Jeremy S. Edwards - Publications

University of California, Berkeley, CA, United States 

57 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
2017 Cho YS, Kim H, Kim HM, Jho S, Jun J, Lee YJ, Chae KS, Kim CG, Kim S, Eriksson A, Edwards JS, Lee S, Kim BC, Manica A, Oh TK, et al. Corrigendum: An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. Nature Communications. 8: 16168. PMID 28991236 DOI: 10.1038/Ncomms16168  0.72
2016 Cho YS, Kim H, Kim HM, Jho S, Jun J, Lee YJ, Chae KS, Kim CG, Kim S, Eriksson A, Edwards JS, Lee S, Kim BC, Manica A, Oh TK, et al. An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. Nature Communications. 7: 13637. PMID 27882922 DOI: 10.1038/Ncomms13637  0.72
2015 Chung O, Jin S, Cho YS, Lim J, Kim H, Jho S, Kim HM, Jun J, Lee H, Chon A, Ko J, Edwards J, Weber JA, Han K, O'Brien SJ, et al. The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures. Genome Biology. 16: 215. PMID 26486310 DOI: 10.1186/S13059-015-0780-4  1
2015 McCabe Pryor M, Steinkamp MP, Halasz AM, Chen Y, Yang S, Smith MS, Zahoransky-Kohalmi G, Swift M, Xu XP, Hanien D, Volkmann N, Lidke DS, Edwards JS, Wilson BS. Orchestration of ErbB3 signaling through hetero and homo-interactions. Molecular Biology of the Cell. PMID 26378253 DOI: 10.1091/Mbc.E14-06-1114  1
2014 Uzzal MM, Zarkesh-Ha P, Edwards JS, Coelho E, Rawat P. A highly sensitive ISFET using pH-to-current conversion for real-time DNA sequencing International System On Chip Conference. 410-414. DOI: 10.1109/SOCC.2014.6948964  1
2013 Halász AM, Lai HJ, McCabe Pryor M, Radhakrishnan K, Edwards JS. Analytical solution of steady-state equations for chemical reaction networks with bilinear rate laws. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 10: 957-69. PMID 24334389 DOI: 10.1109/Tcbb.2013.41  1
2013 Pryor MM, Low-Nam ST, Halász AM, Lidke DS, Wilson BS, Edwards JS. Dynamic transition states of ErbB1 phosphorylation predicted by spatial stochastic modeling. Biophysical Journal. 105: 1533-43. PMID 24048005 DOI: 10.1016/J.Bpj.2013.07.056  1
2012 Archuleta MN, McDermott JE, Edwards JS, Resat H. An adaptive coarse graining method for signal transduction in three dimensions. Fundamenta Informaticae. 118. PMID 24357890 DOI: 10.3233/Fi-2012-720  1
2012 Aragon AD, Torrez-Martinez N, Edwards JS. Genomic analysis of Saccharomyces cerevisiae isolates that grow optimally with glucose as the sole carbon source. Electrophoresis. 33: 3514-20. PMID 23135695 DOI: 10.1002/Elps.201200172  1
2012 Singh AP, Andries E, Edwards JS, Steinberg S. The shuttling scaffold model for prevention of yeast pheromone pathway misactivation. Bulletin of Mathematical Biology. 74: 2861-74. PMID 23104201 DOI: 10.1007/S11538-012-9785-2  1
2012 Radhakrishnan K, Halász Á, McCabe MM, Edwards JS, Wilson BS. Mathematical simulation of membrane protein clustering for efficient signal transduction. Annals of Biomedical Engineering. 40: 2307-18. PMID 22669501 DOI: 10.1007/S10439-012-0599-Z  1
2011 Ho A, Murphy M, Wilson S, Atlas SR, Edwards JS. Sequencing by ligation variation with endonuclease V digestion and deoxyinosine-containing query oligonucleotides. Bmc Genomics. 12: 598. PMID 22151854 DOI: 10.1186/1471-2164-12-598  1
2011 Costa MN, Radhakrishnan K, Edwards JS. Monte Carlo simulations of plasma membrane corral-induced EGFR clustering. Journal of Biotechnology. 151: 261-70. PMID 21167222 DOI: 10.1016/J.Jbiotec.2010.12.009  1
2010 Radhakrishnan K, Halász A, Vlachos D, Edwards JS. Quantitative understanding of cell signaling: the importance of membrane organization. Current Opinion in Biotechnology. 21: 677-82. PMID 20829029 DOI: 10.1016/J.Copbio.2010.08.006  1
2010 Xu MY, Aragon AD, Mascarenas MR, Torrez-Martinez N, Edwards JS. Dual primer emulsion PCR for next- generation DNA sequencing. Biotechniques. 48: 409-12. PMID 20569215 DOI: 10.2144/000113423  1
2010 Hsieh MY, Yang S, Raymond-Stinz MA, Edwards JS, Wilson BS. Spatio-temporal modeling of signaling protein recruitment to EGFR. Bmc Systems Biology. 4: 57. PMID 20459599 DOI: 10.1186/1752-0509-4-57  1
2010 Ogunnaike BA, Gelmi CA, Edwards JS. A probabilistic framework for microarray data analysis: fundamental probability models and statistical inference. Journal of Theoretical Biology. 264: 211-22. PMID 20170665 DOI: 10.1016/J.Jtbi.2010.02.021  1
2009 Radhakrishnan K, Edwards JS, Lidke DS, Jovin TM, Wilson BS, Oliver JM. Sensitivity analysis predicts that the ERK-pMEK interaction regulates ERK nuclear translocation. Iet Systems Biology. 3: 329-41. PMID 21028924 DOI: 10.1049/Iet-Syb.2009.0010  1
2009 Costa MN, Radhakrishnan K, Wilson BS, Vlachos DG, Edwards JS. Coupled stochastic spatial and non-spatial simulations of ErbB1 signaling pathways demonstrate the importance of spatial organization in signal transduction. Plos One. 4: e6316. PMID 19626123 DOI: 10.1371/Journal.Pone.0006316  1
2008 Hsieh MY, Yang S, Raymond-Stinz MA, Steinberg S, Vlachos DG, Shu W, Wilson B, Edwards JS. Stochastic simulations of ErbB homo and heterodimerisation: potential impacts of receptor conformational state and spatial segregation. Iet Systems Biology. 2: 256-72. PMID 19045821 DOI: 10.1049/Iet-Syb:20070073  1
2008 Niehaus AM, Vlachos DG, Edwards JS, Plechac P, Tribe R. Microscopic simulation of membrane molecule diffusion on corralled membrane surfaces. Biophysical Journal. 94: 1551-64. PMID 17993499 DOI: 10.1529/Biophysj.107.106484  1
2007 Merritt J, Roberts KG, Butz JA, Edwards JS. Parallel analysis of tetramerization domain mutants of the human p53 protein using PCR colonies. Genomic Medicine. 1: 113-24. PMID 18923936 DOI: 10.1007/S11568-007-9011-8  1
2007 Mayawala K, Vlachos DG, Edwards JS. The role of reaction engineering in cancer biology: Bio-imaging informatics reveals implications of the plasma membrane heterogeneities Chemical Engineering Science. 62: 5222-5231. DOI: 10.1016/J.Ces.2007.01.048  1
2006 Kauffman KJ, Ogunnaike BA, Edwards JS. Designing experiments that aid in the identification of regulatory networks. Briefings in Functional Genomics & Proteomics. 4: 331-42. PMID 17202124 DOI: 10.1093/Bfgp/Eli004  1
2005 Merritt J, Butz JA, Ogunnaike BA, Edwards JS. Parallel analysis of mutant human glucose 6-phosphate dehydrogenase in yeast using PCR colonies. Biotechnology and Bioengineering. 92: 519-31. PMID 16193512 DOI: 10.1002/Bit.20726  1
2005 Gadkar KG, Doyle Iii FJ, Edwards JS, Mahadevan R. Estimating optimal profiles of genetic alterations using constraint-based models. Biotechnology and Bioengineering. 89: 243-51. PMID 15593263 DOI: 10.1002/Bit.20349  1
2005 Goodkind JR, Edwards JS. Gene expression measurement technologies: Innovations and ethical considerations Computers and Chemical Engineering. 29: 589-596. DOI: 10.1016/J.Compchemeng.2004.08.033  1
2004 Butz JA, Roberts KG, Edwards JS. Detecting changes in the relative expression of KRAS2 splice variants using polymerase colonies. Biotechnology Progress. 20: 1836-9. PMID 15575719 DOI: 10.1021/Bp0343054  1
2004 Mikkilineni V, Mitra RD, Merritt J, DiTonno JR, Church GM, Ogunnaike B, Edwards JS. Digital quantitative measurements of gene expression. Biotechnology and Bioengineering. 86: 117-24. PMID 15052631 DOI: 10.1002/Bit.20048  1
2004 Butz JA, Yan H, Mikkilineni V, Edwards JS. Detection of allelic variations of human gene expression by polymerase colonies. Bmc Genetics. 5: 3. PMID 15040815 DOI: 10.1186/1471-2156-5-3  1
2003 Ibarra RU, Fu P, Palsson BO, DiTonno JR, Edwards JS. Quantitative analysis of Escherichia coli metabolic phenotypes within the context of phenotypic phase planes. Journal of Molecular Microbiology and Biotechnology. 6: 101-8. PMID 15044828 DOI: 10.1159/000076740  1
2003 Lall R, Gao G, Dhurjati P, Edwards J. MRAD: Metabolic reaction analysis database--an entity-relationship approach. Journal of Molecular Microbiology and Biotechnology. 6: 12-8. PMID 14593249 DOI: 10.1159/000073404  1
2003 Kauffman KJ, Prakash P, Edwards JS. Advances in flux balance analysis. Current Opinion in Biotechnology. 14: 491-6. PMID 14580578 DOI: 10.1016/J.Copbio.2003.08.001  0.64
2003 Edwards JS, Battista JR. Using DNA microarray data to understand the ionizing radiation resistance of Deinococcus radiodurans. Trends in Biotechnology. 21: 381-2. PMID 12948669 DOI: 10.1016/S0167-7799(03)00196-3  1
2003 Merritt J, DiTonno JR, Mitra RD, Church GM, Edwards JS. Parallel competition analysis of Saccharomyces cerevisiae strains differing by a single base using polymerase colonies. Nucleic Acids Research. 31: e84. PMID 12888536 DOI: 10.1093/Nar/Gng084  1
2003 Butz J, Wickstrom E, Edwards J. Characterization of mutations and loss of heterozygosity of p53 and K-ras2 in pancreatic cancer cell lines by immobilized polymerase chain reaction. Bmc Biotechnology. 3: 11. PMID 12877750 DOI: 10.1186/1472-6750-3-11  1
2003 Altenbaugh RE, Kauffman KJ, Edwards JS. Suitability and utility of computational analysis tools: characterization of erythrocyte parameter variation. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 104-15. PMID 12603021  0.64
2003 Edwards JS, Kauffman KJ. Biochemical engineering in the 21st century Current Opinion in Biotechnology. 14: 451-453. DOI: 10.1016/J.Copbio.2003.08.007  0.64
2002 Ibarra RU, Edwards JS, Palsson BO. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature. 420: 186-9. PMID 12432395 DOI: 10.1038/Nature01149  1
2002 Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO. Genome-scale metabolic model of Helicobacter pylori 26695. Journal of Bacteriology. 184: 4582-93. PMID 12142428 DOI: 10.1128/Jb.184.16.4582-4593.2002  1
2002 Kauffman KJ, Pajerowski JD, Jamshidi N, Palsson BO, Edwards JS. Description and analysis of metabolic connectivity and dynamics in the human red blood cell. Biophysical Journal. 83: 646-62. PMID 12124254 DOI: 10.1016/S0006-3495(02)75198-9  1
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  1
2002 Edwards JS, Covert M, Palsson B. Metabolic modelling of microbes: the flux-balance approach. Environmental Microbiology. 4: 133-40. PMID 12000313 DOI: 10.1046/J.1462-2920.2002.00282.X  1
2002 Edwards JS, Ramakrishna R, Palsson BO. Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnology and Bioengineering. 77: 27-36. PMID 11745171 DOI: 10.1002/Bit.10047  1
2001 Badarinarayana V, Estep PW, Shendure J, Edwards J, Tavazoie S, Lam F, Church GM. Selection analyses of insertional mutants using subgenic-resolution arrays. Nature Biotechnology. 19: 1060-5. PMID 11689852 DOI: 10.1038/Nbt1101-1060  1
2001 Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson BO. Dynamic simulation of the human red blood cell metabolic network. Bioinformatics (Oxford, England). 17: 286-7. PMID 11294796 DOI: 10.1093/Bioinformatics/17.3.286  1
2001 Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO. Metabolic modeling of microbial strains in silico. Trends in Biochemical Sciences. 26: 179-86. PMID 11246024 DOI: 10.1016/S0968-0004(00)01754-0  1
2001 Edwards JS, Ibarra RU, Palsson BO. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nature Biotechnology. 19: 125-30. PMID 11175725 DOI: 10.1038/84379  1
2001 Ramakrishna R, Edwards JS, McCulloch A, Palsson BO. Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. American Journal of Physiology. Regulatory, Integrative and Comparative Physiology. 280: R695-704. PMID 11171647 DOI: 10.1152/Ajpregu.2001.280.3.R695  1
2000 Schilling CH, Edwards JS, Letscher D, Palsson BØ. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnology and Bioengineering. 71: 286-306. PMID 11291038 DOI: 10.1002/1097-0290(2000)71:4<286::Aid-Bit1018>3.0.Co;2-R  1
2000 Edwards JS, Palsson BO. Robustness analysis of the Escherichia coli metabolic network. Biotechnology Progress. 16: 927-39. PMID 11101318 DOI: 10.1021/Bp0000712  1
2000 Edwards JS, Palsson BO. Multiple steady states in kinetic models of red cell metabolism. Journal of Theoretical Biology. 207: 125-7. PMID 11027485 DOI: 10.1006/Jtbi.2000.2165  1
2000 Edwards JS, Palsson BO. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. Bmc Bioinformatics. 1: 1. PMID 11001586 DOI: 10.1186/1471-2105-1-1  1
2000 Edwards JS, Palsson BO. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proceedings of the National Academy of Sciences of the United States of America. 97: 5528-33. PMID 10805808 DOI: 10.1073/Pnas.97.10.5528  1
1999 Edwards JS, Palsson BO. Systems properties of the Haemophilus influenzae Rd metabolic genotype. The Journal of Biological Chemistry. 274: 17410-6. PMID 10364169 DOI: 10.1074/Jbc.274.25.17410  1
1999 Schilling CH, Edwards JS, Palsson BO. Toward metabolic phenomics: analysis of genomic data using flux balances. Biotechnology Progress. 15: 288-95. PMID 10356245 DOI: 10.1021/Bp9900357  1
1998 Edwards JS, Palsson BO. How will bioinformatics influence metabolic engineering? Biotechnology and Bioengineering. 58: 162-9. PMID 10191386 DOI: 10.1002/(Sici)1097-0290(19980420)58:2/3<162::Aid-Bit8>3.0.Co;2-J  1
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