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Items: 1 to 50 of 51

1.

InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, Finn RD.

Nucleic Acids Res. 2018 Nov 6. doi: 10.1093/nar/gky1100. [Epub ahead of print]

PMID:
30398656
2.

Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources.

Huang LC, Ross KE, Baffi TR, Drabkin H, Kochut KJ, Ruan Z, D'Eustachio P, McSkimming D, Arighi C, Chen C, Natale DA, Smith C, Gaudet P, Newton AC, Wu C, Kannan N.

Sci Rep. 2018 Apr 25;8(1):6518. doi: 10.1038/s41598-018-24457-1.

3.

Scalable Text Mining Assisted Curation of Post-Translationally Modified Proteoforms in the Protein Ontology.

Ross KE, Natale DA, Arighi C, Chen SC, Huang H, Li G, Ren J, Wang M, Vijay-Shanker K, Wu CH.

CEUR Workshop Proc. 2016 Aug;1747. pii: http://ceur-ws.org/Vol-1747/BIT103_ICBO2016.pdf. Epub 2016 Nov 29.

4.

Tutorial on Protein Ontology Resources.

Arighi CN, Drabkin H, Christie KR, Ross KE, Natale DA.

Methods Mol Biol. 2017;1558:57-78. doi: 10.1007/978-1-4939-6783-4_3.

5.

The development of non-coding RNA ontology.

Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, de Silva N, Kasukurthi MV, Jha VK, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M.

Int J Data Min Bioinform. 2016;15(3):214-232.

6.

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.

Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH.

Nucleic Acids Res. 2017 Jan 4;45(D1):D339-D346. doi: 10.1093/nar/gkw1075. Epub 2016 Nov 28.

7.

InterPro in 2017-beyond protein family and domain annotations.

Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL.

Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199. doi: 10.1093/nar/gkw1107. Epub 2016 Nov 29.

8.

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.

Huang J, Gutierrez F, Strachan HJ, Dou D, Huang W, Smith B, Blake JA, Eilbeck K, Natale DA, Lin Y, Wu B, Silva Nd, Wang X, Liu Z, Borchert GM, Tan M, Ruttenberg A.

J Biomed Semantics. 2016 May 10;7:25. doi: 10.1186/s13326-016-0064-2. eCollection 2016.

9.

Computational clustering for viral reference proteomes.

Chen C, Huang H, Mazumder R, Natale DA, McGarvey PB, Zhang J, Polson SW, Wang Y, Wu CH; UniProt Consortium.

Bioinformatics. 2016 Jul 1;32(13):2041-3. doi: 10.1093/bioinformatics/btw110. Epub 2016 Feb 26.

10.

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.

Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M.

J Biomed Semantics. 2016 May 4;7:24. doi: 10.1186/s13326-016-0066-0. eCollection 2016.

11.

Correction: Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework.

Arighi C, Shamovsky V, Masci AM, Ruttenberg A, Smith B, Natale DA, Wu C, D'Eustachio P.

PLoS One. 2015 Jun 18;10(6):e0131148. doi: 10.1371/journal.pone.0131148. eCollection 2015. No abstract available.

12.

Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.

Arighi C, Shamovsky V, Masci AM, Ruttenberg A, Smith B, Natale DA, Wu C, D'Eustachio P.

PLoS One. 2015 Apr 20;10(3):e0122978. doi: 10.1371/journal.pone.0122978. eCollection 2015. Erratum in: PLoS One. 2015;10(6):e0131148.

13.

The InterPro protein families database: the classification resource after 15 years.

Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD.

Nucleic Acids Res. 2015 Jan;43(Database issue):D213-21. doi: 10.1093/nar/gku1243. Epub 2014 Nov 26.

14.

OMIT: dynamic, semi-automated ontology development for the microRNA domain.

Huang J, Dang J, Borchert GM, Eilbeck K, Zhang H, Xiong M, Jiang W, Wu H, Blake JA, Natale DA, Tan M.

PLoS One. 2014 Jul 15;9(7):e100855. doi: 10.1371/journal.pone.0100855. eCollection 2014.

15.

Protein Ontology: a controlled structured network of protein entities.

Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, AlJanahi A, Çelen I, Gan C, Lv M, Schuster-Lezell E, Wu CH.

Nucleic Acids Res. 2014 Jan;42(Database issue):D415-21. doi: 10.1093/nar/gkt1173. Epub 2013 Nov 21.

16.

Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint.

Ross KE, Arighi CN, Ren J, Natale DA, Huang H, Wu CH.

Front Genet. 2013 Apr 26;4:62. doi: 10.3389/fgene.2013.00062. eCollection 2013.

17.

Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.

Chen C, Natale DA, Finn RD, Huang H, Zhang J, Wu CH, Mazumder R.

PLoS One. 2011 Apr 27;6(4):e18910. doi: 10.1371/journal.pone.0018910.

18.

Protein-centric data integration for functional analysis of comparative proteomics data.

McGarvey PB, Zhang J, Natale DA, Wu CH, Huang H.

Methods Mol Biol. 2011;694:323-39. doi: 10.1007/978-1-60761-977-2_20.

PMID:
21082443
19.

Structure-guided rule-based annotation of protein functional sites in UniProt knowledgebase.

Vasudevan S, Vinayaka CR, Natale DA, Huang H, Kahsay RY, Wu CH.

Methods Mol Biol. 2011;694:91-105. doi: 10.1007/978-1-60761-977-2_7.

PMID:
21082430
20.

The Protein Ontology: a structured representation of protein forms and complexes.

Natale DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, D'Eustachio P, Evsikov AV, Huang H, Nchoutmboube J, Roberts NV, Smith B, Zhang J, Wu CH.

Nucleic Acids Res. 2011 Jan;39(Database issue):D539-45. doi: 10.1093/nar/gkq907. Epub 2010 Oct 8.

21.

Community annotation in biology.

Mazumder R, Natale DA, Julio JA, Yeh LS, Wu CH.

Biol Direct. 2010 Feb 18;5:12. doi: 10.1186/1745-6150-5-12.

22.

Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis.

Karp DR, Marthandan N, Marsh SG, Ahn C, Arnett FC, Deluca DS, Diehl AD, Dunivin R, Eilbeck K, Feolo M, Guidry PA, Helmberg W, Lewis S, Mayes MD, Mungall C, Natale DA, Peters B, Petersdorf E, Reveille JD, Smith B, Thomson G, Waller MJ, Scheuermann RH.

Hum Mol Genet. 2010 Feb 15;19(4):707-19. doi: 10.1093/hmg/ddp521. Epub 2009 Nov 18.

23.

Quantitative organelle proteomics of MCF-7 breast cancer cells reveals multiple subcellular locations for proteins in cellular functional processes.

Qattan AT, Mulvey C, Crawford M, Natale DA, Godovac-Zimmermann J.

J Proteome Res. 2010 Jan;9(1):495-508. doi: 10.1021/pr9008332.

24.

TGF-beta signaling proteins and the Protein Ontology.

Arighi CN, Liu H, Natale DA, Barker WC, Drabkin H, Blake JA, Smith B, Wu CH.

BMC Bioinformatics. 2009 May 6;10 Suppl 5:S3. doi: 10.1186/1471-2105-10-S5-S3.

25.

A procedure to recruit members to enlarge protein family databases--the building of UECOG (UniRef-Enriched COG Database) as a model.

Fernandes GR, Barbosa DV, Prosdocimi F, Pena IA, Santana-Santos L, Coelho Junior O, Barbosa-Silva A, Velloso HM, Mudado MA, Natale DA, Faria-Campos AC, Aguiar SC, Ortega JM.

Genet Mol Res. 2008 Sep 30;7(3):910-24.

26.

Framework for a protein ontology.

Natale DA, Arighi CN, Barker WC, Blake J, Chang TC, Hu Z, Liu H, Smith B, Wu CH.

BMC Bioinformatics. 2007 Nov 27;8 Suppl 9:S1.

27.

The Universal Protein Resource (UniProt): an expanding universe of protein information.

Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D187-91.

28.

Computational identification of strain-, species- and genus-specific proteins.

Mazumder R, Natale DA, Murthy S, Thiagarajan R, Wu CH.

BMC Bioinformatics. 2005 Nov 23;6:279.

29.

The Universal Protein Resource (UniProt).

Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D154-9.

30.

Evolution of eukaryotic gene repertoire and gene structure: discovering the unexpected dynamics of genome evolution.

Rogozin IB, Babenko VN, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Mirkin BG, Nikolskaya AN, Rao BS, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA, Koonin EV.

Cold Spring Harb Symp Quant Biol. 2003;68:293-301. No abstract available.

PMID:
15338629
31.

The symptom burden of chronic critical illness.

Nelson JE, Meier DE, Litke A, Natale DA, Siegel RE, Morrison RS.

Crit Care Med. 2004 Jul;32(7):1527-34.

PMID:
15241097
32.

A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.

Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA.

Genome Biol. 2004;5(2):R7. Epub 2004 Jan 15.

33.

UniProt: the Universal Protein knowledgebase.

Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D115-9.

34.

PIRSF: family classification system at the Protein Information Resource.

Wu CH, Nikolskaya A, Huang H, Yeh LS, Natale DA, Vinayaka CR, Hu ZZ, Mazumder R, Kumar S, Kourtesis P, Ledley RS, Suzek BE, Arminski L, Chen Y, Zhang J, Cardenas JL, Chung S, Castro-Alvear J, Dinkov G, Barker WC.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D112-4.

35.

The COG database: an updated version includes eukaryotes.

Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA.

BMC Bioinformatics. 2003 Sep 11;4:41. Epub 2003 Sep 11.

36.

Congruent evolution of different classes of non-coding DNA in prokaryotic genomes.

Rogozin IB, Makarova KS, Natale DA, Spiridonov AN, Tatusov RL, Wolf YI, Yin J, Koonin EV.

Nucleic Acids Res. 2002 Oct 1;30(19):4264-71.

37.

The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens.

Slesarev AI, Mezhevaya KV, Makarova KS, Polushin NN, Shcherbinina OV, Shakhova VV, Belova GI, Aravind L, Natale DA, Rogozin IB, Tatusov RL, Wolf YI, Stetter KO, Malykh AG, Koonin EV, Kozyavkin SA.

Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4644-9.

38.

Independent evolution of heavy metal-associated domains in copper chaperones and copper-transporting atpases.

Jordan IK, Natale DA, Koonin EV, Galperin MY.

J Mol Evol. 2001 Dec;53(6):622-33.

PMID:
11677622
39.

Copper chaperones in bacteria: association with copper-transporting ATPases.

Jordan IK, Natale DA, Galperin MY.

Trends Biochem Sci. 2000 Oct;25(10):480-1. No abstract available.

PMID:
11203382
40.

Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).

Natale DA, Shankavaram UT, Galperin MY, Wolf YI, Aravind L, Koonin EV.

Genome Biol. 2000;1(5):RESEARCH0009. Epub 2000 Nov 6.

41.

Using the COG database to improve gene recognition in complete genomes.

Natale DA, Galperin MY, Tatusov RL, Koonin EV.

Genetica. 2000;108(1):9-17.

PMID:
11145426
42.

A specialized version of the HD hydrolase domain implicated in signal transduction.

Galperin MY, Natale DA, Aravind L, Koonin EV.

J Mol Microbiol Biotechnol. 1999 Nov;1(2):303-5. No abstract available.

43.

Initiation of eukaryotic DNA replication: conservative or liberal?

Bogan JA, Natale DA, Depamphilis ML.

J Cell Physiol. 2000 Aug;184(2):139-50. Review.

PMID:
10867638
45.

Selective activation of pre-replication complexes in vitro at specific sites in mammalian nuclei.

Li CJ, Bogan JA, Natale DA, DePamphilis ML.

J Cell Sci. 2000 Mar;113 ( Pt 5):887-98.

46.

The COG database: new developments in phylogenetic classification of proteins from complete genomes.

Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV.

Nucleic Acids Res. 2001 Jan 1;29(1):22-8.

47.

The COG database: a tool for genome-scale analysis of protein functions and evolution.

Tatusov RL, Galperin MY, Natale DA, Koonin EV.

Nucleic Acids Res. 2000 Jan 1;28(1):33-6.

48.

Absence of an unusual "densely methylated island" at the hamster dhfr ori-beta.

Rein T, Natale DA, Gärtner U, Niggemann M, DePamphilis ML, Zorbas H.

J Biol Chem. 1997 Apr 11;272(15):10021-9.

49.

Ease of DNA unwinding is a conserved property of yeast replication origins.

Natale DA, Umek RM, Kowalski D.

Nucleic Acids Res. 1993 Feb 11;21(3):555-60.

50.

DNA helical stability accounts for mutational defects in a yeast replication origin.

Natale DA, Schubert AE, Kowalski D.

Proc Natl Acad Sci U S A. 1992 Apr 1;89(7):2654-8.

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