Jennifer Leanne Reed - Publications

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

58 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
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2012 Reed JL. Shrinking the metabolic solution space using experimental datasets. Plos Computational Biology. 8: e1002662. PMID 22956899 DOI: 10.1371/journal.pcbi.1002662  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2011 Morris K, Ihnatovych I, Ionetz E, Reed J, Braundmeier A, Strakova Z. Cofilin and slingshot localization in the epithelium of uterine endometrium changes during the menstrual cycle and in endometriosis Reproductive Sciences. 18: 1014-1024. PMID 21693774 DOI: 10.1177/1933719111401663  1
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  1
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  1
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  1
2011 Kim J, Maravelias CT, Reed JL. Predicting immediate behaviors of engineered microbial strains for biofuel production 11aiche - 2011 Aiche Annual Meeting, Conference Proceedings 1
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  1
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  1
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  1
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  1
2010 Strakova Z, Reed J, Ihnatovych I. Human transcriptional coactivator with PDZ-binding motif (TAZ) is downregulated during decidualization Biology of Reproduction. 82: 1112-1118. PMID 20164440 DOI: 10.1095/biolreprod.109.081844  1
2009 Reed JL. Descriptive and predictive applications of constraint-based metabolic models. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 5460-3. PMID 19964681 DOI: 10.1109/IEMBS.2009.5334064  1
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  1
2009 Ihnatovych I, Livak M, Reed J, De Lanerolle P, Strakova Z. Manipulating actin dynamics affects human in vitro decidualization Biology of Reproduction. 81: 222-230. PMID 19339710 DOI: 10.1095/biolreprod.108.074666  1
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  1
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  1
2008 Reed JL, Hua Q, Palsson BO. Determining metabolic fluxes using experimental measurements Aiche Annual Meeting, Conference Proceedings 1
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  1
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  0.8
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2001 Shemesh M, Mizrachi D, Gurevich M, Shore LS, Reed J, Chang SM, Thatcher WW, Fields MJ. Expression of functional luteinizing hormone (LH) receptor and its messenger ribonucleic acid in bovine endometrium: LH augmentation of cAMP and inositol phosphate in vitro and human chorionic gonadotropin (hCG) augmentation of peripheral prostaglandin in vivo. Reproductive Biology. 1: 13-32. PMID 14666165  1
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