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Items: 22

1.

Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery.

Gourdine JF, Brush MH, Vasilevsky NA, Shefchek K, Köhler S, Matentzoglu N, Munoz-Torres MC, McMurry JA, Zhang XA, Robinson PN, Haendel MA.

Database (Oxford). 2019 Jan 1;2019. pii: baz114. doi: 10.1093/database/baz114.

2.

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Rocca MD, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D.

Nucleic Acids Res. 2019 Nov 8. pii: gkz997. doi: 10.1093/nar/gkz997. [Epub ahead of print]

PMID:
31701156
3.

Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics.

Köhler S, Øien NC, Buske OJ, Groza T, Jacobsen JOB, McNamara C, Vasilevsky N, Carmody LC, Gourdine JP, Gargano M, McMurry JA, Danis D, Mungall CJ, Smedley D, Haendel M, Robinson PN.

Curr Protoc Hum Genet. 2019 Sep;103(1):e92. doi: 10.1002/cphg.92.

PMID:
31479590
4.

An analysis and metric of reusable data licensing practices for biomedical resources.

Carbon S, Champieux R, McMurry JA, Winfree L, Wyatt LR, Haendel MA.

PLoS One. 2019 Mar 27;14(3):e0213090. doi: 10.1371/journal.pone.0213090. eCollection 2019.

5.

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.

Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine JP, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Osumi-Sutherland D, Cipriani V, Balhoff JP, Conlin T, Blau H, Baynam G, Palmer R, Gratian D, Dawkins H, Segal M, Jansen AC, Muaz A, Chang WH, Bergerson J, Laulederkind SJF, Yüksel Z, Beltran S, Freeman AF, Sergouniotis PI, Durkin D, Storm AL, Hanauer M, Brudno M, Bello SM, Sincan M, Rageth K, Wheeler MT, Oegema R, Lourghi H, Della Rocca MG, Thompson R, Castellanos F, Priest J, Cunningham-Rundles C, Hegde A, Lovering RC, Hajek C, Olry A, Notarangelo L, Similuk M, Zhang XA, Gómez-Andrés D, Lochmüller H, Dollfus H, Rosenzweig S, Marwaha S, Rath A, Sullivan K, Smith C, Milner JD, Leroux D, Boerkoel CF, Klion A, Carter MC, Groza T, Smedley D, Haendel MA, Mungall C, Robinson PN.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1018-D1027. doi: 10.1093/nar/gky1105.

6.

Uniform resolution of compact identifiers for biomedical data.

Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T.

Sci Data. 2018 May 8;5:180029. doi: 10.1038/sdata.2018.29.

7.

Plain-language medical vocabulary for precision diagnosis.

Vasilevsky NA, Foster ED, Engelstad ME, Carmody L, Might M, Chambers C, Dawkins HJS, Lewis J, Della Rocca MG, Snyder M, Boerkoel CF, Rath A, Terry SF, Kent A, Searle B, Baynam G, Jones E, Gavin P, Bamshad M, Chong J, Groza T, Adams D, Resnick AC, Heath AP, Mungall C, Holm IA, Rageth K, Brownstein CA, Shefchek K, McMurry JA, Robinson PN, Köhler S, Haendel MA.

Nat Genet. 2018 Apr;50(4):474-476. doi: 10.1038/s41588-018-0096-x. No abstract available.

8.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H.

PLoS Biol. 2017 Jun 29;15(6):e2001414. doi: 10.1371/journal.pbio.2001414. eCollection 2017 Jun.

9.

Sharing Clinical and Genomic Data on Cancer - The Need for Global Solutions.

Clinical Cancer Genome Task Team of the Global Alliance for Genomics and Health, Lawler M, Haussler D, Siu LL, Haendel MA, McMurry JA, Knoppers BM, Chanock SJ, Calvo F, The BT, Walia G, Banks I, Yu PP, Staudt LM, Sawyers CL.

N Engl J Med. 2017 May 25;376(21):2006-2009. doi: 10.1056/NEJMp1612254. No abstract available.

10.

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Mungall CJ, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Lewis SE, NguyenXuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, Haendel MA.

Nucleic Acids Res. 2017 Jan 4;45(D1):D712-D722. doi: 10.1093/nar/gkw1128. Epub 2016 Nov 29.

11.

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease.

Smedley D, Schubach M, Jacobsen JOB, Köhler S, Zemojtel T, Spielmann M, Jäger M, Hochheiser H, Washington NL, McMurry JA, Haendel MA, Mungall CJ, Lewis SE, Groza T, Valentini G, Robinson PN.

Am J Hum Genet. 2016 Sep 1;99(3):595-606. doi: 10.1016/j.ajhg.2016.07.005. Epub 2016 Aug 25.

12.

Navigating the Phenotype Frontier: The Monarch Initiative.

McMurry JA, Köhler S, Washington NL, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Xuan JN, Shefchek K, Vasilevsky NA, Yuan Z, Lewis SE, Hochheiser H, Groza T, Smedley D, Robinson PN, Mungall CJ, Haendel MA.

Genetics. 2016 Aug;203(4):1491-5. doi: 10.1534/genetics.116.188870.

13.

Epitope-based vaccination against pneumonic tularemia.

Gregory SH, Mott S, Phung J, Lee J, Moise L, McMurry JA, Martin W, De Groot AS.

Vaccine. 2009 Aug 27;27(39):5299-306. doi: 10.1016/j.vaccine.2009.06.101. Epub 2009 Jul 17.

14.

In silico-accelerated identification of conserved and immunogenic variola/vaccinia T-cell epitopes.

Moise L, McMurry JA, Buus S, Frey S, Martin WD, De Groot AS.

Vaccine. 2009 Oct 30;27(46):6471-9. doi: 10.1016/j.vaccine.2009.06.018. Epub 2009 Jun 24.

15.

Activation of natural regulatory T cells by IgG Fc-derived peptide "Tregitopes".

De Groot AS, Moise L, McMurry JA, Wambre E, Van Overtvelt L, Moingeon P, Scott DW, Martin W.

Blood. 2008 Oct 15;112(8):3303-11. doi: 10.1182/blood-2008-02-138073. Epub 2008 Jul 25.

16.

A call to cellular & humoral arms: enlisting cognate T cell help to develop broad-spectrum vaccines against influenza A.

McMurry JA, Johansson BE, De Groot AS.

Hum Vaccin. 2008 Mar-Apr;4(2):148-57. Epub 2007 Oct 14. Review.

PMID:
18382131
17.

Identification of genome-derived vaccine candidates conserved between human and mouse-adapted strains of H. pylori.

Moise L, McMurry JA, Pappo J, Lee DS, Moss SF, Martin WD, De Groot AS.

Hum Vaccin. 2008 May-Jun;4(3):219-23. Epub 2010 May 8.

PMID:
18376134
18.

Identification of immunogenic HLA-B7 "Achilles' heel" epitopes within highly conserved regions of HIV.

De Groot AS, Rivera DS, McMurry JA, Buus S, Martin W.

Vaccine. 2008 Jun 6;26(24):3059-71. doi: 10.1016/j.vaccine.2007.12.004. Epub 2007 Dec 26.

19.

Tularemia vaccines - an overview.

McMurry JA, Moise L, Gregory SH, De Groot AS.

Med Health R I. 2007 Oct;90(10):311-4. Review.

PMID:
18019188
20.

Epitope-driven TB vaccine development: a streamlined approach using immuno-informatics, ELISpot assays, and HLA transgenic mice.

McMurry JA, Kimball S, Lee JH, Rivera D, Martin W, Weiner DB, Kutzler M, Sherman DR, Kornfeld H, De Groot AS.

Curr Mol Med. 2007 Jun;7(4):351-68.

PMID:
17584075
21.
22.

Confirmation of immunogenic consensus sequence HIV-1 T-cell epitopes in Bamako, Mali and Providence, Rhode Island.

Koita OA, Dabitao D, Mahamadou I, Tall M, Dao S, Tounkara A, Guiteye H, Noumsi C, Thiero O, Kone M, Rivera D, McMurry JA, Martin W, De Groot AS.

Hum Vaccin. 2006 May-Jun;2(3):119-28. Epub 2006 May 25.

PMID:
17012903

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