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Evaluating the efficacy of an algae-based treatment to mitigate elicitation of antibiotic resistance.

Grimes KL, Dunphy LJ, Loudermilk EM, Melara AJ, Kolling GL, Papin JA, Colosi LM.

Chemosphere. 2019 Jul 20;237:124421. doi: 10.1016/j.chemosphere.2019.124421. [Epub ahead of print]


Wisdom of crowds in computational biology.

Papin JA, Mac Gabhann F.

PLoS Comput Biol. 2019 May 23;15(5):e1007032. doi: 10.1371/journal.pcbi.1007032. eCollection 2019 May. No abstract available.


In Vivo Gene Essentiality and Metabolism in Bordetella pertussis.

Gonyar LA, Gelbach PE, McDuffie DG, Koeppel AF, Chen Q, Lee G, Temple LM, Stibitz S, Hewlett EL, Papin JA, Damron FH, Eby JC.

mSphere. 2019 May 22;4(3). pii: e00694-18. doi: 10.1128/mSphere.00694-18.


Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies.

Untaroiu AM, Carey MA, Guler JL, Papin JA.

BMC Bioinformatics. 2019 Apr 15;20(1):186. doi: 10.1186/s12859-019-2756-y.


Mechanistic identification of biofluid metabolite changes as markers of acetaminophen-induced liver toxicity in rats.

Pannala VR, Vinnakota KC, Rawls KD, Estes SK, O'Brien TP, Printz RL, Papin JA, Reifman J, Shiota M, Young JD, Wallqvist A.

Toxicol Appl Pharmacol. 2019 Jun 1;372:19-32. doi: 10.1016/j.taap.2019.04.001. Epub 2019 Apr 8.


Reconciling high-throughput gene essentiality data with metabolic network reconstructions.

Blazier AS, Papin JA.

PLoS Comput Biol. 2019 Apr 11;15(4):e1006507. doi: 10.1371/journal.pcbi.1006507. eCollection 2019 Apr.


Integrated Experimental and Computational Analyses Reveal Differential Metabolic Functionality in Antibiotic-Resistant Pseudomonas aeruginosa.

Dunphy LJ, Yen P, Papin JA.

Cell Syst. 2019 Jan 23;8(1):3-14.e3. doi: 10.1016/j.cels.2018.12.002. Epub 2019 Jan 2.


A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools.

Rawls KD, Dougherty BV, Blais EM, Stancliffe E, Kolling GL, Vinnakota K, Pannala VR, Wallqvist A, Papin JA.

Comput Biol Med. 2019 Feb;105:64-71. doi: 10.1016/j.compbiomed.2018.12.010. Epub 2018 Dec 17.


One thousand simple rules.

Bourne PE, Lewitter F, Markel S, Papin JA.

PLoS Comput Biol. 2018 Dec 20;14(12):e1006670. doi: 10.1371/journal.pcbi.1006670. eCollection 2018 Dec. No abstract available.


Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota.

Medlock GL, Carey MA, McDuffie DG, Mundy MB, Giallourou N, Swann JR, Kolling GL, Papin JA.

Cell Syst. 2018 Sep 26;7(3):245-257.e7. doi: 10.1016/j.cels.2018.08.003. Epub 2018 Sep 5.


Influential Parameters for the Analysis of Intracellular Parasite Metabolomics.

Carey MA, Covelli V, Brown A, Medlock GL, Haaren M, Cooper JG, Papin JA, Guler JL.

mSphere. 2018 Apr 18;3(2). pii: e00097-18. doi: 10.1128/mSphere.00097-18. Print 2018 Apr 25.


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. 2018 Jun;51:70-79. doi: 10.1016/j.copbio.2017.11.014. Epub 2017 Dec 7. 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. Erratum in: J Infect Dis. 2018 Apr 23;217(10):1673.


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.

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