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Items: 1 to 50 of 262

1.

KBase: The United States Department of Energy Systems Biology Knowledgebase.

Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D.

Nat Biotechnol. 2018 Jul 6;36(7):566-569. doi: 10.1038/nbt.4163. No abstract available.

PMID:
29979655
2.

Practitioner Application: Shifts in Medicaid and Uninsured Payer Mix at Safety-Net and Non-Safety-Net Hospitals During the Great Recession.

Stevens RL.

J Healthc Manag. 2018 May-Jun;63(3):173-174. doi: 10.1097/JHM-D-18-00033. No abstract available.

PMID:
29734278
3.

Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae.

Nguyen M, Brettin T, Long SW, Musser JM, Olsen RJ, Olson R, Shukla M, Stevens RL, Xia F, Yoo H, Davis JJ.

Sci Rep. 2018 Jan 11;8(1):421. doi: 10.1038/s41598-017-18972-w.

4.

Provitamin A biofortification of cassava enhances shelf life but reduces dry matter content of storage roots due to altered carbon partitioning into starch.

Beyene G, Solomon FR, Chauhan RD, Gaitán-Solis E, Narayanan N, Gehan J, Siritunga D, Stevens RL, Jifon J, Van Eck J, Linsler E, Gehan M, Ilyas M, Fregene M, Sayre RT, Anderson P, Taylor NJ, Cahoon EB.

Plant Biotechnol J. 2018 Jun;16(6):1186-1200. doi: 10.1111/pbi.12862. Epub 2017 Dec 27.

5.

A communal catalogue reveals Earth's multiscale microbial diversity.

Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project Consortium.

Nature. 2017 Nov 23;551(7681):457-463. doi: 10.1038/nature24621. Epub 2017 Nov 1.

PMID:
29088705
6.

PATRIC as a unique resource for studying antimicrobial resistance.

Antonopoulos DA, Assaf R, Aziz RK, Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S, Kenyon RW, Machi D, Mao C, Murphy-Olson DE, Nordberg EK, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Santerre J, Shukla M, Stevens RL, VanOeffelen M, Vonstein V, Warren AS, Wattam AR, Xia F, Yoo H.

Brief Bioinform. 2017 Jul 31. doi: 10.1093/bib/bbx083. [Epub ahead of print]

PMID:
28968762
7.

Experimental Arthritis Is Dependent on Mouse Mast Cell Protease-5.

Stevens RL, McNeil HP, Wensing LA, Shin K, Wong GW, Hansbro PM, Krilis SA.

J Biol Chem. 2017 Mar 31;292(13):5392-5404. doi: 10.1074/jbc.M116.773416. Epub 2017 Feb 13.

8.

Mutation in an Unannotated Protein Confers Carbapenem Resistance in Mycobacterium tuberculosis.

Kumar P, Kaushik A, Bell DT, Chauhan V, Xia F, Stevens RL, Lamichhane G.

Antimicrob Agents Chemother. 2017 Feb 23;61(3). pii: e02234-16. doi: 10.1128/AAC.02234-16. Print 2017 Mar.

9.

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation.

Faria JP, Davis JJ, Edirisinghe JN, Taylor RC, Weisenhorn P, Olson RD, Stevens RL, Rocha M, Rocha I, Best AA, DeJongh M, Tintle NL, Parrello B, Overbeek R, Henry CS.

Front Microbiol. 2016 Nov 24;7:1819. eCollection 2016.

10.

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.

Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard JL, Gerdes S, Henry CS, Kenyon RW, Machi D, Mao C, Nordberg EK, Olsen GJ, Murphy-Olson DE, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Vonstein V, Warren A, Xia F, Yoo H, Stevens RL.

Nucleic Acids Res. 2017 Jan 4;45(D1):D535-D542. doi: 10.1093/nar/gkw1017. Epub 2016 Nov 29.

11.

The Sin of Prediction: When Mentally Simulated Alternatives Compete With Reality.

Petrocelli JV, Rubin AL, Stevens RL.

Pers Soc Psychol Bull. 2016 Dec;42(12):1635-1652. Epub 2016 Oct 13.

PMID:
27738193
12.

The Trajectory of Pharmacology Education in Dentistry: Is a Course Correction Needed?

Curro FA, Mozaffari MS, Stevens RL, Warner W.

Compend Contin Educ Dent. 2016 Sep;37(8):508-11.

PMID:
27608195
13.

Modeling central metabolism and energy biosynthesis across microbial life.

Edirisinghe JN, Weisenhorn P, Conrad N, Xia F, Overbeek R, Stevens RL, Henry CS.

BMC Genomics. 2016 Aug 8;17:568. doi: 10.1186/s12864-016-2887-8.

14.

REMap: Operon map of M. tuberculosis based on RNA sequence data.

Pelly S, Winglee K, Xia FF, Stevens RL, Bishai WR, Lamichhane G.

Tuberculosis (Edinb). 2016 Jul;99:70-80. doi: 10.1016/j.tube.2016.04.010. Epub 2016 Apr 29.

15.

CD117+ Dendritic and Mast Cells Are Dependent on RasGRP4 to Function as Accessory Cells for Optimal Natural Killer Cell-Mediated Responses to Lipopolysaccharide.

Zhou S, Tanaka K, O'Keeffe M, Qi M, El-Assaad F, Weaver JC, Chen G, Weatherall C, Wang Y, Giannakopoulos B, Chen L, Yu D, Hamilton MJ, Wensing LA, Stevens RL, Krilis SA.

PLoS One. 2016 Mar 16;11(3):e0151638. doi: 10.1371/journal.pone.0151638. eCollection 2016.

16.

The multifaceted mast cell in inflammatory bowel disease.

Hamilton MJ, Frei SM, Stevens RL.

Inflamm Bowel Dis. 2014 Dec;20(12):2364-78. doi: 10.1097/MIB.0000000000000142. Review.

17.

Ras guanine nucleotide-releasing protein 4 is aberrantly expressed in the fibroblast-like synoviocytes of patients with rheumatoid arthritis and controls their proliferation.

Kono M, Yasuda S, Stevens RL, Koide H, Kurita T, Shimizu Y, Kanetsuka Y, Oku K, Bohgaki T, Amengual O, Horita T, Shimizu T, Majima T, Koike T, Atsumi T.

Arthritis Rheumatol. 2015 Feb;67(2):396-407. doi: 10.1002/art.38924.

18.

Mast cell-derived htryptase-beta functions as a potent anticoagulant by proteolytically damaging fibrinogen.

Prieto-García A, Castells MC, Stevens RL.

J Investig Allergol Clin Immunol. 2014;24(4):286-7. No abstract available.

19.

Ancient origin of mast cells.

Wong GW, Zhuo L, Kimata K, Lam BK, Satoh N, Stevens RL.

Biochem Biophys Res Commun. 2014 Aug 22;451(2):314-8. doi: 10.1016/j.bbrc.2014.07.124. Epub 2014 Aug 2.

20.

Standardized metadata for human pathogen/vector genomic sequences.

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH.

PLoS One. 2014 Jun 17;9(6):e99979. doi: 10.1371/journal.pone.0099979. eCollection 2014.

21.

Comparing spatial and temporal changes in metal trends (Cr, Ni, Pb and Zn) on the Portuguese shelf since the 1970s.

Mil-Homens M, Stevens RL, Cato I, Abrantes F.

Environ Monit Assess. 2014 Oct;186(10):6327-40. doi: 10.1007/s10661-014-3857-8. Epub 2014 May 31.

PMID:
24879363
22.

Importance of mast cell Prss31/transmembrane tryptase/tryptase-γ in lung function and experimental chronic obstructive pulmonary disease and colitis.

Hansbro PM, Hamilton MJ, Fricker M, Gellatly SL, Jarnicki AG, Zheng D, Frei SM, Wong GW, Hamadi S, Zhou S, Foster PS, Krilis SA, Stevens RL.

J Biol Chem. 2014 Jun 27;289(26):18214-27. doi: 10.1074/jbc.M114.548594. Epub 2014 May 12.

23.

Mast cell-restricted tetramer-forming tryptases and their beneficial roles in hemostasis and blood coagulation.

Prieto-García A, Castells MC, Hansbro PM, Stevens RL.

Immunol Allergy Clin North Am. 2014 May;34(2):263-81. doi: 10.1016/j.iac.2014.01.001. Epub 2014 Mar 15. Review.

PMID:
24745673
24.

Mouse mast cell proteases 4 and 5 mediate epidermal injury through disruption of tight junctions.

Bankova LG, Lezcano C, Pejler G, Stevens RL, Murphy GF, Austen KF, Gurish MF.

J Immunol. 2014 Mar 15;192(6):2812-20. doi: 10.4049/jimmunol.1301794. Epub 2014 Feb 12.

25.

Development of mast cells and importance of their tryptase and chymase serine proteases in inflammation and wound healing.

Douaiher J, Succar J, Lancerotto L, Gurish MF, Orgill DP, Hamilton MJ, Krilis SA, Stevens RL.

Adv Immunol. 2014;122:211-52. doi: 10.1016/B978-0-12-800267-4.00006-7. Review.

26.

Large-scale modeling of epileptic seizures: scaling properties of two parallel neuronal network simulation algorithms.

Pesce LL, Lee HC, Hereld M, Visser S, Stevens RL, Wildeman A, van Drongelen W.

Comput Math Methods Med. 2013;2013:182145. doi: 10.1155/2013/182145. Epub 2013 Dec 15.

27.

PATRIC, the bacterial bioinformatics database and analysis resource.

Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJ, Yoo HS, Zhang C, Zhang Y, Sobral BW.

Nucleic Acids Res. 2014 Jan;42(Database issue):D581-91. doi: 10.1093/nar/gkt1099. Epub 2013 Nov 12.

28.

A thraustochytrid diacylglycerol acyltransferase 2 with broad substrate specificity strongly increases oleic acid content in engineered Arabidopsis thaliana seeds.

Zhang C, Iskandarov U, Klotz ET, Stevens RL, Cahoon RE, Nazarenus TJ, Pereira SL, Cahoon EB.

J Exp Bot. 2013 Aug;64(11):3189-200. doi: 10.1093/jxb/ert156. Epub 2013 Jun 28.

29.

Mast cell-restricted, tetramer-forming tryptases induce aggrecanolysis in articular cartilage by activating matrix metalloproteinase-3 and -13 zymogens.

Magarinos NJ, Bryant KJ, Fosang AJ, Adachi R, Stevens RL, McNeil HP.

J Immunol. 2013 Aug 1;191(3):1404-12. doi: 10.4049/jimmunol.1300856. Epub 2013 Jun 24.

30.

A new short-term mouse model of chronic obstructive pulmonary disease identifies a role for mast cell tryptase in pathogenesis.

Beckett EL, Stevens RL, Jarnicki AG, Kim RY, Hanish I, Hansbro NG, Deane A, Keely S, Horvat JC, Yang M, Oliver BG, van Rooijen N, Inman MD, Adachi R, Soberman RJ, Hamadi S, Wark PA, Foster PS, Hansbro PM.

J Allergy Clin Immunol. 2013 Mar;131(3):752-62. doi: 10.1016/j.jaci.2012.11.053. Epub 2013 Feb 4.

31.

SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models.

Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Stevens RL, Vonstein V, Xia F.

PLoS One. 2012;7(10):e48053. doi: 10.1371/journal.pone.0048053. Epub 2012 Oct 24.

32.

Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model.

Tanaka K, Henry CS, Zinner JF, Jolivet E, Cohoon MP, Xia F, Bidnenko V, Ehrlich SD, Stevens RL, Noirot P.

Nucleic Acids Res. 2013 Jan 7;41(1):687-99. doi: 10.1093/nar/gks963. Epub 2012 Oct 29.

33.

Interleukin-33 primes mast cells for activation by IgG immune complexes.

Kaieda S, Wang JX, Shnayder R, Fishgal N, Hei H, Lee RT, Stevens RL, Nigrovic PA.

PLoS One. 2012;7(10):e47252. doi: 10.1371/journal.pone.0047252. Epub 2012 Oct 11.

34.

Programming of the lung by early-life infection.

Hansbro PM, Starkey MR, Kim RY, Stevens RL, Foster PS, Horvat JC.

J Dev Orig Health Dis. 2012 Jun;3(3):153-8. doi: 10.1017/S2040174412000050.

PMID:
25102006
35.

The translational repressor T-cell intracellular antigen-1 (TIA-1) is a key modulator of Th2 and Th17 responses driving pulmonary inflammation induced by exposure to house dust mite.

Simarro M, Giannattasio G, Xing W, Lundequist EM, Stewart S, Stevens RL, Orduña A, Boyce JA, Anderson PJ.

Immunol Lett. 2012 Aug 30;146(1-2):8-14. doi: 10.1016/j.imlet.2012.04.001. Epub 2012 Apr 15.

36.

Ras guanine nucleotide-releasing protein-4 (RasGRP4) involvement in experimental arthritis and colitis.

Adachi R, Krilis SA, Nigrovic PA, Hamilton MJ, Chung K, Thakurdas SM, Boyce JA, Anderson P, Stevens RL.

J Biol Chem. 2012 Jun 8;287(24):20047-55. doi: 10.1074/jbc.M112.360388. Epub 2012 Apr 16.

37.

Mast cell restricted mouse and human tryptase·heparin complexes hinder thrombin-induced coagulation of plasma and the generation of fibrin by proteolytically destroying fibrinogen.

Prieto-García A, Zheng D, Adachi R, Xing W, Lane WS, Chung K, Anderson P, Hansbro PM, Castells M, Stevens RL.

J Biol Chem. 2012 Mar 9;287(11):7834-44. doi: 10.1074/jbc.M111.325712. Epub 2012 Jan 10.

38.

Mast cell tryptase deficiency attenuates mouse abdominal aortic aneurysm formation.

Zhang J, Sun J, Lindholt JS, Sukhova GK, Sinnamon M, Stevens RL, Adachi R, Libby P, Thompson RW, Shi GP.

Circ Res. 2011 May 27;108(11):1316-27. doi: 10.1161/CIRCRESAHA.111.243758. Epub 2011 Apr 14.

39.

Connecting genotype to phenotype in the era of high-throughput sequencing.

Henry CS, Overbeek R, Xia F, Best AA, Glass E, Gilbert J, Larsen P, Edwards R, Disz T, Meyer F, Vonstein V, Dejongh M, Bartels D, Desai N, D'Souza M, Devoid S, Keegan KP, Olson R, Wilke A, Wilkening J, Stevens RL.

Biochim Biophys Acta. 2011 Oct;1810(10):967-77. doi: 10.1016/j.bbagen.2011.03.010. Epub 2011 Mar 21. Review.

PMID:
21421023
40.

Essential role for mast cell tryptase in acute experimental colitis.

Hamilton MJ, Sinnamon MJ, Lyng GD, Glickman JN, Wang X, Xing W, Krilis SA, Blumberg RS, Adachi R, Lee DM, Stevens RL.

Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):290-5. doi: 10.1073/pnas.1005758108. Epub 2010 Dec 20.

41.

Systematic comparison of the behaviors produced by computational models of epileptic neocortex.

Warlaumont AS, Lee HC, Benayoun M, Stevens RL, Hereld M.

J Clin Neurophysiol. 2010 Dec;27(6):479-83. doi: 10.1097/WNP.0b013e3181fe074c.

PMID:
21076331
42.

The inflammatory response after an epidermal burn depends on the activities of mouse mast cell proteases 4 and 5.

Younan G, Suber F, Xing W, Shi T, Kunori Y, Abrink M, Pejler G, Schlenner SM, Rodewald HR, Moore FD Jr, Stevens RL, Adachi R, Austen KF, Gurish MF.

J Immunol. 2010 Dec 15;185(12):7681-90. doi: 10.4049/jimmunol.1002803. Epub 2010 Nov 12.

43.

High-throughput generation, optimization and analysis of genome-scale metabolic models.

Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL.

Nat Biotechnol. 2010 Sep;28(9):977-82. doi: 10.1038/nbt.1672. Epub 2010 Aug 29.

PMID:
20802497
44.

Building the blueprint of life.

Henry C, Overbeek R, Stevens RL.

Biotechnol J. 2010 Jul;5(7):695-704. doi: 10.1002/biot.201000076. Review.

PMID:
20665643
45.

Synovial fibroblasts promote the expression and granule accumulation of tryptase via interleukin-33 and its receptor ST-2 (IL1RL1).

Kaieda S, Shin K, Nigrovic PA, Seki K, Lee RT, Stevens RL, Lee DM.

J Biol Chem. 2010 Jul 9;285(28):21478-86. doi: 10.1074/jbc.M110.114991. Epub 2010 Apr 28.

46.

Nutritional vitamin D deficiency: a case report.

Stevens RL, Lyon C.

Cases J. 2009 May 14;2:7000. doi: 10.1186/1757-1626-2-7000.

47.

Critical role of mast cell chymase in mouse abdominal aortic aneurysm formation.

Sun J, Zhang J, Lindholt JS, Sukhova GK, Liu J, He A, Abrink M, Pejler G, Stevens RL, Thompson RW, Ennis TL, Gurish MF, Libby P, Shi GP.

Circulation. 2009 Sep 15;120(11):973-82. doi: 10.1161/CIRCULATIONAHA.109.849679. Epub 2009 Aug 31.

48.

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations.

Henry CS, Zinner JF, Cohoon MP, Stevens RL.

Genome Biol. 2009;10(6):R69. doi: 10.1186/gb-2009-10-6-r69. Epub 2009 Jun 25.

49.

Stress in the ER leads to inflammatory bowel disease.

Hamilton MJ, Stevens RL.

Inflamm Bowel Dis. 2009 Nov;15(11):1765-6. doi: 10.1002/ibd.20969. No abstract available.

PMID:
19408317
50.

Needle thoracostomy for tension pneumothorax: failure predicted by chest computed tomography.

Stevens RL, Rochester AA, Busko J, Blackwell T, Schwartz D, Argenta A, Sing RF.

Prehosp Emerg Care. 2009 Jan-Mar;13(1):14-7. doi: 10.1080/10903120802471998.

PMID:
19145519

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