Loading...

Bernhard Palsson

Title(s)Adjunct Professor, Pediatrics
SchoolAcademic Aff
Phone858-534-5668
vCardDownload vCard

    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 Models of Stress Response for E. coli
    NIH/NIGMS R01GM057089Aug 1, 1998 - Jun 30, 2022
    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.
    List All   |   Timeline
    1. Norsigian CJ, Pusarla N, McConn JL, Yurkovich JT, Dräger A, Palsson BO, King Z. BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic Acids Res. 2019 Nov 07. PMID: 31696234.
      View in: PubMed
    2. Nogales J, Mueller J, Gudmundsson S, Canalejo FJ, Duque E, Monk J, Feist AM, Ramos JL, Niu W, Palsson BO. High-quality genome-scale metabolic modeling of Pseudomonas putida highlights its broad metabolic capabilities. Environ Microbiol. 2019 Oct 27. PMID: 31657101.
      View in: PubMed
    3. Anand A, Chen K, Catoiu E, Sastry AV, Olson CA, Sandberg TE, Seif Y, Xu S, Szubin R, Yang L, Feist AM, Palsson BO. OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states. Mol Biol Evol. 2019 Oct 25. PMID: 31651953.
      View in: PubMed
    4. Du B, Olson CA, Sastry AV, Fang X, Phaneuf PV, Chen K, Wu M, Szubin R, Xu S, Gao Y, Hefner Y, Feist AM, Palsson BO. Adaptive laboratory evolution of Escherichia coli under acid stress. Microbiology. 2019 Oct 18. PMID: 31625833.
      View in: PubMed
    5. Machado H, Weng LL, Dillon N, Seif Y, Holland M, Pekar JE, Monk JM, Nizet V, Palsson BO, Feist AM. Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus. Appl Environ Microbiol. 2019 Nov 01; 85(21). PMID: 31471305.
      View in: PubMed
    6. Smith SR, Dupont CL, McCarthy JK, Broddrick JT, Oborník M, Horák A, Füssy Z, Cihlár J, Kleessen S, Zheng H, McCrow JP, Hixson KK, Araújo WL, Nunes-Nesi A, Fernie A, Nikoloski Z, Palsson BO, Allen AE. Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom. Nat Commun. 2019 Oct 07; 10(1):4552. PMID: 31591397.
      View in: PubMed
    7. Lee Y, Lee N, Jeong Y, Hwang S, Kim W, Cho S, Palsson BO, Cho BK. The Transcription Unit Architecture of Streptomyces lividans TK24. Front Microbiol. 2019; 10:2074. PMID: 31555254.
      View in: PubMed
    8. Seif Y, Monk JM, Machado H, Kavvas E, Palsson BO. Systems Biology and Pangenome of Salmonella O-Antigens. MBio. 2019 Aug 27; 10(4). PMID: 31455646.
      View in: PubMed
    9. Sandberg TE, Salazar MJ, Weng LL, Palsson BO, Feist AM. The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. Metab Eng. 2019 Dec; 56:1-16. PMID: 31401242.
      View in: PubMed
    10. Hwang S, Lee N, Jeong Y, Lee Y, Kim W, Cho S, Palsson BO, Cho BK. Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome. Nucleic Acids Res. 2019 Jul 09; 47(12):6114-6129. PMID: 31131406.
      View in: PubMed
    11. Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ, Sandberg TE, Seo SW, Kim D, Sastry AV, Phaneuf P, Gao Y, Broddrick JT, Chen K, Heckmann D, Szubin R, Hefner Y, Feist AM, Palsson BO. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Proc Natl Acad Sci U S A. 2019 Jul 09; 116(28):14368-14373. PMID: 31270234.
      View in: PubMed
    12. Cheng C, O'Brien EJ, McCloskey D, Utrilla J, Olson C, LaCroix RA, Sandberg TE, Feist AM, Palsson BO, King ZA. Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism. PLoS Comput Biol. 2019 Jun; 15(6):e1007066. PMID: 31158228.
      View in: PubMed
    13. Yang JH, Wright SN, Hamblin M, McCloskey D, Alcantar MA, Schrübbers L, Lopatkin AJ, Satish S, Nili A, Palsson BO, Walker GC, Collins JJ. A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action. Cell. 2019 May 30; 177(6):1649-1661.e9. PMID: 31080069.
      View in: PubMed
    14. Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Pogliano J, Knight R, Nizet V, Palsson BO, Feist AM. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Sci Data. 2019 04 26; 6(1):43. PMID: 31028276.
      View in: PubMed
    15. Lachance JC, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, Rodrigue S, Feist AM, King ZA, Jacques PÉ. BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. PLoS Comput Biol. 2019 04; 15(4):e1006971. PMID: 31009451.
      View in: PubMed
    16. Guzmán GI, Sandberg TE, LaCroix RA, Nyerges Á, Papp H, de Raad M, King ZA, Hefner Y, Northen TR, Notebaart RA, Pál C, Palsson BO, Papp B, Feist AM. Enzyme promiscuity shapes adaptation to novel growth substrates. Mol Syst Biol. 2019 Apr 08; 15(4):e8462. PMID: 30962359.
      View in: PubMed
    17. Ghatak S, King ZA, Sastry A, Palsson BO. The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function. Nucleic Acids Res. 2019 03 18; 47(5):2446-2454. PMID: 30698741.
      View in: PubMed
    18. Lachance JC, Rodrigue S, Palsson BO. Minimal cells, maximal knowledge. Elife. 2019 Mar 12; 8. PMID: 30860025.
      View in: PubMed
    19. Luo H, Hansen ASL, Yang L, Schneider K, Kristensen M, Christensen U, Christensen HB, Du B, Özdemir E, Feist AM, Keasling JD, Jensen MK, Herrgård MJ, Palsson BO. Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses. PLoS Biol. 2019 Mar; 17(3):e2007050. PMID: 30856169.
      View in: PubMed
    20. Broddrick JT, Du N, Smith SR, Tsuji Y, Jallet D, Ware MA, Peers G, Matsuda Y, Dupont CL, Mitchell BG, Palsson BO, Allen AE. Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum. New Phytol. 2019 05; 222(3):1364-1379. PMID: 30636322.
      View in: PubMed
    21. Anand A, Olson CA, Yang L, Sastry AV, Catoiu E, Choudhary KS, Phaneuf PV, Sandberg TE, Xu S, Hefner Y, Szubin R, Feist AM, Palsson BO. Pseudogene repair driven by selection pressure applied in experimental evolution. Nat Microbiol. 2019 03; 4(3):386-389. PMID: 30692668.
      View in: PubMed
    22. Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO. A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. PLoS Comput Biol. 2019 01; 15(1):e1006644. PMID: 30625152.
      View in: PubMed
    23. Yang L, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO. DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression. BMC Syst Biol. 2019 01 09; 13(1):2. PMID: 30626386.
      View in: PubMed
    24. Phaneuf PV, Gosting D, Palsson BO, Feist AM. ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. Nucleic Acids Res. 2019 Jan 08; 47(D1):D1164-D1171. PMID: 30357390.
      View in: PubMed
    25. Guzmán GI, Olson CA, Hefner Y, Phaneuf PV, Catoiu E, Crepaldi LB, Micas LG, Palsson BO, Feist AM. Reframing gene essentiality in terms of adaptive flexibility. BMC Syst Biol. 2018 12 17; 12(1):143. PMID: 30558585.
      View in: PubMed
    26. Heckmann D, Zielinski DC, Palsson BO. Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates. Nat Commun. 2018 12 10; 9(1):5270. PMID: 30532008.
      View in: PubMed
    27. Heckmann D, Lloyd CJ, Mih N, Ha Y, Zielinski DC, Haiman ZB, Desouki AA, Lercher MJ, Palsson BO. Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models. Nat Commun. 2018 12 07; 9(1):5252. PMID: 30531987.
      View in: PubMed
    28. Gao Y, Yurkovich JT, Seo SW, Kabimoldayev I, Dräger A, Chen K, Sastry AV, Fang X, Mih N, Yang L, Eichner J, Cho BK, Kim D, Palsson BO. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. Nucleic Acids Res. 2018 11 16; 46(20):10682-10696. PMID: 30137486.
      View in: PubMed
    29. Lee JS, Park JH, Ha TK, Samoudi M, Lewis NE, Palsson BO, Kildegaard HF, Lee GM. Revealing Key Determinants of Clonal Variation in Transgene Expression in Recombinant CHO Cells Using Targeted Genome Editing. ACS Synth Biol. 2018 12 21; 7(12):2867-2878. PMID: 30388888.
      View in: PubMed
    30. Broddrick JT, Welkie DG, Jallet D, Golden SS, Peers G, Palsson BO. Predicting the metabolic capabilities of Synechococcus elongatus PCC 7942 adapted to different light regimes. Metab Eng. 2019 03; 52:42-56. PMID: 30439494.
      View in: PubMed
    31. Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, Allen-Vercoe E, Palsson BO, Smarr L. Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. Front Microbiol. 2018; 9:2559. PMID: 30425690.
      View in: PubMed
    32. Du B, Zielinski DC, Palsson BO. Estimating Metabolic Equilibrium Constants: Progress and Future Challenges. Trends Biochem Sci. 2018 12; 43(12):960-969. PMID: 30472988.
      View in: PubMed
    33. Kavvas ES, Catoiu E, Mih N, Yurkovich JT, Seif Y, Dillon N, Heckmann D, Anand A, Yang L, Nizet V, Monk JM, Palsson BO. Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance. Nat Commun. 2018 10 17; 9(1):4306. PMID: 30333483.
      View in: PubMed
    34. Dinh HV, King ZA, Palsson BO, Feist AM. Identification of growth-coupled production strains considering protein costs and kinetic variability. Metab Eng Commun. 2018 Dec; 7:e00080. PMID: 30370222.
      View in: PubMed
    35. Du B, Zielinski DC, Monk JM, Palsson BO. Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice. Proc Natl Acad Sci U S A. 2018 10 30; 115(44):11339-11344. PMID: 30309961.
      View in: PubMed
    36. Brunk E, Chang RL, Xia J, Hefzi H, Yurkovich JT, Kim D, Buckmiller E, Wang HH, Cho BK, Yang C, Palsson BO, Church GM, Lewis NE. Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. Proc Natl Acad Sci U S A. 2018 10 23; 115(43):11096-11101. PMID: 30301795.
      View in: PubMed
    37. Rowe E, Palsson BO, King ZA. Escher-FBA: a web application for interactive flux balance analysis. BMC Syst Biol. 2018 09 26; 12(1):84. PMID: 30257674.
      View in: PubMed
    38. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. Nat Commun. 2018 09 18; 9(1):3796. PMID: 30228271.
      View in: PubMed
    39. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions. Appl Environ Microbiol. 2018 10 01; 84(19). PMID: 30054360.
      View in: PubMed
    40. Seif Y, Kavvas E, Lachance JC, Yurkovich JT, Nuccio SP, Fang X, Catoiu E, Raffatellu M, Palsson BO, Monk JM. Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. Nat Commun. 2018 09 14; 9(1):3771. PMID: 30218022.
      View in: PubMed
    41. Santos-Zavaleta A, Sánchez-Pérez M, Salgado H, Velázquez-Ramírez DA, Gama-Castro S, Tierrafría VH, Busby SJW, Aquino P, Fang X, Palsson BO, Galagan JE, Collado-Vides J. A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0. BMC Biol. 2018 08 16; 16(1):91. PMID: 30115066.
      View in: PubMed
    42. Yurkovich JT, Alcantar MA, Haiman ZB, Palsson BO. Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials. PLoS Comput Biol. 2018 08; 14(8):e1006356. PMID: 30086174.
      View in: PubMed
    43. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome. Front Microbiol. 2018; 9:1793. PMID: 30131786.
      View in: PubMed
    44. Lloyd CJ, Ebrahim A, Yang L, King ZA, Catoiu E, O'Brien EJ, Liu JK, Palsson BO. COBRAme: A computational framework for genome-scale models of metabolism and gene expression. PLoS Comput Biol. 2018 07; 14(7):e1006302. PMID: 29975681.
      View in: PubMed
    45. Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z, Palsson BO. ssbio: a Python framework for structural systems biology. Bioinformatics. 2018 06 15; 34(12):2155-2157. PMID: 29444205.
      View in: PubMed
    46. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System. Metab Eng. 2018 07; 48:233-242. PMID: 29906504.
      View in: PubMed
    47. Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L, Palsson BO. Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. BMC Syst Biol. 2018 06 11; 12(1):66. PMID: 29890970.
      View in: PubMed
    48. Du B, Zhang Z, Grubner S, Yurkovich JT, Palsson BO, Zielinski DC. Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method. Biophys J. 2018 06 05; 114(11):2691-2702. PMID: 29874618.
      View in: PubMed
    49. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes. Metab Eng. 2018 07; 48:82-93. PMID: 29842925.
      View in: PubMed
    50. Choudhary KS, Mih N, Monk J, Kavvas E, Yurkovich JT, Sakoulas G, Palsson BO. The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures. Front Microbiol. 2018; 9:1082. PMID: 29887846.
      View in: PubMed
    51. Latif H, Federowicz S, Ebrahim A, Tarasova J, Szubin R, Utrilla J, Zengler K, Palsson BO. ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. PLoS One. 2018; 13(5):e0197272. PMID: 29771928.
      View in: PubMed
    52. Norsigian CJ, Kavvas E, Seif Y, Palsson BO, Monk JM. iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE. Front Genet. 2018; 9:121. PMID: 29692801.
      View in: PubMed
    53. Kim D, Seo SW, Gao Y, Nam H, Guzman GI, Cho BK, Palsson BO. Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP. Nucleic Acids Res. 2018 04 06; 46(6):2901-2917. PMID: 29394395.
      View in: PubMed
    54. Yurkovich JT, Bordbar A, Sigurjónsson ÓE, Palsson BO. Systems biology as an emerging paradigm in transfusion medicine. BMC Syst Biol. 2018 03 07; 12(1):31. PMID: 29514691.
      View in: PubMed
    55. Kavvas ES, Seif Y, Yurkovich JT, Norsigian C, Poudel S, Greenwald WW, Ghatak S, Palsson BO, Monk JM. Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. BMC Syst Biol. 2018 03 02; 12(1):25. PMID: 29499714.
      View in: PubMed
    56. Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlic A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 03; 36(3):272-281. PMID: 29457794.
      View in: PubMed
    57. Yurkovich JT, Palsson BO. Quantitative -omic data empowers bottom-up systems biology. Curr Opin Biotechnol. 2018 06; 51:130-136. PMID: 29414439.
      View in: PubMed
    58. Yang L, Yurkovich JT, King ZA, Palsson BO. Modeling the multi-scale mechanisms of macromolecular resource allocation. Curr Opin Microbiol. 2018 10; 45:8-15. PMID: 29367175.
      View in: PubMed
    59. Abdel-Haleem AM, Hefzi H, Mineta K, Gao X, Gojobori T, Palsson BO, Lewis NE, Jamshidi N. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. PLoS Comput Biol. 2018 01; 14(1):e1005895. PMID: 29300748.
      View in: PubMed
    60. Nilsson A, Nielsen J, Palsson BO. Metabolic Models of Protein Allocation Call for the Kinetome. Cell Syst. 2017 12 27; 5(6):538-541. PMID: 29284126.
      View in: PubMed
    61. Du B, Zielinski DC, Palsson BO. Topological and kinetic determinants of the modal matrices of dynamic models of metabolism. PLoS One. 2017; 12(12):e0189880. PMID: 29267329.
      View in: PubMed
    62. Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR. Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli. Proc Natl Acad Sci U S A. 2018 01 02; 115(1):222-227. PMID: 29255023.
      View in: PubMed
    63. Yang JH, Bhargava P, McCloskey D, Mao N, Palsson BO, Collins JJ. Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function. Cell Host Microbe. 2017 Dec 13; 22(6):757-765.e3. PMID: 29199098.
      View in: PubMed
    64. Yurkovich JT, Zielinski DC, Yang L, Paglia G, Rolfsson O, Sigurjónsson ÓE, Broddrick JT, Bordbar A, Wichuk K, Brynjólfsson S, Palsson S, Gudmundsson S, Palsson BO. Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks. J Biol Chem. 2017 12 01; 292(48):19556-19564. PMID: 29030425.
      View in: PubMed
    65. Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist AM, Palsson BO. iML1515, a knowledgebase that computes Escherichia coli traits. Nat Biotechnol. 2017 10 11; 35(10):904-908. PMID: 29020004.
      View in: PubMed
    66. Chen K, Gao Y, Mih N, O'Brien EJ, Yang L, Palsson BO. Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation. Proc Natl Acad Sci U S A. 2017 10 24; 114(43):11548-11553. PMID: 29073085.
      View in: PubMed
    67. Yurkovich JT, Yurkovich BJ, Dräger A, Palsson BO, King ZA. A Padawan Programmer's Guide to Developing Software Libraries. Cell Syst. 2017 11 22; 5(5):431-437. PMID: 28988801.
      View in: PubMed
    68. Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR. Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring. Metab Eng. 2017 11; 44:100-107. PMID: 28951266.
      View in: PubMed
    69. Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, Palsson BO. Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities. Proc Natl Acad Sci U S A. 2017 09 19; 114(38):10286-10291. PMID: 28874552.
      View in: PubMed
    70. Sastry A, Monk J, Tegel H, Uhlen M, Palsson BO, 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
    71. Sandberg TE, Lloyd CJ, Palsson BO, Feist AM. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies. Appl Environ Microbiol. 2017 07 01; 83(13). PMID: 28455337.
      View in: PubMed
    72. Seo SW, Gao Y, Kim D, Szubin R, Yang J, Cho BK, Palsson BO. 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 05 19; 7(1):2181. PMID: 28526842.
      View in: PubMed
    73. Bordbar A, Yurkovich JT, Paglia G, Rolfsson O, Sigurjónsson ÓE, Palsson BO. Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics. Sci Rep. 2017 04 07; 7:46249. PMID: 28387366.
      View in: PubMed
    74. LaCroix RA, Palsson BO, Feist AM. A Model for Designing Adaptive Laboratory Evolution Experiments. Appl Environ Microbiol. 2017 04 15; 83(8). PMID: 28159796.
      View in: PubMed
    75. Yurkovich JT, Yang L, Palsson BO. Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells. PLoS Comput Biol. 2017 03; 13(3):e1005424. PMID: 28264007.
      View in: PubMed
    76. Levering J, Dupont CL, Allen AE, Palsson BO, 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
    77. Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson BO. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism. Sci Rep. 2017 01 25; 7:41241. PMID: 28120890.
      View in: PubMed
    78. Ma D, Yang L, Fleming RM, Thiele I, Palsson BO, Saunders MA. Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression. Sci Rep. 2017 01 18; 7:40863. PMID: 28098205.
      View in: PubMed
    79. van Wijk XM, Döhrmann S, Hallström BM, Li S, Voldborg BG, Meng BX, McKee KK, van Kuppevelt TH, Yurchenco PD, Palsson BO, 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 01 10; 8(1). PMID: 28074024.
      View in: PubMed
    80. King ZA, O'Brien EJ, Feist AM, Palsson BO. Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion. Metab Eng. 2017 01; 39:220-227. PMID: 27986597.
      View in: PubMed
    81. Broddrick JT, Rubin BE, Welkie DG, Du N, Mih N, Diamond S, Lee JJ, Golden SS, Palsson BO. Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis. Proc Natl Acad Sci U S A. 2016 12 20; 113(51):E8344-E8353. PMID: 27911809.
      View in: PubMed
    82. 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 BO, Andersen MR, Nielsen LK, Borth N, Lee DY, Lewis NE. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Syst. 2016 11 23; 3(5):434-443.e8. PMID: 27883890.
      View in: PubMed
    83. Yang L, Yurkovich JT, Lloyd CJ, Ebrahim A, Saunders MA, Palsson BO. Principles of proteome allocation are revealed using proteomic data and genome-scale models. Sci Rep. 2016 11 18; 6:36734. PMID: 27857205.
      View in: PubMed
    84. D'Alessandro A, Nemkov T, Yoshida T, Bordbar A, Palsson BO, Hansen KC. Citrate metabolism in red blood cells stored in additive solution-3. Transfusion. 2017 02; 57(2):325-336. PMID: 27813142.
      View in: PubMed
    85. Aziz RK, Monk JM, Andrews KA, Nhan J, Khaw VL, Wong H, Palsson BO, 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.
      View in: PubMed
    86. Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM, Palsson BO. Multi-omic data integration enables discovery of hidden biological regularities. Nat Commun. 2016 10 26; 7:13091. PMID: 27782110.
      View in: PubMed
    87. Yang L, Ma D, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO. solveME: fast and reliable solution of nonlinear ME models. BMC Bioinformatics. 2016 Sep 22; 17(1):391. PMID: 27659412.
      View in: PubMed
    88. Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ, Feist AM. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Syst. 2016 09 28; 3(3):238-251.e12. PMID: 27667363.
      View in: PubMed
    89. Paglia G, D'Alessandro A, Rolfsson Ó, Sigurjónsson ÓE, Bordbar A, Palsson S, Nemkov T, Hansen KC, Gudmundsson S, Palsson BO. Biomarkers defining the metabolic age of red blood cells during cold storage. Blood. 2016 09 29; 128(13):e43-50. PMID: 27554084.
      View in: PubMed
    90. Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 2016 08 09; 34(8):828-837. PMID: 27504778.
      View in: PubMed
    91. Paglia G, Sigurjónsson ÓE, Bordbar A, Rolfsson Ó, Magnusdottir M, Palsson S, Wichuk K, Gudmundsson S, Palsson BO. Metabolic fate of adenine in red blood cells during storage in SAGM solution. Transfusion. 2016 Oct; 56(10):2538-2547. PMID: 27491795.
      View in: PubMed
    92. Mih N, Brunk E, Bordbar A, Palsson BO. A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PLoS Comput Biol. 2016 07; 12(7):e1005039. PMID: 27467583.
      View in: PubMed
    93. O'Brien EJ, Utrilla J, Palsson BO. Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. PLoS Comput Biol. 2016 06; 12(6):e1004998. PMID: 27351952.
      View in: PubMed
    94. Du B, Zielinski DC, Kavvas ES, Dräger A, Tan J, Zhang Z, Ruggiero KE, Arzumanyan GA, Palsson BO. Evaluation of rate law approximations in bottom-up kinetic models of metabolism. BMC Syst Biol. 2016 06 06; 10(1):40. PMID: 27266508.
      View in: PubMed
    95. Feist AM, Palsson BO. What do cells actually want? Genome Biol. 2016 05 23; 17(1):110. PMID: 27215675.
      View in: PubMed
    96. Brunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L, O'Brien EJ, Batth TS, Martin HG, Feist A, Adams PD, Keasling JD, Palsson BO, Lee TS. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Syst. 2016 05 25; 2(5):335-46. PMID: 27211860.
      View in: PubMed
    97. Levering J, Broddrick J, Dupont CL, Peers G, Beeri K, Mayers J, Gallina AA, Allen AE, Palsson BO, Zengler K. Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. PLoS One. 2016; 11(5):e0155038. PMID: 27152931.
      View in: PubMed
    98. Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO. Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. Cell Syst. 2016 04 27; 2(4):260-71. PMID: 27135538.
      View in: PubMed
    99. McCloskey D, Young JD, Xu S, Palsson BO, Feist AM. Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale. Anal Chem. 2016 Apr 05; 88(7):3844-52. PMID: 26981784.
      View in: PubMed
    100. Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO. Systems biology of the structural proteome. BMC Syst Biol. 2016 Mar 11; 10:26. PMID: 26969117.
      View in: PubMed
    101. Sandberg TE, Long CP, Gonzalez JE, Feist AM, Antoniewicz MR, Palsson BO. 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.
      View in: PubMed
    102. Golabgir A, Gutierrez JM, Hefzi H, Li S, Palsson BO, 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):621-633. PMID: 26948029.
      View in: PubMed
    103. 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 BO. 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.
      View in: PubMed
    104. McCloskey D, Young JD, Xu S, Palsson BO, 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.
      View in: PubMed
    105. 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 BO, Charusanti P. Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations. Sci Rep. 2015 Nov 04; 5:16025. PMID: 26531810.
      View in: PubMed
    106. Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson BO. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Syst. 2015 Oct 28; 1(4):283-92. PMID: 27136057.
      View in: PubMed
    107. King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res. 2016 Jan 04; 44(D1):D515-22. PMID: 26476456.
      View in: PubMed
    108. 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 BO, 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 Oct 14; 11(10):831. PMID: 26467284.
      View in: PubMed
    109. Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. BMC Syst Biol. 2015 Oct 09; 9:68. PMID: 26452770.
      View in: PubMed
    110. King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO. 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.
      View in: PubMed
    111. Seo SW, Kim D, Szubin R, Palsson BO. 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.
      View in: PubMed
    112. 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 BO. 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.
      View in: PubMed
    113. Seo SW, Kim D, O'Brien EJ, Szubin R, Palsson BO. Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli. Nat Commun. 2015 Aug 10; 6:7970. PMID: 26258987.
      View in: PubMed
    114. Zielinski DC, Filipp FV, Bordbar A, Jensen K, Smith JW, Herrgard MJ, Mo ML, Palsson BO. Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis. Nat Commun. 2015 Jun 09; 6:7101. PMID: 26055627.
      View in: PubMed
    115. Latif H, Szubin R, Tan J, Brunk E, Lechner A, Zengler K, Palsson BO. A streamlined ribosome profiling protocol for the characterization of microorganisms. Biotechniques. 2015 Jun; 58(6):329-32. PMID: 26054770.
      View in: PubMed
    116. O'Brien EJ, Monk JM, Palsson BO. Using Genome-scale Models to Predict Biological Capabilities. Cell. 2015 May 21; 161(5):971-987. PMID: 26000478.
      View in: PubMed
    117. Rolfsson Ó, Palsson BO. Decoding the jargon of bottom-up metabolic systems biology. Bioessays. 2015 Jun; 37(6):588-91. PMID: 25761171.
      View in: PubMed
    118. Pacini T, Fu W, Gudmundsson S, Chiaravalle AE, Brynjolfson S, Palsson BO, Astarita G, Paglia G. Multidimensional analytical approach based on UHPLC-UV-ion mobility-MS for the screening of natural pigments. Anal Chem. 2015 Mar 03; 87(5):2593-9. PMID: 25647265.
      View in: PubMed
    119. O'Brien EJ, Palsson BO. Computing the functional proteome: recent progress and future prospects for genome-scale models. Curr Opin Biotechnol. 2015 Aug; 34:125-34. PMID: 25576845.
      View in: PubMed
    120. King ZA, Lloyd CJ, Feist AM, Palsson BO. Next-generation genome-scale models for metabolic engineering. Curr Opin Biotechnol. 2015 Dec; 35:23-9. PMID: 25575024.
      View in: PubMed
    121. Guzmán GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson BO, 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.
      View in: PubMed
    122. 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 BO, 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.
      View in: PubMed
    123. LaCroix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, Szubin R, Palsson BO, 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; 81(1):17-30. PMID: 25304508.
      View in: PubMed
    124. Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson BO, Feist AM. Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. BMC Syst Biol. 2014 Sep 18; 8:110. PMID: 25227965.
      View in: PubMed
    125. Nam H, Campodonico M, Bordbar A, Hyduke DR, Kim S, Zielinski DC, Palsson BO. A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks. PLoS Comput Biol. 2014 Sep; 10(9):e1003837. PMID: 25232952.
      View in: PubMed
    126. Seo SW, Kim D, Latif H, O'Brien EJ, Szubin R, Palsson BO. Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. Nat Commun. 2014 Sep 15; 5:4910. PMID: 25222563.
      View in: PubMed
    127. Paglia G, Sigurjónsson ÓE, Rolfsson Ó, Hansen MB, Brynjólfsson S, Gudmundsson S, Palsson BO. 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.
      View in: PubMed
    128. Campodonico MA, Andrews BA, Asenjo JA, Palsson BO, 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.
      View in: PubMed
    129. Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson BO, 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.
      View in: PubMed
    130. Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Mol Syst Biol. 2014 Jul 01; 10:737. PMID: 24987116.
      View in: PubMed
    131. Monk J, Palsson BO. Genetics. Predicting microbial growth. Science. 2014 Jun 27; 344(6191):1448-9. PMID: 24970063.
      View in: PubMed
    132. Rohatgi N, Nielsen TK, Bjørn SP, Axelsson I, Paglia G, Voldborg BG, Palsson BO, Rolfsson Ó. 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.
      View in: PubMed
    133. Paglia G, Sigurjónsson ÓE, Rolfsson Ó, Valgeirsdottir S, Hansen MB, Brynjólfsson S, Gudmundsson S, Palsson BO. Comprehensive metabolomic study of platelets reveals the expression of discrete metabolic phenotypes during storage. Transfusion. 2014 Nov; 54(11):2911-23. PMID: 24840017.
      View in: PubMed
    134. Monk J, Nogales J, Palsson BO. Optimizing genome-scale network reconstructions. Nat Biotechnol. 2014 May; 32(5):447-52. PMID: 24811519.
      View in: PubMed
    135. Paglia G, Williams JP, Menikarachchi L, Thompson JW, Tyldesley-Worster R, Halldórsson S, Rolfsson O, Moseley A, Grant D, Langridge J, Palsson BO, Astarita G. Ion mobility derived collision cross sections to support metabolomics applications. Anal Chem. 2014 Apr 15; 86(8):3985-93. PMID: 24640936.
      View in: PubMed
    136. Cho BK, Kim D, Knight EM, Zengler K, Palsson BO. Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states. BMC Biol. 2014 Jan 24; 12:4. PMID: 24461193.
      View in: PubMed
    137. Bordbar A, Monk JM, King ZA, Palsson BO. Constraint-based models predict metabolic and associated cellular functions. Nat Rev Genet. 2014 Feb; 15(2):107-20. PMID: 24430943.
      View in: PubMed
    138. Huang TW, Lam I, Chang HY, Tsai SF, Palsson BO, Charusanti P. Capsule deletion via a ?-Red knockout system perturbs biofilm formation and fimbriae expression in Klebsiella pneumoniae MGH 78578. BMC Res Notes. 2014 Jan 08; 7:13. PMID: 24398052.
      View in: PubMed
    139. Cheng KK, Lee BS, Masuda T, Ito T, Ikeda K, Hirayama A, Deng L, Dong J, Shimizu K, Soga T, Tomita M, Palsson BO, Robert M. Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol. Nat Commun. 2014; 5:3233. PMID: 24481126.
      View in: PubMed
    140. McCloskey D, Gangoiti JA, King ZA, Naviaux RK, Barshop BA, Palsson BO, 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.
      View in: PubMed
    141. Chang RL, Xie L, Bourne PE, Palsson BO. Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst Biol. 2013 Oct 10; 7:102. PMID: 24112686.
      View in: PubMed
    142. Palsson S, Hickling TP, Bradshaw-Pierce EL, Zager M, Jooss K, O'Brien PJ, Spilker ME, Palsson BO, 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 Sep 28; 7:95. PMID: 24074340.
      View in: PubMed
    143. Ebrahim A, Lerman JA, Palsson BO, Hyduke DR. COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst Biol. 2013 Aug 08; 7:74. PMID: 23927696.
      View in: PubMed
    144. Wu W, Jamshidi N, Eraly SA, Liu HC, Bush KT, Palsson BO, Nigam SK. Multispecific drug transporter Slc22a8 (Oat3) regulates multiple metabolic and signaling pathways. Drug Metab Dispos. 2013 Oct; 41(10):1825-34. PMID: 23920220.
      View in: PubMed
    145. 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 BO. 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.
      View in: PubMed
    146. Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO. Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. Science. 2013 Jun 07; 340(6137):1220-3. PMID: 23744946.
      View in: PubMed
    147. Kim YM, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson BO, 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.
      View in: PubMed
    148. Fong NL, Lerman JA, Lam I, Palsson BO, 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.
      View in: PubMed
    149. Qiu Y, Nagarajan H, Embree M, Shieu W, Abate E, Juárez K, Cho BK, Elkins JG, Nevin KP, Barrett CL, Lovley DR, Palsson BO, Zengler K. Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks. Nat Commun. 2013; 4:1755. PMID: 23612296.
      View in: PubMed
    150. 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 BO, 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.
      View in: PubMed
    151. Seo JH, Hong JS, Kim D, Cho BK, Huang TW, Tsai SF, Palsson BO, Charusanti P. Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features. BMC Genomics. 2012 Nov 29; 13:679. PMID: 23194155.
      View in: PubMed
    152. Fu W, Guðmundsson O, Paglia G, Herjólfsson G, Andrésson OS, Palsson BO, 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.
      View in: PubMed
    153. 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 BO, Zhang H, Betenbaugh M. Proteomic analysis of Chinese hamster ovary cells. J Proteome Res. 2012 Nov 02; 11(11):5265-76. PMID: 22971049.
      View in: PubMed
    154. Thiele I, Fleming RM, Que R, Bordbar A, Diep D, Palsson BO. 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.
      View in: PubMed
    155. Nam H, Lewis NE, Lerman JA, Lee DH, Chang RL, Kim D, Palsson BO. Network context and selection in the evolution to enzyme specificity. Science. 2012 Aug 31; 337(6098):1101-4. PMID: 22936779.
      View in: PubMed
    156. Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun. 2012 Jul 03; 3:929. PMID: 22760628.
      View in: PubMed
    157. 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 BO. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol Syst Biol. 2012 Jun 26; 8:558. PMID: 22735334.
      View in: PubMed
    158. Orth JD, Palsson B. Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. BMC Syst Biol. 2012 May 01; 6:30. PMID: 22548736.
      View in: PubMed
    159. Zengler K, Palsson BO. A road map for the development of community systems (CoSy) biology. Nat Rev Microbiol. 2012 03 27; 10(5):366-72. PMID: 22450377.
      View in: PubMed
    160. Charusanti P, Fong NL, Nagarajan H, Pereira AR, Li HJ, Abate EA, Su Y, Gerwick WH, Palsson BO. Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction. PLoS One. 2012; 7(3):e33727. PMID: 22470465.
      View in: PubMed
    161. Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol. 2012 Feb 27; 10(4):291-305. PMID: 22367118.
      View in: PubMed
    162. Bordbar A, Palsson BO. Using the reconstructed genome-scale human metabolic network to study physiology and pathology. J Intern Med. 2012 Feb; 271(2):131-41. PMID: 22142339.
      View in: PubMed
    163. Nogales J, Gudmundsson S, Knight EM, Palsson BO, 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.
      View in: PubMed
    164. Bordbar A, Feist AM, Usaite-Black R, Woodcock J, Palsson BO, Famili I. A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst Biol. 2011 Oct 31; 5:180. PMID: 22041191.
      View in: PubMed
    165. Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson BO. An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. BMC Syst Biol. 2011 Oct 13; 5:163. PMID: 21995956.
      View in: PubMed
    166. 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 BO, Wang J. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nat Biotechnol. 2011 Jul 31; 29(8):735-41. PMID: 21804562.
      View in: PubMed
    167. Bordbar A, Jamshidi N, Palsson BO. 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 Jul 12; 5:110. PMID: 21749716.
      View in: PubMed
    168. McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F. Technologies and approaches to elucidate and model the virulence program of salmonella. Front Microbiol. 2011; 2:121. PMID: 21687430.
      View in: PubMed
    169. Liao YC, Huang TW, Chen FC, Charusanti P, Hong JS, Chang HY, Tsai SF, Palsson BO, 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.
      View in: PubMed
    170. 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 BO, 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 Jan 18; 5:8. PMID: 21244678.
      View in: PubMed
    171. Tremblay PL, Summers ZM, Glaven RH, Nevin KP, Zengler K, Barrett CL, Qiu Y, Palsson BO, 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.
      View in: PubMed
    172. Lerman J, Palsson BO. Microbiology. Topping off a multiscale balancing act. Science. 2010 Nov 19; 330(6007):1058-9. PMID: 21097927.
      View in: PubMed
    173. Barrett CL, Cho BK, Palsson BO. 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.
      View in: PubMed
    174. Feist AM, Palsson BO. The biomass objective function. Curr Opin Microbiol. 2010 Jun; 13(3):344-9. PMID: 20430689.
      View in: PubMed
    175. Jamshidi N, Palsson BO. Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes. BMC Syst Biol. 2009 Apr 30; 3:44. PMID: 19405968.
      View in: PubMed
    176. Lewis NE, Cho BK, Knight EM, Palsson BO. 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.
      View in: PubMed
    177. Mo ML, Palsson BO, Herrgård MJ. Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst Biol. 2009 Mar 25; 3:37. PMID: 19321003.
      View in: PubMed
    178. Sigurdsson MI, Jamshidi N, Jonsson JJ, Palsson BO. Genome-scale network analysis of imprinted human metabolic genes. Epigenetics. 2009 Jan; 4(1):43-6. PMID: 19218833.
      View in: PubMed
    179. Becker SA, Palsson BO. Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol. 2008 May 16; 4(5):e1000082. PMID: 18483554.
      View in: PubMed
    180. Becker SA, Palsson BO. Three factors underlying incorrect in silico predictions of essential metabolic genes. BMC Syst Biol. 2008 Feb 04; 2:14. PMID: 18248675.
      View in: PubMed
    181. Cho BK, Charusanti P, Herrgård MJ, Palsson BO. Microbial regulatory and metabolic networks. Curr Opin Biotechnol. 2007 Aug; 18(4):360-4. PMID: 17719767.
      View in: PubMed
    182. Oh YK, Palsson BO, 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.
      View in: PubMed
    183. Anderson MJ, DeLabarre B, Raghunathan A, Palsson BO, 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.
      View in: PubMed
    184. Vo TD, Paul Lee WN, Palsson BO. 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.
      View in: PubMed
    185. Jamshidi N, Vo TD, Palsson BO. In silico analysis of SNPs and other high-throughput data. Methods Mol Biol. 2007; 366:267-85. PMID: 17568130.
      View in: PubMed
    186. Joyce AR, Palsson BO. Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach. Prog Drug Res. 2007; 64:265, 267-309. PMID: 17195479.
      View in: PubMed
    187. Vo TD, Palsson BO. Isotopomer analysis of myocardial substrate metabolism: a systems biology approach. Biotechnol Bioeng. 2006 Dec 05; 95(5):972-83. PMID: 16878330.
      View in: PubMed
    188. Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO. Systems approach to refining genome annotation. Proc Natl Acad Sci U S A. 2006 Nov 14; 103(46):17480-4. PMID: 17088549.
      View in: PubMed
    189. Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO. Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput Biol. 2006 Aug 11; 2(8):e101. PMID: 16895435.
      View in: PubMed
    190. Vo TD, Palsson BO. 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.
      View in: PubMed
    191. Barrett CL, Palsson BO. Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PLoS Comput Biol. 2006 May; 2(5):e52. PMID: 16710450.
      View in: PubMed
    192. Barrett CL, Price ND, Palsson BO. Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition. BMC Bioinformatics. 2006 Mar 13; 7:132. PMID: 16533395.
      View in: PubMed
    193. Reed JL, Famili I, Thiele I, Palsson BO. Towards multidimensional genome annotation. Nat Rev Genet. 2006 Feb; 7(2):130-41. PMID: 16418748.
      View in: PubMed
    194. Mahadevan R, Bond DR, Butler JE, Esteve-Nuñez A, Coppi MV, Palsson BO, 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.
      View in: PubMed
    195. Cho BK, Knight EM, Palsson BO. PCR-based tandem epitope tagging system for Escherichia coli genome engineering. Biotechniques. 2006 Jan; 40(1):67-72. PMID: 16454042.
      View in: PubMed
    196. Barrett CL, Herring CD, Reed JL, Palsson BO. 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.
      View in: PubMed
    197. Fong SS, Nanchen A, Palsson BO, 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.
      View in: PubMed
    198. Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BO. In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng. 2005 Sep 05; 91(5):643-8. PMID: 15962337.
      View in: PubMed
    199. Papin JA, Hunter T, Palsson BO, 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.
      View in: PubMed
    200. Famili I, Mahadevan R, Palsson BO. k-Cone analysis: determining all candidate values for kinetic parameters on a network scale. Biophys J. 2005 Mar; 88(3):1616-25. PMID: 15626710.
      View in: PubMed
    201. Mahadevan R, Palsson BO. Properties of metabolic networks: structure versus function. Biophys J. 2005 Jan; 88(1):L07-9. PMID: 15574705.
      View in: PubMed
    202. Papin JA, Reed JL, Palsson BO. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends Biochem Sci. 2004 Dec; 29(12):641-7. PMID: 15544950.
      View in: PubMed
    203. Price ND, Schellenberger J, Palsson BO. 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.
      View in: PubMed
    204. Westerhoff HV, Palsson BO. The evolution of molecular biology into systems biology. Nat Biotechnol. 2004 Oct; 22(10):1249-52. PMID: 15470464.
      View in: PubMed
    205. Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO. Comparison of network-based pathway analysis methods. Trends Biotechnol. 2004 Aug; 22(8):400-5. PMID: 15283984.
      View in: PubMed
    206. Papin JA, Palsson BO. 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.
      View in: PubMed
    207. Vo TD, Greenberg HJ, Palsson BO. 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.
      View in: PubMed
    208. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004 May 06; 429(6987):92-6. PMID: 15129285.
      View in: PubMed
    209. Papin JA, Palsson BO. 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.
      View in: PubMed
    210. 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 BO, 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.
      View in: PubMed
    211. Covert MW, Famili I, Palsson BO. 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.
      View in: PubMed
    212. Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BO. Network-based analysis of metabolic regulation in the human red blood cell. J Theor Biol. 2003 Nov 21; 225(2):185-94. PMID: 14575652.
      View in: PubMed
    213. Famili I, Forster J, Nielsen J, Palsson BO. 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.
      View in: PubMed
    214. Famili I, Palsson BO. Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices. J Theor Biol. 2003 Sep 07; 224(1):87-96. PMID: 12900206.
      View in: PubMed
    215. Reed JL, Vo TD, Schilling CH, Palsson BO. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 2003; 4(9):R54. PMID: 12952533.
      View in: PubMed
    216. 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 BO, Smith AL. Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol. 2003 Aug; 185(15):4593-602. PMID: 12867470.
      View in: PubMed
    217. Famili I, Palsson BO. 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.
      View in: PubMed
    218. Palsson BO, 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.
      View in: PubMed
    219. Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO. Metabolic pathways in the post-genome era. Trends Biochem Sci. 2003 May; 28(5):250-8. PMID: 12765837.
      View in: PubMed
    220. Covert MW, Palsson BO. Constraints-based models: regulation of gene expression reduces the steady-state solution space. J Theor Biol. 2003 Apr 07; 221(3):309-25. PMID: 12642111.
      View in: PubMed
    221. Price ND, Papin JA, Schilling CH, Palsson BO. Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol. 2003 Apr; 21(4):162-9. PMID: 12679064.
      View in: PubMed
    222. Raghunathan A, Palsson BO. Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli. Biotechnol Lett. 2003 Mar; 25(5):435-41. PMID: 12882568.
      View in: PubMed
    223. Price ND, Reed JL, Papin JA, Famili I, Palsson BO. Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophys J. 2003 Feb; 84(2 Pt 1):794-804. PMID: 12547764.
      View in: PubMed
    224. Förster J, Famili I, Palsson BO, Nielsen J. Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS. 2003; 7(2):193-202. PMID: 14506848.
      View in: PubMed
    225. Ibarra RU, Fu P, Palsson BO, 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.
      View in: PubMed
    226. Ibarra RU, Edwards JS, Palsson BO. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature. 2002 Nov 14; 420(6912):186-9. PMID: 12432395.
      View in: PubMed
    227. Kauffman KJ, Pajerowski JD, Jamshidi N, Palsson BO, 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.
      View in: PubMed
    228. Wiback SJ, Palsson BO. Extreme pathway analysis of human red blood cell metabolism. Biophys J. 2002 Aug; 83(2):808-18. PMID: 12124266.
      View in: PubMed
    229. Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO. Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol. 2002 Aug; 184(16):4582-93. PMID: 12142428.
      View in: PubMed
    230. Lee GM, Fong SS, Oh DJ, Francis K, Palsson BO. 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.
      View in: PubMed
    231. Edwards JS, Ramakrishna R, Palsson BO. Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol Bioeng. 2002 Jan 05; 77(1):27-36. PMID: 11745171.
      View in: PubMed
    232. Kolker E, Purvine S, Picone A, Cherny T, Akerley BJ, Munson RS, Palsson BO, Daines DA, Smith AL. H. influenzae Consortium: integrative study of H. influenzae-human interactions. OMICS. 2002; 6(4):341-8. PMID: 12626093.
      View in: PubMed
    233. Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson BO. Dynamic simulation of the human red blood cell metabolic network. Bioinformatics. 2001 Mar; 17(3):286-7. PMID: 11294796.
      View in: PubMed
    234. Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO. Metabolic modeling of microbial strains in silico. Trends Biochem Sci. 2001 Mar; 26(3):179-86. PMID: 11246024.
      View in: PubMed
    235. Ramakrishna R, Edwards JS, McCulloch A, Palsson BO. 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.
      View in: PubMed
    236. Edwards JS, Ibarra RU, Palsson BO. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol. 2001 Feb; 19(2):125-30. PMID: 11175725.
      View in: PubMed
    237. Edwards JS, Palsson BO. Multiple steady states in kinetic models of red cell metabolism. J Theor Biol. 2000 Nov 07; 207(1):125-7. PMID: 11027485.
      View in: PubMed
    238. Edwards JS, Palsson BO. Robustness analysis of the Escherichia coli metabolic network. Biotechnol Prog. 2000 Nov-Dec; 16(6):927-39. PMID: 11101318.
      View in: PubMed
    239. Edwards JS, Palsson BO. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics. 2000; 1:1. PMID: 11001586.
      View in: PubMed
    240. Oh DJ, Martinez AR, Lee GM, Francis K, Palsson BO. Extension of osmolality-induced podia is observed from fluorescently labeled hematopoietic cell lines in hyperosmotic medium. Cytometry. 2000 Jun 01; 40(2):109-18. PMID: 10805930.
      View in: PubMed
    241. Oh DJ, Martinez AR, Lee GM, Francis K, Palsson BO. 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 01; 40(2):119-25. PMID: 10805931.
      View in: PubMed
    242. Edwards JS, Palsson BO. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci U S A. 2000 May 09; 97(10):5528-33. PMID: 10805808.
      View in: PubMed
    243. Schilling CH, Letscher D, Palsson BO. 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 07; 203(3):229-48. PMID: 10716907.
      View in: PubMed
    244. Schilling CH, Palsson BO. Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J Theor Biol. 2000 Apr 07; 203(3):249-83. PMID: 10716908.
      View in: PubMed
    245. Lee GM, Fong S, Francis K, Oh DJ, Palsson BO. In situ labeling of adherent cells with PKH26. In Vitro Cell Dev Biol Anim. 2000 Jan; 36(1):4-6. PMID: 10691033.
      View in: PubMed
    246. Holloway W, Martinez AR, Oh DJ, Francis K, Ramakrishna R, Palsson BO. Key adhesion molecules are present on long podia extended by hematopoietic cells. Cytometry. 1999 Nov 01; 37(3):171-7. PMID: 10520196.
      View in: PubMed
    247. Huang S, Law P, Francis K, Palsson BO, 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.
      View in: PubMed
    248. Oh DJ, Lee GM, Francis K, Palsson BO. Phototoxicity of the fluorescent membrane dyes PKH2 and PKH26 on the human hematopoietic KG1a progenitor cell line. Cytometry. 1999 Aug 01; 36(4):312-8. PMID: 10404146.
      View in: PubMed
    249. Edwards JS, Palsson BO. Systems properties of the Haemophilus influenzae Rd metabolic genotype. J Biol Chem. 1999 Jun 18; 274(25):17410-6. PMID: 10364169.
      View in: PubMed
    250. Schilling CH, Edwards JS, Palsson BO. Toward metabolic phenomics: analysis of genomic data using flux balances. Biotechnol Prog. 1999 May-Jun; 15(3):288-95. PMID: 10356245.
      View in: PubMed
    251. Schilling CH, Schuster S, Palsson BO, 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.
      View in: PubMed
    252. Francis K, Ramakrishna R, Holloway W, Palsson BO. 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.
      View in: PubMed
    253. Mandalam RK, Palsson BO. Elemental balancing of biomass and medium composition enhances growth capacity in high-density Chlorella vulgaris cultures. Biotechnol Bioeng. 1998 Sep 05; 59(5):605-11. PMID: 10099378.
      View in: PubMed
    254. Schilling CH, Palsson BO. The underlying pathway structure of biochemical reaction networks. Proc Natl Acad Sci U S A. 1998 Apr 14; 95(8):4193-8. PMID: 9539712.
      View in: PubMed
    255. Edwards JS, Palsson BO. How will bioinformatics influence metabolic engineering? Biotechnol Bioeng. 1998 Apr 20-May 5; 58(2-3):162-9. PMID: 10191386.
      View in: PubMed
    256. Andreadis S, Fuller AO, Palsson BO. 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.
      View in: PubMed
    257. Francis K, Palsson BO. 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.
      View in: PubMed
    258. Koller MR, Manchel I, Palsson BO. Importance of parenchymal:stromal cell ratio for the ex vivo reconstitution of human hematopoiesis. Stem Cells. 1997; 15(4):305-13. PMID: 9253115.
      View in: PubMed
    259. Palsson BO. What lies beyond bioinformatics? Nat Biotechnol. 1997 Jan; 15(1):3-4. PMID: 9035092.
      View in: PubMed
    260. Koller MR, Oxender M, Brott DA, Palsson BO. 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.
      View in: PubMed
    261. Andreadis ST, Palsson BO. Kinetics of retrovirus mediated gene transfer: the importance of intracellular half-life of retroviruses. J Theor Biol. 1996 Sep 07; 182(1):1-20. PMID: 8917734.
      View in: PubMed
    262. Peng CA, Palsson BO. 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.
      View in: PubMed
    263. Rogers CE, Bradley MS, Palsson BO, 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.
      View in: PubMed
    264. Eipers PG, Krauss JC, Palsson BO, 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.
      View in: PubMed
    265. Koller MR, Palsson MA, Manchel I, Palsson BO. Long-term culture-initiating cell expansion is dependent on frequent medium exchange combined with stromal and other accessory cell effects. Blood. 1995 Sep 01; 86(5):1784-93. PMID: 7544642.
      View in: PubMed
    266. Koller MR, Manchel I, Newsom BS, Palsson MA, Palsson BO. 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.
      View in: PubMed
    267. Varma A, Palsson BO. Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism. Biotechnol Bioeng. 1995 Jan 05; 45(1):69-79. PMID: 18623053.
      View in: PubMed
    268. Emerson SG, Palsson BO, 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.
      View in: PubMed
    269. Palsson BO, 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.
      View in: PubMed
    270. Varma A, Palsson BO. 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.
      View in: PubMed
    271. Oh DJ, Koller MR, Palsson BO. 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.
      View in: PubMed
    272. Levee MG, Lee GM, Paek SH, Palsson BO. Microencapsulated human bone marrow cultures: a potential culture system for the clonal outgrowth of hematopoietic progenitor cells. Biotechnol Bioeng. 1994 Apr 05; 43(8):734-9. PMID: 18615796.
      View in: PubMed
    273. Hubbell JA, Palsson BO, Papoutsakis ET. Preface: Tissue engineering and cell therapies: II. Biotechnol Bioeng. 1994 Apr 05; 43(8):683. PMID: 18615791.
      View in: PubMed
    274. Hubbell JA, Palsson BO, Papoutsakis ET. Preface. Tissue engineering and cell therapies. Biotechnol Bioeng. 1994 Mar 25; 43(7):541. PMID: 18615753.
      View in: PubMed
    275. Varma A, Palsson BO. Predictions for oxygen supply control to enhance population stability of engineered production strains. Biotechnol Bioeng. 1994 Feb 20; 43(4):275-85. PMID: 18615690.
      View in: PubMed
    276. Lee GM, Palsson BO. Monoclonal antibody production using free-suspended and entrapped hybridoma cells. Biotechnol Genet Eng Rev. 1994; 12:509-33. PMID: 7727036.
      View in: PubMed
    277. Lee GM, Kim SJ, Palsson BO. Enhanced specific antibody productivity of calcium alginate-entrapped hybridoma is cell line-specific. Cytotechnology. 1994; 16(1):1-15. PMID: 7765785.
      View in: PubMed
    278. Varma A, Palsson BO. Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors. J Theor Biol. 1993 Dec 21; 165(4):477-502. PMID: 21322280.
      View in: PubMed
    279. Lee GM, Palsson BO. Stability of antibody productivity is improved when hybridoma cells are entrapped in calcium alginate beads. Biotechnol Bioeng. 1993 Nov 05; 42(9):1131-5. PMID: 18613244.
      View in: PubMed
    280. Koller MR, Palsson BO. Review: tissue engineering: reconstitution of human hematopoiesis ex vivo. Biotechnol Bioeng. 1993 Oct; 42(8):909-30. PMID: 18613140.
      View in: PubMed
    281. Varma A, Boesch BW, Palsson BO. Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl Environ Microbiol. 1993 Aug; 59(8):2465-73. PMID: 8368835.
      View in: PubMed
    282. Koller MR, Emerson SG, Palsson BO. 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.
      View in: PubMed
    283. Merritt SE, Palsson BO. Loss of antibody productivity is highly reproducible in multiple hybridoma subclones. Biotechnol Bioeng. 1993 Jun 20; 42(2):247-50. PMID: 18612986.
      View in: PubMed
    284. Varma A, Boesch BW, Palsson BO. Biochemical production capabilities of Escherichia coli. Biotechnol Bioeng. 1993 Jun 05; 42(1):59-73. PMID: 18609648.
      View in: PubMed
    285. Meyerhoff ME, Trojanowicz M, Palsson BO. 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.
      View in: PubMed
    286. Palsson BO, Lee ID. Model complexity has a significant effect on the numerical value and interpretation of metabolic sensitivity coefficients. J Theor Biol. 1993 Apr 07; 161(3):299-315. PMID: 8331956.
      View in: PubMed
    287. Palsson BO, 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.
      View in: PubMed
    288. Lee GM, Chuck AS, Palsson BO. Cell Culture conditions determine the enhancement of specific monoclonal antibody productivity of calcium alginate-entrapped S3H5/gamma2bA2 hybridoma cells. Biotechnol Bioeng. 1993 Feb 05; 41(3):330-40. PMID: 18609557.
      View in: PubMed
    289. Lee ID, Palsson BO. A Macintosh software package for simulation of human red blood cell metabolism. Comput Methods Programs Biomed. 1992 Aug; 38(4):195-226. PMID: 1473341.
      View in: PubMed
    290. Keasling JD, Palsson BO, Cooper S. Replication of mini-F plasmids during the bacterial division cycle. Res Microbiol. 1992 Jul-Aug; 143(6):541-8. PMID: 1475515.
      View in: PubMed
    291. Keasling JD, Palsson BO, Cooper S. Replication of prophage P1 is cell-cycle specific. J Bacteriol. 1992 Jul; 174(13):4457-62. PMID: 1624438.
      View in: PubMed
    292. Savinell JM, Palsson BO. 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.
      View in: PubMed
    293. Savinell JM, Palsson BO. 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.
      View in: PubMed
    294. Javanmardian M, Palsson BO. Continuous photoautotrophic cultures of the eukaryotic alga Chlorella vulgaris can exhibit stable oscillatory dynamics. Biotechnol Bioeng. 1992 Mar 05; 39(5):487-97. PMID: 18600974.
      View in: PubMed
    295. Savinell JM, Palsson BO. 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.
      View in: PubMed
    296. Savinell JM, Palsson BO. 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.
      View in: PubMed
    297. Ozturk SS, Riley MR, Palsson BO. Effects of ammonia and lactate on hybridoma growth, metabolism, and antibody production. Biotechnol Bioeng. 1992 Feb 20; 39(4):418-31. PMID: 18600963.
      View in: PubMed
    298. Chuck AS, Palsson BO. Population balance between producing and nonproducing hybridoma clones is very sensitive to serum level, state of inoculum, and medium composition. Biotechnol Bioeng. 1992 Feb 05; 39(3):354-60. PMID: 18600953.
      View in: PubMed
    299. Keasling JD, Palsson BO, Cooper S. Replication of the R6K plasmid during the Escherichia coli cell cycle. J Bacteriol. 1992 Feb; 174(3):1060-2. PMID: 1732198.
      View in: PubMed
    300. Varma A, el-Awar FY, Palsson BO, Emerson SG, Clarke MF. Can Dexter cultures support stem cell proliferation? Exp Hematol. 1992 Jan; 20(1):87-91. PMID: 1577098.
      View in: PubMed
    301. Schwartz RM, Emerson SG, Clarke MF, Palsson BO. In vitro myelopoiesis stimulated by rapid medium exchange and supplementation with hematopoietic growth factors. Blood. 1991 Dec 15; 78(12):3155-61. PMID: 1742483.
      View in: PubMed
    302. Javanmardian M, Palsson BO. High-density photoautotrophic algal cultures: design, construction, and operation of a novel photobioreactor system. Biotechnol Bioeng. 1991 Dec 05; 38(10):1182-9. PMID: 18600714.
      View in: PubMed
    303. Ozturk SS, Palsson BO. 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.
      View in: PubMed
    304. Ozturk SS, Palsson BO. 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.
      View in: PubMed
    305. Lee GM, Varma A, Palsson BO. 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.
      View in: PubMed
    306. Schwartz RM, Palsson BO, 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 01; 88(15):6760-4. PMID: 1862099.
      View in: PubMed
    307. Caldwell J, Palsson BO, 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.
      View in: PubMed
    308. Ozturk SS, Palsson BO. Effect of medium osmolarity on hybridoma growth, metabolism, and antibody production. Biotechnol Bioeng. 1991 Apr 25; 37(10):989-93. PMID: 18597326.
      View in: PubMed
    309. Keasling JD, Palsson BO, 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.
      View in: PubMed
    310. Ozturk SS, Palsson BO. Physiological changes during the adaptation of hybridoma cells to low serum and serum-free media. Biotechnol Bioeng. 1991 Jan 05; 37(1):35-46. PMID: 18597305.
      View in: PubMed
    311. Lee GM, Varma A, Palsson BO. Application of population balance model to the loss of hybridoma antibody productivity. Biotechnol Prog. 1991 Jan-Feb; 7(1):72-5. PMID: 1366981.
      View in: PubMed
    312. Caldwell J, Locey B, Clarke MF, Emerson SG, Palsson BO. 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.
      View in: PubMed
    313. Lee GM, Palsson BO. Immobilization can improve the stability of hybridoma antibody productivity in serum-free media. Biotechnol Bioeng. 1990 Dec 05; 36(10):1049-55. PMID: 18595043.
      View in: PubMed
    314. Ozturk SS, Palsson BO. 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.
      View in: PubMed
    315. Ozturk SS, Palsson BO. 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.
      View in: PubMed
    316. Ozturk SS, Palsson BO. 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.
      View in: PubMed
    317. Joshi A, Palsson BO. Metabolic dynamics in the human red cell. Part IV--Data prediction and some model computations. J Theor Biol. 1990 Jan 09; 142(1):69-85. PMID: 2141094.
      View in: PubMed
    318. Joshi A, Palsson BO. Metabolic dynamics in the human red cell. Part III--Metabolic reaction rates. J Theor Biol. 1990 Jan 09; 142(1):41-68. PMID: 2141093.
      View in: PubMed
    319. Palsson BO, 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.
      View in: PubMed
    320. Lee ID, Palsson BO. A comprehensive model of human erythrocyte metabolism: extensions to include pH effects. Biomed Biochim Acta. 1990; 49(8-9):771-89. PMID: 2082921.
      View in: PubMed
    321. Keasling JD, Palsson BO. ColE1 plasmid replication: a simple kinetic description from a structured model. J Theor Biol. 1989 Dec 19; 141(4):447-61. PMID: 2483575.
      View in: PubMed
    322. Joshi A, Palsson BO. 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.
      View in: PubMed
    323. Joshi A, Palsson BO. 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.
      View in: PubMed
    324. Lee GM, Savinell JM, Palsson BO. Serum can act as a shear protecting agent in agitated hybridoma cell cultures. Hybridoma. 1989 Dec; 8(6):639-45. PMID: 2693339.
      View in: PubMed
    325. Lee GM, Huard TK, Palsson BO. 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.
      View in: PubMed
    326. Keasling JD, Palsson BO. On the kinetics of plasmid replication. J Theor Biol. 1989 Feb 22; 136(4):487-92. PMID: 2811403.
      View in: PubMed
    327. Ozturk SS, Palsson BO, 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 05; 33(6):745-57. PMID: 18587976.
      View in: PubMed
    328. Palsson BO, Narang A, Joshi A. Computer model of human erythrocyte metabolism. Prog Clin Biol Res. 1989; 319:133-50; discussion 151-4. PMID: 2695934.
      View in: PubMed
    329. Palsson BO, Groshans TM. Mathematical modelling of dynamics and control in metabolic networks: VI. Dynamic bifurcations in single biochemical control loops. J Theor Biol. 1988 Mar 07; 131(1):43-53. PMID: 3419192.
      View in: PubMed
    330. Joshi A, Palsson BO. Escherichia coil growth dynamics: A three-pool biochemically based description. Biotechnol Bioeng. 1988 Feb 05; 31(2):102-16. PMID: 18581570.
      View in: PubMed
    331. Palsson BO, Joshi A, Ozturk SS. Reducing complexity in metabolic networks: making metabolic meshes manageable. Fed Proc. 1987 Jun; 46(8):2485-9. PMID: 3297796.
      View in: PubMed
    332. Palsson BO, Joshi A. On the dynamic order of structured Escherichia coli growth models. Biotechnol Bioeng. 1987 Apr; 29(6):789-92. PMID: 18576521.
      View in: PubMed
    333. Palsson BO, 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.
      View in: PubMed
    334. Palsson BO, 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.
      View in: PubMed
    335. Palsson BO, 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.
      View in: PubMed
    336. Palsson BO, 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.
      View in: PubMed
    337. Palsson BO, 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.
      View in: PubMed