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Items: 1 to 50 of 84

1.

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
2.

A family of radical halogenases for the engineering of amino-acid-based products.

Neugebauer ME, Sumida KH, Pelton JG, McMurry JL, Marchand JA, Chang MCY.

Nat Chem Biol. 2019 Oct;15(10):1009-1016. doi: 10.1038/s41589-019-0355-x. Epub 2019 Sep 23.

PMID:
31548692
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.

Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome.

Rusch M, Nakitandwe J, Shurtleff S, Newman S, Zhang Z, Edmonson MN, Parker M, Jiao Y, Ma X, Liu Y, Gu J, Walsh MF, Becksfort J, Thrasher A, Li Y, McMurry J, Hedlund E, Patel A, Easton J, Yergeau D, Vadodaria B, Tatevossian RG, Raimondi S, Hedges D, Chen X, Hagiwara K, McGee R, Robinson GW, Klco JM, Gruber TA, Ellison DW, Downing JR, Zhang J.

Nat Commun. 2018 Sep 27;9(1):3962. doi: 10.1038/s41467-018-06485-7.

7.

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.

8.

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.

9.

SUMO targeting of a stress-tolerant Ulp1 SUMO protease.

Peek J, Harvey C, Gray D, Rosenberg D, Kolla L, Levy-Myers R, Yin R, McMurry JL, Kerscher O.

PLoS One. 2018 Jan 19;13(1):e0191391. doi: 10.1371/journal.pone.0191391. eCollection 2018.

10.

Fluorothreonyl-tRNA deacylase prevents mistranslation in the organofluorine producer Streptomyces cattleya.

McMurry JL, Chang MCY.

Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):11920-11925. doi: 10.1073/pnas.1711482114. Epub 2017 Oct 23.

11.

Breaking in and busting out: cell-penetrating peptides and the endosomal escape problem.

LeCher JC, Nowak SJ, McMurry JL.

Biomol Concepts. 2017 Sep 26;8(3-4):131-141. doi: 10.1515/bmc-2017-0023. Review.

12.

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.

13.

A versatile cell-penetrating peptide-adaptor system for efficient delivery of molecular cargos to subcellular destinations.

Ngwa VM, Axford DS, Healey AN, Nowak SJ, Chrestensen CA, McMurry JL.

PLoS One. 2017 May 26;12(5):e0178648. doi: 10.1371/journal.pone.0178648. eCollection 2017.

14.

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.

15.

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.

16.

The Human Phenotype Ontology in 2017.

Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJ, DeMare LE, Devereau AD, de Vries BB, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MW, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JO, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN.

Nucleic Acids Res. 2017 Jan 4;45(D1):D865-D876. doi: 10.1093/nar/gkw1039. Epub 2016 Nov 28. Review.

17.

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.

18.

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.

19.

Identification of Preferred DNA-Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA.

Van Dyke MW, Beyer MD, Clay E, Hiam KJ, McMurry JL, Xie Y.

PLoS One. 2016 Jul 18;11(7):e0159408. doi: 10.1371/journal.pone.0159408. eCollection 2016.

20.

Novel cell-penetrating peptide-adaptors effect intracellular delivery and endosomal escape of protein cargos.

Salerno JC, Ngwa VM, Nowak SJ, Chrestensen CA, Healey AN, McMurry JL.

J Cell Sci. 2016 Jun 15;129(12):2473-4. doi: 10.1242/jcs.192666. No abstract available.

21.

Localisation and protein-protein interactions of the Helicobacter pylori taxis sensor TlpD and their connection to metabolic functions.

Behrens W, Schweinitzer T, McMurry JL, Loewen PC, Buettner FF, Menz S, Josenhans C.

Sci Rep. 2016 Apr 5;6:23582. doi: 10.1038/srep23582.

22.

The SH3 domain of UNC-89 (obscurin) interacts with paramyosin, a coiled-coil protein, in Caenorhabditis elegans muscle.

Qadota H, Mayans O, Matsunaga Y, McMurry JL, Wilson KJ, Kwon GE, Stanford R, Deehan K, Tinley TL, Ngwa VM, Benian GM.

Mol Biol Cell. 2016 May 15;27(10):1606-20. doi: 10.1091/mbc.E15-09-0675. Epub 2016 Mar 23.

23.

EFN-4 functions in LAD-2-mediated axon guidance in Caenorhabditis elegans.

Dong B, Moseley-Alldredge M, Schwieterman AA, Donelson CJ, McMurry JL, Hudson ML, Chen L.

Development. 2016 Apr 1;143(7):1182-91. doi: 10.1242/dev.128934. Epub 2016 Feb 22.

24.

Novel cell-penetrating peptide-adaptors effect intracellular delivery and endosomal escape of protein cargos.

Salerno JC, Ngwa VM, Nowak SJ, Chrestensen CA, Healey AN, McMurry JL.

J Cell Sci. 2016 Mar 1;129(5):893-7. doi: 10.1242/jcs.182113. Epub 2016 Jan 22. Erratum in: J Cell Sci. 2016 Jun 15;129(12):2473-4.

25.

The Caenorhabditis elegans Ephrin EFN-4 Functions Non-cell Autonomously with Heparan Sulfate Proteoglycans to Promote Axon Outgrowth and Branching.

Schwieterman AA, Steves AN, Yee V, Donelson CJ, Bentley MR, Santorella EM, Mehlenbacher TV, Pital A, Howard AM, Wilson MR, Ereddia DE, Effrein KS, McMurry JL, Ackley BD, Chisholm AD, Hudson ML.

Genetics. 2016 Feb;202(2):639-60. doi: 10.1534/genetics.115.185298. Epub 2015 Dec 8.

26.

Weak Interactions between Salmonella enterica FlhB and Other Flagellar Export Apparatus Proteins Govern Type III Secretion Dynamics.

McMurry JL, Minamino T, Furukawa Y, Francis JW, Hill SA, Helms KA, Namba K.

PLoS One. 2015 Aug 5;10(8):e0134884. doi: 10.1371/journal.pone.0134884. eCollection 2015.

27.

Helicobacter pylori FlhA Binds the Sensor Kinase and Flagellar Gene Regulatory Protein FlgS with High Affinity.

Tsang J, Hirano T, Hoover TR, McMurry JL.

J Bacteriol. 2015 Jun;197(11):1886-92. doi: 10.1128/JB.02610-14. Epub 2015 Mar 23.

28.

Endothelial nitric oxide synthase is regulated by ERK phosphorylation at Ser602.

Salerno JC, Ghosh DK, Razdan R, Helms KA, Brown CC, McMurry JL, Rye EA, Chrestensen CA.

Biosci Rep. 2014 Sep 17;34(5). pii: e00137. doi: 10.1042/BSR20140015.

29.

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.

Nucleic Acids Res. 2014 Jan;42(Database issue):D926-32. doi: 10.1093/nar/gkt1270. Epub 2013 Dec 4.

30.

Characterization of Myxococcus xanthus MazF and implications for a new point of regulation.

Boynton TO, McMurry JL, Shimkets LJ.

Mol Microbiol. 2013 Mar;87(6):1267-76. doi: 10.1111/mmi.12165. Epub 2013 Feb 25.

31.

Helicobacter pylori hydrogenase accessory protein HypA and urease accessory protein UreG compete with each other for UreE recognition.

Benoit SL, McMurry JL, Hill SA, Maier RJ.

Biochim Biophys Acta. 2012 Oct;1820(10):1519-25. doi: 10.1016/j.bbagen.2012.06.002. Epub 2012 Jun 12.

32.

Characterization of crude Echis carinatus venom-induced cytotoxicity in HEK 293T cells.

Pierce RD, Kim ES, Girton LW, McMurry JL, Francis JW, Albrecht EA.

J Venom Res. 2011;2:59-67. Epub 2011 Dec 28.

33.

MAP kinases bind endothelial nitric oxide synthase.

Chrestensen CA, McMurry JL, Salerno JC.

FEBS Open Bio. 2012 Feb 28;2:51-5. doi: 10.1016/j.fob.2012.02.002. Print 2012.

34.

Rate, affinity and calcium dependence of nitric oxide synthase isoform binding to the primary physiological regulator calmodulin.

McMurry JL, Chrestensen CA, Scott IM, Lee EW, Rahn AM, Johansen AM, Forsberg BJ, Harris KD, Salerno JC.

FEBS J. 2011 Dec;278(24):4943-54. doi: 10.1111/j.1742-4658.2011.08395.x. Epub 2011 Nov 11.

35.

Optical biosensing: Kinetics of protein A-IGG binding using biolayer interferometry.

Wilson JL, Scott IM, McMurry JL.

Biochem Mol Biol Educ. 2010 Nov;38(6):400-7. doi: 10.1002/bmb.20442.

36.

Kinetic characterization of Salmonella FliK-FlhB interactions demonstrates complexity of the Type III secretion substrate-specificity switch.

Morris DP, Roush ED, Thompson JW, Moseley MA, Murphy JW, McMurry JL.

Biochemistry. 2010 Aug 3;49(30):6386-93. doi: 10.1021/bi100487p.

37.

Flagellar formation in C-ring-defective mutants by overproduction of FliI, the ATPase specific for flagellar type III secretion.

Konishi M, Kanbe M, McMurry JL, Aizawa S.

J Bacteriol. 2009 Oct;191(19):6186-91. doi: 10.1128/JB.00601-09. Epub 2009 Jul 31.

38.

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.

39.

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.

40.

The Helicobacter pylori anti-sigma factor FlgM is predominantly cytoplasmic and cooperates with the flagellar basal body protein FlhA.

Rust M, Borchert S, Niehus E, Kuehne SA, Gripp E, Bajceta A, McMurry JL, Suerbaum S, Hughes KT, Josenhans C.

J Bacteriol. 2009 Aug;191(15):4824-34. doi: 10.1128/JB.00018-09. Epub 2009 May 22.

41.

Prediction of immunogenicity: in silico paradigms, ex vivo and in vivo correlates.

De Groot AS, McMurry J, Moise L.

Curr Opin Pharmacol. 2008 Oct;8(5):620-6. doi: 10.1016/j.coph.2008.08.002. Epub 2008 Sep 19. Review.

PMID:
18775515
42.

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.

43.

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
44.

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
45.

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.

46.

Novel function of complement C3d as an autologous helper T-cell target.

Knopf PM, Rivera DS, Hai SH, McMurry J, Martin W, De Groot AS.

Immunol Cell Biol. 2008 Mar-Apr;86(3):221-5. doi: 10.1038/sj.icb.7100147. Epub 2008 Jan 8.

PMID:
18180801
47.

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
48.

Progress towards a genome-derived, epitope-driven vaccine for latent TB infection.

Moise L, McMurry J, Rivera DS, Carter EJ, Lee J, Kornfeld H, Martin WD, De Groot AS.

Med Health R I. 2007 Oct;90(10):301-3. Review. No abstract available.

PMID:
18019185
49.

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
50.

Hydrodynamic surface interactions enable Escherichia coli to seek efficient routes to swim upstream.

Hill J, Kalkanci O, McMurry JL, Koser H.

Phys Rev Lett. 2007 Feb 9;98(6):068101. Epub 2007 Feb 6.

PMID:
17358984

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