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Items: 19

1.

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.

2.

Terminal uridylyltransferases target RNA viruses as part of the innate immune system.

Le Pen J, Jiang H, Di Domenico T, Kneuss E, Kosałka J, Leung C, Morgan M, Much C, Rudolph KLM, Enright AJ, O'Carroll D, Wang D, Miska EA.

Nat Struct Mol Biol. 2018 Sep;25(9):778-786. doi: 10.1038/s41594-018-0106-9. Epub 2018 Aug 13.

3.

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.

4.

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription.

Akay A, Di Domenico T, Suen KM, Nabih A, Parada GE, Larance M, Medhi R, Berkyurek AC, Zhang X, Wedeles CJ, Rudolph KLM, Engelhardt J, Hemberg M, Ma P, Lamond AI, Claycomb JM, Miska EA.

Dev Cell. 2017 Aug 7;42(3):241-255.e6. doi: 10.1016/j.devcel.2017.07.002.

5.

The Profile and Dynamics of RNA Modifications in Animals.

van Delft P, Akay A, Huber SM, Bueschl C, Rudolph KLM, Di Domenico T, Schuhmacher R, Miska EA, Balasubramanian S.

Chembiochem. 2017 Jun 1;18(11):979-984. doi: 10.1002/cbic.201700093. Epub 2017 Apr 27.

6.

Highlights from the tenth ISCB Student Council Symposium 2014.

Rahman F, Wilkins K, Jacobsen A, Junge A, Vicedo E, DeBlasio D, Jigisha A, Di Domenico T.

BMC Bioinformatics. 2015;16 Suppl 2:A1-10. Epub 2015 Jan 28.

7.

MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins.

Potenza E, Di Domenico T, Walsh I, Tosatto SC.

Nucleic Acids Res. 2015 Jan;43(Database issue):D315-20. doi: 10.1093/nar/gku982. Epub 2014 Oct 31.

8.

Comprehensive large-scale assessment of intrinsic protein disorder.

Walsh I, Giollo M, Di Domenico T, Ferrari C, Zimmermann O, Tosatto SC.

Bioinformatics. 2015 Jan 15;31(2):201-8. doi: 10.1093/bioinformatics/btu625. Epub 2014 Sep 21.

PMID:
25246432
9.

RUBI: rapid proteomic-scale prediction of lysine ubiquitination and factors influencing predictor performance.

Walsh I, Di Domenico T, Tosatto SC.

Amino Acids. 2014 Apr;46(4):853-62. doi: 10.1007/s00726-013-1645-3. Epub 2013 Dec 23.

PMID:
24363213
10.

RepeatsDB: a database of tandem repeat protein structures.

Di Domenico T, Potenza E, Walsh I, Parra RG, Giollo M, Minervini G, Piovesan D, Ihsan A, Ferrari C, Kajava AV, Tosatto SC.

Nucleic Acids Res. 2014 Jan;42(Database issue):D352-7. doi: 10.1093/nar/gkt1175. Epub 2013 Dec 5.

11.

ISCB computational biology Wikipedia competition.

Bateman A, Kelso J, Mietchen D, Macintyre G, Di Domenico T, Abeel T, Logan DW, Radivojac P, Rost B.

PLoS Comput Biol. 2013;9(9):e1003242. doi: 10.1371/journal.pcbi.1003242. Epub 2013 Sep 19. No abstract available.

12.

Analysis and consensus of currently available intrinsic protein disorder annotation sources in the MobiDB database.

Di Domenico T, Walsh I, Tosatto SC.

BMC Bioinformatics. 2013;14 Suppl 7:S3. doi: 10.1186/1471-2105-14-S7-S3. Epub 2013 Apr 22.

13.

RAPHAEL: recognition, periodicity and insertion assignment of solenoid protein structures.

Walsh I, Sirocco FG, Minervini G, Di Domenico T, Ferrari C, Tosatto SC.

Bioinformatics. 2012 Dec 15;28(24):3257-64. doi: 10.1093/bioinformatics/bts550. Epub 2012 Sep 8.

PMID:
22962341
14.

MobiDB: a comprehensive database of intrinsic protein disorder annotations.

Di Domenico T, Walsh I, Martin AJ, Tosatto SC.

Bioinformatics. 2012 Aug 1;28(15):2080-1. doi: 10.1093/bioinformatics/bts327. Epub 2012 Jun 1.

PMID:
22661649
15.

ESpritz: accurate and fast prediction of protein disorder.

Walsh I, Martin AJ, Di Domenico T, Tosatto SC.

Bioinformatics. 2012 Feb 15;28(4):503-9. doi: 10.1093/bioinformatics/btr682. Epub 2011 Dec 20.

PMID:
22190692
16.

CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs.

Walsh I, Martin AJ, Di Domenico T, Vullo A, Pollastri G, Tosatto SC.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W190-6. doi: 10.1093/nar/gkr411. Epub 2011 Jun 6.

17.

RING: networking interacting residues, evolutionary information and energetics in protein structures.

Martin AJ, Vidotto M, Boscariol F, Di Domenico T, Walsh I, Tosatto SC.

Bioinformatics. 2011 Jul 15;27(14):2003-5. doi: 10.1093/bioinformatics/btr191. Epub 2011 Apr 14.

PMID:
21493660
18.

Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification.

Marino Buslje C, Teppa E, Di Doménico T, Delfino JM, Nielsen M.

PLoS Comput Biol. 2010 Nov 4;6(11):e1000978. doi: 10.1371/journal.pcbi.1000978.

19.

Age is more than just a number: implications for an aging workforce in the US transportation sector.

Popkin SM, Morrow SL, Di Domenico TE, Howarth HD.

Appl Ergon. 2008 Sep;39(5):542-9. doi: 10.1016/j.apergo.2008.02.003. Epub 2008 Mar 28. Review.

PMID:
18374896

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