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Bernhard Palsson

Title(s)Professor, Bioengineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Research 
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    Systems Biology Approach to Redefine Susceptibility Testing and Treatment of MDR Pathogens in the Context of Host Immunity
    NIH U01AI124316Mar 15, 2016 - Feb 28, 2021
    Role: Principal Investigator
    Model-guided Identification of Synthetic Lethal Genes for Drug Target Development
    NIH R01GM098105Jul 1, 2011 - Jun 30, 2015
    Role: Principal Investigator
    A Genome-Scale Regulated Metabolic Model of Yeast
    NIH R01GM071808Aug 1, 2004 - Jul 31, 2009
    Role: Principal Investigator
    Network-based Analysis of Kinetics and Regulation
    NIH R01GM068837Jul 15, 2003 - Mar 31, 2014
    Role: Principal Investigator
    Testable in silico Hypotheses for E. coli Growth
    NIH R01GM062791Apr 1, 2001 - May 31, 2010
    Role: Principal Investigator
    Genome-Scale Models of Stress Response for E. coli
    NIH R01GM057089Aug 1, 1998 - Jun 30, 2022
    Role: Principal Investigator
    MECHANISMS OF STEM CELL MIGRATION
    NIH R01HL060398Jul 10, 1998 - Jun 30, 2002
    Role: Principal Investigator
    HEMATOPOIETIC STEM CELL
    NIH R01HL059234Feb 1, 1998 - Jan 31, 2002
    Role: Principal Investigator
    METABOLIC DYNAMICS &THE RED BLOOD CELL
    NIH 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. Improved red blood cell storage quality of blood from donors carrying the hypermorphic PIMT I120 variant. Hemasphere. 2026 Apr; 10(4):e70361. Bevers S, Issaian AV, Hay A, Keele GR, Dzieciatkowska M, Reisz JA, Haiman ZB, Nemkov T, Stephenson D, Moore AL, Deng X, Stone M, Hansen KC, Kleinman S, Norris PJ, Busch MP, Palsson BO, Roubinian NH, Janetzko J, V?geli B, Page GP, Jones DN, Henen MA, Eisenmesser EZ, Zimring JC, D'Alessandro A. PMID: 42007445; PMCID: PMC13084699.
      View in: PubMed   Mentions:
    2. Multi-strain analysis of Pseudomonas putida reveals the metabolic and genetic diversity of the species. mSystems. 2026 Apr 21; 11(4):e0159425. Mueller J, Krishnan J, Wei Q, Hefner Y, Monk JM, Verkler H, Tibocha-Bonilla JD, Ayala A, Palsson BO, Feist AM, Niu W. PMID: 41919942; PMCID: PMC13098254.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    3. Dissecting host stress responses for predictable heterologous gene expression in E. coli. Nucleic Acids Res. 2026 Mar 19; 54(6). Rode C, Beulig F, Jönsson M, Nørholm MHH, Jahn LJ, Zielinski DC, Palsson BO, Özdemir E, Yang L. PMID: 41909945; PMCID: PMC13034041.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    4. Revealing transcriptomic responses in Escherichia coli during early antibiotic exposure. mSystems. 2026 Apr 21; 11(4):e0158425. Yuan Y, Hefner Y, Szubin R, Sung J, Palsson BO. PMID: 41805196; PMCID: PMC13098195.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    5. The transcriptional regulatory network of the Escherichia coli MG1655 reference strain. Nucleic Acids Res. 2026 Jan 22; 54(3). Bajpe H, Shin J, Hefner Y, Szubin R, Sung J, Yuan Y, Palsson BO. PMID: 41626695; PMCID: PMC12862375.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    6. Aerobicity stimulon in Escherichia coli revealed using multi-scale computational systems biology of respiratory variants. iScience. 2026 Feb 20; 29(2):114715. Patel A, Banwani N, Mink R, Prabhakaran DM, Khairnar SV, Feist AM, Palsson BO, Anand A. PMID: 41675058; PMCID: PMC12886548.
      View in: PubMed   Mentions:
    7. Approaches for accelerating microbial gene function discovery using artificial intelligence. Nat Microbiol. 2026 Feb; 11(2):350-358. Palsson BO, Lee SY, Kim GB. PMID: 41501479.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    8. Multi-strain Analysis of Pseudomonas putida Reveals the Metabolic and Genetic Diversity of the Species. bioRxiv. 2025 Nov 17. Mueller J, Krishnan KJ, Wei Q, Hefner Y, Monk JM, Verkler H, Tibocha-Bonilla JD, Ayala A, Palsson BO, Feist AM, Niu W. PMID: 41332517; PMCID: PMC12667986.
      View in: PubMed   Mentions:
    9. Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli. Genome Biol Evol. 2025 09 30; 17(10). Rychel K, Chen K, Catoiu EA, Olson E, Sandberg TE, Gao Y, Xu S, Hefner Y, Szubin R, Patel A, Feist AM, Palsson BO. PMID: 41041937; PMCID: PMC12492005.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    10. Microbial production of creatine using growth-coupled selection systems. Metab Eng. 2025 Nov; 92:148-160. Li J, Krarup SR, Pieters P, Alter TB, Jacottin P, Johnsen J, Mohamed ET, Harris T, Ahonen L, Adhikari KB, Palsson BO, Feist AM, Yang L. PMID: 40712832.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    11. Reframing the role of the objective function in its proper context for metabolic network modeling. Cell Syst. 2025 Jun 18; 16(6):101298. Islam MM, Shao W, Batavia M, Ford RM, Palsson BO, Nielsen J, Maranas CD, Lee SY, Papin JA. PMID: 40541323.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    12. Evolution-guided tolerance engineering of Pseudomonas putida KT2440 for production of the aviation fuel precursor isoprenol. Metab Eng. 2025 Sep; 91:322-335. Lim HG, Srinivasan A, Menchavez R, Yunus IS, Noh MH, White M, Chen Y, Gin JW, Palsson BO, Lee TS, Petzold CJ, Eng T, Mukhopadhyay A, Feist AM. PMID: 40398593.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    13. A live bacteria enzyme assay for identification of human disease mutations and drug screening. Nat Biomed Eng. 2025 Sep; 9(9):1547-1556. Choe D, Palsson BO. PMID: 40307426; PMCID: PMC12443593.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    14. Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction. Elife. 2025 Apr 30; 12. Poudel S, Hyun J, Hefner Y, Monk J, Nizet V, Palsson BO. PMID: 40305082; PMCID: PMC12043316.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    15. Rapid identification of key antibiotic resistance genes in E. coli using high-resolution genome-scale CRISPRi screening. iScience. 2025 May 16; 28(5):112435. Choe D, Lee E, Kim K, Hwang S, Jeong KJ, Palsson BO, Cho BK, Cho S. PMID: 40352728; PMCID: PMC12063145.
      View in: PubMed   Mentions:
    16. Extracellular respiration is a latent energy metabolism in Escherichia coli. Cell. 2025 May 29; 188(11):2907-2924.e23. Kundu BB, Krishnan J, Szubin R, Patel A, Palsson BO, Zielinski DC, Ajo-Franklin CM. PMID: 40215961.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    17. RBC-GEM: A genome-scale metabolic model for systems biology of the human red blood cell. PLoS Comput Biol. 2025 Mar; 21(3):e1012109. Haiman ZB, Key A, D'Alessandro A, Palsson BO. PMID: 40072998; PMCID: PMC11925312.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    18. Machine learning uncovers the transcriptional regulatory network for the production host Streptomyces albidoflavus. Cell Rep. 2025 Mar 25; 44(3):115392. Jönsson M, Sigrist R, Gren T, Semenov Petrov M, Marcussen NEJ, Svetlova A, Charusanti P, Gockel P, Palsson BO, Yang L, Özdemir E. PMID: 40057950.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    19. Metabolic growth-coupling strategies for in vivo enzyme selection systems. Metab Eng Commun. 2025 Jun; 20:e00257. Alter TB, Pieters PA, Lloyd CJ, Feist AM, Özdemir E, Palsson BO, Zielinski DC. PMID: 40070513; PMCID: PMC11894327.
      View in: PubMed   Mentions: 1  
    20. Pangenome mining of the Streptomyces genus redefines species' biosynthetic potential. Genome Biol. 2025 Jan 14; 26(1):9. Mohite OS, Jørgensen TS, Booth TJ, Charusanti P, Phaneuf PV, Weber T, Palsson BO. PMID: 39810189; PMCID: PMC11734326.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    21. iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets. Nucleic Acids Res. 2025 Jan 06; 53(D1):D99-D106. Catoiu EA, Krishnan J, Li G, Lou XA, Rychel K, Yuan Y, Bajpe H, Patel A, Choe D, Shin J, Burrows J, Phaneuf PV, Zielinski DC, Palsson BO. PMID: 39494532; PMCID: PMC11701608.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    22. Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase. mSystems. 2025 Jan 21; 10(1):e0131524. Lim HG, Gao Y, Rychel K, Lamoureux C, Lou XA, Palsson BO. PMID: 39714213; PMCID: PMC11748552.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    23. Diversity of Transcriptional Regulatory Adaptation in E. coli. Mol Biol Evol. 2024 Nov 01; 41(11). Dalldorf C, Hefner Y, Szubin R, Johnsen J, Mohamed E, Li G, Krishnan J, Feist AM, Palsson BO, Zielinski DC. PMID: 39531644; PMCID: PMC11588850.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    24. iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia. PLoS Comput Biol. 2024 Oct; 20(10):e1012546. Sastry AV, Yuan Y, Poudel S, Rychel K, Yoo R, Lamoureux CR, Li G, Burrows JT, Chauhan S, Haiman ZB, Al Bulushi T, Seif Y, Palsson BO, Zielinski DC. PMID: 39441835; PMCID: PMC11534266.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    25. Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules. Nucleic Acids Res. 2024 Oct 14; 52(18):11362-11377. Shin J, Zielinski DC, Palsson BO. PMID: 39193902; PMCID: PMC11472167.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    26. CyuR is a dual regulator for L-cysteine dependent antimicrobial resistance in Escherichia coli. Commun Biol. 2024 09 17; 7(1):1160. Rodionova IA, Lim HG, Gao Y, Rodionov DA, Hutchison Y, Szubin R, Dalldorf C, Monk J, Palsson BO. PMID: 39289465; PMCID: PMC11408624.
      View in: PubMed   Mentions: 2  Translation:Cells
    27. Machine learning reveals the transcriptional regulatory network and circadian dynamics of Synechococcus elongatus PCC 7942. Proc Natl Acad Sci U S A. 2024 Sep 17; 121(38):e2410492121. Yuan Y, Al Bulushi T, Sastry AV, Sancar C, Szubin R, Golden SS, Palsson BO. PMID: 39269777; PMCID: PMC11420160.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    28. Machine-Learning Analysis of Streptomyces coelicolor Transcriptomes Reveals a Transcription Regulatory Network Encompassing Biosynthetic Gene Clusters. Adv Sci (Weinh). 2024 11; 11(41):e2403912. Lee Y, Choe D, Palsson BO, Cho BK. PMID: 39264300; PMCID: PMC11538686.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    29. Diagnosis and mitigation of the systemic impact of genome reduction in Escherichia coli DGF-298. mBio. 2024 Oct 16; 15(10):e0087324. Champie A, Lachance J-C, Sastry A, Matteau D, Lloyd CJ, Grenier F, Lamoureux CR, Jeanneau S, Feist AM, Jacques P-É, Palsson BO, Rodrigue S. PMID: 39207109; PMCID: PMC11481515.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    30. A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of Streptococcus pyogenes. mSystems. 2024 Sep 17; 9(9):e0073624. Hirose Y, Zielinski DC, Poudel S, Rychel K, Baker JL, Toya Y, Yamaguchi M, Heinken A, Thiele I, Kawabata S, Palsson BO, Nizet V. PMID: 39158303; PMCID: PMC11406949.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    31. Biological and genetic determinants of glycolysis: Phosphofructokinase isoforms boost energy status of stored red blood cells and transfusion outcomes. Cell Metab. 2024 Sep 03; 36(9):1979-1997.e13. Nemkov T, Stephenson D, Earley EJ, Keele GR, Hay A, Key A, Haiman ZB, Erickson C, Dzieciatkowska M, Reisz JA, Moore A, Stone M, Deng X, Kleinman S, Spitalnik SL, Hod EA, Hudson KE, Hansen KC, Palsson BO, Churchill GA, Roubinian N, Norris PJ, Busch MP, Zimring JC, Page GP, D'Alessandro A. PMID: 38964323; PMCID: PMC11374506.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimalsCells
    32. Proteome allocation is linked to transcriptional regulation through a modularized transcriptome. Nat Commun. 2024 Jun 19; 15(1):5234. Patel A, McGrosso D, Hefner Y, Campeau A, Sastry AV, Maurya S, Rychel K, Gonzalez DJ, Palsson BO. PMID: 38898010; PMCID: PMC11187210.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    33. BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets. Nucleic Acids Res. 2024 Jun 10; 52(10):5478-5495. Nuhamunada M, Mohite OS, Phaneuf PV, Palsson BO, Weber T. PMID: 38686794; PMCID: PMC11162802.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    34. The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. mSystems. 2024 Jul 23; 9(7):e0030524. Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski DC, Palsson BO. PMID: 38829048; PMCID: PMC11264592.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    35. Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment. Nat Commun. 2024 Mar 15; 15(1):2356. Choe D, Olson CA, Szubin R, Yang H, Sung J, Feist AM, Palsson BO. PMID: 38490991; PMCID: PMC10943186.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    36. Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning. mSystems. 2024 Mar 19; 9(3):e0125723. Josephs-Spaulding J, Rajput A, Hefner Y, Szubin R, Balasubramanian A, Li G, Zielinski DC, Jahn L, Sommer M, Phaneuf P, Palsson BO. PMID: 38349131; PMCID: PMC10949432.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    37. StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. PLoS Comput Biol. 2024 Feb; 20(2):e1011865. Zhao J, Chen K, Palsson BO, Yang L. PMID: 38346086; PMCID: PMC10890762.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    38. A data-driven approach for timescale decomposition of biochemical reaction networks. mSystems. 2024 Feb 20; 9(2):e0100123. Akbari A, Haiman ZB, Palsson BO. PMID: 38259168; PMCID: PMC10946255.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    39. Inferred regulons are consistent with regulator binding sequences in E. coli. PLoS Comput Biol. 2024 Jan; 20(1):e1011824. Qiu S, Wan X, Liang Y, Lamoureux CR, Akbari A, Palsson BO, Zielinski DC. PMID: 38252668; PMCID: PMC10833566.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    40. CRISPR-aided genome engineering for secondary metabolite biosynthesis in Streptomyces. J Ind Microbiol Biotechnol. 2024 Jan 09; 51. Lee Y, Hwang S, Kim W, Kim JH, Palsson BO, Cho BK. PMID: 38439699; PMCID: PMC10949845.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    41. Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii. mSystems. 2024 Feb 20; 9(2):e0060623. Menon ND, Poudel S, Sastry AV, Rychel K, Szubin R, Dillon N, Tsunemoto H, Hirose Y, Nair BG, Kumar GB, Palsson BO, Nizet V. PMID: 38189271; PMCID: PMC10878099.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    42. Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution. Front Microbiol. 2023; 14:1271121. Lee SM, Le HT, Taizhanova A, Nong LK, Park JY, Lee EJ, Palsson BO, Kim D. PMID: 38239730; PMCID: PMC10794520.
      View in: PubMed   Mentions: 3  
    43. Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species. Nat Commun. 2023 11 24; 14(1):7690. Hyun JC, Monk JM, Szubin R, Hefner Y, Palsson BO. PMID: 38001096; PMCID: PMC10673929.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    44. Functional annotation of enzyme-encoding genes using deep learning with transformer layers. Nat Commun. 2023 11 14; 14(1):7370. Kim GB, Kim JY, Lee JA, Norsigian CJ, Palsson BO, Lee SY. PMID: 37963869; PMCID: PMC10645960.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    45. Modeling Red Blood Cell Metabolism in the Omics Era. Metabolites. 2023 Nov 11; 13(11). Key A, Haiman Z, Palsson BO, D'Alessandro A. PMID: 37999241; PMCID: PMC10673375.
      View in: PubMed   Mentions: 6  
    46. Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways. Metabolites. 2023 Nov 03; 13(11). Mattei G, Gan Z, Ramazzotti M, Palsson BO, Zielinski DC. PMID: 37999223; PMCID: PMC10672963.
      View in: PubMed   Mentions:
    47. Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance. Cell Rep. 2023 09 26; 42(9):113105. Rychel K, Tan J, Patel A, Lamoureux C, Hefner Y, Szubin R, Johnsen J, Mohamed ETT, Phaneuf PV, Anand A, Olson CA, Park JH, Sastry AV, Yang L, Feist AM, Palsson BO. PMID: 37713311; PMCID: PMC10591938.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    48. Machine learning uncovers the Pseudomonas syringae transcriptome in microbial communities and during infection. mSystems. 2023 10 26; 8(5):e0043723. Bajpe H, Rychel K, Lamoureux CR, Sastry AV, Palsson BO. PMID: 37638727; PMCID: PMC10654099.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    49. Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome. Genome Biol. 2023 08 08; 24(1):183. Hyun JC, Palsson BO. PMID: 37553643; PMCID: PMC10411014.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    50. Adaptive evolution of a minimal organism with a synthetic genome. iScience. 2023 Sep 15; 26(9):107500. Sandberg TE, Wise KS, Dalldorf C, Szubin R, Feist AM, Glass JI, Palsson BO. PMID: 37636038; PMCID: PMC10448532.
      View in: PubMed   Mentions: 11  
    51. Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains TCH1516 and LAC. mSystems. 2023 08 31; 8(4):e0027923. Gao Y, Poudel S, Seif Y, Shen Z, Palsson BO. PMID: 37310465; PMCID: PMC10470025.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    52. Empowering drug off-target discovery with metabolic and structural analysis. Nat Commun. 2023 06 09; 14(1):3390. Chowdhury S, Zielinski DC, Dalldorf C, Rodrigues JV, Palsson BO, Shakhnovich EI. PMID: 37296102; PMCID: PMC10256842.
      View in: PubMed   Mentions: 5     Fields:    
    53. Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins. mSystems. 2023 06 29; 8(3):e0024723. Hirose Y, Poudel S, Sastry AV, Rychel K, Lamoureux CR, Szubin R, Zielinski DC, Lim HG, Menon ND, Bergsten H, Uchiyama S, Hanada T, Kawabata S, Palsson BO, Nizet V. PMID: 37278526; PMCID: PMC10308926.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    54. The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets. Nucleic Acids Res. 2023 05 08; 51(8):3618-3630. Gao Y, Bang I, Seif Y, Kim D, Palsson BO. PMID: 37026477; PMCID: PMC10164565.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    55. The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. Res Sq. 2023 Apr 12. Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski DC, Palsson BO. PMID: 37090546; PMCID: PMC10120744.
      View in: PubMed   Mentions:
    56. A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century. Microb Biotechnol. 2023 06; 16(6):1203-1231. Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C. PMID: 37002859; PMCID: PMC10221552.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    57. Proteome allocation is linked to transcriptional regulation through a modularized transcriptome. bioRxiv. 2023 Feb 21. Patel A, McGrosso D, Hefner Y, Campeau A, Sastry AV, Maurya S, Rychel K, Gonzalez DJ, Palsson BO. PMID: 36865326; PMCID: PMC9980150.
      View in: PubMed   Mentions:
    58. Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals. Metab Eng. 2023 03; 76:179-192. Lennen RM, Lim HG, Jensen K, Mohammed ET, Phaneuf PV, Noh MH, Malla S, Börner RA, Chekina K, Özdemir E, Bonde I, Koza A, Maury J, Pedersen LE, Schöning LY, Sonnenschein N, Palsson BO, Nielsen AT, Sommer MOA, Herrgård MJ, Feist AM. PMID: 36738854.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    59. Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains. mSystems. 2022 12 20; 7(6):e0048022. Poudel S, Hefner Y, Szubin R, Sastry A, Gao Y, Nizet V, Palsson BO. PMID: 36321827; PMCID: PMC9765215.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    60. Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures. mSystems. 2022 12 20; 7(6):e0046722. Yuan Y, Seif Y, Rychel K, Yoo R, Chauhan S, Poudel S, Al-Bulushi T, Palsson BO, Sastry AV. PMID: 36317888; PMCID: PMC9764980.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    61. Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes. mSystems. 2022 12 20; 7(6):e0016522. Kavvas ES, Long CP, Sastry A, Poudel S, Antoniewicz MR, Ding Y, Mohamed ET, Szubin R, Monk JM, Feist AM, Palsson BO. PMID: 36226969; PMCID: PMC9765567.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    62. Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa. Nucleic Acids Res. 2022 09 23; 50(17):9675-9688. Rajput A, Tsunemoto H, Sastry AV, Szubin R, Rychel K, Chauhan SM, Pogliano J, Palsson BO. PMID: 36095122; PMCID: PMC9508857.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    63. Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism. Plant J. 2022 11; 112(3):603-621. Broddrick JT, Ware MA, Jallet D, Palsson BO, Peers G. PMID: 36053127; PMCID: PMC9826171.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    64. Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism. PLoS Comput Biol. 2022 08; 18(8):e1010377. Akbari A, Palsson BO. PMID: 35976973; PMCID: PMC9423644.
      View in: PubMed   Mentions: 4     Fields:    
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    260. Microbial regulatory and metabolic networks. Curr Opin Biotechnol. 2007 Aug; 18(4):360-4. Cho BK, Charusanti P, Herrgård MJ, Palsson BO. PMID: 17719767.
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    261. 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):28791-28799. Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R. PMID: 17573341.
      View in: PubMed   Mentions: 214     Fields:    Translation:Cells
    262. Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome. Mol Genet Metab. 2007 May; 91(1):15-22. Vo TD, Paul Lee WN, Palsson BO. PMID: 17336115.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    263. In silico analysis of SNPs and other high-throughput data. Methods Mol Biol. 2007; 366:267-85. Jamshidi N, Vo TD, Palsson BO. PMID: 17568130.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    264. Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach. Prog Drug Res. 2007; 64:265, 267-309. Joyce AR, Palsson BO. PMID: 17195479.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    265. Isotopomer analysis of myocardial substrate metabolism: a systems biology approach. Biotechnol Bioeng. 2006 Dec 05; 95(5):972-83. Vo TD, Palsson BO. PMID: 16878330.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    266. Systems approach to refining genome annotation. Proc Natl Acad Sci U S A. 2006 Nov 14; 103(46):17480-4. Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO. PMID: 17088549; PMCID: PMC1859954.
      View in: PubMed   Mentions: 154     Fields:    Translation:Cells
    267. 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. Vo TD, Palsson BO. PMID: 16885397.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    268. Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PLoS Comput Biol. 2006 May; 2(5):e52. Barrett CL, Palsson BO. PMID: 16710450; PMCID: PMC1463018.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    269. 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. Barrett CL, Price ND, Palsson BO. PMID: 16533395; PMCID: PMC1421444.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    270. Towards multidimensional genome annotation. Nat Rev Genet. 2006 Feb; 7(2):130-41. Reed JL, Famili I, Thiele I, Palsson BO. PMID: 16418748.
      View in: PubMed   Mentions: 149     Fields:    
    271. PCR-based tandem epitope tagging system for Escherichia coli genome engineering. Biotechniques. 2006 Jan; 40(1):67-72. Cho BK, Knight EM, Palsson BO. PMID: 16454042.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    272. 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. Barrett CL, Herring CD, Reed JL, Palsson BO. PMID: 16357206; PMCID: PMC1323155.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    273. 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. Fong SS, Nanchen A, Palsson BO, Sauer U. PMID: 16319065.
      View in: PubMed   Mentions: 93     Fields:    Translation:AnimalsCells
    274. In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng. 2005 Sep 05; 91(5):643-8. Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BO. PMID: 15962337.
      View in: PubMed   Mentions: 132     Fields:    Translation:Cells
    275. Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol. 2005 Feb; 6(2):99-111. Papin JA, Hunter T, Palsson BO, Subramaniam S. PMID: 15654321.
      View in: PubMed   Mentions: 170     Fields:    Translation:HumansAnimalsCells
    276. k-Cone analysis: determining all candidate values for kinetic parameters on a network scale. Biophys J. 2005 Mar; 88(3):1616-25. Famili I, Mahadevan R, Palsson BO. PMID: 15626710; PMCID: PMC1305218.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    277. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends Biochem Sci. 2004 Dec; 29(12):641-7. Papin JA, Reed JL, Palsson BO. PMID: 15544950.
      View in: PubMed   Mentions: 76     Fields:    Translation:HumansAnimalsCells
    278. Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. Biophys J. 2004 Oct; 87(4):2172-86. Price ND, Schellenberger J, Palsson BO. PMID: 15454420; PMCID: PMC1304643.
      View in: PubMed   Mentions: 71     Fields:    Translation:HumansAnimalsCells
    279. Comparison of network-based pathway analysis methods. Trends Biotechnol. 2004 Aug; 22(8):400-5. Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO. PMID: 15283984.
      View in: PubMed   Mentions: 89     Fields:    Translation:HumansCells
    280. The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. Biophys J. 2004 Jul; 87(1):37-46. Papin JA, Palsson BO. PMID: 15240442; PMCID: PMC1304358.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansCells
    281. 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. Vo TD, Greenberg HJ, Palsson BO. PMID: 15205464.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansCells
    282. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004 May 06; 429(6987):92-6. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. PMID: 15129285.
      View in: PubMed   Mentions: 319     Fields:    Translation:Cells
    283. 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. Papin JA, Palsson BO. PMID: 14990392.
      View in: PubMed   Mentions: 35     Fields:    Translation:AnimalsCells
    284. In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium. OMICS. 2004; 8(1):25-41. 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. PMID: 15107235.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    285. 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. Covert MW, Famili I, Palsson BO. PMID: 14708117.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    286. Network-based analysis of metabolic regulation in the human red blood cell. J Theor Biol. 2003 Nov 21; 225(2):185-94. Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BO. PMID: 14575652.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    287. 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. Famili I, Forster J, Nielsen J, Palsson BO. PMID: 14578455; PMCID: PMC263729.
      View in: PubMed   Mentions: 121     Fields:    Translation:AnimalsCells
    288. Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices. J Theor Biol. 2003 Sep 07; 224(1):87-96. Famili I, Palsson BO. PMID: 12900206.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    289. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 2003; 4(9):R54. Reed JL, Vo TD, Schilling CH, Palsson BO. PMID: 12952533; PMCID: PMC193654.
      View in: PubMed   Mentions: 393     Fields:    Translation:Cells
    290. 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. Famili I, Palsson BO. PMID: 12829460; PMCID: PMC1303061.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    291. Metabolic pathways in the post-genome era. Trends Biochem Sci. 2003 May; 28(5):250-8. Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO. PMID: 12765837.
      View in: PubMed   Mentions: 84     Fields:    
    292. Constraints-based models: regulation of gene expression reduces the steady-state solution space. J Theor Biol. 2003 Apr 07; 221(3):309-25. Covert MW, Palsson BO. PMID: 12642111.
      View in: PubMed   Mentions: 45     Fields:    Translation:AnimalsCells
    293. Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol. 2003 Apr; 21(4):162-9. Price ND, Papin JA, Schilling CH, Palsson BO. PMID: 12679064.
      View in: PubMed   Mentions: 132     Fields:    Translation:HumansAnimalsCells
    294. Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli. Biotechnol Lett. 2003 Mar; 25(5):435-41. Raghunathan A, Palsson BO. PMID: 12882568.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    295. Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophys J. 2003 Feb; 84(2 Pt 1):794-804. Price ND, Reed JL, Papin JA, Famili I, Palsson BO. PMID: 12547764; PMCID: PMC1302660.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    296. Quantitative analysis of Escherichia coli metabolic phenotypes within the context of phenotypic phase planes. J Mol Microbiol Biotechnol. 2003; 6(2):101-8. Ibarra RU, Fu P, Palsson BO, DiTonno JR, Edwards JS. PMID: 15044828.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    297. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature. 2002 Nov 14; 420(6912):186-9. Ibarra RU, Edwards JS, Palsson BO. PMID: 12432395.
      View in: PubMed   Mentions: 327     Fields:    Translation:Cells
    298. Extreme pathway analysis of human red blood cell metabolism. Biophys J. 2002 Aug; 83(2):808-18. Wiback SJ, Palsson BO. PMID: 12124266; PMCID: PMC1302188.
      View in: PubMed   Mentions: 53     Fields:    Translation:HumansCells
    299. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    300. 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. Ramakrishna R, Edwards JS, McCulloch A, Palsson BO. PMID: 11171647.
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    301. Metabolic modeling of microbial strains in silico. Trends Biochem Sci. 2001 Mar; 26(3):179-86. Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO. PMID: 11246024.
      View in: PubMed   Mentions: 81     Fields:    
    302. Dynamic simulation of the human red blood cell metabolic network. Bioinformatics. 2001 Mar; 17(3):286-7. Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson BO. PMID: 11294796.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    303. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol. 2001 Feb; 19(2):125-30. Edwards JS, Ibarra RU, Palsson BO. PMID: 11175725.
      View in: PubMed   Mentions: 332     Fields:    Translation:Cells
    304. Robustness analysis of the Escherichia coli metabolic network. Biotechnol Prog. 2000 Nov-Dec; 16(6):927-39. Edwards JS, Palsson BO. PMID: 11101318.
      View in: PubMed   Mentions: 73     Fields:    Translation:Cells
    305. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics. 2000; 1:1. Edwards JS, Palsson BO. PMID: 11001586; PMCID: PMC29061.
      View in: PubMed   Mentions: 87     Fields:    Translation:Cells
    306. 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. Edwards JS, Palsson BO. PMID: 10805808; PMCID: PMC25862.
      View in: PubMed   Mentions: 293     Fields:    Translation:Cells
    307. 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. Schilling CH, Letscher D, Palsson BO. PMID: 10716907.
      View in: PubMed   Mentions: 174     Fields:    Translation:AnimalsCells
    308. 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. Schilling CH, Palsson BO. PMID: 10716908.
      View in: PubMed   Mentions: 67     Fields:    Translation:Cells
    309. Key adhesion molecules are present on long podia extended by hematopoietic cells. Cytometry. 1999 Nov 01; 37(3):171-7. Holloway W, Martinez AR, Oh DJ, Francis K, Ramakrishna R, Palsson BO. PMID: 10520196.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    310. 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. Huang S, Law P, Francis K, Palsson BO, Ho AD. PMID: 10515863.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    311. 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. Oh DJ, Lee GM, Francis K, Palsson BO. PMID: 10404146.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    312. Systems properties of the Haemophilus influenzae Rd metabolic genotype. J Biol Chem. 1999 Jun 18; 274(25):17410-6. Edwards JS, Palsson BO. PMID: 10364169.
      View in: PubMed   Mentions: 145     Fields:    Translation:Cells
    313. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol Prog. 1999 May-Jun; 15(3):296-303. Schilling CH, Schuster S, Palsson BO, Heinrich R. PMID: 10356246.
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    314. Toward metabolic phenomics: analysis of genomic data using flux balances. Biotechnol Prog. 1999 May-Jun; 15(3):288-95. Schilling CH, Edwards JS, Palsson BO. PMID: 10356245.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    315. 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. Francis K, Ramakrishna R, Holloway W, Palsson BO. PMID: 9808555.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    316. The underlying pathway structure of biochemical reaction networks. Proc Natl Acad Sci U S A. 1998 Apr 14; 95(8):4193-8. Schilling CH, Palsson BO. PMID: 9539712; PMCID: PMC22464.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    317. How will bioinformatics influence metabolic engineering? Biotechnol Bioeng. 1998 Apr 20-May 5; 58(2-3):162-9. Edwards JS, Palsson BO. PMID: 10191386.
      View in: PubMed   Mentions: 17     Fields:    
    318. 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. Francis K, Palsson BO. PMID: 9356436; PMCID: PMC24899.
      View in: PubMed   Mentions: 107     Fields:    Translation:HumansAnimals
    319. What lies beyond bioinformatics? Nat Biotechnol. 1997 Jan; 15(1):3-4. Palsson BO. PMID: 9035092.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
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