Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 70

1.

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

Martinez-Gomez L, Abascal F, Jungreis I, Pozo F, Kellis M, Mudge JM, Tress ML.

NAR Genom Bioinform. 2020 Mar;2(1):lqz023. doi: 10.1093/nargab/lqz023. Epub 2019 Dec 19.

2.

Viscoelasticity in associating oligomers and polymers: experimental test of the bond lifetime renormalization model.

Ge S, Tress M, Xing K, Cao PF, Saito T, Sokolov AP.

Soft Matter. 2020 Jan 2;16(2):390-401. doi: 10.1039/c9sm01930h.

PMID:
31840152
3.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

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, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I.

Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8.

4.

What dielectric spectroscopy can tell us about supramolecular networks.

Tress M, Xing K, Ge S, Cao P, Saito T, Sokolov A.

Eur Phys J E Soft Matter. 2019 Oct 18;42(10):133. doi: 10.1140/epje/i2019-11897-4.

PMID:
31624934
5.

Corrigendum: Loose ends: almost one in five human genes still have unresolved coding status.

Abascal F, Juan D, Jungreis I, Kellis M, Martinez L, Rigau M, Rodriguez JM, Vazquez J, Tress ML.

Nucleic Acids Res. 2018 Dec 14;46(22):12194. doi: 10.1093/nar/gky1146. No abstract available.

6.

GENCODE reference annotation for the human and mouse genomes.

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, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P.

Nucleic Acids Res. 2019 Jan 8;47(D1):D766-D773. doi: 10.1093/nar/gky955.

7.

Wetting of soft superhydrophobic micropillar arrays.

Papadopoulos P, Pinchasik BE, Tress M, Vollmer D, Kappl M, Butt HJ.

Soft Matter. 2018 Sep 19;14(36):7429-7434. doi: 10.1039/c8sm01333k.

8.

Loose ends: almost one in five human genes still have unresolved coding status.

Abascal F, Juan D, Jungreis I, Kellis M, Martinez L, Rigau M, Rodriguez JM, Vazquez J, Tress ML.

Nucleic Acids Res. 2018 Aug 21;46(14):7070-7084. doi: 10.1093/nar/gky587. Erratum in: Nucleic Acids Res. 2018 Dec 14;46(22):12194.

9.

Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.

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, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A.

Genome Res. 2018 Jul;28(7):1096. doi: 10.1101/gr.239137.118. No abstract available.

10.

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.

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, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A.

Genome Res. 2018 Feb 9. doi: 10.1101/gr.222976.117. [Epub ahead of print] Erratum in: Genome Res. 2018 Jul;28(7):1096.

11.

Hydrogen-bond strength changes network dynamics in associating telechelic PDMS.

Xing K, Tress M, Cao P, Cheng S, Saito T, Novikov VN, Sokolov AP.

Soft Matter. 2018 Feb 14;14(7):1235-1246. doi: 10.1039/c7sm01805c.

PMID:
29355867
12.

APPRIS 2017: principal isoforms for multiple gene sets.

Rodriguez JM, Rodriguez-Rivas J, Di Domenico T, Vázquez J, Valencia A, Tress ML.

Nucleic Acids Res. 2018 Jan 4;46(D1):D213-D217. doi: 10.1093/nar/gkx997.

13.

Most Alternative Isoforms Are Not Functionally Important.

Tress ML, Abascal F, Valencia A.

Trends Biochem Sci. 2017 Jun;42(6):408-410. doi: 10.1016/j.tibs.2017.04.002. Epub 2017 May 5. No abstract available.

14.

Shape of a sessile drop on a flat surface covered with a liquid film.

Tress M, Karpitschka S, Papadopoulos P, Snoeijer JH, Vollmer D, Butt HJ.

Soft Matter. 2017 May 24;13(20):3760-3767. doi: 10.1039/c7sm00437k.

PMID:
28470269
15.

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.

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, Ribeca P, Capella-Gutiérrez S, Rodríguez JM, Câmara F, Lowy E, Cozzuto L, Erb I, Tress ML, Rodriguez-Ales JL, Ruiz-Orera J, Reverter F, Casas-Marce M, Soriano L, Arango JR, Derdak S, Galán B, Blanc J, Gut M, Lorente-Galdos B, Andrés-Nieto M, López-Otín C, Valencia A, Gut I, García JL, Guigó R, Murphy WJ, Ruiz-Herrera A, Marques-Bonet T, Roma G, Notredame C, Mailund T, Albà MM, Gabaldón T, Alioto T, Godoy JA.

Genome Biol. 2016 Dec 14;17(1):251.

16.

Alternative Splicing May Not Be the Key to Proteome Complexity.

Tress ML, Abascal F, Valencia A.

Trends Biochem Sci. 2017 Feb;42(2):98-110. doi: 10.1016/j.tibs.2016.08.008. Epub 2016 Oct 3. Review.

17.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

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, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

18.

Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors (HRPBC) Uncovers Potential Novel Drivers of Hormonal Resistance.

Manso L, Mourón S, Tress M, Gómez-López G, Morente M, Ciruelos E, Rubio-Camarillo M, Rodriguez-Peralto JL, Pujana MA, Pisano DG, Quintela-Fandino M.

PLoS One. 2016 May 19;11(5):e0155840. doi: 10.1371/journal.pone.0155840. eCollection 2016.

19.

Confinement for More Space: A Larger Free Volume and Enhanced Glassy Dynamics of 2-Ethyl-1-hexanol in Nanopores.

Kipnusu WK, Elsayed M, Kossack W, Pawlus S, Adrjanowicz K, Tress M, Mapesa EU, Krause-Rehberg R, Kaminski K, Kremer F.

J Phys Chem Lett. 2015 Sep 17;6(18):3708-12. doi: 10.1021/acs.jpclett.5b01533. Epub 2015 Sep 4.

PMID:
26722745
20.

The potential clinical impact of the release of two drafts of the human proteome.

Ezkurdia I, Calvo E, Del Pozo A, Vázquez J, Valencia A, Tress ML.

Expert Rev Proteomics. 2015;12(6):579-93. doi: 10.1586/14789450.2015.1103186. Epub 2015 Oct 23.

21.

Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level.

Abascal F, Ezkurdia I, Rodriguez-Rivas J, Rodriguez JM, del Pozo A, Vázquez J, Valencia A, Tress ML.

PLoS Comput Biol. 2015 Jun 10;11(6):e1004325. doi: 10.1371/journal.pcbi.1004325. eCollection 2015 Jun.

22.

APPRIS WebServer and WebServices.

Rodriguez JM, Carro A, Valencia A, Tress ML.

Nucleic Acids Res. 2015 Jul 1;43(W1):W455-9. doi: 10.1093/nar/gkv512. Epub 2015 May 18.

23.

The evolutionary fate of alternatively spliced homologous exons after gene duplication.

Abascal F, Tress ML, Valencia A.

Genome Biol Evol. 2015 Apr 29;7(6):1392-403. doi: 10.1093/gbe/evv076.

24.

Correction to "Analyzing the first drafts of the human proteome".

Ezkurdia I, Vázquez J, Valencia A, Tress M.

J Proteome Res. 2015 Apr 3;14(4):1991. doi: 10.1021/acs.jproteome.5b00186. Epub 2015 Mar 10. No abstract available.

25.

Glassy dynamics of poly(2-vinyl-pyridine) brushes with varying grafting density.

Neubauer N, Winkler R, Tress M, Uhlmann P, Reiche M, Kipnusu WK, Kremer F.

Soft Matter. 2015 Apr 21;11(15):3062-6. doi: 10.1039/c5sm00213c.

PMID:
25740018
26.

Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals.

Abascal F, Tress ML, Valencia A.

Bioinformatics. 2015 Jul 15;31(14):2257-61. doi: 10.1093/bioinformatics/btv132. Epub 2015 Mar 2.

27.

Most highly expressed protein-coding genes have a single dominant isoform.

Ezkurdia I, Rodriguez JM, Carrillo-de Santa Pau E, Vázquez J, Valencia A, Tress ML.

J Proteome Res. 2015 Apr 3;14(4):1880-7. doi: 10.1021/pr501286b. Epub 2015 Mar 11.

28.

Analyzing the first drafts of the human proteome.

Ezkurdia I, Vázquez J, Valencia A, Tress M.

J Proteome Res. 2014 Aug 1;13(8):3854-5. doi: 10.1021/pr500572z. Epub 2014 Jul 16. Erratum in: J Proteome Res. 2015 Apr 3;14(4):1991.

29.

Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes.

Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A, Tress ML.

Hum Mol Genet. 2014 Nov 15;23(22):5866-78. doi: 10.1093/hmg/ddu309. Epub 2014 Jun 16.

30.

The kinetics of mutarotation in L-fucose as monitored by dielectric and infrared spectroscopy.

Kossack W, Kipnusu WK, Dulski M, Adrjanowicz K, Madejczyk O, Kaminska E, Mapesa EU, Tress M, Kaminski K, Kremer F.

J Chem Phys. 2014 Jun 7;140(21):215101. doi: 10.1063/1.4880718.

PMID:
24908041
31.

FireDB: a compendium of biological and pharmacologically relevant ligands.

Maietta P, Lopez G, Carro A, Pingilley BJ, Leon LG, Valencia A, Tress ML.

Nucleic Acids Res. 2014 Jan;42(Database issue):D267-72. doi: 10.1093/nar/gkt1127. Epub 2013 Nov 15.

32.

Glassy dynamics in condensed isolated polymer chains.

Tress M, Mapesa EU, Kossack W, Kipnusu WK, Reiche M, Kremer F.

Science. 2013 Sep 20;341(6152):1371-4. doi: 10.1126/science.1238950.

33.

APPRIS: annotation of principal and alternative splice isoforms.

Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, Valencia A, Tress ML.

Nucleic Acids Res. 2013 Jan;41(Database issue):D110-7. doi: 10.1093/nar/gks1058. Epub 2012 Nov 17.

34.

GENCODE: the reference human genome annotation for The ENCODE Project.

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, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ.

Genome Res. 2012 Sep;22(9):1760-74. doi: 10.1101/gr.135350.111.

35.

Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.

Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R, Valencia A.

Genome Res. 2012 Jul;22(7):1231-42. doi: 10.1101/gr.130062.111. Epub 2012 May 15.

36.

Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.

Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML.

Mol Biol Evol. 2012 Sep;29(9):2265-83. doi: 10.1093/molbev/mss100. Epub 2012 Mar 22.

37.

Evidence for transcript networks composed of chimeric RNAs in human cells.

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, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpí JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR.

PLoS One. 2012;7(1):e28213. doi: 10.1371/journal.pone.0028213. Epub 2012 Jan 4.

38.

Protein structural domains: definition and prediction.

Ezkurdia I, Tress ML.

Curr Protoc Protein Sci. 2011 Nov;Chapter 2:Unit2.14. doi: 10.1002/0471140864.ps0214s66.

PMID:
22045561
39.

firestar--advances in the prediction of functionally important residues.

Lopez G, Maietta P, Rodriguez JM, Valencia A, Tress ML.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W235-41. doi: 10.1093/nar/gkr437. Epub 2011 Jun 14.

40.

The glass transition of thin polymer films in relation to the interfacial dynamics.

Serghei A, Tress M, Kremer F.

J Chem Phys. 2009 Oct 21;131(15):154904. doi: 10.1063/1.3248368.

PMID:
20568881
41.

Predicted residue-residue contacts can help the scoring of 3D models.

Tress ML, Valencia A.

Proteins. 2010 Jun;78(8):1980-91. doi: 10.1002/prot.22714.

PMID:
20408174
42.

Effectiveness of oral self-care among adult Gullah-speaking African Americans with diabetes.

Yuen HK, Tress ME, Salinas CF, Slate EH.

Spec Care Dentist. 2009 May-June;29(3):128-33.

43.

Assessment of ligand binding residue predictions in CASP8.

López G, Ezkurdia I, Tress ML.

Proteins. 2009;77 Suppl 9:138-46. doi: 10.1002/prot.22557.

44.

Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8.

Ezkurdia I, Graña O, Izarzugaza JM, Tress ML.

Proteins. 2009;77 Suppl 9:196-209. doi: 10.1002/prot.22554.

PMID:
19714769
45.

Target domain definition and classification in CASP8.

Tress ML, Ezkurdia I, Richardson JS.

Proteins. 2009;77 Suppl 9:10-7. doi: 10.1002/prot.22497.

46.

Progress and challenges in predicting protein-protein interaction sites.

Ezkurdia I, Bartoli L, Fariselli P, Casadio R, Valencia A, Tress ML.

Brief Bioinform. 2009 May;10(3):233-46. doi: 10.1093/bib/bbp021. Epub 2009 Apr 3.

PMID:
19346321
47.

Sequence-based feature prediction and annotation of proteins.

Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S.

Genome Biol. 2009 Feb 2;10(2):206. doi: 10.1186/gb-2009-10-2-206.

48.

Proteomics studies confirm the presence of alternative protein isoforms on a large scale.

Tress ML, Bodenmiller B, Aebersold R, Valencia A.

Genome Biol. 2008;9(11):R162. doi: 10.1186/gb-2008-9-11-r162. Epub 2008 Nov 18.

49.

Determination and validation of principal gene products.

Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A.

Bioinformatics. 2008 Jan 1;24(1):11-7. Epub 2007 Nov 15.

50.

Assessment of predictions submitted for the CASP7 domain prediction category.

Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo JH, Lee J, Baker D, Chivian D, Kim D, Ezkurdia I.

Proteins. 2007;69 Suppl 8:137-51.

PMID:
17680686

Supplemental Content

Support Center