Jennifer Leanne Reed - Publications

2005 University of California, San Diego, La Jolla, CA 

69 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

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  0.456
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  0.331
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  0.441
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  0.334
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  0.405
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  0.327
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  0.497
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  0.318
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  0.449
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  0.336
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  0.411
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  0.476
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  0.488
2016 Long MR, Reed JL. Improving Flux Predictions by Integrating Data from Multiple Strains. Bioinformatics (Oxford, England). PMID 27998937 DOI: 10.1093/Bioinformatics/Btw706  0.383
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  0.372
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  0.375
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  0.483
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  0.628
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  0.327
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  0.398
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  0.398
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  0.417
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  0.309
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  0.489
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  0.428
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  0.469
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  0.432
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  0.479
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  0.506
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  0.431
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  0.416
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  0.403
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  0.404
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  0.422
2012 Reed JL. Shrinking the metabolic solution space using experimental datasets. Plos Computational Biology. 8: e1002662. PMID 22956899 DOI: 10.1371/Journal.Pcbi.1002662  0.45
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  0.528
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  0.47
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  0.309
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  0.42
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  0.327
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  0.44
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  0.479
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  0.767
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  0.45
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  0.432
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  0.452
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  0.484
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  0.475
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  0.464
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  0.315
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  0.525
2009 Feist AM, HerrgÃ¥rd 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  0.788
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  0.353
2008 Reed JL, Hua Q, Palsson BO. Determining metabolic fluxes using experimental measurements Aiche Annual Meeting, Conference Proceedings 0.451
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  0.485
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  0.814
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  0.718
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  0.623
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  0.66
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  0.634
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  0.485
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  0.812
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  0.78
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  0.374
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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