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Items: 1 to 50 of 152

1.

Emerging concepts in pseudoenzyme classification, evolution, and signaling.

Ribeiro AJM, Das S, Dawson N, Zaru R, Orchard S, Thornton JM, Orengo C, Zeqiraj E, Murphy JM, Eyers PA.

Sci Signal. 2019 Aug 13;12(594). pii: eaat9797. doi: 10.1126/scisignal.aat9797. Review.

PMID:
31409758
2.

Recruiting general practice patients for large clinical trials: lessons from the Aspirin in Reducing Events in the Elderly (ASPREE) study.

Lockery JE, Collyer TA, Abhayaratna WP, Fitzgerald SM, McNeil JJ, Nelson MR, Orchard SG, Reid C, Stocks NP, Trevaks RE, Woods R.

Med J Aust. 2019 Mar;210(4):168-173. doi: 10.5694/mja2.12060. Epub 2018 Dec 21.

PMID:
30835844
3.

Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

IMEx Consortium contributing authors, Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P.

Nat Commun. 2019 Mar 4;10(1):1098. doi: 10.1038/s41467-019-08814-w.

4.

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.

Perfetto L, Acencio ML, Bradley G, Cesareni G, Del Toro N, Fazekas D, Hermjakob H, Korcsmaros T, Kuiper M, Lægreid A, Lo Surdo P, Lovering RC, Orchard S, Porras P, Thomas PD, Touré V, Zobolas J, Licata L.

Bioinformatics. 2019 Feb 21. pii: btz132. doi: 10.1093/bioinformatics/btz132. [Epub ahead of print]

PMID:
30793173
5.

Integration of macromolecular complex data into the Saccharomyces Genome Database.

Wong ED, Skrzypek MS, Weng S, Binkley G, Meldal BHM, Perfetto L, Orchard SE, Engel SR, Cherry JM; SGD Project.

Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz008.

6.

Baseline Characteristics of Participants in the ASPREE (Aspirin in Reducing Events in the Elderly) Study.

McNeil JJ, Woods RL, Nelson MR, Murray AM, Reid CM, Kirpach B, Storey E, Shah RC, Wolfe RS, Tonkin AM, Newman AB, Williamson JD, Lockery JE, Margolis KL, Ernst ME, Abhayaratna WP, Stocks N, Fitzgerald SM, Trevaks RE, Orchard SG, Beilin LJ, Donnan GA, Gibbs P, Johnston CI, Grimm RH; ASPREE Investigator Group.

J Gerontol A Biol Sci Med Sci. 2019 Jan 22. doi: 10.1093/gerona/gly278. [Epub ahead of print] No abstract available.

7.

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

IMEx Consortium Curators, Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P.

Nat Commun. 2019 Jan 2;10(1):10. doi: 10.1038/s41467-018-07709-6. Erratum in: Nat Commun. 2019 Mar 4;10(1):1098.

8.

Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data.

Kramarz B, Roncaglia P, Meldal BHM, Huntley RP, Martin MJ, Orchard S, Parkinson H, Brough D, Bandopadhyay R, Hooper NM, Lovering RC.

Genes (Basel). 2018 Nov 29;9(12). pii: E593. doi: 10.3390/genes9120593.

9.

Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes.

Meldal BHM, Bye-A-Jee H, Gajdoš L, Hammerová Z, Horácková A, Melicher F, Perfetto L, Pokorný D, Lopez MR, Türková A, Wong ED, Xie Z, Casanova EB, Del-Toro N, Koch M, Porras P, Hermjakob H, Orchard S.

Nucleic Acids Res. 2019 Jan 8;47(D1):D550-D558. doi: 10.1093/nar/gky1001.

10.

Effect of Aspirin on Cardiovascular Events and Bleeding in the Healthy Elderly.

McNeil JJ, Wolfe R, Woods RL, Tonkin AM, Donnan GA, Nelson MR, Reid CM, Lockery JE, Kirpach B, Storey E, Shah RC, Williamson JD, Margolis KL, Ernst ME, Abhayaratna WP, Stocks N, Fitzgerald SM, Orchard SG, Trevaks RE, Beilin LJ, Johnston CI, Ryan J, Radziszewska B, Jelinek M, Malik M, Eaton CB, Brauer D, Cloud G, Wood EM, Mahady SE, Satterfield S, Grimm R, Murray AM; ASPREE Investigator Group.

N Engl J Med. 2018 Oct 18;379(16):1509-1518. doi: 10.1056/NEJMoa1805819. Epub 2018 Sep 16.

11.

Effect of Aspirin on Disability-free Survival in the Healthy Elderly.

McNeil JJ, Woods RL, Nelson MR, Reid CM, Kirpach B, Wolfe R, Storey E, Shah RC, Lockery JE, Tonkin AM, Newman AB, Williamson JD, Margolis KL, Ernst ME, Abhayaratna WP, Stocks N, Fitzgerald SM, Orchard SG, Trevaks RE, Beilin LJ, Donnan GA, Gibbs P, Johnston CI, Ryan J, Radziszewska B, Grimm R, Murray AM; ASPREE Investigator Group.

N Engl J Med. 2018 Oct 18;379(16):1499-1508. doi: 10.1056/NEJMoa1800722. Epub 2018 Sep 16.

12.

Effect of Aspirin on All-Cause Mortality in the Healthy Elderly.

McNeil JJ, Nelson MR, Woods RL, Lockery JE, Wolfe R, Reid CM, Kirpach B, Shah RC, Ives DG, Storey E, Ryan J, Tonkin AM, Newman AB, Williamson JD, Margolis KL, Ernst ME, Abhayaratna WP, Stocks N, Fitzgerald SM, Orchard SG, Trevaks RE, Beilin LJ, Donnan GA, Gibbs P, Johnston CI, Radziszewska B, Grimm R, Murray AM; ASPREE Investigator Group.

N Engl J Med. 2018 Oct 18;379(16):1519-1528. doi: 10.1056/NEJMoa1803955. Epub 2018 Sep 16.

13.

Best practice data life cycle approaches for the life sciences.

Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV.

Version 2. F1000Res. 2017 Aug 31 [revised 2018 Jan 1];6:1618. doi: 10.12688/f1000research.12344.2. eCollection 2017.

14.

Normative performance of healthy older individuals on the Modified Mini-Mental State (3MS) examination according to ethno-racial group, gender, age, and education level.

Ryan J, Woods RL, Britt C, Murray AM, Shah RC, Reid CM, Kirpach B, Wolfe RS, Nelson MR, Lockery JE, Orchard SG, Trevaks RE, McNeil JJ, Storey E; ASPREE Investigator Group.

Clin Neuropsychol. 2019 May;33(4):779-797. doi: 10.1080/13854046.2018.1488996. Epub 2018 Jul 5.

PMID:
29976121
15.

JAMI: a Java library for molecular interactions and data interoperability.

Sivade Dumousseau M, Koch M, Shrivastava A, Alonso-López D, De Las Rivas J, Del-Toro N, Combe CW, Meldal BHM, Heimbach J, Rappsilber J, Sullivan J, Yehudi Y, Orchard S.

BMC Bioinformatics. 2018 Apr 11;19(1):133. doi: 10.1186/s12859-018-2119-0.

16.

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard-Blum S, Roechert B, Salwinski L, Shrivastava A, Sullivan J, Thierry-Mieg N, Yehudi Y, Van Roey K, Orchard S.

BMC Bioinformatics. 2018 Apr 11;19(1):134. doi: 10.1186/s12859-018-2118-1.

17.

Searching and Extracting Data from the EMBL-EBI Complex Portal.

Meldal BHM, Orchard S.

Methods Mol Biol. 2018;1764:377-390. doi: 10.1007/978-1-4939-7759-8_24.

PMID:
29605928
18.

A mycorrhizal revolution.

Hoysted GA, Kowal J, Jacob A, Rimington WR, Duckett JG, Pressel S, Orchard S, Ryan MH, Field KJ, Bidartondo MI.

Curr Opin Plant Biol. 2018 Aug;44:1-6. doi: 10.1016/j.pbi.2017.12.004. Epub 2017 Dec 29. Review.

19.

ComplexViewer: visualization of curated macromolecular complexes.

Combe CW, Sivade MD, Hermjakob H, Heimbach J, Meldal BHM, Micklem G, Orchard S, Rappsilber J.

Bioinformatics. 2017 Nov 15;33(22):3673-3675. doi: 10.1093/bioinformatics/btx497.

20.

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR.

J Proteome Res. 2017 Dec 1;16(12):4288-4298. doi: 10.1021/acs.jproteome.7b00370. Epub 2017 Sep 15.

21.

Age-related macular degeneration in a randomized controlled trial of low-dose aspirin: Rationale and study design of the ASPREE-AMD study.

Robman L, Guymer R, Woods R, Ward S, Wolfe R, Phung J, Hodgson L, Makeyeva G, Aung KZ, Gilbert T, Lockery J, Le-Pham YA, Orchard S, Storey E, Abhayaratna W, Reid D, Ernst ME, Nelson M, Reid C, McNeil J.

Contemp Clin Trials Commun. 2017 Jun;6:105-114. doi: 10.1016/j.conctc.2017.03.005. Epub 2017 Mar 27.

22.

The yeast noncoding RNA interaction network.

Panni S, Prakash A, Bateman A, Orchard S.

RNA. 2017 Oct;23(10):1479-1492. doi: 10.1261/rna.060996.117. Epub 2017 Jul 12.

23.

Fine root endophytes under scrutiny: a review of the literature on arbuscule-producing fungi recently suggested to belong to the Mucoromycotina.

Orchard S, Standish RJ, Dickie IA, Renton M, Walker C, Moot D, Ryan MH.

Mycorrhiza. 2017 Oct;27(7):619-638. doi: 10.1007/s00572-017-0782-z. Epub 2017 Jun 7. Review.

24.

Baseline Characteristics of Participants in the ASPREE (ASPirin in Reducing Events in the Elderly) Study.

McNeil JJ, Woods RL, Nelson MR, Murray AM, Reid CM, Kirpach B, Storey E, Shah RC, Wolfe RS, Tonkin AM, Newman AB, Williamson JD, Lockery JE, Margolis KL, Ernst ME, Abhayaratna WP, Stocks N, Fitzgerald SM, Trevaks RE, Orchard SG, Beilin LJ, Donnan GA, Gibbs P, Johnston CI, Grimm RH; ASPREE Investigator Group.

J Gerontol A Biol Sci Med Sci. 2017 Oct 12;72(11):1586-1593. doi: 10.1093/gerona/glw342. Erratum in: J Gerontol A Biol Sci Med Sci. 2019 Jan 22;:.

25.

Farmer Perceptions and Responses to Soil Degradation in Swaziland.

Orchard SE, Stringer LC, Manyatsi AM.

Land Degrad Dev. 2017 Jan;28(1):46-56. doi: 10.1002/ldr.2595. Epub 2016 Sep 13.

26.

Fine endophytes (Glomus tenue) are related to Mucoromycotina, not Glomeromycota.

Orchard S, Hilton S, Bending GD, Dickie IA, Standish RJ, Gleeson DB, Jeffery RP, Powell JR, Walker C, Bass D, Monk J, Simonin A, Ryan MH.

New Phytol. 2017 Jan;213(2):481-486. doi: 10.1111/nph.14268. Epub 2016 Oct 21. No abstract available.

27.

Overview of the interactive task in BioCreative V.

Wang Q, S Abdul S, Almeida L, Ananiadou S, Balderas-Martínez YI, Batista-Navarro R, Campos D, Chilton L, Chou HJ, Contreras G, Cooper L, Dai HJ, Ferrell B, Fluck J, Gama-Castro S, George N, Gkoutos G, Irin AK, Jensen LJ, Jimenez S, Jue TR, Keseler I, Madan S, Matos S, McQuilton P, Milacic M, Mort M, Natarajan J, Pafilis E, Pereira E, Rao S, Rinaldi F, Rothfels K, Salgado D, Silva RM, Singh O, Stefancsik R, Su CH, Subramani S, Tadepally HD, Tsaprouni L, Vasilevsky N, Wang X, Chatr-Aryamontri A, Laulederkind SJ, Matis-Mitchell S, McEntyre J, Orchard S, Pundir S, Rodriguez-Esteban R, Van Auken K, Lu Z, Schaeffer M, Wu CH, Hirschman L, Arighi CN.

Database (Oxford). 2016 Sep 1;2016. pii: baw119. doi: 10.1093/database/baw119. Print 2016.

28.
29.

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.

Tripathi S, Vercruysse S, Chawla K, Christie KR, Blake JA, Huntley RP, Orchard S, Hermjakob H, Thommesen L, Lægreid A, Kuiper M.

Database (Oxford). 2016 Jun 5;2016. pii: baw088. doi: 10.1093/database/baw088. Print 2016.

30.

The MIntAct Project and Molecular Interaction Databases.

Licata L, Orchard S.

Methods Mol Biol. 2016;1415:55-69. doi: 10.1007/978-1-4939-3572-7_3.

PMID:
27115627
31.

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.

Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M.

Database (Oxford). 2015 May 9;2015:bav043. doi: 10.1093/database/bav043. Print 2015.

32.

Shared resources, shared costs--leveraging biocuration resources.

Orchard S, Hermjakob H.

Database (Oxford). 2015 Mar 16;2015. pii: bav009. doi: 10.1093/database/bav009. Print 2015.

33.

Development of data representation standards by the human proteome organization proteomics standards initiative.

Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS, Orchard S, Vizcaíno JA, Hermjakob H.

J Am Med Inform Assoc. 2015 May;22(3):495-506. doi: 10.1093/jamia/ocv001. Epub 2015 Feb 28. Review.

34.

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.

Villaveces JM, Jiménez RC, Porras P, Del-Toro N, Duesbury M, Dumousseau M, Orchard S, Choi H, Ping P, Zong NC, Askenazi M, Habermann BH, Hermjakob H.

Database (Oxford). 2015 Feb 4;2015. pii: bau131. doi: 10.1093/database/bau131. Print 2015.

35.

A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology.

Porras P, Duesbury M, Fabregat A, Ueffing M, Orchard S, Gloeckner CJ, Hermjakob H.

Proteomics. 2015 Apr;15(8):1390-404. doi: 10.1002/pmic.201400390. Epub 2015 Mar 21. Review.

36.

The complex portal--an encyclopaedia of macromolecular complexes.

Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S.

Nucleic Acids Res. 2015 Jan;43(Database issue):D479-84. doi: 10.1093/nar/gku975. Epub 2014 Oct 13.

37.

Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany.

Orchard S, Albar JP, Binz PA, Kettner C, Jones AR, Salek RM, Vizcaino JA, Deutsch EW, Hermjakob H.

Proteomics. 2014 Nov;14(21-22):2363-8. doi: 10.1002/pmic.201470164. Epub 2014 Oct 9.

PMID:
25297050
38.

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.

Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H.

Nucleic Acids Res. 2014 Jan;42(Database issue):D358-63. doi: 10.1093/nar/gkt1115. Epub 2013 Nov 13.

39.

Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.

Orchard S, Binz PA, Jones AR, Vizcaino JA, Deutsch EW, Hermjakob H.

Proteomics. 2013 Oct;13(20):2931-7. doi: 10.1002/pmic.201370166.

PMID:
24108681
40.

Capturing cooperative interactions with the PSI-MI format.

Van Roey K, Orchard S, Kerrien S, Dumousseau M, Ricard-Blum S, Hermjakob H, Gibson TJ.

Database (Oxford). 2013 Sep 25;2013:bat066. doi: 10.1093/database/bat066. Print 2013.

41.

A new reference implementation of the PSICQUIC web service.

del-Toro N, Dumousseau M, Orchard S, Jimenez RC, Galeota E, Launay G, Goll J, Breuer K, Ono K, Salwinski L, Hermjakob H.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W601-6. doi: 10.1093/nar/gkt392. Epub 2013 May 13.

42.

Exploring higher-order EGFR oligomerisation and phosphorylation--a combined experimental and theoretical approach.

Kozer N, Barua D, Orchard S, Nice EC, Burgess AW, Hlavacek WS, Clayton AH.

Mol Biosyst. 2013 Jul;9(7):1849-63. doi: 10.1039/c3mb70073a. Epub 2013 Apr 30.

43.

Data standardization and sharing-the work of the HUPO-PSI.

Orchard S.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):82-7. doi: 10.1016/j.bbapap.2013.03.011. Epub 2013 Mar 20. Review.

PMID:
23524294
44.

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaíno JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M; HUPO-PSI Group.

Database (Oxford). 2013 Mar 12;2013:bat009. doi: 10.1093/database/bat009. Print 2013.

45.

BioJS: an open source JavaScript framework for biological data visualization.

Gómez J, García LJ, Salazar GA, Villaveces J, Gore S, García A, Martín MJ, Launay G, Alcántara R, Del-Toro N, Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, Ping P, Corpas M, Jiménez RC.

Bioinformatics. 2013 Apr 15;29(8):1103-4. doi: 10.1093/bioinformatics/btt100. Epub 2013 Feb 23.

46.

Controlled vocabularies and ontologies in proteomics: overview, principles and practice.

Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):98-107. doi: 10.1016/j.bbapap.2013.02.017. Epub 2013 Feb 19. Review.

47.

Ligand binding induces a conformational change in epidermal growth factor receptor dimers.

Walker F, Rothacker J, Henderson C, Nice EC, Catimel B, Zhang HH, Scott AM, Bailey MF, Orchard SG, Adams TE, Liu Z, Garrett TP, Clayton AH, Burgess AW.

Growth Factors. 2012 Dec;30(6):394-409. doi: 10.3109/08977194.2012.739619. Epub 2012 Nov 20.

PMID:
23163584
48.

Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA.

Orchard S, Binz PA, Borchers C, Gilson MK, Jones AR, Nicola G, Vizcaino JA, Deutsch EW, Hermjakob H.

Proteomics. 2012 Sep;12(18):2767-72. doi: 10.1002/pmic.201270126.

49.

Penicillium menonorum, a new species related to P. pimiteouiense.

Peterson SW, Orchard SS, Menon S.

IMA Fungus. 2011 Dec;2(2):121-5. doi: 10.5598/imafungus.2011.02.02.02. Epub 2011 Sep 29.

50.

Molecular interaction databases.

Orchard S.

Proteomics. 2012 May;12(10):1656-62. doi: 10.1002/pmic.201100484. Review.

PMID:
22611057

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