M Diekhans, AM Ferreira, R Johnson, I Jungreis, J Loveland, ...
Nucleic acids research 47 (D1), D766-D773, 2019
19592019
A user's guide to the encyclopedia of DNA elements (ENCODE)
ENCODE Project Consortium
PLoS biology 9 (4), e1001046, 2011
13812011
Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes
I Ezkurdia, D Juan, JM Rodriguez, A Frankish, M Diekhans, J Harrow, ...
Human molecular genetics 23 (22), 5866-5878, 2014
7082014
Expanded encyclopaedias of DNA elements in the human and mouse genomes
JE Moore, MJ Purcaro, HE Pratt, CB Epstein, N Shoresh, J Adrian, T Kawli, ...
Nature 583 (7818), 699-710, 2020
6662020
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Y Jiang, TR Oron, WT Clark, AR Bankapur, D D’Andrea, R Lepore, ...
Genome biology 17 (1), 1-19, 2016
3582016
GENCODE 2021
A Frankish, M Diekhans, I Jungreis, J Lagarde, JE Loveland, JM Mudge, ...
Nucleic acids research 49 (D1), D916-D923, 2021
2812021
Alternative splicing may not be the key to proteome complexity
ML Tress, F Abascal, A Valencia
Trends in biochemical sciences 42 (2), 98-110, 2017
2712017
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ...
Genome biology 20 (1), 1-23, 2019
2482019
The implications of alternative splicing in the ENCODE protein complement
ML Tress, PL Martelli, A Frankish, GA Reeves, JJ Wesselink, C Yeats, ...
Proceedings of the National Academy of Sciences 104 (13), 5495-5500, 2007
2432007
SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
M Tardaguila, L De La Fuente, C Marti, C Pereira, FJ Pardo-Palacios, ...
Genome research 28 (3), 396-411, 2018
2292018
APPRIS: annotation of principal and alternative splice isoforms
JM Rodriguez, P Maietta, I Ezkurdia, A Pietrelli, JJ Wesselink, G Lopez, ...
Nucleic acids research 41 (D1), D110-D117, 2013
2152013
Progress and challenges in predicting protein–protein interaction sites
I Ezkurdia, L Bartoli, P Fariselli, R Casadio, A Valencia, ML Tress
Briefings in bioinformatics 10 (3), 233-246, 2009
1992009
Assessment of predictions submitted for the CASP6 comparative modeling category
M Tress, I Ezkurdia, O Grana, G López, A Valencia
Proteins: Structure, Function, and Bioinformatics 61 (S7), 27-45, 2005
1642005
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts
M Frenkel-Morgenstern, V Lacroix, I Ezkurdia, Y Levin, A Gabashvili, ...
Genome research 22 (7), 1231-1242, 2012
1602012
Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure
DT Jones, M Tress, K Bryson, C Hadley
Proteins: Structure, Function, and Bioinformatics 37 (S3), 104-111, 1999
1351999
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
F Abascal, A Corvelo, F Cruz, JL Villanueva-Cañas, A Vlasova, ...
Genome biology 17 (1), 1-19, 2016
1342016
Expanded encyclopaedias of DNA elements in the human and mouse genomes
ENCODE Project Consortium
Nature 583 (7818), 699-710, 2020
1312020
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