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Items: 1 to 50 of 89


Ten simple rules for biologists learning to program.

Carey MA, Papin JA.

PLoS Comput Biol. 2018 Jan 4;14(1):e1005871. doi: 10.1371/journal.pcbi.1005871. eCollection 2018 Jan. No abstract available.


Biomedical applications of genome-scale metabolic network reconstructions of human pathogens.

Dunphy LJ, Papin JA.

Curr Opin Biotechnol. 2017 Dec 7;51:70-79. doi: 10.1016/j.copbio.2017.11.014. [Epub ahead of print] Review.


How can computation advance microbiome research?

Nussinov R, Papin JA.

PLoS Comput Biol. 2017 Sep 21;13(9):e1005547. doi: 10.1371/journal.pcbi.1005547. eCollection 2017 Sep. No abstract available.


History of antibiotic adaptation influences microbial evolutionary dynamics during subsequent treatment.

Yen P, Papin JA.

PLoS Biol. 2017 Aug 8;15(8):e2001586. doi: 10.1371/journal.pbio.2001586. eCollection 2017 Aug.


Novel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions.

Moutinho TJ Jr, Panagides JC, Biggs MB, Medlock GL, Kolling GL, Papin JA.

PLoS One. 2017 Aug 2;12(8):e0182163. doi: 10.1371/journal.pone.0182163. eCollection 2017.


Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance.

Carey MA, Papin JA, Guler JL.

BMC Genomics. 2017 Jul 19;18(1):543. doi: 10.1186/s12864-017-3905-1.


An engineering design approach to systems biology.

Janes KA, Chandran PL, Ford RM, Lazzara MJ, Papin JA, Peirce SM, Saucerman JJ, Lauffenburger DA.

Integr Biol (Camb). 2017 Jul 17;9(7):574-583. doi: 10.1039/c7ib00014f. Review.


Increased Urinary Trimethylamine N-Oxide Following Cryptosporidium Infection and Protein Malnutrition Independent of Microbiome Effects.

Bolick DT, Mayneris-Perxachs J, Medlock GL, Kolling GL, Papin JA, Swann JR, Guerrant RL.

J Infect Dis. 2017 Jul 1;216(1):64-71. doi: 10.1093/infdis/jix234.


Growth-altering microbial interactions are responsive to chemical context.

Liu A, Archer AM, Biggs MB, Papin JA.

PLoS One. 2017 Mar 20;12(3):e0164919. doi: 10.1371/journal.pone.0164919. eCollection 2017.


Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis.

Bartell JA, Blazier AS, Yen P, Thøgersen JC, Jelsbak L, Goldberg JB, Papin JA.

Nat Commun. 2017 Mar 7;8:14631. doi: 10.1038/ncomms14631.


Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA.

Biggs MB, Papin JA.

PLoS Comput Biol. 2017 Mar 6;13(3):e1005413. doi: 10.1371/journal.pcbi.1005413. eCollection 2017 Mar.


Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions.

Blais EM, Rawls KD, Dougherty BV, Li ZI, Kolling GL, Ye P, Wallqvist A, Papin JA.

Nat Commun. 2017 Feb 8;8:14250. doi: 10.1038/ncomms14250.


Computing the Dynamic Supramolecular Structural Proteome.

Nussinov R, Papin JA, Vakser I.

PLoS Comput Biol. 2017 Jan 19;13(1):e1005290. doi: 10.1371/journal.pcbi.1005290. eCollection 2017 Jan. No abstract available.


Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota.

Biggs MB, Medlock GL, Moutinho TJ, Lees HJ, Swann JR, Kolling GL, Papin JA.

ISME J. 2017 Feb;11(2):426-438. doi: 10.1038/ismej.2016.130. Epub 2016 Nov 8.


Protein- and zinc-deficient diets modulate the murine microbiome and metabolic phenotype.

Mayneris-Perxachs J, Bolick DT, Leng J, Medlock GL, Kolling GL, Papin JA, Swann JR, Guerrant RL.

Am J Clin Nutr. 2016 Nov;104(5):1253-1262. Epub 2016 Oct 12.


Computing Biology.

Nussinov R, Papin JA.

PLoS Comput Biol. 2016 Jul 12;12(7):e1005050. doi: 10.1371/journal.pcbi.1005050. eCollection 2016 Jul. No abstract available.


Day of Surgery Impacts Outcome: Rehabilitation Utilization on Hospital Length of Stay in Patients Undergoing Elective Meningioma Resection.

Sarkiss CA, Papin JA, Yao A, Lee J, Sefcik RK, Oermann EK, Gordon EL, Post KD, Bederson JB, Shrivastava RK.

World Neurosurg. 2016 Sep;93:127-32. doi: 10.1016/j.wneu.2016.06.003. Epub 2016 Jun 11.


Metabolic network-guided binning of metagenomic sequence fragments.

Biggs MB, Papin JA.

Bioinformatics. 2016 Mar 15;32(6):867-74. doi: 10.1093/bioinformatics/btv671. Epub 2015 Nov 14.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


Functional integration of a metabolic network model and expression data without arbitrary thresholding.

Jensen PA, Papin JA.

Bioinformatics. 2011 Feb 15;27(4):541-7. doi: 10.1093/bioinformatics/btq702. Epub 2010 Dec 20.


Systems analysis of small signaling modules relevant to eight human diseases.

Benedict KF, Mac Gabhann F, Amanfu RK, Chavali AK, Gianchandani EP, Glaw LS, Oberhardt MA, Thorne BC, Yang JH, Papin JA, Peirce SM, Saucerman JJ, Skalak TC.

Ann Biomed Eng. 2011 Feb;39(2):621-35. doi: 10.1007/s10439-010-0208-y. Epub 2010 Dec 4.


The application of flux balance analysis in systems biology.

Gianchandani EP, Chavali AK, Papin JA.

Wiley Interdiscip Rev Syst Biol Med. 2010 May-Jun;2(3):372-382. doi: 10.1002/wsbm.60. Review.


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