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Items: 33

1.

A blueprint for human whole-cell modeling.

Szigeti B, Roth YD, Sekar JAP, Goldberg AP, Pochiraju SC, Karr JR.

Curr Opin Syst Biol. 2018 Feb;7:8-15. doi: 10.1016/j.coisb.2017.10.005. Epub 2017 Nov 9.

2.

Emerging whole-cell modeling principles and methods.

Goldberg AP, Szigeti B, Chew YH, Sekar JA, Roth YD, Karr JR.

Curr Opin Biotechnol. 2018 Jun;51:97-102. doi: 10.1016/j.copbio.2017.12.013. Epub 2017 Dec 21. Review.

3.

Guidelines for Reproducibly Building and Simulating Systems Biology Models.

Medley JK, Goldberg AP, Karr JR.

IEEE Trans Biomed Eng. 2016 Oct;63(10):2015-20. doi: 10.1109/TBME.2016.2591960. Epub 2016 Jul 18.

4.

Toward Community Standards and Software for Whole-Cell Modeling.

Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PE, Cantarelli M, Chew YH, Costa RS, Cursons J, Czauderna T, Goldberg AP, Gomez HF, Hahn J, Hameri T, Gardiol DF, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knupfer C, Konig M, Lee D, Lloret-Villas A, Mandrik N, Medley JK, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song JH, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A, Schreiber F.

IEEE Trans Biomed Eng. 2016 Oct;63(10):2007-14. doi: 10.1109/TBME.2016.2560762. Epub 2016 Jun 10.

5.
6.

A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium.

Kazakiewicz D, Karr JR, Langner KM, Plewczynski D.

Comput Biol Chem. 2015 Dec;59 Pt B:91-7. doi: 10.1016/j.compbiolchem.2015.07.007. Epub 2015 Jul 30.

PMID:
26271684
7.

The principles of whole-cell modeling.

Karr JR, Takahashi K, Funahashi A.

Curr Opin Microbiol. 2015 Oct;27:18-24. doi: 10.1016/j.mib.2015.06.004. Epub 2015 Jun 24. Review.

PMID:
26115539
8.

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.

Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C; DREAM8 Parameter Estimation Challenge Consortium, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, Meyer P.

PLoS Comput Biol. 2015 May 28;11(5):e1004096. doi: 10.1371/journal.pcbi.1004096. eCollection 2015 May.

9.

NetworkPainter: dynamic intracellular pathway animation in Cytobank.

Karr JR, Guturu H, Chen EY, Blair SL, Irish JM, Kotecha N, Covert MW.

BMC Bioinformatics. 2015 May 25;16:172. doi: 10.1186/s12859-015-0602-4.

10.

Causal inference in biology networks with integrated belief propagation.

Chang R, Karr JR, Schadt EE.

Pac Symp Biocomput. 2015:359-70.

11.

DREAMTools: a Python package for scoring collaborative challenges.

Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, de la Fuente A, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G, Saez-Rodriguez J.

Version 2. F1000Res. 2015 Oct 9 [revised 2016 Jan 1];4:1030. doi: 10.12688/f1000research.7118.2. eCollection 2015.

12.

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions.

Karr JR, Phillips NC, Covert MW.

Database (Oxford). 2014 Sep 16;2014. pii: bau095. doi: 10.1093/database/bau095. Print 2014.

13.

Reducing livestock effects on public lands in the western United States as the climate changes: a reply to Svejcar et al.

Beschta RL, Donahue DL, DellaSala DA, Rhodes JJ, Karr JR, O'Brien MH, Fleischner TL, Williams CD.

Environ Manage. 2014 Jun;53(6):1039-42. doi: 10.1007/s00267-014-0263-5. Epub 2014 Apr 1.

PMID:
24687319
14.

Accelerated discovery via a whole-cell model.

Sanghvi JC, Regot S, Carrasco S, Karr JR, Gutschow MV, Bolival B Jr, Covert MW.

Nat Methods. 2013 Dec;10(12):1192-5. doi: 10.1038/nmeth.2724. Epub 2013 Nov 3.

15.

WholeCellViz: data visualization for whole-cell models.

Lee R, Karr JR, Covert MW.

BMC Bioinformatics. 2013 Aug 21;14:253. doi: 10.1186/1471-2105-14-253.

16.

Towards a whole-cell modeling approach for synthetic biology.

Purcell O, Jain B, Karr JR, Covert MW, Lu TK.

Chaos. 2013 Jun;23(2):025112. doi: 10.1063/1.4811182.

17.

WholeCellKB: model organism databases for comprehensive whole-cell models.

Karr JR, Sanghvi JC, Macklin DN, Arora A, Covert MW.

Nucleic Acids Res. 2013 Jan;41(Database issue):D787-92. doi: 10.1093/nar/gks1108. Epub 2012 Nov 21.

18.

Adapting to climate change on Western public lands: addressing the ecological effects of domestic, wild, and feral ungulates.

Beschta RL, Donahue DL, DellaSala DA, Rhodes JJ, Karr JR, O'Brien MH, Fleischner TL, Deacon Williams C.

Environ Manage. 2013 Feb;51(2):474-91. doi: 10.1007/s00267-012-9964-9. Epub 2012 Nov 15.

PMID:
23151970
19.

A whole-cell computational model predicts phenotype from genotype.

Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI, Covert MW.

Cell. 2012 Jul 20;150(2):389-401. doi: 10.1016/j.cell.2012.05.044.

20.

Integrating '-omics' and natural product discovery platforms to investigate metabolic exchange in microbiomes.

Yang JY, Karr JR, Watrous JD, Dorrestein PC.

Curr Opin Chem Biol. 2011 Feb;15(1):79-87. doi: 10.1016/j.cbpa.2010.10.025. Epub 2010 Nov 17. Review.

21.

A hinge region cis-proline in ribonuclease A acts as a conformational gatekeeper for C-terminal domain swapping.

Miller KH, Karr JR, Marqusee S.

J Mol Biol. 2010 Jul 16;400(3):567-78. doi: 10.1016/j.jmb.2010.05.017. Epub 2010 May 13. Erratum in: J Mol Biol. 2010 Nov 12;403(5):825.

22.

Heeding a call to action for US coral reefs: the untapped potential of the Clean Water Act.

Fore LS, Karr JR, Fisher WS, Bradley P, Davis WS.

Mar Pollut Bull. 2009 Oct;58(10):1421-3. doi: 10.1016/j.marpolbul.2009.06.003. Epub 2009 Jul 16. No abstract available.

PMID:
19615697
23.

Making waves with the Clean Water Act.

Fore LS, Karr JR, Fisher WS, Davis WS.

Science. 2008 Dec 19;322(5909):1788. doi: 10.1126/science.322.5909.1788a. No abstract available.

PMID:
19095922
24.

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli.

Covert MW, Xiao N, Chen TJ, Karr JR.

Bioinformatics. 2008 Sep 15;24(18):2044-50. doi: 10.1093/bioinformatics/btn352. Epub 2008 Jul 10.

PMID:
18621757
25.

Post-fire logging debate ignores many issues.

DellaSala DA, Karr JR, Schoennagel T, Perry D, Noss RF, Lindenmayer D, Beschta R, Hutto RL, Swanson ME, Evans J.

Science. 2006 Oct 6;314(5796):51-2. No abstract available.

PMID:
17023633
26.

Shifting priorities at the Department of Energy's bomb factories: protecting human and ecological health.

Burger J, Leschine TM, Greenberg M, Karr JR, Gochfeld M, Powers CW.

Environ Manage. 2003 Feb;31(2):157-67.

PMID:
12520373
27.

Biological Integrity: A Long-Neglected Aspect of Water Resource Management.

Karr JR.

Ecol Appl. 1991 Feb;1(1):66-84. doi: 10.2307/1941848.

PMID:
27755684
28.

Breeding Birds of Isolated Woodlots: Area and Habitat Relationships.

Blake JG, Karr JR.

Ecology. 1987 Dec;68(6):1724-1734. doi: 10.2307/1939864.

PMID:
29357170
29.

Australian bird populations: birds of eucalypt forests and woodlands.

Karr JR.

Science. 1986 Oct 31;234(4776):620. No abstract available.

PMID:
17835569
30.
31.

Water resources and the land-water interface.

Karr JR, Schlosser IJ.

Science. 1978 Jul 21;201(4352):229-34.

PMID:
17778646
32.

Controlling hog cholera in Brazil.

KARR JR.

North Am Vet. 1947 Jun;28(6):359-61. No abstract available.

PMID:
20240358
33.

Duties of the veterinary officer in the ATC.

KARR JR.

Air Surg Bull. 1945;2:394. No abstract available.

PMID:
21004518

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