| Year |
Citation |
Score |
| 2020 |
Ong WK, Courtney DK, Pan S, Andrade RB, Kiley PJ, Pfleger BF, Reed JL. Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4. Plos Computational Biology. 16: e1008137. PMID 32804944 DOI: 10.1371/Journal.Pcbi.1008137 |
0.453 |
|
| 2019 |
Kim J, Tremaine M, Grass JA, Purdy HM, Landick R, Kiley PJ, Reed JL. Systems metabolic engineering of Escherichia coli improves co-conversion of lignocellulose-derived sugars. Biotechnology Journal. e1800441. PMID 31297978 DOI: 10.1002/Biot.201800441 |
0.329 |
|
| 2019 |
Jacobson TB, Adamczyk PA, Stevenson DM, Regner M, Ralph J, Reed J, Amador-Noguez D. H and C metabolic flux analysis elucidates in vivo thermodynamics of the ED pathway in Zymomonas mobilis. Metabolic Engineering. PMID 31078792 DOI: 10.1016/J.Ymben.2019.05.006 |
0.439 |
|
| 2018 |
Wu W, Long MR, Zhang X, Reed JL, Maravelias CT. A framework for the identification of promising bio-based chemicals. Biotechnology and Bioengineering. PMID 29940066 DOI: 10.1002/Bit.26779 |
0.333 |
|
| 2018 |
Tian M, Reed JL. Integrating Proteomic or Transcriptomic Data into Metabolic Models Using Linear Bound Flux Balance Analysis. Bioinformatics (Oxford, England). PMID 29878053 DOI: 10.1093/Bioinformatics/Bty445 |
0.404 |
|
| 2018 |
Clark RL, McGinley LL, Purdy HM, Korosh TC, Reed JL, Root TW, Pfleger BF. Light-Optimized Growth of Cyanobacterial Cultures: Growth Phases and Productivity of Biomass and Secreted Molecules in Light-Limited Batch Growth. Metabolic Engineering. PMID 29601856 DOI: 10.1016/J.Ymben.2018.03.017 |
0.326 |
|
| 2017 |
Pan S, Reed JL. Advances in gap-filling genome-scale metabolic models and model-driven experiments lead to novel metabolic discoveries. Current Opinion in Biotechnology. 51: 103-108. PMID 29278837 DOI: 10.1016/J.Copbio.2017.12.012 |
0.494 |
|
| 2017 |
Comer AD, Long MR, Reed JL, Pfleger BF. Flux Balance Analysis Indicates that Methane Is the Lowest Cost Feedstock for Microbial Cell Factories. Metabolic Engineering Communications. 5: 26-33. PMID 28989864 DOI: 10.1016/J.Meteno.2017.07.002 |
0.316 |
|
| 2017 |
Pan S, Nikolakakis K, Adamczyk PA, Pan M, Ruby EG, Reed JL. Model-enabled gene search (MEGS) allows fast and direct discovery of enzymatic and transport gene functions in the marine bacterium Vibrio fischeri. The Journal of Biological Chemistry. PMID 28446608 DOI: 10.1074/Jbc.M116.763193 |
0.447 |
|
| 2017 |
Thompson LR, Nikolakakis K, Pan S, Reed J, Knight R, Ruby EG. Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes. Environmental Microbiology. PMID 28152560 DOI: 10.1111/1462-2920.13684 |
0.335 |
|
| 2017 |
Adamczyk PA, Reed JL. Escherichia coli as a model organism for systems metabolic engineering Current Opinion in Systems Biology. 6: 80-88. DOI: 10.1016/J.Coisb.2017.11.001 |
0.409 |
|
| 2017 |
Purdy HM, Reed JL. Evaluating the capabilities of microbial chemical production using genome-scale metabolic models Current Opinion in Systems Biology. 2: 91-97. DOI: 10.1016/J.Coisb.2017.01.008 |
0.473 |
|
| 2017 |
Pan S, Nikolakakis K, Ruby E, Reed J. Using a Genome-Scale Model and Genomic Library to Discover the Functions of Metabolic Genes Biophysical Journal. 112: 342a. DOI: 10.1016/J.Bpj.2016.11.1855 |
0.485 |
|
| 2016 |
Long MR, Reed JL. Improving Flux Predictions by Integrating Data from Multiple Strains. Bioinformatics (Oxford, England). PMID 27998937 DOI: 10.1093/Bioinformatics/Btw706 |
0.381 |
|
| 2016 |
Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, Avanasi Narasimhan R, McGee MA, Dickinson Q, La Reau A, Xie D, ... ... Reed JL, et al. Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. Plos Genetics. 12: e1006372. PMID 27741250 DOI: 10.1371/Journal.Pgen.1006372 |
0.369 |
|
| 2016 |
Zhang X, Tervo CJ, Reed JL. Metabolic Assessment of E. coli as a Biofactory for Commercial Products. Metabolic Engineering. PMID 26850742 DOI: 10.1016/J.Ymben.2016.01.007 |
0.373 |
|
| 2016 |
Tervo CJ, Reed JL. MapMaker and PathTracer for tracking carbon in genome-scale metabolic models. Biotechnology Journal. PMID 26771089 DOI: 10.1002/Biot.201500267 |
0.48 |
|
| 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, ... ... Reed JL, et al. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11: 831. PMID 26467284 DOI: 10.15252/Msb.20156157 |
0.621 |
|
| 2015 |
Hamilton JJ, Calixto Contreras M, Reed JL. Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community. Plos Computational Biology. 11: e1004364. PMID 26147299 DOI: 10.1371/Journal.Pcbi.1004364 |
0.326 |
|
| 2015 |
Long MR, Ong WK, Reed JL. Computational methods in metabolic engineering for strain design. Current Opinion in Biotechnology. 34: 135-141. PMID 25576846 DOI: 10.1016/J.Copbio.2014.12.019 |
0.396 |
|
| 2014 |
Tervo CJ, Reed JL. Expanding Metabolic Engineering Algorithms Using Feasible Space and Shadow Price Constraint Modules. Metabolic Engineering Communications. 1: 1-11. PMID 25478320 DOI: 10.1016/J.Meteno.2014.06.001 |
0.397 |
|
| 2014 |
Vinay-Lara E, Hamilton JJ, Stahl B, Broadbent JR, Reed JL, Steele JL. Genome-scale reconstruction of metabolic networks of Lactobacillus casei ATCC 334 and 12A. Plos One. 9: e110785. PMID 25365062 DOI: 10.1371/Journal.Pone.0110785 |
0.415 |
|
| 2014 |
Zhang X, Reed JL. Adaptive evolution of synthetic cooperating communities improves growth performance. Plos One. 9: e108297. PMID 25299364 DOI: 10.1371/Journal.Pone.0108297 |
0.308 |
|
| 2014 |
Kim J, Reed JL. Refining metabolic models and accounting for regulatory effects. Current Opinion in Biotechnology. 29: 34-8. PMID 24632483 DOI: 10.1016/J.Copbio.2014.02.009 |
0.486 |
|
| 2014 |
Ong WK, Vu TT, Lovendahl KN, Llull JM, Serres MH, Romine MF, Reed JL. Comparisons of Shewanella strains based on genome annotations, modeling, and experiments. Bmc Systems Biology. 8: 31. PMID 24621294 DOI: 10.1186/1752-0509-8-31 |
0.426 |
|
| 2014 |
Hamilton JJ, Reed JL. Software platforms to facilitate reconstructing genome-scale metabolic networks. Environmental Microbiology. 16: 49-59. PMID 24148076 DOI: 10.1111/1462-2920.12312 |
0.465 |
|
| 2013 |
Tervo CJ, Reed JL. BioMog: a computational framework for the de novo generation or modification of essential biomass components. Plos One. 8: e81322. PMID 24339916 DOI: 10.1371/Journal.Pone.0081322 |
0.43 |
|
| 2013 |
Hamilton JJ, Dwivedi V, Reed JL. Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models. Biophysical Journal. 105: 512-22. PMID 23870272 DOI: 10.1016/J.Bpj.2013.06.011 |
0.475 |
|
| 2013 |
Baumler DJ, Ma B, Reed JL, Perna NT. Inferring ancient metabolism using ancestral core metabolic models of enterobacteria. Bmc Systems Biology. 7: 46. PMID 23758866 DOI: 10.1186/1752-0509-7-46 |
0.502 |
|
| 2013 |
Cotten C, Reed JL. Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering. Biotechnology Journal. 8: 595-604. PMID 23703951 DOI: 10.1002/Biot.201200316 |
0.428 |
|
| 2013 |
Vu TT, Hill EA, Kucek LA, Konopka AE, Beliaev AS, Reed JL. Computational evaluation of Synechococcus sp. PCC 7002 metabolism for chemical production. Biotechnology Journal. 8: 619-30. PMID 23613453 DOI: 10.1002/Biot.201200315 |
0.414 |
|
| 2013 |
Cotten C, Reed JL. Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models. Bmc Bioinformatics. 14: 32. PMID 23360254 DOI: 10.1186/1471-2105-14-32 |
0.402 |
|
| 2012 |
Tervo CJ, Reed JL. FOCAL: an experimental design tool for systematizing metabolic discoveries and model development. Genome Biology. 13: R116. PMID 23236964 DOI: 10.1186/Gb-2012-13-12-R116 |
0.403 |
|
| 2012 |
Kim J, Reed JL. RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations. Genome Biology. 13: R78. PMID 23013597 DOI: 10.1186/Gb-2012-13-9-R78 |
0.419 |
|
| 2012 |
Reed JL. Shrinking the metabolic solution space using experimental datasets. Plos Computational Biology. 8: e1002662. PMID 22956899 DOI: 10.1371/Journal.Pcbi.1002662 |
0.448 |
|
| 2012 |
Hamilton JJ, Reed JL. Identification of functional differences in metabolic networks using comparative genomics and constraint-based models. Plos One. 7: e34670. PMID 22666308 DOI: 10.1371/Journal.Pone.0034670 |
0.524 |
|
| 2012 |
Vu TT, Stolyar SM, Pinchuk GE, Hill EA, Kucek LA, Brown RN, Lipton MS, Osterman A, Fredrickson JK, Konopka AE, Beliaev AS, Reed JL. Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142. Plos Computational Biology. 8: e1002460. PMID 22529767 DOI: 10.1371/Journal.Pcbi.1002460 |
0.468 |
|
| 2012 |
Schwalbach MS, Keating DH, Tremaine M, Marner WD, Zhang Y, Bothfeld W, Higbee A, Grass JA, Cotten C, Reed JL, da Costa Sousa L, Jin M, Balan V, Ellinger J, Dale B, et al. Complex physiology and compound stress responses during fermentation of alkali-pretreated corn stover hydrolysate by an Escherichia coli ethanologen. Applied and Environmental Microbiology. 78: 3442-57. PMID 22389370 DOI: 10.1128/Aem.07329-11 |
0.308 |
|
| 2012 |
Schellenberger J, Zielinski DC, Choi W, Madireddi S, Portnoy V, Scott DA, Reed JL, Osterman AL, Palsson B. Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling. Bmc Systems Biology. 6: 9. PMID 22289253 DOI: 10.1186/1752-0509-6-9 |
0.745 |
|
| 2011 |
Baumler DJ, Peplinski RG, Reed JL, Glasner JD, Perna NT. The evolution of metabolic networks of E. coli. Bmc Systems Biology. 5: 182. PMID 22044664 DOI: 10.1186/1752-0509-5-182 |
0.417 |
|
| 2011 |
Pinchuk GE, Geydebrekht OV, Hill EA, Reed JL, Konopka AE, Beliaev AS, Fredrickson JK. Pyruvate and lactate metabolism by Shewanella oneidensis MR-1 under fermentation, oxygen limitation, and fumarate respiration conditions. Applied and Environmental Microbiology. 77: 8234-40. PMID 21965410 DOI: 10.1128/Aem.05382-11 |
0.325 |
|
| 2011 |
Kim J, Reed JL, Maravelias CT. Large-scale bi-level strain design approaches and mixed-integer programming solution techniques. Plos One. 6: e24162. PMID 21949695 DOI: 10.1371/Journal.Pone.0024162 |
0.439 |
|
| 2011 |
Imam S, Yilmaz S, Sohmen U, Gorzalski AS, Reed JL, Noguera DR, Donohue TJ. iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network. Bmc Systems Biology. 5: 116. PMID 21777427 DOI: 10.1186/1752-0509-5-116 |
0.476 |
|
| 2011 |
Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RM, Hsiung CA, De Keersmaecker SC, Liao YC, Marchal K, Mo ML, Özdemir E, ... Reed JL, et al. A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. Bmc Systems Biology. 5: 8. PMID 21244678 DOI: 10.1186/1752-0509-5-8 |
0.766 |
|
| 2011 |
Chen X, Alonso AP, Allen DK, Reed JL, Shachar-Hill Y. Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli. Metabolic Engineering. 13: 38-48. PMID 21129495 DOI: 10.1016/J.Ymben.2010.11.004 |
0.447 |
|
| 2011 |
Kim J, Reed JL, Maravelias CT. Microbial Strain Design for Biochemical Production Using Mixed-integer Programming Techniques Computer Aided Chemical Engineering. 29: 1306-1310. DOI: 10.1016/B978-0-444-54298-4.50040-4 |
0.43 |
|
| 2010 |
Reed JL, Senger RS, Antoniewicz MR, Young JD. Computational approaches in metabolic engineering. Journal of Biomedicine & Biotechnology. 2010: 207414. PMID 21584279 DOI: 10.1155/2010/207414 |
0.449 |
|
| 2010 |
Barua D, Kim J, Reed JL. An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models. Plos Computational Biology. 6: e1000970. PMID 21060853 DOI: 10.1371/Journal.Pcbi.1000970 |
0.481 |
|
| 2010 |
Pinchuk GE, Hill EA, Geydebrekht OV, De Ingeniis J, Zhang X, Osterman A, Scott JH, Reed SB, Romine MF, Konopka AE, Beliaev AS, Fredrickson JK, Reed JL. Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation. Plos Computational Biology. 6: e1000822. PMID 20589080 DOI: 10.1371/Journal.Pcbi.1000822 |
0.472 |
|
| 2010 |
Kim J, Reed JL. OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. Bmc Systems Biology. 4: 53. PMID 20426856 DOI: 10.1186/1752-0509-4-53 |
0.461 |
|
| 2010 |
Wier AM, Nyholm SV, Mandel MJ, Massengo-Tiassé RP, Schaefer AL, Koroleva I, Splinter-Bondurant S, Brown B, Manzella L, Snir E, Almabrazi H, Scheetz TE, Bonaldo Mde F, Casavant TL, Soares MB, ... ... Reed JL, et al. Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis. Proceedings of the National Academy of Sciences of the United States of America. 107: 2259-64. PMID 20133870 DOI: 10.1073/Pnas.0909712107 |
0.314 |
|
| 2009 |
Raghunathan A, Reed J, Shin S, Palsson B, Daefler S. Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction Bmc Systems Biology. 3. PMID 19356237 DOI: 10.1186/1752-0509-3-38 |
0.518 |
|
| 2009 |
Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BØ. Reconstruction of biochemical networks in microorganisms. Nature Reviews. Microbiology. 7: 129-43. PMID 19116616 DOI: 10.1038/Nrmicro1949 |
0.781 |
|
| 2008 |
Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JL, Saffarini DA, Serres MH, Spormann AM, et al. Towards environmental systems biology of Shewanella. Nature Reviews. Microbiology. 6: 592-603. PMID 18604222 DOI: 10.1038/Nrmicro1947 |
0.351 |
|
| 2008 |
Reed JL, Hua Q, Palsson BO. Determining metabolic fluxes using experimental measurements Aiche Annual Meeting, Conference Proceedings. |
0.443 |
|
| 2007 |
Resendis-Antonio O, Reed JL, Encarnación S, Collado-Vides J, Palsson BØ. Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli. Plos Computational Biology. 3: 1887-95. PMID 17922569 DOI: 10.1371/Journal.Pcbi.0030192 |
0.482 |
|
| 2007 |
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Systems Biology. 3: 121. PMID 17593909 DOI: 10.1038/Msb4100155 |
0.808 |
|
| 2006 |
Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO. Systems approach to refining genome annotation. Proceedings of the National Academy of Sciences of the United States of America. 103: 17480-4. PMID 17088549 DOI: 10.1073/Pnas.0603364103 |
0.761 |
|
| 2006 |
Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BØ, Agarwalla S. Experimental and computational assessment of conditionally essential genes in Escherichia coli. Journal of Bacteriology. 188: 8259-71. PMID 17012394 DOI: 10.1128/Jb.00740-06 |
0.71 |
|
| 2006 |
Reed JL, Famili I, Thiele I, Palsson BO. Towards multidimensional genome annotation. Nature Reviews. Genetics. 7: 130-41. PMID 16418748 DOI: 10.1038/Nrg1769 |
0.767 |
|
| 2005 |
Barrett CL, Herring CD, Reed JL, Palsson BO. The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states. Proceedings of the National Academy of Sciences of the United States of America. 102: 19103-8. PMID 16357206 DOI: 10.1073/Pnas.0505231102 |
0.615 |
|
| 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 |
0.648 |
|
| 2004 |
Price ND, Reed JL, Palsson BØ. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nature Reviews. Microbiology. 2: 886-97. PMID 15494745 DOI: 10.1038/Nrmicro1023 |
0.627 |
|
| 2004 |
Reed JL, Palsson BØ. Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. Genome Research. 14: 1797-805. PMID 15342562 DOI: 10.1101/Gr.2546004 |
0.482 |
|
| 2004 |
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 429: 92-6. PMID 15129285 DOI: 10.1038/Nature02456 |
0.807 |
|
| 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 |
0.768 |
|
| 2003 |
Reed JL, Vo TD, Schilling CH, Palsson BO. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biology. 4: R54. PMID 12952533 DOI: 10.1186/Gb-2003-4-9-R54 |
0.778 |
|
| 2003 |
Reed JL, Palsson BØ. Thirteen years of building constraint-based in silico models of Escherichia coli. Journal of Bacteriology. 185: 2692-9. PMID 12700248 DOI: 10.1128/Jb.185.9.2692-2699.2003 |
0.373 |
|
| 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 |
0.789 |
|
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