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Results: 1 to 20 of 62

1.

MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data.

Jensen PA, Papin JA.

Bioinformatics. 2014 May 1;30(9):1327-8. doi: 10.1093/bioinformatics/btt758. Epub 2014 Jan 9.

PMID:
24413519
[PubMed - indexed for MEDLINE]
2.

Clinical, molecular and genetic validation of a murine orthotopic xenograft model of pancreatic adenocarcinoma using fresh human specimens.

Walters DM, Stokes JB, Adair SJ, Stelow EB, Borgman CA, Lowrey BT, Xin W, Blais EM, Lee JK, Papin JA, Parsons JT, Bauer TW.

PLoS One. 2013 Oct 18;8(10):e77065. doi: 10.1371/journal.pone.0077065. eCollection 2013.

PMID:
24204737
[PubMed - in process]
Free PMC Article
3.

Comparative metabolic systems analysis of pathogenic Burkholderia.

Bartell JA, Yen P, Varga JJ, Goldberg JB, Papin JA.

J Bacteriol. 2014 Jan;196(2):210-26. doi: 10.1128/JB.00997-13. Epub 2013 Oct 25.

PMID:
24163337
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation.

Biggs MB, Papin JA.

PLoS One. 2013 Oct 17;8(10):e78011. doi: 10.1371/journal.pone.0078011. eCollection 2013.

PMID:
24147108
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

MicroRNAs induced in melanoma treated with combination targeted therapy of Temsirolimus and Bevacizumab.

Wagenseller AG, Shada A, D'Auria KM, Murphy C, Sun D, Molhoek KR, Papin JA, Dutta A, Slingluff CL Jr.

J Transl Med. 2013 Sep 18;11:218. doi: 10.1186/1479-5876-11-218.

PMID:
24047116
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

In vivo physiological and transcriptional profiling reveals host responses to Clostridium difficile toxin A and toxin B.

D'Auria KM, Kolling GL, Donato GM, Warren CA, Gray MC, Hewlett EL, Papin JA.

Infect Immun. 2013 Oct;81(10):3814-24. doi: 10.1128/IAI.00869-13. Epub 2013 Jul 29.

PMID:
23897615
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Multiscale computational models of complex biological systems.

Walpole J, Papin JA, Peirce SM.

Annu Rev Biomed Eng. 2013;15:137-54. doi: 10.1146/annurev-bioeng-071811-150104. Epub 2013 Apr 29. Review.

PMID:
23642247
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

A community-driven global reconstruction of human metabolism.

Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ.

Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3.

PMID:
23455439
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Linking genome-scale metabolic modeling and genome annotation.

Blais EM, Chavali AK, Papin JA.

Methods Mol Biol. 2013;985:61-83. doi: 10.1007/978-1-62703-299-5_4.

PMID:
23417799
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Mechanistic systems modeling to guide drug discovery and development.

Schmidt BJ, Papin JA, Musante CJ.

Drug Discov Today. 2013 Feb;18(3-4):116-27. doi: 10.1016/j.drudis.2012.09.003. Epub 2012 Sep 19. Review.

PMID:
22999913
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Integration of expression data in genome-scale metabolic network reconstructions.

Blazier AS, Papin JA.

Front Physiol. 2012 Aug 6;3:299. doi: 10.3389/fphys.2012.00299. eCollection 2012.

PMID:
22934050
[PubMed]
Free PMC Article
12.

Matrix rigidity regulates cancer cell growth by modulating cellular metabolism and protein synthesis.

Tilghman RW, Blais EM, Cowan CR, Sherman NE, Grigera PR, Jeffery ED, Fox JW, Blackman BR, Tschumperlin DJ, Papin JA, Parsons JT.

PLoS One. 2012;7(5):e37231. doi: 10.1371/journal.pone.0037231. Epub 2012 May 18.

PMID:
22623999
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease.

Chavali AK, Blazier AS, Tlaxca JL, Jensen PA, Pearson RD, Papin JA.

BMC Syst Biol. 2012 Apr 27;6:27. doi: 10.1186/1752-0509-6-27.

PMID:
22540944
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A metabolic network approach for the identification and prioritization of antimicrobial drug targets.

Chavali AK, D'Auria KM, Hewlett EL, Pearson RD, Papin JA.

Trends Microbiol. 2012 Mar;20(3):113-23. doi: 10.1016/j.tim.2011.12.004. Epub 2012 Jan 31. Review.

PMID:
22300758
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control.

D'Auria KM, Donato GM, Gray MC, Kolling GL, Warren CA, Cave LM, Solga MD, Lannigan JA, Papin JA, Hewlett EL.

BMC Syst Biol. 2012 Jan 6;6:2. doi: 10.1186/1752-0509-6-2.

PMID:
22225989
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Whole-genome metabolic network reconstruction and constraint-based modeling.

Haggart CR, Bartell JA, Saucerman JJ, Papin JA.

Methods Enzymol. 2011;500:411-33. doi: 10.1016/B978-0-12-385118-5.00021-9.

PMID:
21943909
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks.

Jensen PA, Lutz KA, Papin JA.

BMC Syst Biol. 2011 Sep 23;5:147. doi: 10.1186/1752-0509-5-147.

PMID:
21943338
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii.

Ghamsari L, Balaji S, Shen Y, Yang X, Balcha D, Fan C, Hao T, Yu H, Papin JA, Salehi-Ashtiani K.

BMC Genomics. 2011 Jun 15;12 Suppl 1:S4. doi: 10.1186/1471-2164-12-S1-S4.

PMID:
21810206
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.

Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K, Papin JA.

Mol Syst Biol. 2011 Aug 2;7:518. doi: 10.1038/msb.2011.52.

PMID:
21811229
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis.

Oberhardt MA, Puchałka J, Martins dos Santos VA, Papin JA.

PLoS Comput Biol. 2011 Mar;7(3):e1001116. doi: 10.1371/journal.pcbi.1001116. Epub 2011 Mar 31.

PMID:
21483480
[PubMed - indexed for MEDLINE]
Free PMC Article

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