Search PubMed for lab publications

2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 1997 prior Cover Art

2009 Return to top

  1. Oberhardt, M.A., Palsson, B.O., and Papin, J.A., Applications of genome-scale metabolic reconstructions, Molecular Systems Biology, 5: 320 (2009).

  2. Cho, B.K., Zengler, K., Qiu, Y., Knight, E.M., Park, Y.S., Barrett, C.L., Gao,Y., and Palsson, B.O., Elucidation of the Transcription Unit Architecture of the Escherichia coli K-12 MG1655 Genome, Nature Biotechnology. Published online: 1 November 2009 | doi:10.1038/nbt.1582 Supplemental Data

  3. Feist, A.M., Zielinski, D.C., Orth, J.D., Schellenberger, J., Herrgard, M.J., Palsson, B.O. , Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli , Metabolic Engineering (2009)

  4. Conrad, T.M., Joyce, A.R., Applebee, M., Barrett, C.L., Xie, B., Gao, Y., Palsson, B.O. , Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations, Genome Biology 2009, 10:R118.

  5. Palsson, B.O., Systems Biology of Metabolism, FEBS Letters Sept 19, (2009).

  6. Zhang, Y., Thiele, I., Weekes, D., Li, Z, Jaroszewski, L., Ginalski, K., Deacon, A., Wooley, J., Lesley, S., Wilson, I., Palsson, B.Ø., Osterman, A., Godzik, A. "Three-Dimensional Structural view of the Central Metabolic Network of Thermotoga maritima" Science, 325(5947):1544-1549 (2009). Highlighted in Nature.

  7. Jamshidi, N., Palsson, B.Ø., Flux-concentration duality in dynamic nonequilibrium biological networks. Biophys J. 97(5):L11-3 (2009).

  8. Cho, B.K. and Palsson, B.O., Can the protein occupancy landscape show the topologically isolated chromosomal domains in the E. coli genome?: An exciting prospect. Molecular Cell. 35(3):255-256 (2009). [Previews in Mol. Cell]

  9. Manichaikul A., Ghamsari L., Hom E.F., Lin C., Murray R.R., Chang R.L., Balaji S., Hao T., Shen Y., Chavali A.K., Thiele I., Yang X., Fan C., Mello E., Hill D.E., Vidal M., Salehi-Ashtiani K., Papin J.A., Metabolic network analysis integrated with transcript verification for sequenced genomes. Nature Methods. (2009).

  10. Cho, B.K. and Palsson, B.O., Probing the basis for genotype-phenotype relationships. Nature Methods. 6(8):565-566 (2009). [News and Views in Nat. Methods]

  11. Gianchandi, E.P., Joyce, A.R., Palsson, B.O., and Papin, J.A., Functional States of the Genome-Scale Escherichia coli Transcriptional Regulatory System. PLoS Computational Biology. 5:e1000403 (2009).

  12. Jamshidi, N. and Palsson, B.O., Using In Silico Models to Simulate Dual Perturbation Experiments: Procedure Development and Interpretation of Outcomes. BMC Systems Biology. 3:44 (2009).

  13. Raghunathan, A., Reed, J., Shin, S., Palsson, B.O., Daefler, S., Constraint-based analysis of metabolic capacity of Salmonella typhimurium during hostpathogen interaction. BMC Systems Biology. 3:38 (2009).

  14. Lewis, N.E., Cho, B.K., Knight, E.M., and Palsson, B.O., Gene Expression Profiling and the Use of Genome-scale ''In Silico'' Models of ''Escherichia coli'' for Analysis: Providing Context for Content, J Bacteriol, 191:3437-44 (2009).

  15. Mo, M.L., Palsson, B.O., Herrgard, M.J., Connecting extracellular metabolomic profiles to intracellular metabolic states in yeast. BMC Systems Biology. 3:37 (2009).

  16. Barrett, C.L., Herrgard, M.J., and Palsson, B.Ø.,Decomposing complex reaction networks using random sampling, principal component analysis, and basis rotation, BMC Systems Biology, 3:30 (2009).

  17. Thiele, I., Jamshidi, N., Fleming, R.M.T., Palsson, B.Ø., "Genome-scale reconstruction of ''E. coli'' 's transcriptional and translational machinery: A knowledge-base, its mathematical formulation, and its functional characterization", PLoS Comput Biol 5(3): e1000312. doi:10.1371/journal.pcbi.1000312.

  18. Li, F., Thiele, I., Jamshidi, N., and Palsson, B.O., Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling, PLOS Comput Biol. 5:e1000292. doi:10.1371/journal.pcbi.1000292 (2009).

  19. Sigurdsson, M.I., Jamshidi, N., Jonsson J.J., and Palsson, B.O., ''Genome-scale network analysis of imprinted human metabolic genes''. Epigenetics. (2009)

  20. Schellenberger, J. and Palsson, B.Ø. "The use of randomized sampling for analysis of metabolic networks", JBC Minireview. 2009 Feb;284(9): 5457-61.

  21. Feist, A.M., Herrgard, M.J., Thiele, I., Reed, J.L., Palsson, B.Ø., "Reconstruction of Biochemical Networks in Microbial Organisms" Nature Reviews Microbiology, 7(2)(2009).

  22. Mo, M.L. and Palsson, B.Ø. Understanding human metabolic physiology: A genome-to-systems approach, Trends in Biotechnology. 27(1):37-44 (2009).

2008 Return to top

  1. Portnoy, V.A., Herrgård, M.J., Palsson, B.Ø. Aerobic Fermentation of D-Glucose by an Evolved Cytochrome Oxidase Deficient Escherichia coli Strain, Appl Environ Microbiol. 2008 Dec;74(24):7561-9.

  2. Cho, B.K., Barrett, C.L., Knight, E.M., Park, Y.S., and Palsson B.Ø. Genome-scale reconstruction of Lrp-regulatory network in Escherichia coli, Proc Natl Acad Sci USA, 105:19462-19467 (2008). Supplemental Data

  3. Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novère, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasić, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kırdar, B., Penttilä, M., Klipp, E., Palsson, B. Ø., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J. & Kell, D. B., A consensus yeast metabolic network obtained from a community approach to systems biology., "Nature Biotechnology", 26: 1155-1160 (2008).

  4. Nogales, J. , Palsson, B.Ø., and Thiele, I., A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory., BMC Syst Biol, 2:79.doi:10.1186/1752-0509-2-79 (2008).

  5. Jamshidi, N. and Palsson, B.Ø., Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks, PLoS Computational Biology, 4(9): e1000177. doi:10.1371/journal.pcbi.1000177 (2008).

  6. Shlomi, T., Cabili, M.N., Herrgard, M.J., Palsson, B.O. and Ruppin, E., Network-based prediction of human tissue-specific metabolism, Nature Biotechnology, 26: 1003-1010 (2008).

  7. Lee, J., Yun, H., Feist, A.M., Palsson, B.O., and Lee, S.Y., "Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network", Appl Microbiol Biotechnol, 80(5): 849 - 862 (2008).

  8. Applebee, M.K., Herrgård, M.J. and Palsson, B.Ø., Impact of Individual Mutations on Increased Fitness in Adaptively-evolved strains of Escherichia coli., J Bacteriol, 190(14): 5087-5094 (2008).

  9. Becker, S.A. and Palsson, B.Ø., Context-specific metabolic networks are consistent with experiments., PLoS Comput Biol, 4(5): e1000082 (2008).

  10. Feist, A.M. and Palsson, B.Ø., The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli., Nature Biotechnology, 26(6): 659 - 667 (2008).

  11. Joyce, A.R. and Palsson, B.Ø., Predicting gene essentiality using genome-scale in silico models. Methods Mol Biol, 416: 433-57(2008).

  12. Cho, B.K., Knight, E.M., Barrett, C.L. and Palsson, B.Ø., Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts., Genome Research, 18(6):900-10 (2008). Supplemental Data

  13. Cho, B.K., Knight, E.M., and Palsson, B.Ø., Genome-wide Identification of Protein Binding Locations using Chromatin Immunoprecipitation coupled with Microarrays., Methods in Molecular Biology, 439:131-45 (2008).

  14. Becker, S.A. and Palsson, B.O., Three factors underlying incorrect in silico predictions of essential metabolic genes., BMC Syst Biol., 2(1): 14 (2008).

  15. Jamshidi, N. and Palsson, B.Ø., Formulating genome-scale kinetic models in the post-genome era, Molecular Systems Biology 4:171 (2008).

2007 Return to top

  1. Shlomi, T., Herrgard, M., Portnoy, V., Naim, E., Palsson, B.Ø., Sharan, R., Ruppin, E., Systematic condition-dependent annotation of metabolic genes., Genome Res., 17(11): 1626-33 (2007).

  2. Resendis-Antonio O., Reed J.L., Encarnacion S., Collado-Vides J. and Palsson B.Ø., "Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli., PLoS Comp. Biol., 3(10):e192, (2007).

  3. Oh, Y-K., Palsson, B.Ø., Park, S.M., Schilling, C.H., Mahadevan, R. "Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data., J Biol Chem. 10.1074/jbc.M703759200 (2007).

  4. Yeung, M., Thiele, I., and Palsson, B.Ø., Estimation of the number of extreme pathways for metabolic networks. , BMC Bioinformatics, 8(1): 363 (2007).

  5. Mo, M.L., Jamshidi, N., Palsson, B.Ø., "A Genome-scale, Constraint-based Approach to Systems Biology of Human Metabolism.," Molecular Biosystems. 3:9 (2007).

  6. Herring, C.S., Palsson, B.Ø , "An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes", BMC Genomics 8:274 (2007).

  7. Cho, B.K., Charusanti, P., Herrgard, M.J. and Palsson, B.Ø., "Microbial Regulatory and Metabolic Networks., Current Opinion in Biotechnology, 18(4): 360-364 (2007).

  8. Hua, Q., Joyce, A.R., Palsson, B.Ø., Fong, S.S., Metabolic characterization of Escherichia coli strains adapted to growth on lactate., Appl Environ Microbiol., 73(14): 4639-47 (2007).

  9. Jamshidi, N, Palsson, B.Ø. , Investigating the Metabolic Capabilities of Mycobacterium tuberculosis H37Rv Using the in silico Strain iNJ661 and Proposing Alternative Drug Targets., BMC Systems Biology, 1:26 (2007).

  10. Anderson, M.J., Delabarre, B., Raghunathan, A., Palsson, B.O., Brunger, A.T., Quake, S.R., Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices., Biochemistry, 46(19): 5722-31 (2007).

  11. Vo, T.D., Lee, W. N. P., Palsson, B.Ø. Systems analysis of energy metabolism elucidates the 3 affected respiratory chain complex in Leigh's syndrome., Mol Genet Metab., doi:10.1016/j.ymgme.2007.01.012 (2007).

  12. Duarte, N.D., Becker, S.A., Jamshidi, N., Thiele, I., Mo, M.L., Vo, T.D., Srivas, R., Palsson, B.Ø., Global reconstruction of the human metabolic network based on genomic and bibliomic data , Proc Natl Acad. Sci U S A, 104(6):1777-82 (2007).

  13. Vo, T.D., Palsson, B.Ø., Building the power house: recent advances in mitochondrial studies through proteomics and systems biology., Am J Physiol Cell Physiol., 292(1):C164-77 (2007).

  14. Jamshidi, N., Vo, T.D., Palsson, B.Ø., In silico analysis of SNPs and other high-throughput data.,Methods Mol Biol., 366:267-85 (2007).

  15. Feist, A.M., Henry, C.S., Reed, J.L., Krummenacker, M., Joyce, A.R., Karp, P.D., Broadbelt, L.J., Hatzimanikatis, V., Palsson, B.Ø. , "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information " Molecular Systems Biology, 3:121 (2007)

  16. Becker, S.A., Feist, A.M., Mo, M. L., Hannum, G., Palsson, B.Ø., Herrgard, M.J. Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox., Nat. Protocols, 2, 727-738 (2007).

  17. Joyce, A.R., Palsson, B.O., Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach., Prog Drug Res., 64: 267-309 (2007).

2006 Return to top

  1. Mahadevan, R., Bond, D.R., Butler, J.E., Esteve-Nunez, A., Coppi, M.V., Palsson, B.O., Schilling, C.H., and Lovley, D.R., “Characterization of metabolism in the Fe(III)-reducing organism ''Geobacter sulfurreducens'' by constraint-based modeling,” Appl. Environ, Microbiol., 72: 1558-1568 (2006).

  2. Price, N.D., Thiele, I., Palsson B.Ø. Candidate States of Helicobacter pylori's Genome-Scale Metabolic Network upon Application of "Loop Law" Thermodynamic Constraints " Biophys J, 90:3919-28 (2006)

  3. Herring, C. D., Raghunathan, A., Honisch, C., Patel, T., Applebee, M. K., Joyce, A. J., Albert, T. J., Blattner, F. R., van den Boom, D., Cantor, C. R., Palsson, B.Ø., Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale ", Nature Genetics, 38:1406-1412 (2006) 2007 commentary based on this study

  4. Reed, J. R., Patel, T. R., Chen, K. H., Joyce, A. R., Applebee, M. K., Herring, C. D., Bui, O. T., Knight, E. K., Fong, S. S., Palsson, B.Ø., Systems Approach to Refining Genome Annotation ", Proc Natl Acad Sci U S A, 103(46):17480-4 (2006)

  5. Vo, T. D., Kim, S. K., Lee, W. N. P., Palsson, B.Ø., Isotopomer Analysis of Cellular Metabolism in Tissue Culture: A Comparative study between the pathway and network-based methods ", Metabolomics, 2(4):243-56 (2006)

  6. Gianchandani E. P., Papin J. A., Price N. D., Joyce A. R., Palsson B.Ø., Matrix formalism to describe functional States of transcriptional regulatory systems ," PLoS Comput Biol, 2006 Aug 11;2(8):e101. see Cover Art below

  7. Joyce, A. R., Reed, J.L., White, A., Edwards, R., Osterman, A., Baba, T., Lesley, S.A., Palsson, B.Ø., Agarwalla, S., Experimental and computational assessment of conditionally essential genes in E. coli, " J Bacteriol 188(23):8259-8271 (2006) [supplemental_material/JBact2006/index.html Supplemental Materials ]

  8. Jamshidi, N., Palsson, B.Ø., Systems biology of SNPs ," Molecular Systems Biology 2 doi:10.1038/msb4100077 (2006)

  9. Hua, Q., Joyce, A.R., Fong, S.S., Palsson, B.Ø., Metabolic Analysis of Adaptive Evolution for In Silico-Designed Lactate-Producing Strains ," Biotechnol Bioeng 95(5):992-1002 (2006)

  10. Vo, T.D., Palsson, B.Ø., Isotopomer analysis of myocardial substrate metabolism: A systems biology approach ," Biotechnology and Bioengineering, 95(5):972-83 (2006)

  11. Barrett, C.L., Kim, T.Y., Kim, H.U., Palsson, B.Ø., and Lee, S.Y., Systems biology as a foundation for genome-scale synthetic biology ", Curr Opin Biotechnol 17(5):488-492 (2006)

  12. Herrgard, M.J., Fong, S.F., Palsson, B.Ø., Systematic identification of genome-scale metabolic models using experimentally measured flux profiles .", PLoS Computational Biology, 2(7): e72 (2006).

  13. Cho, B.K., Knight, E.M., Palsson, B.Ø., Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA ", Microbiology, 152, 2207-2219 (2006).

  14. Barrett, C.L. and Palsson, B.Ø., Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach ", PLoS Computational Biology, 2:5 (2006).

  15. Herrgard, M.J., Lee, B-S., Portnoy, V., Palsson, B.Ø., Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae ", Genome Research, 16(5):627-35 (2006)

  16. Clark I.B., Hanania E.G., Stevens J., Gallina M., Fieck A., Brandes R., Palsson, B.Ø, Koller M.R. “Optoinjection for efficient targeted delivery of a broad range of compounds and macromolecules into diverse cell types ”, J. Biomedical Optics, 11(1):14034 (2006).

  17. Jamshidi N, Palsson BO. Systems biology of the human red blood cell ", Blood Cells Mol Dis, 36(2):239-47.

  18. Barrett, C.L., Price, N.D. Palsson, B.Ø. , Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition ", BMC Bioinformatics 7:132 (2006)

  19. Becker, S.A., Price, N.D., Palsson, B.Ø., “Metabolite coupling in genome-scale metabolic networks ”, BMC Bioinformatics, 7:111 (2006).

  20. Joyce A.R. and Palsson B.Ø. The model organism as a system: integrating 'omics' data sets ", Nature Reviews Molecular Cell Biology. 7:198-210 (2006)

  21. Feist, A.M., Scholten, J.C.M., Palsson, B.Ø., Brockman, F.J., and Ideker, T., "Modeling methanogenesis with a genome-scale metabolic reconstruction of ''Methanosarcina barkeri'' ", Molecular Systems Biology, 2:2006.0004 (2006).

  22. Fong S. S., Nanchen A., Palsson B.Ø., Sauer U., Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes ," J Biol Chem, 281(12):8024-33 (2006)

  23. Reed, J.L., Famili, I., Thiele, I., and Palsson, B.Ø., "Towards multidimensional genome annotation ", ",Nature Reviews Genetics, 7(2) :130-41 (2006).

  24. Cho, B.K., Knight, E.M., and Palsson, B.Ø., PCR-based tandem epitope tagging system for E. coli genome engineering ", Biotechniques, 40:67-70 (2006)”.

  25. Allen, T.E., Price, N.D., Joyce, A.R., and Palsson, B.Ø., "Long-range patterns in prokaryotic genome sequences indicate significant chromosomal organization ",PLoS Computational Biology, 13:2(1):e2 (2006). see Cover Art below

2005 Return to top

  1. Barrett, C.B., Herring, C.D., Reed, J.L., and Palsson, B.Ø., "The Global Transcriptional Regulatory Network for Metabolism in ''Escherichia coli'' Exhibits Few Dominant Functional States ", PNAS, 102(52):19103-8 (2005).

  2. Fong, S.S., Joyce, A. R., and Palsson, B.Ø., Parallel adaptive evolution cultures of ''Escherichia coli'' lead to convergent growth phenotypes with different expression states" , Genome Research, 15(10):1365-1372 (2005).

  3. Herring, C.D., Raffaelle, M., Allen, T.E., Kanin, E., Landick, R., Ansari, A.Z., and Palsson, B.Ø., "Immobilization of ''Escherichia coli'' RNA polymerase and location of binding sites using chromatin immunoprecipitation and microarrays" , Journal of Bacteriology, 187(17):6166-6174 (2005).

  4. Thiele, I., Vo, T.D., Price, N.D. and Palsson, B.Ø., "An Expanded Metabolic Reconstruction of Helicobacter pylori (iIT341 GSM/GPR): An in silico genome-scale characterization of single and double deletion mutants.", Journal of Bacteriology, 187(16): 5818-5830 (2005).

  5. Herrgard, M.J. and Palsson, B.Ø., "Untangling the web of functional and physical interactions in yeast" , Journal of Biology,4(2):5(2005).

  6. Hanania, E.G., Fieck, A., Stevens, J., Bodzin, L.J., Palsson, B.Ø., and Koller,M.R., "Automated in situ measurement of cell-specific antibody secretion and laser-mediated purification for rapid cloning of highly-secreting producers" , Biotechnology and Bioengineering, 91(7):872-876 (2005).

  7. Fong, S.S., Burgard, A.P., Herring, C.D., Knight, E.M., Blattner, F.R., Maranas, C.D., and Palsson, B.Ø., "In Silico Design and Adaptive Evolution of ''Escherichia coli'' for Production of Lactic Acid" , Biotechnology and Bioengineering, 91(5):643-648 (2005).

  8. Bell, S.L. and Palsson, B.Ø., "ExPA: A Program for Calculating Extreme Pathways in Biochemical Reaction Networks" , Bioinformatics, 21(8):1739-1740 (2005).

  9. Becker, S.A. and Palsson, B.Ø., "Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation" , BMC Microbiology, 5(1):8 (2005).

  10. Bell, S.L. and Palsson, B.Ø., "Phenotype Phase Plane Analysis Using Interior Point Methods" , Computers & Chemical Engineering,29(3):481-486 (2005).

  11. Thiele, I., Price, N.D., Vo, T.D. and Palsson, B.Ø., "Candidate metabolic network states in human mitochondria: Impact of diabetes, ischemia, and diet" , Journal of Biological Chemistry, 280(12):11683-11695 (2005)

  12. Famili, I., Mahadevan, R. and Palsson, B.Ø., "''K''-Cone Analysis: Determining All Candidate Values for Kinetic Parameters on a Network-scale" , Biophysical Journal, 88(3): 1616-1625 (2005).

  13. Papin, J., Hunter, T., Palsson, B.Ø., and Subramanian, S., "Reconstruction of cellular signalling networks and analysis of their properties" , Nature Reviews Molecular Cell Biology, 6(2):99-111 (2005). see Cover Art below

  14. Mahadevan, R. and Palsson, B.Ø., "Properties of Metabolic Networks: Structure versus Function" , Biophysical Journal,88:L7-L9 (2005).

2004 Return to top

  1. Koller, M.R., Hanania, E.G., Stevens, J., Eisfeld, T.M., Sasaki, G.C., Fieck, A., and Palsson, B.Ø., "High-throughput laser mediated in situ cell purification with high purity and yield", Cytometry, 61A (2):153-161 (2004).

  2. Honisch, C., Raghunathan, A., Cantor, C.R., Palsson, B.Ø, and van den Boom, D., "High-throughput Mutation Detection Underlying Adaptive Evolution of Escherichia coli-K12," Genome Research, 14(12):2495-2502 (2004).

  3. Papin, J.A., Reed, J.L. and Palsson, B.Ø., "Hierarchical thinking in network biology: the unbiased modularization of biochemical networks," Trends in Biochemical Sciences, 29:641-647 (2004).

  4. Price, N.D., Reed, J.L. and Palsson, B.Ø., "Genome-scale Models of Microbial Cells:Evaluating the consequences of constraints," Nature Reviews Microbiology, 2:886-897 (2004).

  5. Duarte, N.C., Palsson, B.Ø., and Fu, P., "Integrated Analysis of Metabolic Phenotypes in ''Saccharomyces cerevisiae''," BMC Genomics, 5:63 (2004).

  6. Fong, S.S. and Palsson, B.Ø., "Metabolic gene-deletion strains of ''Escherichia coli'' evolve to computationally predicted growth phenotypes," Nature Genetics, 36(10):1056-58(2004).

  7. Price, N.D., Schellenberger, J., and Palsson, B.Ø., "Uniform Sampling of Steady State Flux Spaces: Means to Design Experiments and to Interpret Enzymopathies" , Biophysical Journal, 87:2172-2186(2004).

  8. Vo, T.D., Greenberg, H.J., and Palsson, B.Ø., "Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data ", Journal of Biological Chemistry, 279(38):39532-40 (2004).

  9. Reed, J.L. and Palsson, B.Ø., "Genome-scale in silico models of ''E. coli'' have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states" , Genome Research, 14:1797-1805(2004).

  10. Papin, J.A., Stelling, J., Price, N.D., Klamt, S., Schuster, S., and Palsson, B.Ø., "Comparison of Network-Based Pathway Analysis Methods ", Trends in Biotechnology, 22(8): 400-4055 (2004).

  11. Papin, J.A. and Palsson, B.Ø., "The JAK-STAT Signaling Network in the Human B-Cell: An Extreme Signaling Pathway Analysis ", Biophysical Journal, 87: 37-46(2004).

  12. Duarte, N.C., Herrgard, M.J., and Palsson, B.Ø., "Reconstruction and Validation of ''Saccharomyces cerevisiae'' iND750, a Fully Compartmentalized Genome-scale Metabolic Model ", Genome Research, 14: 1298-1309 (2004).

  13. Wiback, S.J., Famili, I., Greenberg, H.J., and Palsson, B.Ø., "Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space ", Journal of Theoretical Biology, 228(4): 437-447 (2004).

  14. Covert, M.W., Knight, E.M., Reed, J.L., Herrgard, M.J., and Palsson, B.Ø., "Integrating high-throughput and computational data elucidates bacterial networks ", Nature, 429: 92-96 (2004).

  15. Wiback, S.J., Mahadevan, R., and Palsson, B.Ø., "Using Metabolic Flux Data to Further Constrain the Metabolic Solution space and Predict Internal Flux Patterns: The ''Escherichia coli'' spectrum ", Biotechnology & Bioengineering, 86(3): 317-331 (2004).

  16. Raghunathan, A., Price, N.D., Galperin, M.Y., Makarova, K.S., Purvine, S., Picone, A.F., Cherny, T., Xie, T., Reilly, T.J., Munson,Jr., R., Tyler, R.E., Akerley, B.J., Smith, A.L., Palsson, B.Ø., and Kolker, E. ""In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium ", OMICS 8(1): 25-42 (2004).

  17. Ibarra, R.U., Fu, P, Palsson, B.Ø., DiTonno, J.R., and Edwards, J.S., "Quantitative Analysis of ''E.'' ''coli'' Metabolic Phenotypes within the Context of Phenotypic Phase Planes ", J Mol Microbiol Biotechnol, 6(2): 101-108 (2003).

  18. Palsson, B.Ø., "''In silico'' biotechnology: Era of reconstruction and interrogation ", Current Opinion in Biotechnology, 15(1): 50-51(2004).

  19. Herrgard, M.J., Covert,M.W., Palsson, B.Ø., "Reconstruction of Microbioal Transcriptional Regulatory Networks ", Current Opinion in Biotechnology, 15(1): 70-77(2004).

  20. Papin, J.A. and Palsson, B.Ø., "Topological Analysis of Mass-Balanced Signaling Networks: A Framework to Obtain Emergent Properties Including Crosstalk ", Journal of Theoretical Biology, 227: 283-297(2004).

2003 Return to top

  1. Covert, M.W., Famili, I. and Palsson, B.Ø., "Identifying Constraints that Govern Cell Behavior: A Key to Converting Conceptual to Computational Models in Biology? ", Biotechnology & Bioengineering, 84(7): 763-772 (2003).

  2. Famili,I., Förster, J., Nielsen, J., and Palsson, B.Ø.,"Saccharomyces cerevisiae Phenotypes can be Predicted using Constraint-based Analysis of a Genome-scale Reconstructed Metabolic Network ", PNAS, 100: 13134-13139 (2003).

  3. Herrgard, M., Covert, M.W. and Palsson, B.Ø., “Reconciling Gene Expression Data with Known Genome-scale Regulatory Network Structure ,” Genome Research, 13: 2423-2434 (2003).

  4. Fong, S.S., Marciniak, J.Y. and Palsson, B.Ø., "Description and Interpretation of Adaptive Evolution of Escherichia coli K12 MG1655 Using a Genome-scale ''in silico'' Metabolic Model ", Journal of Bacteriology, 185(21):6400-6408 (2003).

  5. Allen, T.E., Herrgard, M.J., Mingzhu, L., Qiu, Y., Glasner, J.D., Blattner, F.R., Palsson, B.Ø., "Genome-scale analysis of the uses of the Escherichia coli genome: a model-driven analysis of heterogeneous datasets ", Journal of Bacteriology, 185(21):6392-6399 (2003).

  6. Price, N.D., Reed, J.L., Papin, J.A., Wiback, S.J., and Palsson, B.Ø., "Network-based Analysis of Regulation in the Human Red Blood Cell ", Journal of Theoretical Biology, 225(2): 1985-194 (2003).

  7. Wiback, S.J, Mahadevan, R., and Palsson, B.Ø., "Reconstructing Metabolic Flux Vectors from Extreme Pathways: Defining the alpha-Spectrum ", Journal of Theoretical Biology, 24(3): 313-324 (2003).

  8. Reed, J.L., Vo, T.D., Schilling, C.H., and Palsson, B.Ø., "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) ", Genome Biology, 4(9): R54.1-R54.12 (2003).

  9. Kolker, E., Purvine, S., Galperin, M.Y., Stolyar, S., Goodlett, D.R., Nesvizhskii, A.I., Keller, A., Xie, T., Eng, J.K., Yi, E., Hood, L., Picone, A.F., Cherny, T., Tjaden, B.C., Siegel, A.F., Reilly, T.J., Makarova, K.S., Palsson, B.Ø. and Smith, A.L., "Initial Proteome Analysis of Model Microorganism Haemophilus influenzae Strain Rd KW20 ", Journal of Bacteriology, 185:4593-4602 (2003).

  10. Famili, I., and Palsson, B.Ø., "Systemic Metabolic Reactions are Obtained by Singular Value Decomposition of Genome-Scale Stoichiometric Matrices ", Journal of Theoretical Biology, 224(1):87-96 (2003).

  11. Förster, J., Famili, I., Palsson, B.Ø., and Nielsen, J., "Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae," OMICS, 7(2):193-202 (2003).

  12. Papin, J.A., Price, N.D., Wiback, S.J., Fell, D.A., and Palsson, B.Ø.; "Metabolic Pathways in the Post-Genome Era ," Trends in Biochemical Sciences, 28: 250-258 (2003). see Cover Art below

  13. Famili, I. and Palsson, B.Ø., "The Convex Basis of the Left Null Space of the Stoichiometric Matrix Leads to the Definition of Metabolically Meaningful Pools ", Biophysical Journal, 85: 16-26 (2003).

  14. Reed, J.L. and Palsson, B.Ø.; "Thirteen Years of Building Constraint-Based ''in silico'' Models of Escherichia coli ," Journal of Bacteriology, 185(9): pp. 2692-2699 (2003).

  15. Palsson, B.Ø., Price, N.D., Papin, J.A., "Development of network-based pathway definitions: the need to analyze real metabolic networks ," Trends in Biotechnology, 21(5): pp. 195-198 (2003).

  16. Price, N.D., Papin, J.A., Schilling, C.H., and Palsson, B.Ø.; "Genome-Scale Microbial In Silico Models: The Constraints-Based Approach ," Trends in Biotechnology, 21(4): pp. 162-169 (2003)

  17. Covert, M.W. and Palsson, B.Ø., "Constraints-Based Models: Regulation of Gene Expression Reduces the Steady-state Solution Space ", Journal of Theoretical Biology, 221(3): pp. 309-325 (2003).

  18. Raghunathan, A. and Palsson, B.Ø.; "Scalable Method to Determine Mutations that Occur During Adaptive Evolution of Escherichia coli ," Biotech Letters, 25(5): pp. 435-441 (2003).

  19. Allen, T.E., and Palsson, B.Ø., "Sequence-Based Analysis of Metabolic Demands for Protein Synthesis in Prokaryotes ", Journal of Theoretical Biology, 220: pp. 1-18 (2003).

  20. Price, N.D., Reed, J.L., Papin, J.A., Famili, I. and Palsson, B.Ø.; "Analysis of Metabolic Capabilities using Singular Value Decomposition of Extreme Pathway Matrices ", Biophysical Journal 84:794-804 (2003).

  21. Förster, J., Famili, I., Fu, P., Palsson, B.Ø., and Nielsen, J.; "Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network ," Genome Research, 13(2): pp. 244-253 (2003).

2002 Return to top

  1. Papin, J.A., Price, N.D., and Palsson, B.Ø.; "Extreme Pathway Lengths and Reaction Participation in Genome-Scale Metabolic Networks ," Genome Research, 12: pp. 1889-1900 (2002).

  2. Ibarra, R.U., Edwards, J.S., and Palsson, B.Ø.; "Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth ," Nature, 420: pp. 186-189 (2002).

  3. Jamshidi, N., Wiback, S.J., and Palsson, B.Ø., "''In Silico'' Model-Driven Assessment of the Effects of Single Nucleotide Polymorphisms (SNPs) on Human Red Blood Cell Metabolism ", Genome Research, 12: pp. 1687-1692 (2002).

  4. Kauffman, K.J., Pajerowski, J.D., Jamshidi, N., Palsson, B.Ø., and Edwards, J.S., "Description and Analysis of Metabolic Connectivity and Dynamics in the Human Red Blood Cell ", Biophysical Journal, 83: pp. 646-662 (2002).

  5. Price, N.D., Famili, I., Beard, D.A., and Palsson, B.Ø., "Extreme Pathways and Kirchhoff's Second Law ", Biophysical Journal, 83: pp. 2879-2882. (2002).

  6. Schilling, C. H., Covert, M.W., Famili, I., Church, G.M., Edwards, J.S., and Palsson, B.Ø., "Genome-scale metabolic model of Helicobacter pylori 26695 ", Journal of Bacteriology, 184(16): pp. 4582-4593 (2002).

  7. Wiback, S.J., and Palsson, B.Ø., "Extreme Pathway Analysis of Human Red Blood Cell Metabolism ", Biophysical Journal, 83(2): pp. 808-818 (2002).

  8. Papin, J.A., Price, N.D., Edwards, J.S., and Palsson, B.Ø., "The Genome-Scale Metabolic Extreme Pathway Structure in Haemophilus influenzae Shows Significant Network Redundancy ", Journal of Theoretical Biology, 215(1): pp. 67-82 (2002).

  9. Covert, M.W., and Palsson, B.Ø., "Transcriptional Regulation in Constraints-Based Metabolic Models of Escherichia coli ", Journal of Biological Chemistry, 277(31): pp. 28058-28064 (2002).

  10. Edwards, J.S., Covert, M., and Palsson, B.Ø., "Metabolic Modeling of Microbes: the Flux Balance Approach ", Environmental Microbiology, 4(3): pp. 133-140 (2002).

  11. Price, N.D., Papin, J.A., Palsson, B.Ø., "Determination of Redundancy and Systems Properties of the Metabolic Network of Helicobacter pylori Using Genome-Scale Extreme Pathway Analysis",Genome Research, 12: 760-769 (2002).

  12. Edwards, J.S., Ramakrishna R., Palsson, B.Ø., "Characterizing the metabolic phenotype: A phenotype phase plane analysis" , Biotechnology and Bioengineering, 77(1): pp. 27-36 (2002).

  13. Lee, G.M., Fong, S., Francis, K., Palsson, B.Ø., "Characterization and Efficacy of PKH26 as a Probe to Study the Replication History of the Human Hematopoietic KG1a Progenitor Cell Line" , In Vitro Cellular and Developmental Biology: Animal 38(2) :90-96 (2002).

  14. Francis, K., Palsson, B.Ø., "Comment on Time Dependent Concentration Profile of Secreted Molecules in the Intercellular Signaling" , Journal of the Japan Physical Society, 71(2) :1005-1006 (2002).

  15. Francis, K., Palsson, B.Ø., Carrier, E., "Murine Sca-1+/Lin- Cells and Human KG1a Cells Exhibit Multiple Pseudopod Morphologies During Migration" , Experimental Hematology, 30(5): 460-462 (2002).

  16. Francis, K., Lee, G.M., Palsson, B.Ø., "Characterization of the KG1a Cell Line for use in a Cell Migration Based Screening Assay", Biotechnology and Bioprocess Engineering, 7(3): 178-184 (2002)

2001 Return to top

  1. Covert, M., Schilling, C. H., Palsson, B.Ø., "Regulation of Gene Expression in Flux Balance Models of Metabolism" , Journal of Theoretical Biology, 213(1): pp. 73-88 (2001).

  2. Jamshidi, N.,Edwards, J. S., Fahland, T., Church, G. M., Palsson, B.Ø. "Dynamic simulation of the human red blood cell metabolic network" , Bioinformatics, 17(3): p. 286-7. (2001).

  3. Ramakrishna, R., Edwards, J.S., McCulloch, A., and Palsson, B.Ø., "Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints" , Am J Physiol Regulatory Integrative Comp Physiol 280: R695-R704 (2001).

  4. Covert, M.W., Schilling, C.H., Famili, I., Edwards, J.S., Goryanin, I.I., Selkov, E., and Palsson, B.Ø., "Metabolic modeling of microbial strains ''in silico''", Trends in Biochemical Sciences 26: 179-186(2001).

  5. Edwards, J.S., Ibarra, R.U., and Palsson, B.Ø., "In silico predictions of Escherichi coli metabolic capabilities are consistent with experimental data" , Nature Biotechnology 19: 125-130(2001). "Living on the edges," by Harvey Bialy, Same Issue see Cover Art below

  6. Schilling,C.H., Edwards, J.S., Letscher, D.L., and Palsson, B.Ø., "Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems" , Biotechnology and Bioengineering 71: 286-306 (2001).

2000 Return to top

  1. Edwards, J.S., and Palsson, B.Ø., "Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions", BMC Bioinformatics 1/1(2000).

  2. J.S. Edwards and B.Ø. Palsson,"Letter to the Editor: Multiple Steady States in Kinetic Models of Red Cell Metabolism" , J. Theor. Biol. 207: 125-127. (2000).

  3. Edwards, J.S., and Palsson, B.Ø., "Robustness Analysis of the ''Escherichia coli'' Metabolic Network" , Biotechnol Prog., 16: 927-939, (2000).

  4. Lee, G.M., Fong, S., Francis, K., Oh, D.J., and Palsson, B.Ø., "In Situ Labeling of Adherent Cells with PKH26" , In Vitro Cellular and Developmental Biology: Animal 36: 4-6 (2000).

  5. Oh, D.J., Martinez, A., Lee, G.M., Francis, K., and Palsson, B.Ø., "Extension of Osmolarity Induced Podia is Observed from Fluorescently Labeled Hematopoietic Cell Lines in Hyperosmotic Medium" , Cytometry 40: 109-118 (2000).

  6. Oh, D.J., Martinez, A., Lee, G.M., Francis, K., and Palsson, B.Ø., "Inter-Cellular Adhesion can be visualized using Fluorescently Labeled Fibrosarcoma HT1080 Cells Co-Cultured with Hematopoietic Cell Lines or CD34+ Enriched Human Mobilized Peripheral Blood Cells", Cytometry 40: 119-125 (2000).

  7. Edwards, J.S., and Palsson, B.Ø., "The ''Escherichia coli'' MG1655 ''in silico'' Metabolic Genotype: Its Definition, Characteristics, and Capabilities" , Proc. Nat’l Acad. Sci. USA, 97: 5528-5533, (2000).

  8. Schilling, C.H., Letscher, D., and Palsson, B.Ø., "Theory for the Systemic Definition of Metabolic Pathways and their use in Interpreting Metabolic Function from a Pathway-Oriented Perspective" , J. theor. Biol, 203: 229-248, (2000).

  9. Schilling, C.H., and Palsson, B.Ø., "Assesment of the Metabolic Capabilities of ''Haemophilus influenzae'' Rd through a Genome-scale Pathway Analysis" , J. theor. Biol., 203: 249-283, (2000).

1999 Return to top

  1. Holloway, W., Martinez, A., Oh, D.J., Francis, K., Ramakrishna, R., and Palsson, B.Ø., "Key Adhesion Molecules are Present on Long Podia Extended by Hematopoietic Cells" , Cytometry, 37: 171-177, (1999).

  2. Huang, S., Law, P., Francis, K., Palsson, B.Ø. and Ho, A., "Symmetry of Initial Cell Divisions Among Primitive Hematopoietic Progenitors Is Independent of Ontogenic Age and Regulatory Molecules" , Blood, 94: 2595-2604, (1999).

  3. Francis, K., Oh, D.J., Martinez, A., Palsson, B.Ø., "Response to Tenupodia Formation by Blasts in Bone Marrow Aspirate Smears from a Patient with Acute Monoblastic Leukemia" , Blood, 94: 3955, (1999).

  4. Oh, D.J., Lee, G.M., Francis, K., and Palsson, B.Ø., "Phototoxicity of the Fluorescent Membrane Dyes PKH2 and PKH26 on the Human Hematopoietic KG1a Progenitor Cell Line" , Cytometry, 36: 312-318, (1999).

  5. Edwards, J.S., and Palsson, B.Ø., "Systems Properties of the Haemophilus influenzae Rd Metabolic Genotype" , The Journal of Biological Chemistry, 274: 17410-17416, (1999).

  6. Schilling, C.H., Schuster, S., Palsson, B.Ø., and Heinrich, R., "Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post-genomic Era" , Biotechnology Progress, 15: 296-303, (1999).

  7. Schilling, C.H., Edwards, J.S., and Palsson, B.Ø., "Toward Metabolic Phenomics: Analysis of Genomic Data Using Flux Balances" , Biotechnology Progress, 15: 288-295, (1999).

1998 Return to top

  1. Francis, K., Holloway, W., Ramakrishna, P. and B.Ø. Palsson, "Two New Pseudopod Morphologies Displayed by the Human Hematopoietic KG1a Progenitor Cell Line and by Primary Human CD34+ Cells." , Blood, 92:3616-3623, (1998). see Cover Art below

  2. Schilling, C.H. and Palsson B.Ø., "The underlying pathway structure of biochemical reaction networks." , Proc. Nat’l Acad. Sci. USA 95: 4193-4198, (1998).

1997 Return to top

  1. Edwards, J.S. and Palsson, B.Ø., "How will Bioinformatics Influence Metabolic Engineering?", Biotechnology & Bioengineering, 58:162-169, (1997).

  2. Francis, K., Palsson, B.Ø., "Effective intercellular communication distances are determined by the relative time constants for cyto/chemokine secretion and diffusion." , Proc. Natl. Acad. Sci. USA, Vol. 94, pp. 12258-12262. November 1997.

  3. Cover Art:

Two New Pseudopod Morphologies Displayed by the Human Hematopoietic KG1a Progenitor Cell Line and by Primary Human CD34+ Cells In silico predictions of Escherichi coli metabolic capabilities are consistent with experimental data Metabolic Pathways in the Post-Genome Era Reconstruction of cellular signalling networks and analysis of their properties
Long-range patterns in prokaryotic genome sequences indicate significant chromosomal organization Systematic identification of genome-scale metabolic models using experimentally measured flux profiles. Elucidation of the Transcription Unit Architecture of the Escherichia coli K-12 MG1655 Genome.

* DISCLOSURE: Some of the publications listed on this web site contain subject matter that is or potentially could be related to patent filings from UCSD that have been licensed. UCSD and BØP hold interests in this company. No patents have been issued. The patent applications involved are: