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Items: 1 to 20 of 72

1.

Metabolic network-guided binning of metagenomic sequence fragments.

Biggs MB, Papin JA.

Bioinformatics. 2015 Nov 14. pii: btv671. [Epub ahead of print]

PMID:
26568626
2.

Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains.

Varga JJ, Barbier M, Mulet X, Bielecki P, Bartell JA, Owings JP, Martinez-Ramos I, Hittle LE, Davis MR Jr, Damron FH, Liechti GW, Puchałka J, dos Santos VA, Ernst RK, Papin JA, Albertí S, Oliver A, Goldberg JB.

BMC Genomics. 2015 Oct 30;16:883. doi: 10.1186/s12864-015-2069-0.

3.

Do genome-scale models need exact solvers or clearer standards?

Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.

4.

Pilot Study on Early Postoperative Discharge in Pituitary Adenoma Patients: Effect of Socioeconomic Factors and Benefit of Specialized Pituitary Centers.

Sarkiss CA, Lee J, Papin JA, Geer EB, Banik R, Rucker JC, Oudheusden B, Govindaraj S, Shrivastava RK.

J Neurol Surg B Skull Base. 2015 Aug;76(4):323-30. doi: 10.1055/s-0035-1549004. Epub 2015 Apr 27.

PMID:
26225324
5.

From "What Is?" to "What Isn't?" Computational Biology.

Nussinov R, Bonhoeffer S, Papin JA, Sporns O.

PLoS Comput Biol. 2015 Jul 2;11(7):e1004318. doi: 10.1371/journal.pcbi.1004318. eCollection 2015 Jul. No abstract available.

6.

Metabolic network modeling of microbial communities.

Biggs MB, Medlock GL, Kolling GL, Papin JA.

Wiley Interdiscip Rev Syst Biol Med. 2015 Sep-Oct;7(5):317-34. doi: 10.1002/wsbm.1308. Epub 2015 Jun 24. Review.

PMID:
26109480
7.

Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome.

Steinway SN, Biggs MB, Loughran TP Jr, Papin JA, Albert R.

PLoS Comput Biol. 2015 Jun 23;11(5):e1004338. doi: 10.1371/journal.pcbi.1004338. eCollection 2015 May.

8.

High temporal resolution of glucosyltransferase dependent and independent effects of Clostridium difficile toxins across multiple cell types.

D'Auria KM, Bloom MJ, Reyes Y, Gray MC, van Opstal EJ, Papin JA, Hewlett EL.

BMC Microbiol. 2015 Feb 4;15:7. doi: 10.1186/s12866-015-0361-4.

9.

Miniaturized plate readers for low-cost, high-throughput phenotypic screening.

Jensen PA, Dougherty BV, Moutinho TJ Jr, Papin JA.

J Lab Autom. 2015 Feb;20(1):51-5. doi: 10.1177/2211068214555414. Epub 2014 Nov 3.

10.

A thirteen-gene expression signature predicts survival of patients with pancreatic cancer and identifies new genes of interest.

Newhook TE, Blais EM, Lindberg JM, Adair SJ, Xin W, Lee JK, Papin JA, Parsons JT, Bauer TW.

PLoS One. 2014 Sep 2;9(9):e105631. doi: 10.1371/journal.pone.0105631. eCollection 2014.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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