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Bernhard Palsson

Title(s)Adjunct Professor, Pediatrics
SchoolAcademic Aff
Address9500 Gilman Drive #0412
La Jolla CA 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 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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. A biochemically-interpretable machine learning classifier for microbial GWAS. Nat Commun. 2020 May 22; 11(1):2580. Kavvas ES, Yang L, Monk JM, Heckmann D, Palsson BO. PMID: 32444610.
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    2. Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. BMC Bioinformatics. 2020 Apr 29; 21(1):162. Mih N, Monk JM, Fang X, Catoiu E, Heckmann D, Yang L, Palsson BO. PMID: 32349661.
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    3. Multiplex secretome engineering enhances recombinant protein production and purity. Nat Commun. 2020 Apr 20; 11(1):1908. Kol S, Ley D, Wulff T, Decker M, Arnsdorf J, Schoffelen S, Hansen AH, Jensen TL, Gutierrez JM, Chiang AWT, Masson HO, Palsson BO, Voldborg BG, Pedersen LE, Kildegaard HF, Lee GM, Lewis NE. PMID: 32313013.
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    4. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020 Apr; 38(4):504. Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Sheriff RSM, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. PMID: 32265554.
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    5. Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus. mSystems. 2020 Mar 31; 5(2). Salazar MJ, Machado H, Dillon NA, Tsunemoto H, Szubin R, Dahesh S, Pogliano J, Sakoulas G, Palsson BO, Nizet V, Feist AM. PMID: 32234776.
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    6. An atlas of human metabolism. Sci Signal. 2020 Mar 24; 13(624). Robinson JL, Kocabas P, Wang H, Cholley PE, Cook D, Nilsson A, Anton M, Ferreira R, Domenzain I, Billa V, Limeta A, Hedin A, Gustafsson J, Kerkhoven EJ, Svensson LT, Palsson BO, Mardinoglu A, Hansson L, Uhlén M, Nielsen J. PMID: 32209698.
      View in: PubMed   Mentions: 1     Fields:    
    7. Metabolic and genetic basis for auxotrophies in Gram-negative species. Proc Natl Acad Sci U S A. 2020 03 17; 117(11):6264-6273. Seif Y, Choudhary KS, Hefner Y, Anand A, Yang L, Palsson BO. PMID: 32132208.
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    8. Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen. Front Genet. 2020; 11:116. Jensen CS, Norsigian CJ, Fang X, Nielsen XC, Christensen JJ, Palsson BO, Monk JM. PMID: 32194617.
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    9. Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. PLoS Comput Biol. 2020 03; 16(3):e1007608. Hyun JC, Kavvas ES, Monk JM, Palsson BO. PMID: 32119670.
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    10. MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020 03; 38(3):272-276. Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Malik Sheriff RS, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. PMID: 32123384.
      View in: PubMed   Mentions: 2     Fields:    
    11. OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States. Mol Biol Evol. 2020 03 01; 37(3):660-667. Anand A, Chen K, Catoiu E, Sastry AV, Olson CA, Sandberg TE, Seif Y, Xu S, Szubin R, Yang L, Feist AM, Palsson BO. PMID: 31651953.
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    12. BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic Acids Res. 2020 01 08; 48(D1):D402-D406. Norsigian CJ, Pusarla N, McConn JL, Yurkovich JT, Dräger A, Palsson BO, King Z. PMID: 31696234.
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    13. Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion. Nat Commun. 2020 01 02; 11(1):68. Gutierrez JM, Feizi A, Li S, Kallehauge TB, Hefzi H, Grav LM, Ley D, Baycin Hizal D, Betenbaugh MJ, Voldborg B, Faustrup Kildegaard H, Min Lee G, Palsson BO, Nielsen J, Lewis NE. PMID: 31896772.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    14. Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. PLoS Comput Biol. 2019 12; 15(12):e1007562. Yan J, Estanbouli H, Liao C, Kim W, Monk JM, Rahman R, Kamboj M, Palsson BO, Qiu W, Xavier JB. PMID: 31860667.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    15. A workflow for generating multi-strain genome-scale metabolic models of prokaryotes. Nat Protoc. 2020 01; 15(1):1-14. Norsigian CJ, Fang X, Seif Y, Monk JM, Palsson BO. PMID: 31863076.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    16. Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media. Sci Data. 2019 12 17; 6(1):322. Rajput A, 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, Knight R, Nizet V, Palsson BO, Feist AM, Pogliano J. PMID: 31848353.
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    17. Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli. PLoS Comput Biol. 2019 12; 15(12):e1007525. Du B, Yang L, Lloyd CJ, Fang X, Palsson BO. PMID: 31809503.
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    18. The Escherichia coli transcriptome mostly consists of independently regulated modules. Nat Commun. 2019 12 04; 10(1):5536. Sastry AV, Gao Y, Szubin R, Hefner Y, Xu S, Kim D, Choudhary KS, Yang L, King ZA, Palsson BO. PMID: 31797920.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    19. Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration. Proc Natl Acad Sci U S A. 2019 12 10; 116(50):25287-25292. Anand A, Chen K, Yang L, Sastry AV, Olson CA, Poudel S, Seif Y, Hefner Y, Phaneuf PV, Xu S, Szubin R, Feist AM, Palsson BO. PMID: 31767748.
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    20. High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities. Environ Microbiol. 2020 Jan; 22(1):255-269. Nogales J, Mueller J, Gudmundsson S, Canalejo FJ, Duque E, Monk J, Feist AM, Ramos JL, Niu W, Palsson BO. PMID: 31657101.
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    21. Expanding the uses of genome-scale models with protein structures. Mol Syst Biol. 2019 11; 15(11):e8601. Mih N, Palsson BO. PMID: 31777175.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    22. Adaptive laboratory evolution of Escherichia coli under acid stress. Microbiology. 2020 02; 166(2):141-148. 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. PMID: 31625833.
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    23. Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus. Appl Environ Microbiol. 2019 11 01; 85(21). Machado H, Weng LL, Dillon N, Seif Y, Holland M, Pekar JE, Monk JM, Nizet V, Palsson BO, Feist AM. PMID: 31471305.
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    24. Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom. Nat Commun. 2019 10 07; 10(1):4552. 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. PMID: 31591397.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    25. The Transcription Unit Architecture of Streptomyces lividans TK24. Front Microbiol. 2019; 10:2074. Lee Y, Lee N, Jeong Y, Hwang S, Kim W, Cho S, Palsson BO, Cho BK. PMID: 31555254.
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    26. Systems Biology and Pangenome of Salmonella O-Antigens. mBio. 2019 08 27; 10(4). Seif Y, Monk JM, Machado H, Kavvas E, Palsson BO. PMID: 31455646.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    27. The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. Metab Eng. 2019 12; 56:1-16. Sandberg TE, Salazar MJ, Weng LL, Palsson BO, Feist AM. PMID: 31401242.
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    28. Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome. Nucleic Acids Res. 2019 07 09; 47(12):6114-6129. Hwang S, Lee N, Jeong Y, Lee Y, Kim W, Cho S, Palsson BO, Cho BK. PMID: 31131406.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    29. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Proc Natl Acad Sci U S A. 2019 07 09; 116(28):14368-14373. 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. PMID: 31270234.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    30. Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism. PLoS Comput Biol. 2019 06; 15(6):e1007066. Cheng C, O'Brien EJ, McCloskey D, Utrilla J, Olson C, LaCroix RA, Sandberg TE, Feist AM, Palsson BO, King ZA. PMID: 31158228.
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    31. A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action. Cell. 2019 05 30; 177(6):1649-1661.e9. Yang JH, Wright SN, Hamblin M, McCloskey D, Alcantar MA, Schrübbers L, Lopatkin AJ, Satish S, Nili A, Palsson BO, Walker GC, Collins JJ. PMID: 31080069.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    32. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Sci Data. 2019 04 26; 6(1):43. 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. PMID: 31028276.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    33. BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. PLoS Comput Biol. 2019 04; 15(4):e1006971. Lachance JC, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, Rodrigue S, Feist AM, King ZA, Jacques PÉ. PMID: 31009451.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    34. Enzyme promiscuity shapes adaptation to novel growth substrates. Mol Syst Biol. 2019 04 08; 15(4):e8462. 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. PMID: 30962359.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    35. 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. Ghatak S, King ZA, Sastry A, Palsson BO. PMID: 30698741.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    36. Minimal cells, maximal knowledge. Elife. 2019 03 12; 8. Lachance JC, Rodrigue S, Palsson BO. PMID: 30860025.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    37. Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses. PLoS Biol. 2019 03; 17(3):e2007050. 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. PMID: 30856169.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    38. Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum. New Phytol. 2019 05; 222(3):1364-1379. Broddrick JT, Du N, Smith SR, Tsuji Y, Jallet D, Ware MA, Peers G, Matsuda Y, Dupont CL, Mitchell BG, Palsson BO, Allen AE. PMID: 30636322.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    39. Pseudogene repair driven by selection pressure applied in experimental evolution. Nat Microbiol. 2019 03; 4(3):386-389. 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. PMID: 30692668.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    40. A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. PLoS Comput Biol. 2019 01; 15(1):e1006644. Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO. PMID: 30625152.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    41. DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression. BMC Syst Biol. 2019 01 09; 13(1):2. Yang L, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO. PMID: 30626386.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    42. ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. Nucleic Acids Res. 2019 01 08; 47(D1):D1164-D1171. Phaneuf PV, Gosting D, Palsson BO, Feist AM. PMID: 30357390.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    43. Reframing gene essentiality in terms of adaptive flexibility. BMC Syst Biol. 2018 12 17; 12(1):143. Guzmán GI, Olson CA, Hefner Y, Phaneuf PV, Catoiu E, Crepaldi LB, Micas LG, Palsson BO, Feist AM. PMID: 30558585.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    44. Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates. Nat Commun. 2018 12 10; 9(1):5270. Heckmann D, Zielinski DC, Palsson BO. PMID: 30532008.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    45. Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models. Nat Commun. 2018 12 07; 9(1):5252. Heckmann D, Lloyd CJ, Mih N, Ha Y, Zielinski DC, Haiman ZB, Desouki AA, Lercher MJ, Palsson BO. PMID: 30531987.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    46. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. Nucleic Acids Res. 2018 11 16; 46(20):10682-10696. 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. PMID: 30137486.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    47. 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. Lee JS, Park JH, Ha TK, Samoudi M, Lewis NE, Palsson BO, Kildegaard HF, Lee GM. PMID: 30388888.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    48. Predicting the metabolic capabilities of Synechococcus elongatus PCC 7942 adapted to different light regimes. Metab Eng. 2019 03; 52:42-56. Broddrick JT, Welkie DG, Jallet D, Golden SS, Peers G, Palsson BO. PMID: 30439494.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    49. 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. 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. PMID: 30425690.
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    50. Estimating Metabolic Equilibrium Constants: Progress and Future Challenges. Trends Biochem Sci. 2018 12; 43(12):960-969. Du B, Zielinski DC, Palsson BO. PMID: 30472988.
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    51. Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance. Nat Commun. 2018 10 17; 9(1):4306. Kavvas ES, Catoiu E, Mih N, Yurkovich JT, Seif Y, Dillon N, Heckmann D, Anand A, Yang L, Nizet V, Monk JM, Palsson BO. PMID: 30333483.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    52. Identification of growth-coupled production strains considering protein costs and kinetic variability. Metab Eng Commun. 2018 Dec; 7:e00080. Dinh HV, King ZA, Palsson BO, Feist AM. PMID: 30370222.
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    53. 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. Du B, Zielinski DC, Monk JM, Palsson BO. PMID: 30309961.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    54. Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. Proc Natl Acad Sci U S A. 2018 10 23; 115(43):11096-11101. 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. PMID: 30301795.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    55. Escher-FBA: a web application for interactive flux balance analysis. BMC Syst Biol. 2018 09 26; 12(1):84. Rowe E, Palsson BO, King ZA. PMID: 30257674.
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    56. Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. Nat Commun. 2018 09 18; 9(1):3796. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 30228271.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    57. Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions. Appl Environ Microbiol. 2018 10 01; 84(19). McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 30054360.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    58. Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. Nat Commun. 2018 09 14; 9(1):3771. Seif Y, Kavvas E, Lachance JC, Yurkovich JT, Nuccio SP, Fang X, Catoiu E, Raffatellu M, Palsson BO, Monk JM. PMID: 30218022.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    59. 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. 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. PMID: 30115066.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    60. Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome. Front Microbiol. 2018; 9:1793. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 30131786.
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    61. 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. Yurkovich JT, Alcantar MA, Haiman ZB, Palsson BO. PMID: 30086174.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    62. COBRAme: A computational framework for genome-scale models of metabolism and gene expression. PLoS Comput Biol. 2018 07; 14(7):e1006302. Lloyd CJ, Ebrahim A, Yang L, King ZA, Catoiu E, O'Brien EJ, Liu JK, Palsson BO. PMID: 29975681.
      View in: PubMed   Mentions: 6     Fields:    
    63. 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. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 29906504.
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    248. 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. Lee GM, Fong SS, Oh DJ, Francis K, Palsson BO. PMID: 11929001.
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    309. High-density photoautotrophic algal cultures: design, construction, and operation of a novel photobioreactor system. Biotechnol Bioeng. 1991 Dec 05; 38(10):1182-9. Javanmardian M, Palsson BO. PMID: 18600714.
      View in: PubMed   Mentions: 5     Fields:    
    310. 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. Ozturk SS, Palsson BO. PMID: 1367749.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    311. 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. Ozturk SS, Palsson BO. PMID: 1367750.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    312. Production of monoclonal antibody using free-suspended and immobilized hybridoma cells: Effect of serum. Biotechnol Bioeng. 1991 Oct 20; 38(8):821-30. Lee GM, Varma A, Palsson BO. PMID: 18600839.
      View in: PubMed   Mentions: 10     Fields:    
    313. 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. Caldwell J, Palsson BO, Locey B, Emerson SG. PMID: 2040665.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    314. Effect of medium osmolarity on hybridoma growth, metabolism, and antibody production. Biotechnol Bioeng. 1991 Apr 25; 37(10):989-93. Ozturk SS, Palsson BO. PMID: 18597326.
      View in: PubMed   Mentions: 29     Fields:    
    315. Cell-cycle-specific F plasmid replication: regulation by cell size control of initiation. J Bacteriol. 1991 Apr; 173(8):2673-80. Keasling JD, Palsson BO, Cooper S. PMID: 2013579.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    316. Physiological changes during the adaptation of hybridoma cells to low serum and serum-free media. Biotechnol Bioeng. 1991 Jan 05; 37(1):35-46. Ozturk SS, Palsson BO. PMID: 18597305.
      View in: PubMed   Mentions: 7     Fields:    
    317. 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. Caldwell J, Locey B, Clarke MF, Emerson SG, Palsson BO. PMID: 1366977.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    318. Application of population balance model to the loss of hybridoma antibody productivity. Biotechnol Prog. 1991 Jan-Feb; 7(1):72-5. Lee GM, Varma A, Palsson BO. PMID: 1366981.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    319. Immobilization can improve the stability of hybridoma antibody productivity in serum-free media. Biotechnol Bioeng. 1990 Dec 05; 36(10):1049-55. Lee GM, Palsson BO. PMID: 18595043.
      View in: PubMed   Mentions: 8     Fields:    
    320. 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. Ozturk SS, Palsson BO. PMID: 1366834.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    321. 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. Ozturk SS, Palsson BO. PMID: 2347598.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    322. Metabolic dynamics in the human red cell. Part III--Metabolic reaction rates. J Theor Biol. 1990 Jan 09; 142(1):41-68. Joshi A, Palsson BO. PMID: 2141093.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    323. 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. Joshi A, Palsson BO. PMID: 2141094.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    324. A comprehensive model of human erythrocyte metabolism: extensions to include pH effects. Biomed Biochim Acta. 1990; 49(8-9):771-89. Lee ID, Palsson BO. PMID: 2082921.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    325. 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. Palsson BO, Keasling JD, Emerson SG. PMID: 2405389.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    326. ColE1 plasmid replication: a simple kinetic description from a structured model. J Theor Biol. 1989 Dec 19; 141(4):447-61. Keasling JD, Palsson BO. PMID: 2483575.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    327. Metabolic dynamics in the human red cell. Part II--Interactions with the environment. J Theor Biol. 1989 Dec 19; 141(4):529-45. Joshi A, Palsson BO. PMID: 2630804.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    328. Metabolic dynamics in the human red cell. Part I--A comprehensive kinetic model. J Theor Biol. 1989 Dec 19; 141(4):515-28. Joshi A, Palsson BO. PMID: 2630803.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    329. Serum can act as a shear protecting agent in agitated hybridoma cell cultures. Hybridoma. 1989 Dec; 8(6):639-45. Lee GM, Savinell JM, Palsson BO. PMID: 2693339.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    330. Effect of serum concentration on hybridoma cell growth and monoclonal antibody production at various initial cell densities. Hybridoma. 1989 Jun; 8(3):369-75. Lee GM, Huard TK, Palsson BO. PMID: 2744789.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    331. On the kinetics of plasmid replication. J Theor Biol. 1989 Feb 22; 136(4):487-92. Keasling JD, Palsson BO. PMID: 2811403.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    332. 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. Ozturk SS, Palsson BO, Thiele JH. PMID: 18587976.
      View in: PubMed   Mentions: 3     Fields:    
    333. Computer model of human erythrocyte metabolism. Prog Clin Biol Res. 1989; 319:133-50; discussion 151-4. Palsson BO, Narang A, Joshi A. PMID: 2695934.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    334. 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. Palsson BO, Groshans TM. PMID: 3419192.
      View in: PubMed   Mentions:    Fields:    
    335. Escherichia coil growth dynamics: A three-pool biochemically based description. Biotechnol Bioeng. 1988 Feb 05; 31(2):102-16. Joshi A, Palsson BO. PMID: 18581570.
      View in: PubMed   Mentions: 3     Fields:    
    336. Reducing complexity in metabolic networks: making metabolic meshes manageable. Fed Proc. 1987 Jun; 46(8):2485-9. Palsson BO, Joshi A, Ozturk SS. PMID: 3297796.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    337. On the dynamic order of structured Escherichia coli growth models. Biotechnol Bioeng. 1987 Apr; 29(6):789-92. Palsson BO, Joshi A. PMID: 18576521.
      View in: PubMed   Mentions: 4     Fields:    
    338. 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. Palsson BO, Lightfoot EN. PMID: 3999779.
      View in: PubMed   Mentions: 6     Fields:    
    339. Mathematical modelling of dynamics and control in metabolic networks. III. Linear reaction sequences. J Theor Biol. 1985 Mar 21; 113(2):231-59. Palsson BO, Palsson H, Lightfoot EN. PMID: 3999777.
      View in: PubMed   Mentions: 2     Fields:    
    340. 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. Palsson BO, Lightfoot EN. PMID: 3999778.
      View in: PubMed   Mentions: 3     Fields:    
    341. Mathematical modelling of dynamics and control in metabolic networks. I. On Michaelis-Menten kinetics. J Theor Biol. 1984 Nov 21; 111(2):273-302. Palsson BO, Lightfoot EN. PMID: 6513572.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    342. Mathematical modelling of dynamics and control in metabolic networks. II. Simple dimeric enzymes. J Theor Biol. 1984 Nov 21; 111(2):303-21. Palsson BO, Jamier R, Lightfoot EN. PMID: 6513573.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
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