| Year |
Citation |
Score |
| 2024 |
Cerdán-Vélez D, Tress ML. The T2T-CHM13 reference assembly uncovers essential WASH1 and GPRIN2 paralogues. Bioinformatics Advances. 4: vbae029. PMID 38464973 DOI: 10.1093/bioadv/vbae029 |
0.339 |
|
| 2022 |
Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, Arnan C, Barnes I, Banerjee A, Bennett R, Berry A, Bignell A, Boix C, ... ... Tress ML, et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Research. PMID 36420896 DOI: 10.1093/nar/gkac1071 |
0.351 |
|
| 2022 |
Rodriguez JM, Pozo F, Cerdán-Vélez D, Di Domenico T, Vázquez J, Tress ML. APPRIS: selecting functionally important isoforms. Nucleic Acids Research. 50: D54-D59. PMID 34755885 DOI: 10.1093/nar/gkab1058 |
0.393 |
|
| 2021 |
Pozo F, Martinez-Gomez L, Walsh TA, Rodriguez JM, Di Domenico T, Abascal F, Vazquez J, Tress ML. Assessing the functional relevance of splice isoforms. Nar Genomics and Bioinformatics. 3: lqab044. PMID 34046593 DOI: 10.1093/nargab/lqab044 |
0.359 |
|
| 2020 |
Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, ... ... Tress ML, et al. GENCODE 2021. Nucleic Acids Research. PMID 33270111 DOI: 10.1093/nar/gkaa1087 |
0.343 |
|
| 2020 |
Martinez-Gomez L, Abascal F, Jungreis I, Pozo F, Kellis M, Mudge JM, Tress ML. Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation. Nar Genomics and Bioinformatics. 2: lqz023. PMID 31886458 DOI: 10.1093/nargab/lqz023 |
0.313 |
|
| 2019 |
Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, ... ... Tress ML, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. 20: 244. PMID 31744546 DOI: 10.1186/S13059-019-1835-8 |
0.314 |
|
| 2018 |
Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, ... ... Tress ML, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Research. PMID 30357393 DOI: 10.1093/Nar/Gky955 |
0.32 |
|
| 2018 |
Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, et al. Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Research. 28: 1096. PMID 29967126 DOI: 10.1101/Gr.239137.118 |
0.317 |
|
| 2018 |
Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, et al. SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Research. PMID 29440222 DOI: 10.1101/Gr.222976.117 |
0.378 |
|
| 2017 |
Rodriguez JM, Rodriguez-Rivas J, Di Domenico T, Vázquez J, Valencia A, Tress ML. APPRIS 2017: principal isoforms for multiple gene sets. Nucleic Acids Research. PMID 29069475 DOI: 10.1093/Nar/Gkx997 |
0.535 |
|
| 2017 |
Tress ML, Abascal F, Valencia A. Most Alternative Isoforms Are Not Functionally Important. Trends in Biochemical Sciences. 42: 408-410. PMID 28483377 DOI: 10.1016/J.Tibs.2017.04.002 |
0.499 |
|
| 2016 |
Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, ... ... Tress ML, et al. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biology. 17: 251. PMID 27964752 DOI: 10.1186/S13059-016-1090-1 |
0.401 |
|
| 2016 |
Tress ML, Abascal F, Valencia A. Alternative Splicing May Not Be the Key to Proteome Complexity. Trends in Biochemical Sciences. PMID 27712956 DOI: 10.1016/J.Tibs.2016.08.008 |
0.542 |
|
| 2016 |
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, ... ... Tress ML, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 17: 184. PMID 27604469 DOI: 10.1186/S13059-016-1037-6 |
0.512 |
|
| 2015 |
Ezkurdia I, Calvo E, Del Pozo A, Vázquez J, Valencia A, Tress ML. The potential clinical impact of the release of two drafts of the human proteome. Expert Review of Proteomics. 12: 579-593. PMID 26496066 DOI: 10.1586/14789450.2015.1103186 |
0.461 |
|
| 2015 |
Abascal F, Ezkurdia I, Rodriguez-Rivas J, Rodriguez JM, Del Pozo A, Vázquez J, Valencia A, Tress ML. Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. Plos Computational Biology. 11: e1004325. PMID 26061177 DOI: 10.1371/Journal.Pcbi.1004325 |
0.537 |
|
| 2015 |
Rodriguez JM, Carro A, Valencia A, Tress ML. APPRIS WebServer and WebServices. Nucleic Acids Research. PMID 25990727 DOI: 10.1093/Nar/Gkv512 |
0.548 |
|
| 2015 |
Abascal F, Tress ML, Valencia A. The evolutionary fate of alternatively spliced homologous exons after gene duplication. Genome Biology and Evolution. 7: 1392-403. PMID 25931610 DOI: 10.1093/Gbe/Evv076 |
0.481 |
|
| 2015 |
Ezkurdia I, Vázquez J, Valencia A, Tress M. Correction to "Analyzing the first drafts of the human proteome". Journal of Proteome Research. 14: 1991. PMID 25756922 DOI: 10.1021/Acs.Jproteome.5B00186 |
0.461 |
|
| 2015 |
Abascal F, Tress ML, Valencia A. Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals. Bioinformatics (Oxford, England). PMID 25735770 DOI: 10.1093/Bioinformatics/Btv132 |
0.52 |
|
| 2015 |
Ezkurdia I, Rodriguez JM, Carrillo-de Santa Pau E, Vázquez J, Valencia A, Tress ML. Most highly expressed protein-coding genes have a single dominant isoform. Journal of Proteome Research. 14: 1880-7. PMID 25732134 DOI: 10.1021/Pr501286B |
0.542 |
|
| 2014 |
Ezkurdia I, Vázquez J, Valencia A, Tress M. Analyzing the first drafts of the human proteome. Journal of Proteome Research. 13: 3854-5. PMID 25014353 DOI: 10.1021/Pr500572Z |
0.529 |
|
| 2014 |
Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A, Tress ML. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Human Molecular Genetics. 23: 5866-78. PMID 24939910 DOI: 10.1093/Hmg/Ddu309 |
0.517 |
|
| 2014 |
Maietta P, Lopez G, Carro A, Pingilley BJ, Leon LG, Valencia A, Tress ML. FireDB: a compendium of biological and pharmacologically relevant ligands. Nucleic Acids Research. 42: D267-72. PMID 24243844 DOI: 10.1093/Nar/Gkt1127 |
0.451 |
|
| 2013 |
Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, Valencia A, Tress ML. APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Research. 41: D110-7. PMID 23161672 DOI: 10.1093/Nar/Gks1058 |
0.576 |
|
| 2012 |
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, ... ... Tress M, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Research. 22: 1760-74. PMID 22955987 DOI: 10.1101/Gr.135350.111 |
0.572 |
|
| 2012 |
Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R, Valencia A. Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Genome Research. 22: 1231-42. PMID 22588898 DOI: 10.1101/Gr.130062.111 |
0.494 |
|
| 2012 |
Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML. Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. Molecular Biology and Evolution. 29: 2265-83. PMID 22446687 DOI: 10.1093/Molbev/Mss100 |
0.577 |
|
| 2012 |
Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, ... ... Tress ML, et al. Evidence for transcript networks composed of chimeric RNAs in human cells. Plos One. 7: e28213. PMID 22238572 DOI: 10.1371/Journal.Pone.0028213 |
0.476 |
|
| 2011 |
Ezkurdia I, Tress ML. Protein structural domains: definition and prediction. Current Protocols in Protein Science / Editorial Board, John E. Coligan ... [Et Al.]. Unit2.14. PMID 22045561 DOI: 10.1002/0471140864.ps0214s66 |
0.302 |
|
| 2011 |
Lopez G, Maietta P, Rodriguez JM, Valencia A, Tress ML. firestar--advances in the prediction of functionally important residues. Nucleic Acids Research. 39: W235-41. PMID 21672959 DOI: 10.1093/Nar/Gkr437 |
0.508 |
|
| 2010 |
Tress ML, Valencia A. Predicted residue-residue contacts can help the scoring of 3D models. Proteins. 78: 1980-91. PMID 20408174 DOI: 10.1002/Prot.22714 |
0.45 |
|
| 2010 |
Searle S, Frankish A, Bignell A, Aken B, Derrien T, Diekhans M, Harte R, Howald C, Kokocinski F, Lin M, Tress M, Van Baren M, Barnes I, Hunt T, Carvalho-Silva D, et al. The GENCODE human gene set Genome Biology. 11: P36. DOI: 10.1186/Gb-2010-11-S1-P36 |
0.509 |
|
| 2009 |
Ezkurdia I, Bartoli L, Fariselli P, Casadio R, Valencia A, Tress ML. Progress and challenges in predicting protein-protein interaction sites. Briefings in Bioinformatics. 10: 233-46. PMID 19346321 DOI: 10.1093/Bib/Bbp021 |
0.499 |
|
| 2009 |
Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S. Sequence-based feature prediction and annotation of proteins. Genome Biology. 10: 206. PMID 19226438 DOI: 10.1186/Gb-2009-10-2-206 |
0.539 |
|
| 2009 |
Bignell A, Frankish A, Aken B, Diekhans M, Kokocinski F, Lin M, Tress M, Baren JV, Barnes I, Hunt T, Carvalho-Silva D, Davidson C, Donaldson S, Gilbert J, Hart E, et al. GENCODE: Creating a Validated Manually Annotated Geneset for the Whole Human Genome Nature Precedings. 4: 1-1. DOI: 10.1038/Npre.2009.3155.1 |
0.348 |
|
| 2008 |
Tress ML, Bodenmiller B, Aebersold R, Valencia A. Proteomics studies confirm the presence of alternative protein isoforms on a large scale. Genome Biology. 9: R162. PMID 19017398 DOI: 10.1186/gb-2008-9-11-r162 |
0.517 |
|
| 2008 |
Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A. Determination and validation of principal gene products. Bioinformatics (Oxford, England). 24: 11-7. PMID 18006548 DOI: 10.1093/Bioinformatics/Btm547 |
0.546 |
|
| 2007 |
Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo JH, Lee J, Baker D, Chivian D, Kim D, Ezkurdia I. Assessment of predictions submitted for the CASP7 domain prediction category. Proteins. 69: 137-51. PMID 17680686 DOI: 10.1002/Prot.21675 |
0.359 |
|
| 2007 |
Izarzugaza JM, Graña O, Tress ML, Valencia A, Clarke ND. Assessment of intramolecular contact predictions for CASP7. Proteins. 69: 152-8. PMID 17671976 DOI: 10.1002/Prot.21637 |
0.472 |
|
| 2007 |
Clarke ND, Ezkurdia I, Kopp J, Read RJ, Schwede T, Tress M. Domain definition and target classification for CASP7. Proteins. 69: 10-8. PMID 17654725 DOI: 10.1002/Prot.21686 |
0.342 |
|
| 2007 |
López G, Rojas A, Tress M, Valencia A. Assessment of predictions submitted for the CASP7 function prediction category. Proteins. 69: 165-74. PMID 17654548 DOI: 10.1002/prot.21651 |
0.498 |
|
| 2007 |
López G, Valencia A, Tress ML. firestar--prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Research. 35: W573-7. PMID 17584799 DOI: 10.1093/Nar/Gkm297 |
0.499 |
|
| 2007 |
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Tress ML, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874 |
0.501 |
|
| 2007 |
Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, et al. The implications of alternative splicing in the ENCODE protein complement. Proceedings of the National Academy of Sciences of the United States of America. 104: 5495-500. PMID 17372197 DOI: 10.1073/Pnas.0700800104 |
0.537 |
|
| 2007 |
Lopez G, Valencia A, Tress M. FireDB--a database of functionally important residues from proteins of known structure. Nucleic Acids Research. 35: D219-23. PMID 17132832 DOI: 10.1093/Nar/Gkl897 |
0.49 |
|
| 2006 |
Carro A, Tress M, de Juan D, Pazos F, Lopez-Romero P, del Sol A, Valencia A, Rojas AM. TreeDet: a web server to explore sequence space. Nucleic Acids Research. 34: W110-5. PMID 16844971 DOI: 10.1093/Nar/Gkl203 |
0.466 |
|
| 2006 |
Tress ML, Cozzetto D, Tramontano A, Valencia A. An analysis of the Sargasso Sea resource and the consequences for database composition. Bmc Bioinformatics. 7: 213. PMID 16623953 DOI: 10.1186/1471-2105-7-213 |
0.472 |
|
| 2005 |
Graña O, Baker D, MacCallum RM, Meiler J, Punta M, Rost B, Tress ML, Valencia A. CASP6 assessment of contact prediction. Proteins. 61: 214-24. PMID 16187364 DOI: 10.1002/Prot.20739 |
0.461 |
|
| 2005 |
Tress M, Ezkurdia I, Graña O, López G, Valencia A. Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins. 61: 27-45. PMID 16187345 DOI: 10.1002/Prot.20720 |
0.53 |
|
| 2005 |
Tress M, Tai CH, Wang G, Ezkurdia I, López G, Valencia A, Lee B, Dunbrack RL. Domain definition and target classification for CASP6. Proteins. 61: 8-18. PMID 16187342 DOI: 10.1002/Prot.20717 |
0.498 |
|
| 2005 |
Tress M, de Juan D, Graña O, Gómez MJ, Gómez-Puertas P, González JM, López G, Valencia A. Scoring docking models with evolutionary information. Proteins. 60: 275-80. PMID 15981273 DOI: 10.1002/Prot.20570 |
0.57 |
|
| 2005 |
Contreras-Moreira B, Ezkurdia I, Tress ML, Valencia A. Empirical limits for template-based protein structure prediction: the CASP5 example. Febs Letters. 579: 1203-7. PMID 15710414 DOI: 10.1016/J.Febslet.2005.01.014 |
0.483 |
|
| 2004 |
Tress ML, Graña O, Valencia A. SQUARE--determining reliable regions in sequence alignments. Bioinformatics (Oxford, England). 20: 974-5. PMID 14764569 DOI: 10.1093/Bioinformatics/Bth032 |
0.482 |
|
| 2003 |
Tress ML, Jones D, Valencia A. Predicting reliable regions in protein alignments from sequence profiles. Journal of Molecular Biology. 330: 705-18. PMID 12850141 DOI: 10.1016/S0022-2836(03)00622-3 |
0.502 |
|
| 1999 |
Jones DT, Tress M, Bryson K, Hadley C. Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure. Proteins. 104-11. PMID 10526358 DOI: 10.1002/(Sici)1097-0134(1999)37:3+<104::Aid-Prot14>3.0.Co;2-P |
0.429 |
|
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