| Year |
Citation |
Score |
| 2024 |
Islam MM, Kolling GL, Glass EM, Goldberg JB, Papin JA. Model-driven characterization of functional diversity of clinical isolates with broadly representative phenotypes. Microbial Genomics. 10. PMID 38836744 DOI: 10.1099/mgen.0.001259 |
0.36 |
|
| 2024 |
Kuper TJ, Islam MM, Peirce-Cottler SM, Papin JA, Ford RM. Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment. Plos Computational Biology. 20: e1012031. PMID 38669236 DOI: 10.1371/journal.pcbi.1012031 |
0.35 |
|
| 2024 |
Dougherty BV, Moore CJ, Rawls KD, Jenior ML, Chun B, Nagdas S, Saucerman JJ, Kolling GL, Wallqvist A, Papin JA. Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism. Plos Computational Biology. 20: e1011919. PMID 38422168 DOI: 10.1371/journal.pcbi.1011919 |
0.366 |
|
| 2023 |
Tubergen PJ, Medlock G, Moore A, Zhang X, Papin JA, Danna CH. A computational model of Pseudomonas syringae metabolism unveils a role for branched-chain amino acids in Arabidopsis leaf colonization. Plos Computational Biology. 19: e1011651. PMID 38150474 DOI: 10.1371/journal.pcbi.1011651 |
0.302 |
|
| 2023 |
Islam MM, Kolling GL, Glass EM, Goldberg JB, Papin JA. Model-driven characterization of functional diversity of clinical isolates with broadly representative phenotypes. Biorxiv : the Preprint Server For Biology. PMID 37873245 DOI: 10.1101/2023.10.08.561426 |
0.361 |
|
| 2023 |
Jenior ML, Leslie JL, Kolling GL, Archbald-Pannone L, Powers DA, Petri WA, Papin JA. Systems-ecology designed bacterial consortium protects from severe infection. Biorxiv : the Preprint Server For Biology. PMID 37609255 DOI: 10.1101/2023.08.08.552483 |
0.489 |
|
| 2023 |
Moore CJ, Holstege CP, Papin JA. Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses. Plos Computational Biology. 19: e1010927. PMID 37603574 DOI: 10.1371/journal.pcbi.1010927 |
0.306 |
|
| 2023 |
Potter AD, Baiocco CM, Papin JA, Criss AK. Transcriptome-guided metabolic network analysis reveals rearrangements of carbon flux distribution in during neutrophil co-culture. Msystems. e0126522. PMID 37387581 DOI: 10.1128/msystems.01265-22 |
0.384 |
|
| 2023 |
Jenior ML, Glass EM, Papin JA. Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling. Bioinformatics (Oxford, England). 39. PMID 37279743 DOI: 10.1093/bioinformatics/btad367 |
0.393 |
|
| 2023 |
Powers DA, Jenior ML, Kolling GL, Papin JA. Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies. Plos Computational Biology. 19: e1011076. PMID 37099624 DOI: 10.1371/journal.pcbi.1011076 |
0.332 |
|
| 2023 |
Fernandes P, Sharma Y, Zulqarnain F, McGrew B, Shrivastava A, Ehsan L, Payne D, Dillard L, Powers D, Aldridge I, Matthews J, Kugathasan S, Fernández FM, Gaul D, Papin JA, et al. Identifying metabolic shifts in Crohn's disease using' omics-driven contextualized computational metabolic network models. Scientific Reports. 13: 203. PMID 36604447 DOI: 10.1038/s41598-022-26816-5 |
0.307 |
|
| 2022 |
Dillard LR, Glass EM, Lewis AL, Thomas-White K, Papin JA. Metabolic Network Models of the Pangenome Identify Key Interactions with the Vaginal Environment. Msystems. e0068922. PMID 36511689 DOI: 10.1128/msystems.00689-22 |
0.377 |
|
| 2022 |
Jenior ML, Dickenson ME, Papin JA. Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae. Npj Systems Biology and Applications. 8: 41. PMID 36307414 DOI: 10.1038/s41540-022-00252-7 |
0.327 |
|
| 2022 |
Carey MA, Medlock GL, Stolarczyk M, Petri WA, Guler JL, Papin JA. Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models. Plos Computational Biology. 18: e1009870. PMID 35196325 DOI: 10.1371/journal.pcbi.1009870 |
0.827 |
|
| 2022 |
Moutinho TJ, Neubert BC, Jenior ML, Papin JA. Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions. Plos Computational Biology. 18: e1009341. PMID 35130271 DOI: 10.1371/journal.pcbi.1009341 |
0.423 |
|
| 2021 |
Jenior ML, Papin JA. Computational approaches to understanding Clostridioides difficile metabolism and virulence. Current Opinion in Microbiology. 65: 108-115. PMID 34839237 DOI: 10.1016/j.mib.2021.11.002 |
0.332 |
|
| 2021 |
Payne DD, Renz A, Dunphy LJ, Lewis T, Dräger A, Papin JA. An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism. Npj Systems Biology and Applications. 7: 37. PMID 34625561 DOI: 10.1038/s41540-021-00198-2 |
0.434 |
|
| 2021 |
Jenior ML, Leslie JL, Powers DA, Garrett EM, Walker KA, Dickenson ME, Petri WA, Tamayo R, Papin JA. Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis. Msystems. e0091921. PMID 34609164 DOI: 10.1128/mSystems.00919-21 |
0.562 |
|
| 2021 |
Carey MA, Medlock GL, Alam M, Kabir M, Uddin MJ, Nayak U, Papin J, Faruque ASG, Haque R, Petri WA, Gilchrist CA. Megasphaera in the stool microbiota is negatively associated with diarrheal cryptosporidiosis. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 33684930 DOI: 10.1093/cid/ciab207 |
0.751 |
|
| 2020 |
Rawls KD, Dougherty BV, Vinnakota KC, Pannala VR, Wallqvist A, Kolling GL, Papin JA. Predicting changes in renal metabolism after compound exposure with a genome-scale metabolic model. Toxicology and Applied Pharmacology. 115390. PMID 33387578 DOI: 10.1016/j.taap.2020.115390 |
0.356 |
|
| 2020 |
Jenior ML, Papin JA. Clostridioides difficile: Sometimes It Pays To Be Difficult. Cell Host & Microbe. 28: 358-359. PMID 32910918 DOI: 10.1016/J.Chom.2020.08.010 |
0.325 |
|
| 2020 |
Carey MA, Dräger A, Beber ME, Papin JA, Yurkovich JT. Community standards to facilitate development and address challenges in metabolic modeling. Molecular Systems Biology. 16: e9235. PMID 32845080 DOI: 10.15252/Msb.20199235 |
0.798 |
|
| 2020 |
Medlock GL, Moutinho TJ, Papin JA. Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions. Plos Computational Biology. 16: e1007847. PMID 32348298 DOI: 10.1371/Journal.Pcbi.1007847 |
0.827 |
|
| 2020 |
Jenior ML, Moutinho TJ, Dougherty BV, Papin JA. Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments. Plos Computational Biology. 16: e1007099. PMID 32298268 DOI: 10.1371/Journal.Pcbi.1007099 |
0.535 |
|
| 2020 |
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, ... ... Papin JA, et al. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. 38: 504. PMID 32265554 DOI: 10.1038/S41587-020-0477-4 |
0.791 |
|
| 2020 |
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, ... ... Papin JA, et al. MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. PMID 32123384 DOI: 10.1038/S41587-020-0446-Y |
0.793 |
|
| 2020 |
Medlock GL, Papin JA. Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning. Cell Systems. 10: 109-119.e3. PMID 31926940 DOI: 10.1016/J.Cels.2019.11.006 |
0.799 |
|
| 2020 |
Rawls K, Dougherty BV, Papin J. Metabolic Network Reconstructions to Predict Drug Targets and Off-Target Effects. Methods in Molecular Biology (Clifton, N.J.). 2088: 315-330. PMID 31893380 DOI: 10.1007/978-1-0716-0159-4_14 |
0.396 |
|
| 2020 |
Dougherty BV, Papin JA. Systems biology approaches help to facilitate interpretation of cross-species comparisons Current Opinion in Toxicology. 74-79. DOI: 10.1016/J.Cotox.2020.06.002 |
0.348 |
|
| 2019 |
Pannala VR, Vinnakota KC, Estes SK, Trenary I, OˈBrien TP, Printz RL, Papin JA, Reifman J, Oyama T, Shiota M, Young JD, Wallqvist A. Genome-scale model-based identification of metabolite indicators for early detection of kidney toxicity. Toxicological Sciences : An Official Journal of the Society of Toxicology. PMID 31722432 DOI: 10.1093/Toxsci/Kfz228 |
0.398 |
|
| 2019 |
Rawls KD, Blais EM, Dougherty BV, Vinnakota KC, Pannala VR, Wallqvist A, Kolling GL, Papin JA. Genome-Scale Characterization of Toxicity-Induced Metabolic Alterations in Primary Hepatocytes. Toxicological Sciences : An Official Journal of the Society of Toxicology. PMID 31501904 DOI: 10.1093/Toxsci/Kfz197 |
0.764 |
|
| 2019 |
Gonyar LA, Gelbach PE, McDuffie DG, Koeppel AF, Chen Q, Lee G, Temple LM, Stibitz S, Hewlett EL, Papin JA, Damron FH, Eby JC. Gene Essentiality and Metabolism in Bordetella pertussis. Msphere. 4. PMID 31118307 DOI: 10.1128/mSphere.00694-18 |
0.302 |
|
| 2019 |
Untaroiu AM, Carey MA, Guler JL, Papin JA. Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies. Bmc Bioinformatics. 20: 186. PMID 30987583 DOI: 10.1186/S12859-019-2756-Y |
0.744 |
|
| 2019 |
Pannala VR, Vinnakota KC, Rawls KD, Estes SK, O'Brien TP, Printz RL, Papin JA, Reifman J, Shiota M, Young JD, Wallqvist A. Mechanistic identification of biofluid metabolite changes as markers of acetaminophen-induced liver toxicity in rats. Toxicology and Applied Pharmacology. PMID 30974156 DOI: 10.1016/J.Taap.2019.04.001 |
0.322 |
|
| 2019 |
Blazier AS, Papin JA. Reconciling high-throughput gene essentiality data with metabolic network reconstructions. Plos Computational Biology. 15: e1006507. PMID 30973869 DOI: 10.1371/Journal.Pcbi.1006507 |
0.458 |
|
| 2018 |
Dunphy LJ, Yen P, Papin JA. Integrated Experimental and Computational Analyses Reveal Differential Metabolic Functionality in Antibiotic-Resistant Pseudomonas aeruginosa. Cell Systems. PMID 30611675 DOI: 10.1016/J.Cels.2018.12.002 |
0.436 |
|
| 2018 |
Rawls KD, Dougherty BV, Blais EM, Stancliffe E, Kolling GL, Vinnakota K, Pannala VR, Wallqvist A, Papin JA. A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools. Computers in Biology and Medicine. 105: 64-71. PMID 30584952 DOI: 10.1016/J.Compbiomed.2018.12.010 |
0.776 |
|
| 2018 |
Medlock GL, Carey MA, McDuffie DG, Mundy MB, Giallourou N, Swann JR, Kolling GL, Papin JA. Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota. Cell Systems. PMID 30195437 DOI: 10.1016/J.Cels.2018.08.003 |
0.8 |
|
| 2018 |
Carey MA, Covelli V, Brown A, Medlock GL, Haaren M, Cooper JG, Papin JA, Guler JL. Influential Parameters for the Analysis of Intracellular Parasite Metabolomics. Msphere. 3. PMID 29669882 DOI: 10.1128/mSphere.00097-18 |
0.79 |
|
| 2018 |
Carey MA, Papin JA. Ten simple rules for biologists learning to program. Plos Computational Biology. 14: e1005871. PMID 29300745 DOI: 10.1371/Journal.Pcbi.1005871 |
0.728 |
|
| 2017 |
Dunphy LJ, Papin JA. Biomedical applications of genome-scale metabolic network reconstructions of human pathogens. Current Opinion in Biotechnology. 51: 70-79. PMID 29223465 DOI: 10.1016/J.Copbio.2017.11.014 |
0.449 |
|
| 2017 |
Moutinho TJ, Panagides JC, Biggs MB, Medlock GL, Kolling GL, Papin JA. Novel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions. Plos One. 12: e0182163. PMID 28767660 DOI: 10.1371/Journal.Pone.0182163 |
0.752 |
|
| 2017 |
Bartelt LA, Bolick DT, Mayneris-Perxachs J, Kolling GL, Medlock GL, Zaenker EI, Donowitz J, Thomas-Beckett RV, Rogala A, Carroll IM, Singer SM, Papin J, Swann JR, Guerrant RL. Cross-modulation of pathogen-specific pathways enhances malnutrition during enteric co-infection with Giardia lamblia and enteroaggregative Escherichia coli. Plos Pathogens. 13: e1006471. PMID 28750066 DOI: 10.1371/Journal.Ppat.1006471 |
0.777 |
|
| 2017 |
Carey MA, Papin JA, Guler JL. Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance. Bmc Genomics. 18: 543. PMID 28724354 DOI: 10.1186/S12864-017-3905-1 |
0.784 |
|
| 2017 |
Janes KA, Chandran PL, Ford RM, Lazzara MJ, Papin JA, Peirce SM, Saucerman JJ, Lauffenburger DA. An engineering design approach to systems biology. Integrative Biology : Quantitative Biosciences From Nano to Macro. PMID 28590470 DOI: 10.1039/C7Ib00014F |
0.304 |
|
| 2017 |
Bolick DT, Mayneris-Perxachs J, Medlock GL, Kolling GL, Papin J, Swann JR, Guerrant RL. Increased urinary trimethylamine N-oxide (TMAO) following Cryptosporidium infection and protein malnutrition independent of microbiome effects. The Journal of Infectious Diseases. PMID 28520899 DOI: 10.1093/Infdis/Jix234 |
0.773 |
|
| 2017 |
Bartell JA, Blazier AS, Yen P, Thøgersen JC, Jelsbak L, Goldberg JB, Papin JA. Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis. Nature Communications. 8: 14631. PMID 28266498 DOI: 10.1038/Ncomms14631 |
0.418 |
|
| 2017 |
Biggs MB, Papin JA. Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA. Plos Computational Biology. 13: e1005413. PMID 28263984 DOI: 10.1371/Journal.Pcbi.1005413 |
0.464 |
|
| 2017 |
Blais EM, Rawls KD, Dougherty BV, Li ZI, Kolling GL, Ye P, Wallqvist A, Papin JA. Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions. Nature Communications. 8: 14250. PMID 28176778 DOI: 10.1038/Ncomms14250 |
0.759 |
|
| 2016 |
Biggs MB, Medlock GL, Moutinho TJ, Lees HJ, Swann JR, Kolling GL, Papin JA. Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota. The Isme Journal. PMID 27824342 DOI: 10.1038/Ismej.2016.130 |
0.807 |
|
| 2016 |
Mayneris-Perxachs J, Bolick DT, Leng J, Medlock GL, Kolling GL, Papin JA, Swann JR, Guerrant RL. Protein- and zinc-deficient diets modulate the murine microbiome and metabolic phenotype. The American Journal of Clinical Nutrition. PMID 27733402 DOI: 10.3945/Ajcn.116.131797 |
0.769 |
|
| 2016 |
Chaiboonchoe A, Ghamsari L, Dohai B, Ng P, Khraiwesh B, Jaiswal A, Jijakli K, Koussa J, Nelson DR, Cai H, Yang X, Chang RL, Papin J, Yu H, Balaji S, et al. Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation. Molecular Biosystems. PMID 27357594 DOI: 10.1039/C6Mb00237D |
0.68 |
|
| 2015 |
Biggs MB, Papin JA. Metabolic Network-Guided Binning of Metagenomic Sequence Fragments. Bioinformatics (Oxford, England). PMID 26568626 DOI: 10.1093/Bioinformatics/Btv671 |
0.347 |
|
| 2015 |
Varga JJ, Barbier M, Mulet X, Bielecki P, Bartell JA, Owings JP, Martinez-Ramos I, Hittle LE, Davis MR, Damron FH, Liechti GW, Puchałka J, Dos Santos VA, Ernst RK, Papin JA, et al. Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains. Bmc Genomics. 16: 883. PMID 26519161 DOI: 10.1186/S12864-015-2069-0 |
0.321 |
|
| 2015 |
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, ... ... Papin JA, et al. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11: 831. PMID 26467284 DOI: 10.15252/Msb.20156157 |
0.739 |
|
| 2015 |
Biggs MB, Medlock GL, Kolling GL, Papin JA. Metabolic network modeling of microbial communities. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. PMID 26109480 DOI: 10.1002/Wsbm.1308 |
0.812 |
|
| 2015 |
Steinway SN, Biggs MB, Loughran TP, Papin JA, Albert R. Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome. Plos Computational Biology. 11: e1004338. PMID 26102287 DOI: 10.1371/Journal.Pcbi.1004338 |
0.428 |
|
| 2015 |
Jensen PA, Dougherty BV, Moutinho TJ, Papin JA. Miniaturized plate readers for low-cost, high-throughput phenotypic screening. Journal of Laboratory Automation. 20: 51-5. PMID 25366331 DOI: 10.1177/2211068214555414 |
0.58 |
|
| 2014 |
Newhook TE, Blais EM, Lindberg JM, Adair SJ, Xin W, Lee JK, Papin JA, Parsons JT, Bauer TW. A thirteen-gene expression signature predicts survival of patients with pancreatic cancer and identifies new genes of interest. Plos One. 9: e105631. PMID 25180633 DOI: 10.1371/Journal.Pone.0105631 |
0.667 |
|
| 2014 |
Jensen PA, Papin JA. MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data. Bioinformatics (Oxford, England). 30: 1327-8. PMID 24413519 DOI: 10.1093/Bioinformatics/Btt758 |
0.687 |
|
| 2014 |
Bartell JA, Yen P, Varga JJ, Goldberg JB, Papin JA. Comparative metabolic systems analysis of pathogenic Burkholderia. Journal of Bacteriology. 196: 210-26. PMID 24163337 DOI: 10.1128/Jb.00997-13 |
0.409 |
|
| 2014 |
Newhook TE, Lindberg JM, Adair SJ, Blais E, Papin J, Gray L, Parsons JT, Bauer TW. Abstract 808: Combination therapy with a MEK inhibitor plus T-type calcium channel inhibitor is highly effective in patient-derived pancreatic ductal adenocarcinomas Cancer Research. 74: 808-808. DOI: 10.1158/1538-7445.Am2014-808 |
0.66 |
|
| 2013 |
Walters DM, Stokes JB, Adair SJ, Stelow EB, Borgman CA, Lowrey BT, Xin W, Blais EM, Lee JK, Papin JA, Parsons JT, Bauer TW. Clinical, molecular and genetic validation of a murine orthotopic xenograft model of pancreatic adenocarcinoma using fresh human specimens. Plos One. 8: e77065. PMID 24204737 DOI: 10.1371/Journal.Pone.0077065 |
0.679 |
|
| 2013 |
Biggs MB, Papin JA. Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation. Plos One. 8: e78011. PMID 24147108 DOI: 10.1371/Journal.Pone.0078011 |
0.402 |
|
| 2013 |
D'Auria KM, Kolling GL, Donato GM, Warren CA, Gray MC, Hewlett EL, Papin JA. In vivo physiological and transcriptional profiling reveals host responses to Clostridium difficile toxin A and toxin B. Infection and Immunity. 81: 3814-24. PMID 23897615 DOI: 10.1128/Iai.00869-13 |
0.321 |
|
| 2013 |
Walpole J, Papin JA, Peirce SM. Multiscale computational models of complex biological systems. Annual Review of Biomedical Engineering. 15: 137-54. PMID 23642247 DOI: 10.1146/Annurev-Bioeng-071811-150104 |
0.339 |
|
| 2013 |
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, ... ... Papin JA, et al. A community-driven global reconstruction of human metabolism. Nature Biotechnology. 31: 419-25. PMID 23455439 DOI: 10.1038/Nbt.2488 |
0.808 |
|
| 2013 |
Blais EM, Chavali AK, Papin JA. Linking genome-scale metabolic modeling and genome annotation. Methods in Molecular Biology (Clifton, N.J.). 985: 61-83. PMID 23417799 DOI: 10.1007/978-1-62703-299-5_4 |
0.837 |
|
| 2013 |
Schmidt BJ, Papin JA, Musante CJ. Mechanistic systems modeling to guide drug discovery and development. Drug Discovery Today. 18: 116-27. PMID 22999913 DOI: 10.1016/J.Drudis.2012.09.003 |
0.302 |
|
| 2013 |
Koskimaki JE, Blazier AS, Clarens AF, Papin JA. Computational models of algae metabolism for industrial applications Industrial Biotechnology. 9: 185-195. DOI: 10.1089/Ind.2013.0012 |
0.428 |
|
| 2012 |
Blazier AS, Papin JA. Integration of expression data in genome-scale metabolic network reconstructions. Frontiers in Physiology. 3: 299. PMID 22934050 DOI: 10.3389/Fphys.2012.00299 |
0.506 |
|
| 2012 |
Tilghman RW, Blais EM, Cowan CR, Sherman NE, Grigera PR, Jeffery ED, Fox JW, Blackman BR, Tschumperlin DJ, Papin JA, Parsons JT. Matrix rigidity regulates cancer cell growth by modulating cellular metabolism and protein synthesis. Plos One. 7: e37231. PMID 22623999 DOI: 10.1371/Journal.Pone.0037231 |
0.706 |
|
| 2012 |
Chavali AK, Blazier AS, Tlaxca JL, Jensen PA, Pearson RD, Papin JA. Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease. Bmc Systems Biology. 6: 27. PMID 22540944 DOI: 10.1186/1752-0509-6-27 |
0.799 |
|
| 2012 |
Chavali AK, D'Auria KM, Hewlett EL, Pearson RD, Papin JA. A metabolic network approach for the identification and prioritization of antimicrobial drug targets. Trends in Microbiology. 20: 113-23. PMID 22300758 DOI: 10.1016/J.Tim.2011.12.004 |
0.803 |
|
| 2011 |
Haggart CR, Bartell JA, Saucerman JJ, Papin JA. Whole-genome metabolic network reconstruction and constraint-based modeling. Methods in Enzymology. 500: 411-33. PMID 21943909 DOI: 10.1016/B978-0-12-385118-5.00021-9 |
0.484 |
|
| 2011 |
Jensen PA, Lutz KA, Papin JA. TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks. Bmc Systems Biology. 5: 147. PMID 21943338 DOI: 10.1186/1752-0509-5-147 |
0.725 |
|
| 2011 |
Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K, Papin JA. Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Molecular Systems Biology. 7: 518. PMID 21811229 DOI: 10.1038/Msb.2011.52 |
0.796 |
|
| 2011 |
Ghamsari L, Balaji S, Shen Y, Yang X, Balcha D, Fan C, Hao T, Yu H, Papin JA, Salehi-Ashtiani K. Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii. Bmc Genomics. 12: S4. PMID 21810206 DOI: 10.1186/1471-2164-12-S1-S4 |
0.475 |
|
| 2011 |
Oberhardt MA, Pucha?ka J, Martins dos Santos VA, Papin JA. Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis. Plos Computational Biology. 7: e1001116. PMID 21483480 DOI: 10.1371/Journal.Pcbi.1001116 |
0.766 |
|
| 2011 |
Jensen PA, Papin JA. Functional integration of a metabolic network model and expression data without arbitrary thresholding. Bioinformatics (Oxford, England). 27: 541-7. PMID 21172910 DOI: 10.1093/Bioinformatics/Btq702 |
0.701 |
|
| 2011 |
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. Systems analysis of small signaling modules relevant to eight human diseases. Annals of Biomedical Engineering. 39: 621-35. PMID 21132372 DOI: 10.1007/S10439-010-0208-Y |
0.768 |
|
| 2010 |
Gianchandani EP, Chavali AK, Papin JA. The application of flux balance analysis in systems biology. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 2: 372-82. PMID 20836035 DOI: 10.1002/Wsbm.60 |
0.823 |
|
| 2010 |
Oberhardt MA, Goldberg JB, Hogardt M, Papin JA. Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection. Journal of Bacteriology. 192: 5534-48. PMID 20709898 DOI: 10.1128/Jb.00900-10 |
0.748 |
|
| 2010 |
Ruppin E, Papin JA, de Figueiredo LF, Schuster S. Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks. Current Opinion in Biotechnology. 21: 502-10. PMID 20692823 DOI: 10.1016/J.Copbio.2010.07.002 |
0.506 |
|
| 2010 |
Schmidt BJ, Lin-Schmidt X, Chamberlin A, Salehi-Ashtiani K, Papin JA. Metabolic systems analysis to advance algal biotechnology. Biotechnology Journal. 5: 660-70. PMID 20665641 DOI: 10.1002/Biot.201000129 |
0.466 |
|
| 2010 |
Sefcik LS, Wilson JL, Papin JA, Botchwey EA. Harnessing systems biology approaches to engineer functional microvascular networks. Tissue Engineering. Part B, Reviews. 16: 361-70. PMID 20121415 DOI: 10.1089/Ten.Teb.2009.0611 |
0.394 |
|
| 2009 |
Jensen PA, Papin JA. A scalable systems analysis approach for regulated metabolic networks. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 5464-5. PMID 19964682 DOI: 10.1109/IEMBS.2009.5334060 |
0.686 |
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| 2009 |
Oberhardt MA, Palsson BØ, Papin JA. Applications of genome-scale metabolic reconstructions. Molecular Systems Biology. 5: 320. PMID 19888215 DOI: 10.1038/Msb.2009.77 |
0.79 |
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| 2009 |
Manichaikul A, Ghamsari L, Hom EF, Lin C, Murray RR, Chang RL, Balaji S, Hao T, Shen Y, Chavali AK, Thiele I, Yang X, Fan C, Mello E, Hill DE, ... ... Papin JA, et al. Metabolic network analysis integrated with transcript verification for sequenced genomes. Nature Methods. 6: 589-92. PMID 19597503 DOI: 10.1038/Nmeth.1348 |
0.834 |
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| 2009 |
Gianchandani EP, Joyce AR, Palsson BØ, Papin JA. Functional states of the genome-scale Escherichia coli transcriptional regulatory system. Plos Computational Biology. 5: e1000403. PMID 19503608 DOI: 10.1371/Journal.Pcbi.1000403 |
0.812 |
|
| 2009 |
Roberts SB, Robichaux JL, Chavali AK, Manque PA, Lee V, Lara AM, Papin JA, Buck GA. Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi. Bmc Systems Biology. 3: 52. PMID 19445715 DOI: 10.1186/1752-0509-3-52 |
0.822 |
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| 2009 |
Mandell JW, Glass G, Gianchandani EP, Locke CN, Amos S, Bourne TD, Schiff D, Papin JA. Dephosphorylation of beta-arrestin 1 in glioblastomas. Journal of Neuropathology and Experimental Neurology. 68: 535-41. PMID 19404096 DOI: 10.1097/Nen.0B013E3181A2B8F4-9 |
0.721 |
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| 2009 |
Oberhardt MA, Chavali AK, Papin JA. Flux balance analysis: interrogating genome-scale metabolic networks. Methods in Molecular Biology (Clifton, N.J.). 500: 61-80. PMID 19399432 DOI: 10.1007/978-1-59745-525-1_3 |
0.823 |
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| 2009 |
Wieghaus KA, Gianchandani EP, Neal RA, Paige MA, Brown ML, Papin JA, Botchwey EA. Phthalimide neovascular factor 1 (PNF1) modulates MT1-MMP activity in human microvascular endothelial cells. Biotechnology and Bioengineering. 103: 796-807. PMID 19326468 DOI: 10.1002/Bit.22310 |
0.755 |
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| 2009 |
Allen T, Saucerman J, Papin J, Peirce-Cottler S. Development and assessment of a novel systems bioengineering course integrating modeling and experimentation Asee Annual Conference and Exposition, Conference Proceedings. |
0.538 |
|
| 2008 |
Pucha?ka J, Oberhardt MA, Godinho M, Bielecka A, Regenhardt D, Timmis KN, Papin JA, Martins dos Santos VA. Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. Plos Computational Biology. 4: e1000210. PMID 18974823 DOI: 10.1371/Journal.Pcbi.1000210 |
0.794 |
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| 2008 |
Chavali AK, Gianchandani EP, Tung KS, Lawrence MB, Peirce SM, Papin JA. Characterizing emergent properties of immunological systems with multi-cellular rule-based computational modeling. Trends in Immunology. 29: 589-99. PMID 18964301 DOI: 10.1016/J.It.2008.08.006 |
0.775 |
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| 2008 |
Wieghaus KA, Gianchandani EP, Paige MA, Brown ML, Botchwey EA, Papin JA. Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule. Bioinformatics (Oxford, England). 24: 2384-90. PMID 18718940 DOI: 10.1093/Bioinformatics/Btn451 |
0.759 |
|
| 2008 |
Lee JM, Min Lee J, Gianchandani EP, Eddy JA, Papin JA. Dynamic analysis of integrated signaling, metabolic, and regulatory networks. Plos Computational Biology. 4: e1000086. PMID 18483615 DOI: 10.1371/Journal.Pcbi.1000086 |
0.831 |
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| 2008 |
Chavali AK, Whittemore JD, Eddy JA, Williams KT, Papin JA. Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major. Molecular Systems Biology. 4: 177. PMID 18364711 DOI: 10.1038/Msb.2008.15 |
0.822 |
|
| 2008 |
Gianchandani EP, Oberhardt MA, Burgard AP, Maranas CD, Papin JA. Predicting biological system objectives de novo from internal state measurements. Bmc Bioinformatics. 9: 43. PMID 18218092 DOI: 10.1186/1471-2105-9-43 |
0.813 |
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| 2008 |
Oberhardt MA, Pucha?ka J, Fryer KE, Martins dos Santos VA, Papin JA. Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. Journal of Bacteriology. 190: 2790-803. PMID 18192387 DOI: 10.1128/Jb.01583-07 |
0.793 |
|
| 2008 |
Lee JM, Gianchandani EP, Eddy JA, Papin JA. Application of a novel optimization-based approach to characterize integrated signalling, regulatory Ifac Proceedings Volumes (Ifac-Papersonline). 17. DOI: 10.3182/20080706-5-KR-1001.2567 |
0.727 |
|
| 2008 |
Lee JM, Gianchandani EP, Eddy JA, Papin JA. Application of a novel optimization-based approach to characterize integrated signalling, regulatory, and metabolic biochemical networks Ifac Proceedings Volumes. 41: 11630-11635. DOI: 10.3182/20080706-5-Kr-1001.01971 |
0.806 |
|
| 2008 |
Lee JM, Gianchandani EP, Eddy JA, Papin JA. Correction: Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks Plos Computational Biology. 4. DOI: 10.1371/Annotation/5594348B-De00-446A-Bdd0-Ec56E70B3553 |
0.8 |
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| 2007 |
Robertson SH, Smith CK, Langhans AL, McLinden SE, Oberhardt MA, Jakab KR, Dzamba B, DeSimone DW, Papin JA, Peirce SM. Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior. Bmc Systems Biology. 1: 46. PMID 17953751 DOI: 10.1186/1752-0509-1-46 |
0.702 |
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| 2007 |
Wieghaus KA, Gianchandani EP, Brown ML, Papin JA, Botchwey EA. Mechanistic exploration of phthalimide neovascular factor 1 using network analysis tools. Tissue Engineering. 13: 2561-75. PMID 17723106 DOI: 10.1089/Ten.2007.0023 |
0.768 |
|
| 2006 |
Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO. Matrix formalism to describe functional states of transcriptional regulatory systems. Plos Computational Biology. 2: e101. PMID 16895435 DOI: 10.1371/Journal.Pcbi.0020101 |
0.792 |
|
| 2006 |
Lee JM, Gianchandani EP, Papin JA. Flux balance analysis in the era of metabolomics. Briefings in Bioinformatics. 7: 140-50. PMID 16772264 DOI: 10.1093/Bib/Bbl007 |
0.812 |
|
| 2006 |
Gianchandani EP, Brautigan DL, Papin JA. Systems analyses characterize integrated functions of biochemical networks. Trends in Biochemical Sciences. 31: 284-91. PMID 16616498 DOI: 10.1016/J.Tibs.2006.03.007 |
0.817 |
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| 2006 |
Peirce SM, Skalak TC, Papin JA. Multiscale biosystems integration: Coupling intracellular network analysis with tissue-patterning simulations Ibm Journal of Research and Development. 50: 601-615. DOI: 10.1147/Rd.506.0601 |
0.393 |
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| 2005 |
Papin JA, Hunter T, Palsson BO, Subramaniam S. Reconstruction of cellular signalling networks and analysis of their properties. Nature Reviews. Molecular Cell Biology. 6: 99-111. PMID 15654321 DOI: 10.1038/Nrm1570 |
0.519 |
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| 2004 |
Papin JA, Reed JL, Palsson BO. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends in Biochemical Sciences. 29: 641-7. PMID 15544950 DOI: 10.1016/J.Tibs.2004.10.001 |
0.63 |
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| 2004 |
Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO. Comparison of network-based pathway analysis methods. Trends in Biotechnology. 22: 400-5. PMID 15283984 DOI: 10.1016/J.Tibtech.2004.06.010 |
0.694 |
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| 2004 |
Papin JA, Palsson BO. The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. Biophysical Journal. 87: 37-46. PMID 15240442 DOI: 10.1529/Biophysj.103.029884 |
0.521 |
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| 2004 |
Papin J, Subramaniam S. Bioinformatics and cellular signaling Current Opinion in Biotechnology. 15: 78-81. PMID 15102471 DOI: 10.1016/J.Copbio.2004.01.003 |
0.401 |
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| 2004 |
Papin JA, Palsson BO. Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. Journal of Theoretical Biology. 227: 283-97. PMID 14990392 DOI: 10.1016/J.Jtbi.2003.11.016 |
0.551 |
|
| 2003 |
Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BO. Network-based analysis of metabolic regulation in the human red blood cell. Journal of Theoretical Biology. 225: 185-94. PMID 14575652 DOI: 10.1016/S0022-5193(03)00237-6 |
0.824 |
|
| 2003 |
Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO. Metabolic pathways in the post-genome era. Trends in Biochemical Sciences. 28: 250-8. PMID 12765837 DOI: 10.1016/S0968-0004(03)00064-1 |
0.839 |
|
| 2003 |
Palsson BO, Price ND, Papin JA. Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends in Biotechnology. 21: 195-8. PMID 12727379 DOI: 10.1016/S0167-7799(03)00080-5 |
0.64 |
|
| 2003 |
Price ND, Papin JA, Schilling CH, Palsson BO. Genome-scale microbial in silico models: the constraints-based approach. Trends in Biotechnology. 21: 162-9. PMID 12679064 DOI: 10.1016/S0167-7799(03)00030-1 |
0.771 |
|
| 2003 |
Price ND, Reed JL, Papin JA, Famili I, Palsson BO. Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophysical Journal. 84: 794-804. PMID 12547764 DOI: 10.1016/S0006-3495(03)74899-1 |
0.828 |
|
| 2002 |
Papin JA, Price ND, Palsson BØ. Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Research. 12: 1889-900. PMID 12466293 DOI: 10.1101/Gr.327702 |
0.66 |
|
| 2002 |
Papin JA, Price ND, Edwards JS, Palsson B BØ. The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. Journal of Theoretical Biology. 215: 67-82. PMID 12051985 DOI: 10.1006/Jtbi.2001.2499 |
0.727 |
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| 2002 |
Price ND, Papin JA, Palsson BØ. Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Research. 12: 760-9. PMID 11997342 DOI: 10.1101/Gr.218002 |
0.684 |
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