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    Bernhard Palsson

    TitleProfessor
    SchoolUniversity of California, San Diego
    DepartmentBioengineering
    Address9500 Gilman Drive #0412
    CA La Jolla 92093
    Phone858-534-5668
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      Collapse Research 
      Collapse Research Activities and Funding
      Systems Biology Approach to Redefine Susceptibility Testing and Treatment of MDR Pathogens in the Context of Host Immunity
      NIH/NIAID U01AI124316Mar 15, 2016 - Feb 28, 2021
      Role: Principal Investigator
      Model-guided Identification of Synthetic Lethal Genes for Drug Target Development
      NIH/NIGMS R01GM098105Jul 1, 2011 - Jun 30, 2014
      Role: Principal Investigator
      A Genome-Scale Regulated Metabolic Model of Yeast
      NIH/NIGMS R01GM071808Aug 1, 2004 - Jul 31, 2009
      Role: Principal Investigator
      Network-based Analysis of Kinetics and Regulation
      NIH/NIGMS R01GM068837Jul 15, 2003 - Mar 31, 2014
      Role: Principal Investigator
      Testable in silico Hypotheses for E. coli Growth
      NIH/NIGMS R01GM062791Apr 1, 2001 - May 31, 2010
      Role: Principal Investigator
      Genome-Scale in silico Model for E. Coli
      NIH/NIGMS R01GM057089Aug 1, 1998 - Apr 30, 2015
      Role: Principal Investigator
      MECHANISMS OF STEM CELL MIGRATION
      NIH/NHLBI R01HL060398Jul 10, 1998 - Jun 30, 2002
      Role: Principal Investigator
      HEMATOPOIETIC STEM CELL
      NIH/NHLBI R01HL059234Feb 1, 1998 - Jan 31, 2002
      Role: Principal Investigator
      METABOLIC DYNAMICS &THE RED BLOOD CELL
      NIH/NIDDK R29DK039256Sep 1, 1987 - Aug 31, 1992
      Role: Principal Investigator

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, Palsson B. Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities. Proc Natl Acad Sci U S A. 2017 Sep 05. PMID: 28874552.
        View in: PubMed
      2. Sastry A, Monk J, Tegel H, Uhlen M, Palsson B, Rockberg J, Brunk E. Machine learning in computational biology to accelerate high-throughput protein expression. Bioinformatics. 2017 Aug 15; 33(16):2487-2495. PMID: 28398465.
        View in: PubMed
      3. Sandberg TE, Lloyd CJ, Palsson B, Feist AM. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies. Appl Environ Microbiol. 2017 Jul 01; 83(13). PMID: 28455337.
        View in: PubMed
      4. Seo SW, Gao Y, Kim D, Szubin R, Yang J, Cho BK, Palsson B. Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655. Sci Rep. 2017 May 19; 7(1):2181. PMID: 28526842.
        View in: PubMed
      5. Yurkovich JT, Yang L, Palsson B. Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells. PLoS Comput Biol. 2017 Mar; 13(3):e1005424. PMID: 28264007.
        View in: PubMed
      6. Levering J, Dupont CL, Allen AE, Palsson B, Zengler K. Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels. mSystems. 2017 Jan-Feb; 2(1). PMID: 28217746.
        View in: PubMed
      7. LaCroix RA, Palsson B, Feist AM. A Model for Designing Adaptive Laboratory Evolution Experiments. Appl Environ Microbiol. 2017 Feb 03. PMID: 28159796.
        View in: PubMed
      8. Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson B. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism. Sci Rep. 2017 Jan 25; 7:41241. PMID: 28120890.
        View in: PubMed
      9. Ma D, Yang L, Fleming RM, Thiele I, Palsson B, Saunders MA. Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression. Sci Rep. 2017 Jan 18; 7:40863. PMID: 28098205.
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      10. van Wijk XM, Döhrmann S, Hallström BM, Li S, Voldborg BG, Meng BX, McKee KK, van Kuppevelt TH, Yurchenco PD, Palsson B, Lewis NE, Nizet V, Esko JD. Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin a2 as a Host Factor for Bacterial Invasion. MBio. 2017 Jan 10; 8(1). PMID: 28074024.
        View in: PubMed
      11. King ZA, O'Brien EJ, Feist AM, Palsson B. Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion. Metab Eng. 2016 Dec 13. PMID: 27986597.
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      12. Broddrick JT, Rubin BE, Welkie DG, Du N, Mih N, Diamond S, Lee JJ, Golden SS, Palsson B. Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis. Proc Natl Acad Sci U S A. 2016 Dec 01. PMID: 27911809.
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      13. Hefzi H, Ang KS, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D, Martinez VS, Kyriakopoulos S, Jiménez NE, Zielinski DC, Quek LE, Wulff T, Arnsdorf J, Li S, Lee JS, Paglia G, Loira N, Spahn PN, Pedersen LE, Gutierrez JM, King ZA, Lund AM, Nagarajan H, Thomas A, Abdel-Haleem AM, Zanghellini J, Kildegaard HF, Voldborg BG, Gerdtzen ZP, Betenbaugh MJ, Palsson B, Andersen MR, Nielsen LK, Borth N, Lee DY, Lewis NE. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Syst. 2016 Nov 23; 3(5):434-443.e8. PMID: 27883890.
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      14. Yang L, Yurkovich JT, Lloyd CJ, Ebrahim A, Saunders MA, Palsson B. Principles of proteome allocation are revealed using proteomic data and genome-scale models. Sci Rep. 2016 Nov 18; 6:36734. PMID: 27857205.
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      15. Aziz RK, Monk JM, Andrews KA, Nhan J, Khaw VL, Wong H, Palsson B, Charusanti P. The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli. Microbiol Res. 2017 Jan; 194:47-52. PMID: 27938862.
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      16. D'Alessandro A, Nemkov T, Yoshida T, Bordbar A, Palsson B, Hansen KC. Citrate metabolism in red blood cells stored in additive solution-3. Transfusion. 2017 Feb; 57(2):325-336. PMID: 27813142.
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      17. Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM, Palsson B. Multi-omic data integration enables discovery of hidden biological regularities. Nat Commun. 2016 Oct 26; 7:13091. PMID: 27782110.
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      18. Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson B, Herrgård MJ, Feist AM. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Syst. 2016 Sep 28; 3(3):238-251.e12. PMID: 27667363.
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      19. Yang L, Ma D, Ebrahim A, Lloyd CJ, Saunders MA, Palsson B. solveME: fast and reliable solution of nonlinear ME models. BMC Bioinformatics. 2016 Sep 22; 17(1):391. PMID: 27659412.
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      20. Mih N, Brunk E, Bordbar A, Palsson B. A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PLoS Comput Biol. 2016 Jul; 12(7):e1005039. PMID: 27467583.
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      21. O'Brien EJ, Utrilla J, Palsson B. Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. PLoS Comput Biol. 2016 Jun; 12(6):e1004998. PMID: 27351952.
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      22. Du B, Zielinski DC, Kavvas ES, Dräger A, Tan J, Zhang Z, Ruggiero KE, Arzumanyan GA, Palsson B. Evaluation of rate law approximations in bottom-up kinetic models of metabolism. BMC Syst Biol. 2016; 10(1):40. PMID: 27266508.
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      23. Feist AM, Palsson B. What do cells actually want? Genome Biol. 2016; 17(1):110. PMID: 27215675.
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      24. Levering J, Broddrick J, Dupont CL, Peers G, Beeri K, Mayers J, Gallina AA, Allen AE, Palsson B, Zengler K. Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. PLoS One. 2016; 11(5):e0155038. PMID: 27152931.
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      25. Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson B. Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. Cell Syst. 2016 Apr 27; 2(4):260-71. PMID: 27135538.
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      26. McCloskey D, Young JD, Xu S, Palsson B, Feist AM. Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale. Anal Chem. 2016 Apr 5; 88(7):3844-52. PMID: 26981784.
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      27. Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson B. Systems biology of the structural proteome. BMC Syst Biol. 2016; 10(1):26. PMID: 26969117.
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      28. Sandberg TE, Long CP, Gonzalez JE, Feist AM, Antoniewicz MR, Palsson B. Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology. PLoS One. 2016; 11(3):e0151130. PMID: 26964043.
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      29. Golabgir A, Gutierrez JM, Hefzi H, Li S, Palsson B, Herwig C, Lewis NE. Quantitative feature extraction from the Chinese hamster ovary bioprocess bibliome using a novel meta-analysis workflow. Biotechnol Adv. 2016 Sep-Oct; 34(5):621-33. PMID: 26948029.
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      30. Bordbar A, Johansson PI, Paglia G, Harrison SJ, Wichuk K, Magnusdottir M, Valgeirsdottir S, Gybel-Brask M, Ostrowski SR, Palsson S, Rolfsson O, Sigurjónsson OE, Hansen MB, Gudmundsson S, Palsson B. Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomes. Transfusion. 2016 Apr; 56(4):852-62. PMID: 26749434.
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      31. McCloskey D, Young JD, Xu S, Palsson B, Feist AM. MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications. Anal Chem. 2016 Jan 19; 88(2):1362-70. PMID: 26666286.
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      32. Aziz RK, Monk JM, Lewis RM, In Loh S, Mishra A, Abhay Nagle A, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Fong NL, Li HJ, Palsson B, Charusanti P. Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations. Sci Rep. 2015; 5:16025. PMID: 26531810.
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      33. Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson B. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Syst. 2015 Oct 28; 1(4):283-92. PMID: 27136057.
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      34. King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson B, Lewis NE. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res. 2016 Jan 4; 44(D1):D515-22. PMID: 26476456.
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      35. 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, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson B, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I. Do genome-scale models need exact solvers or clearer standards? Mol Syst Biol. 2015; 11(10):831. PMID: 26467284.
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      36. Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson B, Zell A. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. BMC Syst Biol. 2015; 9(1):68. PMID: 26452770.
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      37. King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson B. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput Biol. 2015 Aug; 11(8):e1004321. PMID: 26313928.
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      38. Seo SW, Kim D, Szubin R, Palsson B. Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655. Cell Rep. 2015 Aug 25; 12(8):1289-99. PMID: 26279566.
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      39. Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT, Du B, Dräger A, Thomas A, Sun Y, Saunders MA, Palsson B. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proc Natl Acad Sci U S A. 2015 Aug 25; 112(34):10810-5. PMID: 26261351.
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      40. Seo SW, Kim D, O'Brien EJ, Szubin R, Palsson B. Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli. Nat Commun. 2015; 6:7970. PMID: 26258987.
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      41. Zielinski DC, Filipp FV, Bordbar A, Jensen K, Smith JW, Herrgard MJ, Mo ML, Palsson B. Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis. Nat Commun. 2015; 6:7101. PMID: 26055627.
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      42. Latif H, Szubin R, Tan J, Brunk E, Lechner A, Zengler K, Palsson B. A streamlined ribosome profiling protocol for the characterization of microorganisms. Biotechniques. 2014; 58(6):329-32. PMID: 26054770.
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      43. O'Brien EJ, Monk JM, Palsson B. Using Genome-scale Models to Predict Biological Capabilities. Cell. 2015 May 21; 161(5):971-87. PMID: 26000478.
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      44. Rolfsson Ó, Palsson B. Decoding the jargon of bottom-up metabolic systems biology. Bioessays. 2015 Jun; 37(6):588-91. PMID: 25761171.
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      45. Pacini T, Fu W, Gudmundsson S, Chiaravalle AE, Brynjolfson S, Palsson B, Astarita G, Paglia G. Multidimensional Analytical Approach Based on UHPLC-UV-Ion Mobility-MS for the Screening of Natural Pigments. Anal Chem. 2015 Mar 3; 87(5):2593-9. PMID: 25647265.
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      46. O'Brien EJ, Palsson B. Computing the functional proteome: recent progress and future prospects for genome-scale models. Curr Opin Biotechnol. 2015 Aug; 34:125-34. PMID: 25576845.
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      47. King ZA, Lloyd CJ, Feist AM, Palsson B. Next-generation genome-scale models for metabolic engineering. Curr Opin Biotechnol. 2015 Dec; 35:23-9. PMID: 25575024.
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      48. Guzmán GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson B, Feist AM. Model-driven discovery of underground metabolic functions in Escherichia coli. Proc Natl Acad Sci U S A. 2015 Jan 20; 112(3):929-34. PMID: 25564669.
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      49. Paglia G, Angel P, Williams JP, Richardson K, Olivos HJ, Thompson JW, Menikarachchi L, Lai S, Walsh C, Moseley A, Plumb RS, Grant DF, Palsson B, Langridge J, Geromanos S, Astarita G. Ion mobility-derived collision cross section as an additional measure for lipid fingerprinting and identification. Anal Chem. 2015 Jan 20; 87(2):1137-44. PMID: 25495617.
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      50. LaCroix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, Szubin R, Palsson B, Feist AM. Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium. Appl Environ Microbiol. 2015 Jan 1; 81(1):17-30. PMID: 25304508.
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      51. Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson B, Feist AM. Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. BMC Syst Biol. 2014; 8(1):110. PMID: 25227965.
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      52. Nam H, Campodonico M, Bordbar A, Hyduke DR, Kim S, Zielinski DC, Palsson B. A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks. PLoS Comput Biol. 2014 Sep; 10(9):e1003837. PMID: 25232952.
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      53. Seo SW, Kim D, Latif H, O'Brien EJ, Szubin R, Palsson B. Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. Nat Commun. 2014; 5:4910. PMID: 25222563.
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      54. Paglia G, Sigurjónsson ÓE, Rolfsson Ó, Hansen MB, Brynjólfsson S, Gudmundsson S, Palsson B. Metabolomic analysis of platelets during storage: a comparison between apheresis- and buffy coat-derived platelet concentrates. Transfusion. 2015 Feb; 55(2):301-13. PMID: 25156572.
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      55. Campodonico MA, Andrews BA, Asenjo JA, Palsson B, Feist AM. Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metab Eng. 2014 Sep; 25:140-58. PMID: 25080239.
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      56. Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson B, Sommer M, Feist AM. Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations. Mol Biol Evol. 2014 Oct; 31(10):2647-62. PMID: 25015645.
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      57. Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson B. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Mol Syst Biol. 2014; 10(7):737. PMID: 24987116.
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      58. Monk J, Palsson B. Genetics. Predicting microbial growth. Science. 2014 Jun 27; 344(6191):1448-9. PMID: 24970063.
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      59. Rohatgi N, Nielsen TK, Bjørn SP, Axelsson I, Paglia G, Voldborg BG, Palsson B, Rolfsson O. Biochemical characterization of human gluconokinase and the proposed metabolic impact of gluconic Acid as determined by constraint based metabolic network analysis. PLoS One. 2014; 9(6):e98760. PMID: 24896608.
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      60. Paglia G, Sigurjónsson ÓE, Rolfsson Ó, Valgeirsdottir S, Hansen MB, Brynjólfsson S, Gudmundsson S, Palsson B. Comprehensive metabolomic study of platelets reveals the expression of discrete metabolic phenotypes during storage. Transfusion. 2014 Nov; 54(11):2911-23. PMID: 24840017.
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      61. Monk J, Nogales J, Palsson B. Optimizing genome-scale network reconstructions. Nat Biotechnol. 2014 May 8; 32(5):447-52. PMID: 24811519.
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      62. Paglia G, Williams JP, Menikarachchi L, Thompson JW, Tyldesley-Worster R, Halldórsson S, Rolfsson O, Moseley A, Grant D, Langridge J, Palsson B, Astarita G. Ion mobility derived collision cross sections to support metabolomics applications. Anal Chem. 2014 Apr 15; 86(8):3985-93. PMID: 24640936; PMCID: PMC4004193 [Available on 03/18/15].
      63. Cheng KK, Lee BS, Masuda T, Ito T, Ikeda K, Hirayama A, Deng L, Dong J, Shimizu K, Soga T, Tomita M, Palsson B, Robert M. Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol. Nat Commun. 2014 Jan 31; 5:3233. PMID: 24481126.
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      64. Cho BK, Kim D, Knight EM, Zengler K, Palsson B. Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states. BMC Biol. 2014; 12(1):4. PMID: 24461193.
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      65. Bordbar A, Monk JM, King ZA, Palsson B. Constraint-based models predict metabolic and associated cellular functions. Nat Rev Genet. 2014 Feb; 15(2):107-20. PMID: 24430943.
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      66. Huang TW, Lam I, Chang HY, Tsai SF, Palsson B, Charusanti P. Capsule deletion via a ?-Red knockout system perturbs biofilm formation and fimbriae expression in Klebsiella pneumoniae MGH 78578. BMC Res Notes. 2014; 7(1):13. PMID: 24398052.
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      67. McCloskey D, Gangoiti JA, King ZA, Naviaux RK, Barshop BA, Palsson B, Feist AM. A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent. Biotechnol Bioeng. 2014 Apr; 111(4):803-15. PMID: 24249002.
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      68. Chang RL, Xie L, Bourne PE, Palsson B. Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst Biol. 2013; 7:102. PMID: 24112686.
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      69. Palsson S, Hickling TP, Bradshaw-Pierce EL, Zager M, Jooss K, O'Brien PJ, Spilker ME, Palsson B, Vicini P. The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models. BMC Syst Biol. 2013; 7:95. PMID: 24074340.
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      70. Ebrahim A, Lerman JA, Palsson B, Hyduke DR. COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst Biol. 2013; 7:74. PMID: 23927696.
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      71. Wu W, Jamshidi N, Eraly SA, Liu HC, Bush KT, Palsson B, Nigam SK. Multispecific drug transporter Slc22a8 (Oat3) regulates multiple metabolic and signaling pathways. Drug Metab Dispos. 2013 Oct; 41(10):1825-34. PMID: 23920220.
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      72. Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C, Xie M, Chen W, Li N, Baycin-Hizal D, Latif H, Forster J, Betenbaugh MJ, Famili I, Xu X, Wang J, Palsson B. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nat Biotechnol. 2013 Aug; 31(8):759-65. PMID: 23873082.
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      73. Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson B. Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. Science. 2013 Jun 7; 340(6137):1220-3. PMID: 23744946.
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      74. Kim YM, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson B, McDermott JE, Heffron F, Smith RD, Peterson SN, Ansong C, Hyduke DR, Metz TO, Adkins JN. Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. Mol Biosyst. 2013 Jun; 9(6):1522-34. PMID: 23559334.
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      75. Fong NL, Lerman JA, Lam I, Palsson B, Charusanti P. Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant. FEMS Microbiol Lett. 2013 May; 342(1):62-9. PMID: 23432746.
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      76. Ansong C, Deatherage BL, Hyduke D, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P, Kim YM, Nakayasu ES, Li J, Kidwai A, Niemann G, Brown RN, Metz TO, McAteer K, Heffron F, Peterson SN, Motin V, Palsson B, Smith RD, Adkins JN. Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling. Curr Top Microbiol Immunol. 2013; 363:21-41. PMID: 22886542.
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      77. Qiu Y, Nagarajan H, Embree M, Shieu W, Abate E, Juárez K, Cho BK, Elkins JG, Nevin KP, Barrett CL, Lovley DR, Palsson B, Zengler K. Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks. Nat Commun. 2013; 4:1755. PMID: 23612296.
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      78. Seo JH, Hong JS, Kim D, Cho BK, Huang TW, Tsai SF, Palsson B, Charusanti P. Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features. BMC Genomics. 2012; 13:679. PMID: 23194155.
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      79. Fu W, Guðmundsson O, Paglia G, Herjólfsson G, Andrésson OS, Palsson B, Brynjólfsson S. Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution. Appl Microbiol Biotechnol. 2013 Mar; 97(6):2395-403. PMID: 23095941.
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      80. Baycin-Hizal D, Tabb DL, Chaerkady R, Chen L, Lewis NE, Nagarajan H, Sarkaria V, Kumar A, Wolozny D, Colao J, Jacobson E, Tian Y, O'Meally RN, Krag SS, Cole RN, Palsson B, Zhang H, Betenbaugh M. Proteomic analysis of Chinese hamster ovary cells. J Proteome Res. 2012 Nov 2; 11(11):5265-76. PMID: 22971049.
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      81. Thiele I, Fleming RM, Que R, Bordbar A, Diep D, Palsson B. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PLoS One. 2012; 7(9):e45635. PMID: 23029152.
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      82. Nam H, Lewis NE, Lerman JA, Lee DH, Chang RL, Kim D, Palsson B. Network context and selection in the evolution to enzyme specificity. Science. 2012 Aug 31; 337(6098):1101-4. PMID: 22936779.
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      83. Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson B. In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun. 2012; 3:929. PMID: 22760628.
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      84. Bordbar A, Mo ML, Nakayasu ES, Schrimpe-Rutledge AC, Kim YM, Metz TO, Jones MB, Frank BC, Smith RD, Peterson SN, Hyduke DR, Adkins JN, Palsson B. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol Syst Biol. 2012; 8:558. PMID: 22735334.
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      85. Orth JD, Palsson B. Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. BMC Syst Biol. 2012; 6:30. PMID: 22548736.
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      86. Zengler K, Palsson B. A road map for the development of community systems (CoSy) biology. Nat Rev Microbiol. 2012 May; 10(5):366-72. PMID: 22450377.
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      87. Charusanti P, Fong NL, Nagarajan H, Pereira AR, Li HJ, Abate EA, Su Y, Gerwick WH, Palsson B. Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction. PLoS One. 2012; 7(3):e33727. PMID: 22470465.
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      88. Lewis NE, Nagarajan H, Palsson B. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol. 2012 Apr; 10(4):291-305. PMID: 22367118.
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      89. Bordbar A, Palsson B. Using the reconstructed genome-scale human metabolic network to study physiology and pathology. J Intern Med. 2012 Feb; 271(2):131-41. PMID: 22142339.
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      90. Nogales J, Gudmundsson S, Knight EM, Palsson B, Thiele I. Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis. Proc Natl Acad Sci U S A. 2012 Feb 14; 109(7):2678-83. PMID: 22308420.
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      91. Bordbar A, Feist AM, Usaite-Black R, Woodcock J, Palsson B, Famili I. A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst Biol. 2011; 5:180. PMID: 22041191.
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      92. Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson B. An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. BMC Syst Biol. 2011; 5:163. PMID: 21995956.
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      93. Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S, Andersen MR, Neff N, Passarelli B, Koh W, Fan HC, Wang J, Gui Y, Lee KH, Betenbaugh MJ, Quake SR, Famili I, Palsson B, Wang J. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nat Biotechnol. 2011 Aug; 29(8):735-41. PMID: 21804562.
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      94. Bordbar A, Jamshidi N, Palsson B. iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. BMC Syst Biol. 2011; 5:110. PMID: 21749716.
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      95. McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson B, Adkins JN, Heffron F. Technologies and approaches to elucidate and model the virulence program of salmonella. Front Microbiol. 2011; 2:121. PMID: 21687430.
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      96. Liao YC, Huang TW, Chen FC, Charusanti P, Hong JS, Chang HY, Tsai SF, Palsson B, Hsiung CA. An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. J Bacteriol. 2011 Apr; 193(7):1710-7. PMID: 21296962.
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      97. 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, Raghunathan A, Reed JL, Shin SI, Sigurbjörnsdóttir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson B, Adkins JN, Bumann D. A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst Biol. 2011; 5:8. PMID: 21244678.
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      98. Tremblay PL, Summers ZM, Glaven RH, Nevin KP, Zengler K, Barrett CL, Qiu Y, Palsson B, Lovley DR. A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution. Environ Microbiol. 2011 Jan; 13(1):13-23. PMID: 20636372.
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      99. Lerman J, Palsson B. Microbiology. Topping off a multiscale balancing act. Science. 2010 Nov 19; 330(6007):1058-9. PMID: 21097927.
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      100. Barrett CL, Cho BK, Palsson B. Sensitive and accurate identification of protein-DNA binding events in ChIP-chip assays using higher order derivative analysis. Nucleic Acids Res. 2011 Mar; 39(5):1656-65. PMID: 21051353.
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      101. Feist AM, Palsson B. The biomass objective function. Curr Opin Microbiol. 2010 Jun; 13(3):344-9. PMID: 20430689.
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      102. Jamshidi N, Palsson B. Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes. BMC Syst Biol. 2009; 3:44. PMID: 19405968.
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      103. Lewis NE, Cho BK, Knight EM, Palsson B. Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content. J Bacteriol. 2009 Jun; 191(11):3437-44. PMID: 19363119.
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      104. Mo ML, Palsson B, Herrgård MJ. Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst Biol. 2009; 3:37. PMID: 19321003.
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      105. Sigurdsson MI, Jamshidi N, Jonsson JJ, Palsson B. Genome-scale network analysis of imprinted human metabolic genes. Epigenetics. 2009 Jan; 4(1):43-6. PMID: 19218833.
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      106. Becker SA, Palsson B. Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol. 2008 May; 4(5):e1000082. PMID: 18483554.
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      107. Becker SA, Palsson B. Three factors underlying incorrect in silico predictions of essential metabolic genes. BMC Syst Biol. 2008; 2:14. PMID: 18248675.
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      108. Cho BK, Charusanti P, Herrgård MJ, Palsson B. Microbial regulatory and metabolic networks. Curr Opin Biotechnol. 2007 Aug; 18(4):360-4. PMID: 17719767.
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      109. Oh YK, Palsson B, Park SM, Schilling CH, Mahadevan R. Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem. 2007 Sep 28; 282(39):28791-9. PMID: 17573341.
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      110. Anderson MJ, DeLabarre B, Raghunathan A, Palsson B, Brunger AT, Quake SR. Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices. Biochemistry. 2007 May 15; 46(19):5722-31. PMID: 17441732.
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      111. Vo TD, Paul Lee WN, Palsson B. Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome. Mol Genet Metab. 2007 May; 91(1):15-22. PMID: 17336115.
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      112. Jamshidi N, Vo TD, Palsson B. In silico analysis of SNPs and other high-throughput data. Methods Mol Biol. 2007; 366:267-85. PMID: 17568130.
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      113. Joyce AR, Palsson B. Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach. Prog Drug Res. 2007; 64:265, 267-309. PMID: 17195479.
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      114. Vo TD, Palsson B. Isotopomer analysis of myocardial substrate metabolism: a systems biology approach. Biotechnol Bioeng. 2006 Dec 5; 95(5):972-83. PMID: 16878330.
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      115. Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson B. Systems approach to refining genome annotation. Proc Natl Acad Sci U S A. 2006 Nov 14; 103(46):17480-4. PMID: 17088549.
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      116. Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson B. Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput Biol. 2006 Aug 11; 2(8):e101. PMID: 16895435.
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      117. Vo TD, Palsson B. Building the power house: recent advances in mitochondrial studies through proteomics and systems biology. Am J Physiol Cell Physiol. 2007 Jan; 292(1):C164-77. PMID: 16885397.
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      118. Barrett CL, Palsson B. Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PLoS Comput Biol. 2006 May; 2(5):e52. PMID: 16710450.
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      119. Barrett CL, Price ND, Palsson B. Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition. BMC Bioinformatics. 2006; 7:132. PMID: 16533395.
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      120. Reed JL, Famili I, Thiele I, Palsson B. Towards multidimensional genome annotation. Nat Rev Genet. 2006 Feb; 7(2):130-41. PMID: 16418748.
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      121. Mahadevan R, Bond DR, Butler JE, Esteve-Nuñez A, Coppi MV, Palsson B, Schilling CH, Lovley DR. Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Appl Environ Microbiol. 2006 Feb; 72(2):1558-68. PMID: 16461711.
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      122. Cho BK, Knight EM, Palsson B. PCR-based tandem epitope tagging system for Escherichia coli genome engineering. Biotechniques. 2006 Jan; 40(1):67-72. PMID: 16454042.
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      123. Barrett CL, Herring CD, Reed JL, Palsson B. The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states. Proc Natl Acad Sci U S A. 2005 Dec 27; 102(52):19103-8. PMID: 16357206.
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      124. Fong SS, Nanchen A, Palsson B, Sauer U. Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes. J Biol Chem. 2006 Mar 24; 281(12):8024-33. PMID: 16319065.
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      125. Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson B. In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng. 2005 Sep 5; 91(5):643-8. PMID: 15962337.
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      126. Papin JA, Hunter T, Palsson B, Subramaniam S. Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol. 2005 Feb; 6(2):99-111. PMID: 15654321.
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      127. Famili I, Mahadevan R, Palsson B. k-Cone analysis: determining all candidate values for kinetic parameters on a network scale. Biophys J. 2005 Mar; 88(3):1616-25. PMID: 15626710.
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      128. Mahadevan R, Palsson B. Properties of metabolic networks: structure versus function. Biophys J. 2005 Jan; 88(1):L07-9. PMID: 15574705.
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      129. Papin JA, Reed JL, Palsson B. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends Biochem Sci. 2004 Dec; 29(12):641-7. PMID: 15544950.
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      130. Price ND, Schellenberger J, Palsson B. Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. Biophys J. 2004 Oct; 87(4):2172-86. PMID: 15454420.
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      131. Westerhoff HV, Palsson B. The evolution of molecular biology into systems biology. Nat Biotechnol. 2004 Oct; 22(10):1249-52. PMID: 15470464.
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      132. Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson B. Comparison of network-based pathway analysis methods. Trends Biotechnol. 2004 Aug; 22(8):400-5. PMID: 15283984.
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      133. Papin JA, Palsson B. The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. Biophys J. 2004 Jul; 87(1):37-46. PMID: 15240442.
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      134. Vo TD, Greenberg HJ, Palsson B. Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J Biol Chem. 2004 Sep 17; 279(38):39532-40. PMID: 15205464.
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      135. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson B. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004 May 6; 429(6987):92-6. PMID: 15129285.
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      136. Papin JA, Palsson B. Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. J Theor Biol. 2004 Mar 21; 227(2):283-97. PMID: 14990392.
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      137. Raghunathan A, Price ND, Galperin MY, Makarova KS, Purvine S, Picone AF, Cherny T, Xie T, Reilly TJ, Munson R, Tyler RE, Akerley BJ, Smith AL, Palsson B, Kolker E. In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium. OMICS. 2004; 8(1):25-41. PMID: 15107235.
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      138. Covert MW, Famili I, Palsson B. Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology? Biotechnol Bioeng. 2003 Dec 30; 84(7):763-72. PMID: 14708117.
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      139. Price ND, Reed JL, Papin JA, Wiback SJ, Palsson B. Network-based analysis of metabolic regulation in the human red blood cell. J Theor Biol. 2003 Nov 21; 225(2):185-94. PMID: 14575652.
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      140. Famili I, Forster J, Nielsen J, Palsson B. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc Natl Acad Sci U S A. 2003 Nov 11; 100(23):13134-9. PMID: 14578455.
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      141. Famili I, Palsson B. Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices. J Theor Biol. 2003 Sep 7; 224(1):87-96. PMID: 12900206.
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      142. Reed JL, Vo TD, Schilling CH, Palsson B. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 2003; 4(9):R54. PMID: 12952533.
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      143. Kolker E, Purvine S, Galperin MY, Stolyar S, Goodlett DR, Nesvizhskii AI, Keller A, Xie T, Eng JK, Yi E, Hood L, Picone AF, Cherny T, Tjaden BC, Siegel AF, Reilly TJ, Makarova KS, Palsson B, Smith AL. Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol. 2003 Aug; 185(15):4593-602. PMID: 12867470.
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      144. Famili I, Palsson B. The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools. Biophys J. 2003 Jul; 85(1):16-26. PMID: 12829460.
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      145. Palsson B, Price ND, Papin JA. Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends Biotechnol. 2003 May; 21(5):195-8. PMID: 12727379.
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      146. Papin JA, Price ND, Wiback SJ, Fell DA, Palsson B. Metabolic pathways in the post-genome era. Trends Biochem Sci. 2003 May; 28(5):250-8. PMID: 12765837.
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      147. Covert MW, Palsson B. Constraints-based models: regulation of gene expression reduces the steady-state solution space. J Theor Biol. 2003 Apr 7; 221(3):309-25. PMID: 12642111.
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      148. Price ND, Papin JA, Schilling CH, Palsson B. Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol. 2003 Apr; 21(4):162-9. PMID: 12679064.
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      149. Raghunathan A, Palsson B. Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli. Biotechnol Lett. 2003 Mar; 25(5):435-41. PMID: 12882568.
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      150. Price ND, Reed JL, Papin JA, Famili I, Palsson B. Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophys J. 2003 Feb; 84(2 Pt 1):794-804. PMID: 12547764.
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      151. Ibarra RU, Fu P, Palsson B, DiTonno JR, Edwards JS. Quantitative analysis of Escherichia coli metabolic phenotypes within the context of phenotypic phase planes. J Mol Microbiol Biotechnol. 2003; 6(2):101-8. PMID: 15044828.
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      152. Förster J, Famili I, Palsson B, Nielsen J. Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS. 2003; 7(2):193-202. PMID: 14506848.
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      153. Ibarra RU, Edwards JS, Palsson B. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature. 2002 Nov 14; 420(6912):186-9. PMID: 12432395.
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      154. Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson B. Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol. 2002 Aug; 184(16):4582-93. PMID: 12142428.
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      155. Wiback SJ, Palsson B. Extreme pathway analysis of human red blood cell metabolism. Biophys J. 2002 Aug; 83(2):808-18. PMID: 12124266.
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      156. Kauffman KJ, Pajerowski JD, Jamshidi N, Palsson B, Edwards JS. Description and analysis of metabolic connectivity and dynamics in the human red blood cell. Biophys J. 2002 Aug; 83(2):646-62. PMID: 12124254.
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      157. Lee GM, Fong SS, Oh DJ, Francis K, Palsson B. Characterization and efficacy of PKH26 as a probe to study the replication history of the human hematopoietic KG1a progenitor cell line. In Vitro Cell Dev Biol Anim. 2002 Feb; 38(2):90-6. PMID: 11929001.
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      158. Edwards JS, Ramakrishna R, Palsson B. Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol Bioeng. 2002 Jan 5; 77(1):27-36. PMID: 11745171.
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      159. Kolker E, Purvine S, Picone A, Cherny T, Akerley BJ, Munson RS, Palsson B, Daines DA, Smith AL. H. influenzae Consortium: integrative study of H. influenzae-human interactions. OMICS. 2002; 6(4):341-8. PMID: 12626093.
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      160. Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson B. Dynamic simulation of the human red blood cell metabolic network. Bioinformatics. 2001 Mar; 17(3):286-7. PMID: 11294796.
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      161. Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson B. Metabolic modeling of microbial strains in silico. Trends Biochem Sci. 2001 Mar; 26(3):179-86. PMID: 11246024.
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      162. Ramakrishna R, Edwards JS, McCulloch A, Palsson B. Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. Am J Physiol Regul Integr Comp Physiol. 2001 Mar; 280(3):R695-704. PMID: 11171647.
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      163. Edwards JS, Ibarra RU, Palsson B. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol. 2001 Feb; 19(2):125-30. PMID: 11175725.
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      164. Edwards JS, Palsson B. Multiple steady states in kinetic models of red cell metabolism. J Theor Biol. 2000 Nov 7; 207(1):125-7. PMID: 11027485.
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      165. Edwards JS, Palsson B. Robustness analysis of the Escherichia coli metabolic network. Biotechnol Prog. 2000 Nov-Dec; 16(6):927-39. PMID: 11101318.
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      166. Edwards JS, Palsson B. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics. 2000; 1:1. PMID: 11001586.
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      167. Oh DJ, Martinez AR, Lee GM, Francis K, Palsson B. Intercellular adhesion can be visualized using fluorescently labeled fibrosarcoma HT1080 cells cocultured with hematopoietic cell lines or CD34(+) enriched human mobilized peripheral blood cells. Cytometry. 2000 Jun 1; 40(2):119-25. PMID: 10805931.
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      168. Oh DJ, Martinez AR, Lee GM, Francis K, Palsson B. Extension of osmolality-induced podia is observed from fluorescently labeled hematopoietic cell lines in hyperosmotic medium. Cytometry. 2000 Jun 1; 40(2):109-18. PMID: 10805930.
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      169. Edwards JS, Palsson B. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci U S A. 2000 May 9; 97(10):5528-33. PMID: 10805808.
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      170. Schilling CH, Letscher D, Palsson B. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J Theor Biol. 2000 Apr 7; 203(3):229-48. PMID: 10716907.
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      171. Schilling CH, Palsson B. Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J Theor Biol. 2000 Apr 7; 203(3):249-83. PMID: 10716908.
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      172. Lee GM, Fong S, Francis K, Oh DJ, Palsson B. In situ labeling of adherent cells with PKH26. In Vitro Cell Dev Biol Anim. 2000 Jan; 36(1):4-6. PMID: 10691033.
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      173. Holloway W, Martinez AR, Oh DJ, Francis K, Ramakrishna R, Palsson B. Key adhesion molecules are present on long podia extended by hematopoietic cells. Cytometry. 1999 Nov 1; 37(3):171-7. PMID: 10520196.
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      174. Huang S, Law P, Francis K, Palsson B, Ho AD. Symmetry of initial cell divisions among primitive hematopoietic progenitors is independent of ontogenic age and regulatory molecules. Blood. 1999 Oct 15; 94(8):2595-604. PMID: 10515863.
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      175. Oh DJ, Lee GM, Francis K, Palsson B. Phototoxicity of the fluorescent membrane dyes PKH2 and PKH26 on the human hematopoietic KG1a progenitor cell line. Cytometry. 1999 Aug 1; 36(4):312-8. PMID: 10404146.
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      176. Edwards JS, Palsson B. Systems properties of the Haemophilus influenzae Rd metabolic genotype. J Biol Chem. 1999 Jun 18; 274(25):17410-6. PMID: 10364169.
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      177. Schilling CH, Edwards JS, Palsson B. Toward metabolic phenomics: analysis of genomic data using flux balances. Biotechnol Prog. 1999 May-Jun; 15(3):288-95. PMID: 10356245.
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      178. Schilling CH, Schuster S, Palsson B, Heinrich R. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol Prog. 1999 May-Jun; 15(3):296-303. PMID: 10356246.
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      179. Francis K, Ramakrishna R, Holloway W, Palsson B. Two new pseudopod morphologies displayed by the human hematopoietic KG1a progenitor cell line and by primary human CD34(+) cells. Blood. 1998 Nov 15; 92(10):3616-23. PMID: 9808555.
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      180. Mandalam RK, Palsson B. Elemental balancing of biomass and medium composition enhances growth capacity in high-density Chlorella vulgaris cultures. Biotechnol Bioeng. 1998 Sep 5; 59(5):605-11. PMID: 10099378.
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      181. Schilling CH, Palsson B. The underlying pathway structure of biochemical reaction networks. Proc Natl Acad Sci U S A. 1998 Apr 14; 95(8):4193-8. PMID: 9539712.
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      182. Edwards JS, Palsson B. How will bioinformatics influence metabolic engineering? Biotechnol Bioeng. 1998 Apr 20-May 5; 58(2-3):162-9. PMID: 10191386.
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      183. Andreadis S, Fuller AO, Palsson B. Cell cycle dependence of retroviral transduction: An issue of overlapping time scales. Biotechnol Bioeng. 1998 Apr 20-May 5; 58(2-3):272-81. PMID: 10191401.
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      184. Francis K, Palsson B. Effective intercellular communication distances are determined by the relative time constants for cyto/chemokine secretion and diffusion. Proc Natl Acad Sci U S A. 1997 Nov 11; 94(23):12258-62. PMID: 9356436.
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      185. Palsson B. What lies beyond bioinformatics? Nat Biotechnol. 1997 Jan; 15(1):3-4. PMID: 9035092.
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      186. Koller MR, Manchel I, Palsson B. Importance of parenchymal:stromal cell ratio for the ex vivo reconstitution of human hematopoiesis. Stem Cells. 1997; 15(4):305-13. PMID: 9253115.
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      187. Koller MR, Oxender M, Brott DA, Palsson B. flt-3 ligand is more potent than c-kit ligand for the synergistic stimulation of ex vivo hematopoietic cell expansion. J Hematother. 1996 Oct; 5(5):449-59. PMID: 8938517.
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      188. Andreadis ST, Palsson B. Kinetics of retrovirus mediated gene transfer: the importance of intracellular half-life of retroviruses. J Theor Biol. 1996 Sep 7; 182(1):1-20. PMID: 8917734.
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      189. Peng CA, Palsson B. Determination of specific oxygen uptake rates in human hematopoietic cultures and implications for bioreactor design. Ann Biomed Eng. 1996 May-Jun; 24(3):373-81. PMID: 8734058.
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      190. Rogers CE, Bradley MS, Palsson B, Koller MR. Flow cytometric analysis of human bone marrow perfusion cultures: erythroid development and relationship with burst-forming units-erythroid. Exp Hematol. 1996 Apr; 24(5):597-604. PMID: 8605964.
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      191. Eipers PG, Krauss JC, Palsson B, Emerson SG, Todd RF, Clarke MF. Retroviral-mediated gene transfer in human bone marrow cells growth in continuous perfusion culture vessels. Blood. 1995 Nov 15; 86(10):3754-62. PMID: 7579342.
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      192. Koller MR, Palsson MA, Manchel I, Palsson B. Long-term culture-initiating cell expansion is dependent on frequent medium exchange combined with stromal and other accessory cell effects. Blood. 1995 Sep 1; 86(5):1784-93. PMID: 7544642.
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      193. Koller MR, Manchel I, Newsom BS, Palsson MA, Palsson B. Bioreactor expansion of human bone marrow: comparison of unprocessed, density-separated, and CD34-enriched cells. J Hematother. 1995 Jun; 4(3):159-69. PMID: 7551915.
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      194. Varma A, Palsson B. Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism. Biotechnol Bioeng. 1995 Jan 5; 45(1):69-79. PMID: 18623053.
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      195. Emerson SG, Palsson B, Clarke MF, Silver SM, Adams PT, Koller MR, Van Zant G, Rummel S, Armstrong RD, Maluta J. In vitro expansion of hematopoietic cells for clinical application. Cancer Treat Res. 1995; 76:215-23. PMID: 7577336.
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      196. Palsson B, Oh DJ, Koller MR. Replating of bioreactor expanded human bone marrow results in extended growth of primitive and mature cells. Cytotechnology. 1995 Jan; 18(1-2):125-31. PMID: 22358645.
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      197. Varma A, Palsson B. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol. 1994 Oct; 60(10):3724-31. PMID: 7986045.
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      198. Oh DJ, Koller MR, Palsson B. Frequent harvesting from perfused bone marrow cultures results in increased overall cell and progenitor expansion. Biotechnol Bioeng. 1994 Aug 20; 44(5):609-16. PMID: 18618796.
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      199. Hubbell JA, Palsson B, Papoutsakis ET. Preface: Tissue engineering and cell therapies: II. Biotechnol Bioeng. 1994 Apr 5; 43(8):683. PMID: 18615791.
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      200. Levee MG, Lee GM, Paek SH, Palsson B. Microencapsulated human bone marrow cultures: a potential culture system for the clonal outgrowth of hematopoietic progenitor cells. Biotechnol Bioeng. 1994 Apr 5; 43(8):734-9. PMID: 18615796.
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      201. Hubbell JA, Palsson B, Papoutsakis ET. Preface. Tissue engineering and cell therapies. Biotechnol Bioeng. 1994 Mar 25; 43(7):541. PMID: 18615753.
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      202. Varma A, Palsson B. Predictions for oxygen supply control to enhance population stability of engineered production strains. Biotechnol Bioeng. 1994 Feb 20; 43(4):275-85. PMID: 18615690.
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      203. Lee GM, Kim SJ, Palsson B. Enhanced specific antibody productivity of calcium alginate-entrapped hybridoma is cell line-specific. Cytotechnology. 1994; 16(1):1-15. PMID: 7765785.
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      204. Lee GM, Palsson B. Monoclonal antibody production using free-suspended and entrapped hybridoma cells. Biotechnol Genet Eng Rev. 1994; 12:509-33. PMID: 7727036.
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      205. Varma A, Palsson B. Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors. J Theor Biol. 1993 Dec 21; 165(4):477-502. PMID: 21322280.
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      206. Lee GM, Palsson B. Stability of antibody productivity is improved when hybridoma cells are entrapped in calcium alginate beads. Biotechnol Bioeng. 1993 Nov 5; 42(9):1131-5. PMID: 18613244.
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      207. Koller MR, Palsson B. Review: tissue engineering: reconstitution of human hematopoiesis ex vivo. Biotechnol Bioeng. 1993 Oct; 42(8):909-30. PMID: 18613140.
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      208. Varma A, Boesch BW, Palsson B. Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl Environ Microbiol. 1993 Aug; 59(8):2465-73. PMID: 8368835.
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      209. Koller MR, Emerson SG, Palsson B. Large-scale expansion of human stem and progenitor cells from bone marrow mononuclear cells in continuous perfusion cultures. Blood. 1993 Jul 15; 82(2):378-84. PMID: 8329697.
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      210. Merritt SE, Palsson B. Loss of antibody productivity is highly reproducible in multiple hybridoma subclones. Biotechnol Bioeng. 1993 Jun 20; 42(2):247-50. PMID: 18612986.
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      211. Varma A, Boesch BW, Palsson B. Biochemical production capabilities of Escherichia coli. Biotechnol Bioeng. 1993 Jun 5; 42(1):59-73. PMID: 18609648.
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      212. Meyerhoff ME, Trojanowicz M, Palsson B. Simultaneous enzymatic/electrochemical determination of glucose and L-glutamine in hybridoma media by flow-injection analysis. Biotechnol Bioeng. 1993 Apr 25; 41(10):964-9. PMID: 18601278.
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      213. Palsson B, Lee ID. Model complexity has a significant effect on the numerical value and interpretation of metabolic sensitivity coefficients. J Theor Biol. 1993 Apr 7; 161(3):299-315. PMID: 8331956.
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      214. Palsson B, Paek SH, Schwartz RM, Palsson M, Lee GM, Silver S, Emerson SG. Expansion of human bone marrow progenitor cells in a high cell density continuous perfusion system. Biotechnology (N Y). 1993 Mar; 11(3):368-72. PMID: 7763438.
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      215. Lee GM, Chuck AS, Palsson B. Cell Culture conditions determine the enhancement of specific monoclonal antibody productivity of calcium alginate-entrapped S3H5/gamma2bA2 hybridoma cells. Biotechnol Bioeng. 1993 Feb 5; 41(3):330-40. PMID: 18609557.
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      216. Lee ID, Palsson B. A Macintosh software package for simulation of human red blood cell metabolism. Comput Methods Programs Biomed. 1992 Aug; 38(4):195-226. PMID: 1473341.
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      217. Keasling JD, Palsson B, Cooper S. Replication of prophage P1 is cell-cycle specific. J Bacteriol. 1992 Jul; 174(13):4457-62. PMID: 1624438.
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      218. Savinell JM, Palsson B. Optimal selection of metabolic fluxes for in vivo measurement. I. Development of mathematical methods. J Theor Biol. 1992 Mar 21; 155(2):201-14. PMID: 1453697.
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      219. Savinell JM, Palsson B. Optimal selection of metabolic fluxes for in vivo measurement. II. Application to Escherichia coli and hybridoma cell metabolism. J Theor Biol. 1992 Mar 21; 155(2):215-42. PMID: 1453698.
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      220. Javanmardian M, Palsson B. Continuous photoautotrophic cultures of the eukaryotic alga Chlorella vulgaris can exhibit stable oscillatory dynamics. Biotechnol Bioeng. 1992 Mar 5; 39(5):487-97. PMID: 18600974.
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      221. Savinell JM, Palsson B. Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism. J Theor Biol. 1992 Feb 21; 154(4):421-54. PMID: 1593896.
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      222. Savinell JM, Palsson B. Network analysis of intermediary metabolism using linear optimization. II. Interpretation of hybridoma cell metabolism. J Theor Biol. 1992 Feb 21; 154(4):455-73. PMID: 1593897.
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      223. Ozturk SS, Riley MR, Palsson B. Effects of ammonia and lactate on hybridoma growth, metabolism, and antibody production. Biotechnol Bioeng. 1992 Feb 20; 39(4):418-31. PMID: 18600963.
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      224. Chuck AS, Palsson B. Population balance between producing and nonproducing hybridoma clones is very sensitive to serum level, state of inoculum, and medium composition. Biotechnol Bioeng. 1992 Feb 5; 39(3):354-60. PMID: 18600953.
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      225. Keasling JD, Palsson B, Cooper S. Replication of the R6K plasmid during the Escherichia coli cell cycle. J Bacteriol. 1992 Feb; 174(3):1060-2. PMID: 1732198.
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      226. Varma A, el-Awar FY, Palsson B, Emerson SG, Clarke MF. Can Dexter cultures support stem cell proliferation? Exp Hematol. 1992 Jan; 20(1):87-91. PMID: 1577098.
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      227. Schwartz RM, Emerson SG, Clarke MF, Palsson B. In vitro myelopoiesis stimulated by rapid medium exchange and supplementation with hematopoietic growth factors. Blood. 1991 Dec 15; 78(12):3155-61. PMID: 1742483.
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      228. Javanmardian M, Palsson B. High-density photoautotrophic algal cultures: design, construction, and operation of a novel photobioreactor system. Biotechnol Bioeng. 1991 Dec 5; 38(10):1182-9. PMID: 18600714.
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      229. Ozturk SS, Palsson B. Growth, metabolic, and antibody production kinetics of hybridoma cell culture: 1. Analysis of data from controlled batch reactors. Biotechnol Prog. 1991 Nov-Dec; 7(6):471-80. PMID: 1367749.
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      230. Ozturk SS, Palsson B. Growth, metabolic, and antibody production kinetics of hybridoma cell culture: 2. Effects of serum concentration, dissolved oxygen concentration, and medium pH in a batch reactor. Biotechnol Prog. 1991 Nov-Dec; 7(6):481-94. PMID: 1367750.
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      231. Lee GM, Varma A, Palsson B. Production of monoclonal antibody using free-suspended and immobilized hybridoma cells: Effect of serum. Biotechnol Bioeng. 1991 Oct 20; 38(8):821-30. PMID: 18600839.
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      232. Schwartz RM, Palsson B, Emerson SG. Rapid medium perfusion rate significantly increases the productivity and longevity of human bone marrow cultures. Proc Natl Acad Sci U S A. 1991 Aug 1; 88(15):6760-4. PMID: 1862099.
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      233. Caldwell J, Palsson B, Locey B, Emerson SG. Culture perfusion schedules influence the metabolic activity and granulocyte-macrophage colony-stimulating factor production rates of human bone marrow stromal cells. J Cell Physiol. 1991 May; 147(2):344-53. PMID: 2040665.
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      234. Ozturk SS, Palsson B. Effect of medium osmolarity on hybridoma growth, metabolism, and antibody production. Biotechnol Bioeng. 1991 Apr 25; 37(10):989-93. PMID: 18597326.
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      235. Keasling JD, Palsson B, Cooper S. Cell-cycle-specific F plasmid replication: regulation by cell size control of initiation. J Bacteriol. 1991 Apr; 173(8):2673-80. PMID: 2013579.
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      236. Ozturk SS, Palsson B. Physiological changes during the adaptation of hybridoma cells to low serum and serum-free media. Biotechnol Bioeng. 1991 Jan 5; 37(1):35-46. PMID: 18597305.
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      237. Lee GM, Varma A, Palsson B. Application of population balance model to the loss of hybridoma antibody productivity. Biotechnol Prog. 1991 Jan-Feb; 7(1):72-5. PMID: 1366981.
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      238. Caldwell J, Locey B, Clarke MF, Emerson SG, Palsson B. Influence of medium exchange schedules on metabolic, growth, and GM-CSF secretion rates of genetically engineered NIH-3T3 cells. Biotechnol Prog. 1991 Jan-Feb; 7(1):1-8. PMID: 1366977.
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      239. Lee GM, Palsson B. Immobilization can improve the stability of hybridoma antibody productivity in serum-free media. Biotechnol Bioeng. 1990 Dec 5; 36(10):1049-55. PMID: 18595043.
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      240. Ozturk SS, Palsson B. Effects of dissolved oxygen on hybridoma cell growth, metabolism, and antibody production kinetics in continuous culture. Biotechnol Prog. 1990 Nov-Dec; 6(6):437-46. PMID: 1366834.
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      241. Ozturk SS, Palsson B. Loss of antibody productivity during long-term cultivation of a hybridoma cell line in low serum and serum-free media. Hybridoma. 1990 Apr; 9(2):167-75. PMID: 2347598.
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      242. Ozturk SS, Palsson B. Chemical decomposition of glutamine in cell culture media: effect of media type, pH, and serum concentration. Biotechnol Prog. 1990 Mar-Apr; 6(2):121-8. PMID: 1366484.
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      243. Joshi A, Palsson B. Metabolic dynamics in the human red cell. Part IV--Data prediction and some model computations. J Theor Biol. 1990 Jan 9; 142(1):69-85. PMID: 2141094.
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      244. Joshi A, Palsson B. Metabolic dynamics in the human red cell. Part III--Metabolic reaction rates. J Theor Biol. 1990 Jan 9; 142(1):41-68. PMID: 2141093.
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      245. Palsson B, Keasling JD, Emerson SG. The regulatory mechanisms of human immunodeficiency virus replication predict multiple expression rates. Proc Natl Acad Sci U S A. 1990 Jan; 87(2):772-6. PMID: 2405389.
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      246. Lee ID, Palsson B. A comprehensive model of human erythrocyte metabolism: extensions to include pH effects. Biomed Biochim Acta. 1990; 49(8-9):771-89. PMID: 2082921.
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      247. Joshi A, Palsson B. Metabolic dynamics in the human red cell. Part I--A comprehensive kinetic model. J Theor Biol. 1989 Dec 19; 141(4):515-28. PMID: 2630803.
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      248. Keasling JD, Palsson B. ColE1 plasmid replication: a simple kinetic description from a structured model. J Theor Biol. 1989 Dec 19; 141(4):447-61. PMID: 2483575.
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      249. Joshi A, Palsson B. Metabolic dynamics in the human red cell. Part II--Interactions with the environment. J Theor Biol. 1989 Dec 19; 141(4):529-45. PMID: 2630804.
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      250. Lee GM, Savinell JM, Palsson B. Serum can act as a shear protecting agent in agitated hybridoma cell cultures. Hybridoma. 1989 Dec; 8(6):639-45. PMID: 2693339.
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      251. Lee GM, Huard TK, Palsson B. Effect of serum concentration on hybridoma cell growth and monoclonal antibody production at various initial cell densities. Hybridoma. 1989 Jun; 8(3):369-75. PMID: 2744789.
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      252. Keasling JD, Palsson B. On the kinetics of plasmid replication. J Theor Biol. 1989 Feb 22; 136(4):487-92. PMID: 2811403.
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      253. Ozturk SS, Palsson B, Thiele JH. Control of interspecies electron transfer flow during anaerobic digestion: dynamic diffusion reaction models for hydrogen gas transfer in microbial flocs. Biotechnol Bioeng. 1989 Feb 5; 33(6):745-57. PMID: 18587976.
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      254. Palsson B, Narang A, Joshi A. Computer model of human erythrocyte metabolism. Prog Clin Biol Res. 1989; 319:133-50; discussion 151-4. PMID: 2695934.
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      255. Palsson B, Groshans TM. Mathematical modelling of dynamics and control in metabolic networks: VI. Dynamic bifurcations in single biochemical control loops. J Theor Biol. 1988 Mar 7; 131(1):43-53. PMID: 3419192.
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      256. Joshi A, Palsson B. Escherichia coil growth dynamics: A three-pool biochemically based description. Biotechnol Bioeng. 1988 Feb 5; 31(2):102-16. PMID: 18581570.
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      257. Palsson B, Joshi A, Ozturk SS. Reducing complexity in metabolic networks: making metabolic meshes manageable. Fed Proc. 1987 Jun; 46(8):2485-9. PMID: 3297796.
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      258. Palsson B, Joshi A. On the dynamic order of structured Escherichia coli growth models. Biotechnol Bioeng. 1987 Apr; 29(6):789-92. PMID: 18576521.
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      259. Palsson B, Palsson H, Lightfoot EN. Mathematical modelling of dynamics and control in metabolic networks. III. Linear reaction sequences. J Theor Biol. 1985 Mar 21; 113(2):231-59. PMID: 3999777.
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      260. Palsson B, Lightfoot EN. Mathematical modelling of dynamics and control in metabolic networks. V. Static bifurcations in single biochemical control loops. J Theor Biol. 1985 Mar 21; 113(2):279-98. PMID: 3999779.
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      261. Palsson B, Lightfoot EN. Mathematical modelling of dynamics and control in metabolic networks. IV. Local stability analysis of single biochemical control loops. J Theor Biol. 1985 Mar 21; 113(2):261-77. PMID: 3999778.
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      262. Palsson B, Lightfoot EN. Mathematical modelling of dynamics and control in metabolic networks. I. On Michaelis-Menten kinetics. J Theor Biol. 1984 Nov 21; 111(2):273-302. PMID: 6513572.
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      263. Palsson B, Jamier R, Lightfoot EN. Mathematical modelling of dynamics and control in metabolic networks. II. Simple dimeric enzymes. J Theor Biol. 1984 Nov 21; 111(2):303-21. PMID: 6513573.
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