Bernhard O. Palsson, PhD - Publications

1984-1995 Chemical Engineering University of Michigan, Ann Arbor, Ann Arbor, MI 
 1995- Bioengineering University of California, San Diego, La Jolla, CA 

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Year Citation  Score
2022 Rajput A, Tsunemoto H, Sastry AV, Szubin R, Rychel K, Chauhan SM, Pogliano J, Palsson BO. Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa. Nucleic Acids Research. 50: 9675-9688. PMID 36095122 DOI: 10.1093/nar/gkac743  0.678
2022 Broddrick JT, Ware MA, Jallet D, Palsson BO, Peers G. Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism. The Plant Journal : For Cell and Molecular Biology. PMID 36053127 DOI: 10.1111/tpj.15965  0.807
2022 Fait A, Seif Y, Mikkelsen K, Poudel S, Wells JM, Palsson BO, Ingmer H. Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories. Proceedings of the National Academy of Sciences of the United States of America. 119: e2118262119. PMID 35858453 DOI: 10.1073/pnas.2118262119  0.737
2022 Yang L, Malla S, Özdemir E, Kim SH, Lennen R, Christensen HB, Christensen U, Munro LJ, Herrgård MJ, Kell DB, Palsson BØ. Identification and Engineering of Transporters for Efficient Melatonin Production in . Frontiers in Microbiology. 13: 880847. PMID 35794920 DOI: 10.3389/fmicb.2022.880847  0.782
2022 Anand A, Patel A, Chen K, Olson CA, Phaneuf PV, Lamoureux C, Hefner Y, Szubin R, Feist AM, Palsson BO. Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity. Nature Communications. 13: 3682. PMID 35760776 DOI: 10.1038/s41467-022-30877-5  0.812
2022 Mohite OS, Lloyd CJ, Monk JM, Weber T, Palsson BO. Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets. Synthetic and Systems Biotechnology. 7: 900-910. PMID 35647330 DOI: 10.1016/j.synbio.2022.04.011  0.818
2022 Rodionova IA, Gao Y, Monk J, Hefner Y, Wong N, Szubin R, Lim HG, Rodionov DA, Zhang Z, Saier MH, Palsson BO. A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli. Scientific Reports. 12: 7274. PMID 35508583 DOI: 10.1038/s41598-022-11134-7  0.743
2022 Lim HG, Rychel K, Sastry AV, Bentley GJ, Mueller J, Schindel HS, Larsen PE, Laible PD, Guss AM, Niu W, Johnson CW, Beckham GT, Feist AM, Palsson BO. Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network. Metabolic Engineering. PMID 35489688 DOI: 10.1016/j.ymben.2022.04.004  0.795
2022 Norsigian CJ, Danhof HA, Brand CK, Midani FS, Broddrick JT, Savidge TC, Britton RA, Palsson BO, Spinler JK, Monk JM. Systems biology approach to functionally assess the pangenome reveals genetic diversity with discriminatory power. Proceedings of the National Academy of Sciences of the United States of America. 119: e2119396119. PMID 35476524 DOI: 10.1073/pnas.2119396119  0.795
2022 Rajput A, Tsunemoto H, Sastry AV, Szubin R, Rychel K, Sugie J, Pogliano J, Palsson BO. Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators. Nucleic Acids Research. PMID 35357493 DOI: 10.1093/nar/gkac187  0.71
2022 Yoo R, Rychel K, Poudel S, Al-Bulushi T, Yuan Y, Chauhan S, Lamoureux C, Palsson BO, Sastry A. Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection. Msphere. e0003322. PMID 35306876 DOI: 10.1128/msphere.00033-22  0.71
2022 Palsson BO, Yurkovich JT. Is the kinetome conserved? Molecular Systems Biology. 18: e10782. PMID 35188334 DOI: 10.15252/msb.202110782  0.693
2022 Hyun JC, Monk JM, Palsson BO. Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity. Bmc Genomics. 23: 7. PMID 34983386 DOI: 10.1186/s12864-021-08223-8  0.6
2021 McConn JL, Lamoureux CR, Poudel S, Palsson BO, Sastry AV. Optimal dimensionality selection for independent component analysis of transcriptomic data. Bmc Bioinformatics. 22: 584. PMID 34879815 DOI: 10.1186/s12859-021-04497-7  0.679
2021 Decker KT, Gao Y, Rychel K, Al Bulushi T, Chauhan SM, Kim D, Cho BK, Palsson BO. proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. Nucleic Acids Research. PMID 34791440 DOI: 10.1093/nar/gkab1043  0.724
2021 Chauhan SM, Poudel S, Rychel K, Lamoureux C, Yoo R, Al Bulushi T, Yuan Y, Palsson BO, Sastry AV. Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile . Frontiers in Microbiology. 12: 753521. PMID 34777307 DOI: 10.3389/fmicb.2021.753521  0.711
2021 Phaneuf PV, Zielinski DC, Yurkovich JT, Johnsen J, Szubin R, Yang L, Kim SH, Schulz S, Wu M, Dalldorf C, Ozdemir E, Lennen RM, Palsson BO, Feist AM. Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data. Acs Synthetic Biology. PMID 34762392 DOI: 10.1021/acssynbio.1c00337  0.79
2021 Choe D, Szubin R, Poudel S, Sastry A, Song Y, Lee Y, Cho S, Palsson B, Cho BK. RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics. Plos Genetics. 17: e1009821. PMID 34570751 DOI: 10.1371/journal.pgen.1009821  0.65
2021 Seif Y, Palsson BØ. Path to improving the life cycle and quality of genome-scale models of metabolism. Cell Systems. 12: 842-859. PMID 34555324 DOI: 10.1016/j.cels.2021.06.005  0.758
2021 Sastry AV, Dillon N, Anand A, Poudel S, Hefner Y, Xu S, Szubin R, Feist AM, Nizet V, Palsson B. Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility. Msphere. 6: e0044321. PMID 34431696 DOI: 10.1128/mSphere.00443-21  0.797
2021 Gao Y, Lim HG, Verkler H, Szubin R, Quach D, Rodionova I, Chen K, Yurkovich JT, Cho BK, Palsson BO. Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo. Nucleic Acids Research. PMID 34428301 DOI: 10.1093/nar/gkab735  0.744
2021 Rodionova IA, Gao Y, Sastry A, Hefner Y, Lim HG, Rodionov DA, Saier MH, Palsson BO. Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli. Communications Biology. 4: 991. PMID 34413462 DOI: 10.1038/s42003-021-02516-0  0.762
2021 Lachance JC, Matteau D, Brodeur J, Lloyd CJ, Mih N, King ZA, Knight TF, Feist AM, Monk JM, Palsson BO, Jacques PÉ, Rodrigue S. Genome-scale metabolic modeling reveals key features of a minimal gene set. Molecular Systems Biology. 17: e10099. PMID 34288418 DOI: 10.15252/msb.202010099  0.845
2021 Machado H, Seif Y, Sakoulas G, Olson CA, Hefner Y, Anand A, Jones YZ, Szubin R, Palsson BO, Nizet V, Feist AM. Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus. Communications Biology. 4: 793. PMID 34172889 DOI: 10.1038/s42003-021-02339-z  0.775
2021 Lloyd CJ, Monk J, Yang L, Ebrahim A, Palsson BO. Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. Plos Computational Biology. 17: e1007817. PMID 34161321 DOI: 10.1371/journal.pcbi.1007817  0.837
2021 Akbari A, Yurkovich JT, Zielinski DC, Palsson BO. The quantitative metabolome is shaped by abiotic constraints. Nature Communications. 12: 3178. PMID 34039963 DOI: 10.1038/s41467-021-23214-9  0.772
2021 Anand A, Olson CA, Sastry AV, Patel A, Szubin R, Yang L, Feist AM, Palsson BO. Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications. Cell Reports. 35: 108961. PMID 33826886 DOI: 10.1016/j.celrep.2021.108961  0.808
2021 Wilken SE, Monk JM, Leggieri PA, Lawson CE, Lankiewicz TS, Seppälä S, Daum CG, Jenkins J, Lipzen AM, Mondo SJ, Barry KW, Grigoriev IV, Henske JK, Theodorou MK, Palsson BO, et al. Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus. Msystems. 6. PMID 33594000 DOI: 10.1128/mSystems.00002-21  0.694
2021 Sastry AV, Hu A, Heckmann D, Poudel S, Kavvas E, Palsson BO. Independent component analysis recovers consistent regulatory signals from disparate datasets. Plos Computational Biology. 17: e1008647. PMID 33529205 DOI: 10.1371/journal.pcbi.1008647  0.809
2021 Haiman ZB, Zielinski DC, Koike Y, Yurkovich JT, Palsson BO. MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. Plos Computational Biology. 17: e1008208. PMID 33507922 DOI: 10.1371/journal.pcbi.1008208  0.79
2021 Rajput A, Seif Y, Choudhary KS, Dalldorf C, Poudel S, Monk JM, Palsson BO. Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens. Msystems. 6. PMID 33500331 DOI: 10.1128/mSystems.00981-20  0.791
2021 Chen K, Anand A, Olson C, Sandberg TE, Gao Y, Mih N, Palsson BO. Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types. Plos Computational Biology. 17: e1008596. PMID 33465077 DOI: 10.1371/journal.pcbi.1008596  0.824
2021 Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Seif Y, Lamsa A, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, ... ... Palsson BO, et al. Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media. Gigascience. 10. PMID 33420779 DOI: 10.1093/gigascience/giaa156  0.769
2021 Lee N, Hwang S, Kim W, Lee Y, Kim JH, Cho S, Kim HU, Yoon YJ, Oh MK, Palsson BO, Cho BK. Systems and synthetic biology to elucidate secondary metabolite biosynthetic gene clusters encoded in genomes. Natural Product Reports. PMID 33393961 DOI: 10.1039/d0np00071j  0.325
2021 Kim GB, Gao Y, Palsson BO, Lee SY. DeepTFactor: A deep learning-based tool for the prediction of transcription factors. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33372147 DOI: 10.1073/pnas.2021171118  0.551
2020 Zielinski DC, Patel A, Palsson BO. The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale. Microorganisms. 8. PMID 33371386 DOI: 10.3390/microorganisms8122050  0.613
2020 Nemkov T, Stefanoni D, Bordbar A, Issaian A, Palsson BO, Dumont LJ, Hay AM, Song A, Xia Y, Redzic JS, Eisenmesser EZ, Zimring JC, Kleinman S, Hansen KC, Busch M, et al. Blood donor exposome and impact of common drugs on red blood cell metabolism. Jci Insight. PMID 33351786 DOI: 10.1172/jci.insight.146175  0.527
2020 Rychel K, Sastry AV, Palsson BO. Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome. Nature Communications. 11: 6338. PMID 33311500 DOI: 10.1038/s41467-020-20153-9  0.698
2020 Broddrick JT, Szubin R, Norsigian CJ, Monk JM, Palsson BO, Parenteau MN. High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies. Frontiers in Microbiology. 11: 596626. PMID 33281796 DOI: 10.3389/fmicb.2020.596626  0.819
2020 Choudhary KS, Kleinmanns JA, Decker K, Sastry AV, Gao Y, Szubin R, Seif Y, Palsson BO. Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships. Msystems. 5. PMID 33172971 DOI: 10.1128/mSystems.00980-20  0.818
2020 Norsigian CJ, Danhof HA, Brand CK, Oezguen N, Midani FS, Palsson BO, Savidge TC, Britton RA, Spinler JK, Monk JM. Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence. Npj Systems Biology and Applications. 6: 31. PMID 33082337 DOI: 10.1038/s41540-020-00151-9  0.837
2020 Rychel K, Decker K, Sastry AV, Phaneuf PV, Poudel S, Palsson BO. iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. Nucleic Acids Research. PMID 33045728 DOI: 10.1093/nar/gkaa810  0.805
2020 Fang X, Vázquez-Baeza Y, Elijah E, Vargas F, Ackermann G, Humphrey G, Lau R, Weldon KC, Sanders JG, Panitchpakdi M, Carpenter C, Jarmusch AK, Neill J, Miralles A, Dulai P, ... ... Palsson BO, et al. Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity. Inflammatory Bowel Diseases. PMID 33026068 DOI: 10.1093/ibd/izaa262  0.338
2020 Shiratsubaki IS, Fang X, Souza ROO, Palsson BO, Silber AM, Siqueira-Neto JL. Genome-scale metabolic models highlight stage-specific differences in essential metabolic pathways in Trypanosoma cruzi. Plos Neglected Tropical Diseases. 14: e0008728. PMID 33021977 DOI: 10.1371/journal.pntd.0008728  0.51
2020 Lamoureux CR, Choudhary KS, King ZA, Sandberg TE, Gao Y, Sastry AV, Phaneuf PV, Choe D, Cho BK, Palsson BO. The Bitome: digitized genomic features reveal fundamental genome organization. Nucleic Acids Research. PMID 32976587 DOI: 10.1093/nar/gkaa774  0.803
2020 Fang X, Lloyd CJ, Palsson BO. Reconstructing organisms in silico: genome-scale models and their emerging applications. Nature Reviews. Microbiology. PMID 32958892 DOI: 10.1038/S41579-020-00440-4  0.833
2020 Heckmann D, Campeau A, Lloyd CJ, Phaneuf PV, Hefner Y, Carrillo-Terrazas M, Feist AM, Gonzalez DJ, Palsson BO. Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers. Proceedings of the National Academy of Sciences of the United States of America. PMID 32873645 DOI: 10.1073/Pnas.2001562117  0.835
2020 Botero D, Monk J, Rodríguez Cubillos MJ, Rodríguez Cubillos A, Restrepo M, Bernal-Galeano V, Reyes A, González Barrios A, Palsson BØ, Restrepo S, Bernal A. Genome-Scale Metabolic Model of pv. : An Approach to Elucidate Pathogenicity at the Metabolic Level. Frontiers in Genetics. 11: 837. PMID 32849823 DOI: 10.3389/Fgene.2020.00837  0.677
2020 Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, ... ... Palsson B, et al. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology. 16: e9110. PMID 32845085 DOI: 10.15252/Msb.20199110  0.34
2020 Lee Y, Lee N, Hwang S, Kim K, Kim W, Kim J, Cho S, Palsson BO, Cho BK. System-level understanding of gene expression and regulation for engineering secondary metabolite production in Streptomyces. Journal of Industrial Microbiology & Biotechnology. PMID 32778981 DOI: 10.1007/S10295-020-02298-0  0.346
2020 Sandberg TE, Szubin R, Phaneuf PV, Palsson BO. Synthetic cross-phyla gene replacement and evolutionary assimilation of major enzymes. Nature Ecology & Evolution. PMID 32778753 DOI: 10.1038/S41559-020-1271-X  0.788
2020 Phaneuf PV, Yurkovich JT, Heckmann D, Wu M, Sandberg TE, King ZA, Tan J, Palsson BO, Feist AM. Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity. Bmc Genomics. 21: 514. PMID 32711472 DOI: 10.1186/S12864-020-06920-4  0.785
2020 Tan J, Sastry AV, Fremming KS, Bjørn SP, Hoffmeyer A, Seo S, Voldborg BG, Palsson BO. Independent component analysis of E. coli's transcriptome reveals the cellular processes that respond to heterologous gene expression. Metabolic Engineering. PMID 32710928 DOI: 10.1016/J.Ymben.2020.07.002  0.8
2020 Mejía-Almonte C, Busby SJW, Wade JT, van Helden J, Arkin AP, Stormo GD, Eilbeck K, Palsson BO, Galagan JE, Collado-Vides J. Redefining fundamental concepts of transcription initiation in bacteria. Nature Reviews. Genetics. PMID 32665585 DOI: 10.1038/S41576-020-0254-8  0.381
2020 Hawkey J, Monk JM, Billman-Jacobe H, Palsson B, Holt KE. Impact of insertion sequences on convergent evolution of Shigella species. Plos Genetics. 16: e1008931. PMID 32644999 DOI: 10.1371/Journal.Pgen.1008931  0.669
2020 Lee N, Hwang S, Kim J, Cho S, Palsson B, Cho BK. Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in . Computational and Structural Biotechnology Journal. 18: 1548-1556. PMID 32637051 DOI: 10.1016/J.Csbj.2020.06.024  0.395
2020 Poudel S, Tsunemoto H, Seif Y, Sastry AV, Szubin R, Xu S, Machado H, Olson CA, Anand A, Pogliano J, Nizet V, Palsson BO. Revealing 29 sets of independently modulated genes in , their regulators, and role in key physiological response. Proceedings of the National Academy of Sciences of the United States of America. PMID 32616573 DOI: 10.1073/Pnas.2008413117  0.806
2020 Dahal S, Yurkovich JT, Xu H, Palsson BO, Yang L. Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models. Proteomics. e1900282. PMID 32579720 DOI: 10.1002/Pmic.201900282  0.832
2020 Luo H, Schneider K, Christensen U, Lei Y, Herrgard M, Palsson BØ. Microbial Synthesis of Human-Hormone Melatonin at Gram Scales. Acs Synthetic Biology. PMID 32501000 DOI: 10.1021/Acssynbio.0C00065  0.594
2020 Hwang S, Lee N, Cho S, Palsson B, Cho BK. Repurposing Modular Polyketide Synthases and Non-ribosomal Peptide Synthetases for Novel Chemical Biosynthesis. Frontiers in Molecular Biosciences. 7: 87. PMID 32500080 DOI: 10.3389/Fmolb.2020.00087  0.313
2020 Kavvas ES, Yang L, Monk JM, Heckmann D, Palsson BO. A biochemically-interpretable machine learning classifier for microbial GWAS. Nature Communications. 11: 2580. PMID 32444610 DOI: 10.1038/S41467-020-16310-9  0.803
2020 Kim W, Hwang S, Lee N, Lee Y, Cho S, Palsson B, Cho BK. Transcriptome and translatome profiles of Streptomyces species in different growth phases. Scientific Data. 7: 138. PMID 32385251 DOI: 10.1038/S41597-020-0476-9  0.35
2020 Sales MJ, Sakoulas G, Szubin R, Palsson B, Arias C, Singh KV, Murray BE, Monk JM. Genome Sequence Comparison of Staphylococcus aureus TX0117 and a Beta-Lactamase-Cured Derivative Shows Increased Cationic Peptide Resistance Accompanying Mutations in and . Microbiology Resource Announcements. 9. PMID 32354985 DOI: 10.1128/MRA.01515-19  0.564
2020 Mih N, Monk JM, Fang X, Catoiu E, Heckmann D, Yang L, Palsson BO. Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. Bmc Bioinformatics. 21: 162. PMID 32349661 DOI: 10.1186/S12859-020-3505-Y  0.808
2020 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, et al. Multiplex secretome engineering enhances recombinant protein production and purity. Nature Communications. 11: 1908. PMID 32313013 DOI: 10.1038/S41467-020-15866-W  0.791
2020 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, ... ... Palsson BO, et al. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. 38: 504. PMID 32265554 DOI: 10.1038/S41587-020-0477-4  0.814
2020 Salazar MJ, Machado H, Dillon NA, Tsunemoto H, Szubin R, Dahesh S, Pogliano J, Sakoulas G, Palsson BO, Nizet V, Feist AM. Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus. Msystems. 5. PMID 32234776 DOI: 10.1128/mSystems.00828-19  0.774
2020 Robinson JL, Kocabaş 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, et al. An atlas of human metabolism. Science Signaling. 13. PMID 32209698 DOI: 10.1126/Scisignal.Aaz1482  0.502
2020 Jensen CS, Norsigian CJ, Fang X, Nielsen XC, Christensen JJ, Palsson BO, Monk JM. Reconstruction and Validation of a Genome-Scale Metabolic Model of (iCJ415), a Human Commensal and Opportunistic Pathogen. Frontiers in Genetics. 11: 116. PMID 32194617 DOI: 10.3389/Fgene.2020.00116  0.831
2020 Luo H, Yang L, Kim SH, Wulff T, Feist AM, Herrgard M, Palsson BØ. Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in . Acs Synthetic Biology. PMID 32149495 DOI: 10.1021/Acssynbio.9B00488  0.743
2020 Seif Y, Choudhary KS, Hefner Y, Anand A, Yang L, Palsson BO. Metabolic and genetic basis for auxotrophies in Gram-negative species. Proceedings of the National Academy of Sciences of the United States of America. PMID 32132208 DOI: 10.1073/Pnas.1910499117  0.832
2020 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, ... ... Palsson BO, et al. MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. PMID 32123384 DOI: 10.1038/S41587-020-0446-Y  0.82
2020 Hyun JC, Kavvas ES, Monk JM, Palsson BO. Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. Plos Computational Biology. 16: e1007608. PMID 32119670 DOI: 10.1371/Journal.Pcbi.1007608  0.649
2020 Lee N, Kim W, Hwang S, Lee Y, Cho S, Palsson B, Cho BK. Thirty complete Streptomyces genome sequences for mining novel secondary metabolite biosynthetic gene clusters. Scientific Data. 7: 55. PMID 32054853 DOI: 10.1038/S41597-020-0395-9  0.39
2020 Choe D, Palsson B, Cho BK. STATR: A simple analysis pipeline of Ribo-Seq in bacteria. Journal of Microbiology (Seoul, Korea). PMID 31989542 DOI: 10.1007/S12275-020-9536-2  0.328
2020 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. Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion. Nature Communications. 11: 68. PMID 31896772 DOI: 10.1038/S41467-019-13867-Y  0.816
2020 Lim HG, Fong B, Alarcon G, Magurudeniya HD, Eng T, Szubin R, Olson CA, Palsson BO, Gladden JM, Simmons BA, Mukhopadhyay A, Singer SW, Feist AM. Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution Green Chemistry. 22: 5677-5690. DOI: 10.1039/D0Gc01663B  0.679
2019 Norsigian CJ, Fang X, Seif Y, Monk JM, Palsson BO. A workflow for generating multi-strain genome-scale metabolic models of prokaryotes. Nature Protocols. PMID 31863076 DOI: 10.1038/S41596-019-0254-3  0.811
2019 Yan J, Estanbouli H, Liao C, Kim W, Monk JM, Rahman R, Kamboj M, Palsson BO, Qiu W, Xavier JB. Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. Plos Computational Biology. 15: e1007562. PMID 31860667 DOI: 10.1371/Journal.Pcbi.1007562  0.629
2019 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, ... ... Palsson BO, et al. Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media. Scientific Data. 6: 322. PMID 31848353 DOI: 10.1038/S41597-019-0331-Z  0.785
2019 Rosas-Lemus M, Minasov G, Shuvalova L, Wawrzak Z, Kiryukhina O, Mih N, Jaroszewski L, Palsson B, Godzik A, Satchell KJF. Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment. Protein Science : a Publication of the Protein Society. PMID 31811683 DOI: 10.1002/Pro.3796  0.731
2019 Du B, Yang L, Lloyd CJ, Fang X, Palsson BO. Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli. Plos Computational Biology. 15: e1007525. PMID 31809503 DOI: 10.1371/Journal.Pcbi.1007525  0.818
2019 Sastry AV, Gao Y, Szubin R, Hefner Y, Xu S, Kim D, Choudhary KS, Yang L, King ZA, Palsson BO. The Escherichia coli transcriptome mostly consists of independently regulated modules. Nature Communications. 10: 5536. PMID 31797920 DOI: 10.1038/S41467-019-13483-W  0.809
2019 Mih N, Palsson BO. Expanding the uses of genome-scale models with protein structures. Molecular Systems Biology. 15: e8601. PMID 31777175 DOI: 10.15252/Msb.20188601  0.788
2019 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. Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration. Proceedings of the National Academy of Sciences of the United States of America. PMID 31767748 DOI: 10.1073/Pnas.1909987116  0.812
2019 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 Research. PMID 31696234 DOI: 10.1093/Nar/Gkz1054  0.822
2019 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. Environmental Microbiology. PMID 31657101 DOI: 10.1111/1462-2920.14843  0.803
2019 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. Molecular Biology and Evolution. PMID 31651953 DOI: 10.1093/Molbev/Msz251  0.814
2019 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 under acid stress. Microbiology (Reading, England). PMID 31625833 DOI: 10.1099/Mic.0.000867  0.806
2019 Smith SR, Dupont CL, McCarthy JK, Broddrick JT, Oborník M, Horák A, Füssy Z, Cihlář J, Kleessen S, Zheng H, McCrow JP, Hixson KK, Araújo WL, Nunes-Nesi A, Fernie A, ... ... Palsson BO, et al. Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom. Nature Communications. 10: 4552. PMID 31591397 DOI: 10.1038/S41467-019-12407-Y  0.831
2019 Lee Y, Lee N, Jeong Y, Hwang S, Kim W, Cho S, Palsson BO, Cho BK. The Transcription Unit Architecture of TK24. Frontiers in Microbiology. 10: 2074. PMID 31555254 DOI: 10.3389/Fmicb.2019.02074  0.323
2019 Machado H, Weng LL, Dillon N, Seif Y, Holland M, Pekar JE, Monk JM, Nizet V, Palsson BO, Feist AM. A defined minimal medium for systems analyses of reveals strain-specific metabolic requirements. Applied and Environmental Microbiology. PMID 31471305 DOI: 10.1128/Aem.01773-19  0.827
2019 Seif Y, Monk JM, Machado H, Kavvas E, Palsson BO. Systems Biology and Pangenome of O-Antigens. Mbio. 10. PMID 31455646 DOI: 10.1128/Mbio.01247-19  0.787
2019 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. Metabolic Engineering. PMID 31401242 DOI: 10.1016/J.Ymben.2019.08.004  0.639
2019 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, ... ... Palsson BO, et al. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Proceedings of the National Academy of Sciences of the United States of America. PMID 31270234 DOI: 10.1073/Pnas.1905039116  0.773
2019 Norsigian CJ, Attia H, Szubin R, Yassin AS, Palsson BØ, Aziz RK, Monk JM. Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase-Producing Multidrug-Resistant Clinical Isolates. Frontiers in Cellular and Infection Microbiology. 9: 161. PMID 31179245 DOI: 10.3389/fcimb.2019.00161  0.81
2019 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 Computational Biology. 15: e1007066. PMID 31158228 DOI: 10.1371/Journal.Pcbi.1007066  0.82
2019 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 Research. PMID 31131406 DOI: 10.1093/Nar/Gkz471  0.411
2019 Lee N, Hwang S, Lee Y, Cho S, Palsson B, Cho BK. Synthetic biology tools for novel secondary metabolite discovery in . Journal of Microbiology and Biotechnology. PMID 31091862 DOI: 10.4014/Jmb.1904.04015  0.41
2019 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. PMID 31080069 DOI: 10.1016/J.Cell.2019.04.016  0.813
2019 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, ... ... Palsson BO, et al. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Scientific Data. 6: 43. PMID 31028276 DOI: 10.1038/S41597-019-0051-4  0.781
2019 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 Computational Biology. 15: e1006971. PMID 31009451 DOI: 10.1371/Journal.Pcbi.1006971  0.831
2019 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. Molecular Systems Biology. 15: e8462. PMID 30962359 DOI: 10.15252/Msb.20188462  0.769
2019 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 Biology. 17: e2007050. PMID 30856169 DOI: 10.1371/Journal.Pbio.2007050  0.777
2019 Choe D, Lee JH, Yoo M, Hwang S, Sung BH, Cho S, Palsson B, Kim SC, Cho BK. Adaptive laboratory evolution of a genome-reduced Escherichia coli. Nature Communications. 10: 935. PMID 30804335 DOI: 10.1038/S41467-019-08888-6  0.461
2019 Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, ... ... Palsson BØ, et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nature Protocols. PMID 30787451 DOI: 10.1038/S41596-018-0098-2  0.81
2019 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 Research. PMID 30698741 DOI: 10.1093/Nar/Gkz030  0.709
2019 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. Nature Microbiology. PMID 30692668 DOI: 10.1038/S41564-018-0340-2  0.787
2019 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. The New Phytologist. PMID 30636322 DOI: 10.1111/Nph.15685  0.821
2019 Yang L, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO. DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression. Bmc Systems Biology. 13: 2. PMID 30626386 DOI: 10.1186/S12918-018-0675-6  0.831
2019 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 Computational Biology. 15: e1006644. PMID 30625152 DOI: 10.1371/Journal.Pcbi.1006644  0.831
2018 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 Systems Biology. 12: 143. PMID 30558585 DOI: 10.1186/S12918-018-0653-Z  0.811
2018 Pekar JE, Phaneuf P, Szubin R, Palsson B, Feist A, Monk JM. Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology. Microbiology Resource Announcements. 7. PMID 30533692 DOI: 10.1128/MRA.00890-18  0.797
2018 Heckmann D, Zielinski DC, Palsson BO. Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates. Nature Communications. 9: 5270. PMID 30532008 DOI: 10.1038/S41467-018-07649-1  0.826
2018 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. Nature Communications. 9: 5252. PMID 30531987 DOI: 10.1038/S41467-018-07652-6  0.819
2018 Du B, Zielinski DC, Palsson BO. Estimating Metabolic Equilibrium Constants: Progress and Future Challenges. Trends in Biochemical Sciences. 43: 960-969. PMID 30472988 DOI: 10.1016/J.Tibs.2018.09.009  0.667
2018 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. Metabolic Engineering. PMID 30439494 DOI: 10.1016/J.Ymben.2018.11.001  0.83
2018 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, ... ... Palsson BO, et al. Metagenomics-Based, Strain-Level Analysis of From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. Frontiers in Microbiology. 9: 2559. PMID 30425690 DOI: 10.3389/Fmicb.2018.02559  0.686
2018 Lee JS, Park JH, Ha TK, Samoudi M, Lewis N, Palsson BØ, Kildegaard HF, Lee GM. Revealing key determinants of clonal variation in transgene expression in recombinant CHO cells using targeted genome editing. Acs Synthetic Biology. PMID 30388888 DOI: 10.1021/Acssynbio.8B00290  0.668
2018 Dinh HV, King ZA, Palsson BO, Feist AM. Identification of growth-coupled production strains considering protein costs and kinetic variability. Metabolic Engineering Communications. 7: e00080. PMID 30370222 DOI: 10.1016/J.Mec.2018.E00080  0.666
2018 Phaneuf PV, Gosting D, Palsson BO, Feist AM. ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. Nucleic Acids Research. PMID 30357390 DOI: 10.1093/Nar/Gky983  0.784
2018 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. Nature Communications. 9: 4306. PMID 30333483 DOI: 10.1038/S41467-018-06634-Y  0.799
2018 Du B, Zielinski DC, Monk JM, Palsson BO. Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice. Proceedings of the National Academy of Sciences of the United States of America. PMID 30309961 DOI: 10.1073/Pnas.1805367115  0.789
2018 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 30301795 DOI: 10.1073/Pnas.1811971115  0.839
2018 Rowe E, Palsson BO, King ZA. Escher-FBA: a web application for interactive flux balance analysis. Bmc Systems Biology. 12: 84. PMID 30257674 DOI: 10.1186/S12918-018-0607-5  0.39
2018 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. Nature Communications. 9: 3796. PMID 30228271 DOI: 10.1038/S41467-018-06219-9  0.828
2018 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. Nature Communications. 9: 3771. PMID 30218022 DOI: 10.1038/S41467-018-06112-5  0.831
2018 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 Research. PMID 30137486 DOI: 10.1093/Nar/Gky752  0.806
2018 McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Growth Adaptation of and Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome. Frontiers in Microbiology. 9: 1793. PMID 30131786 DOI: 10.3389/Fmicb.2018.01793  0.824
2018 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 Biology. 16: 91. PMID 30115066 DOI: 10.1186/S12915-018-0555-Y  0.553
2018 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 Computational Biology. 14: e1006356. PMID 30086174 DOI: 10.1371/Journal.Pcbi.1006356  0.694
2018 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 knockout evolutions. Applied and Environmental Microbiology. PMID 30054360 DOI: 10.1128/Aem.00823-18  0.823
2018 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 Computational Biology. 14: e1006302. PMID 29975681 DOI: 10.1371/Journal.Pcbi.1006302  0.82
2018 Jóhannsson F, Guðmundsson S, Paglia G, Guðmundsson S, Palsson B, Sigurjónsson ÓE, Rolfsson Ó. Systems analysis of metabolism in platelet concentrates during storage in platelet additive solution. The Biochemical Journal. PMID 29914982 DOI: 10.1042/Bcj20170921  0.356
2018 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. Metabolic Engineering. PMID 29906504 DOI: 10.1016/J.Ymben.2018.06.005  0.802
2018 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 Systems Biology. 12: 66. PMID 29890970 DOI: 10.1186/S12918-018-0587-5  0.791
2018 Choudhary KS, Mih N, Monk J, Kavvas E, Yurkovich JT, Sakoulas G, Palsson BO. The Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures. Frontiers in Microbiology. 9: 1082. PMID 29887846 DOI: 10.3389/Fmicb.2018.01082  0.804
2018 Du B, Zhang Z, Grubner S, Yurkovich JT, Palsson BO, Zielinski DC. Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method. Biophysical Journal. 114: 2691-2702. PMID 29874618 DOI: 10.1016/J.Bpj.2018.04.030  0.791
2018 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. Metabolic Engineering. PMID 29842925 DOI: 10.1016/J.Ymben.2018.05.012  0.826
2018 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. 13: e0197272. PMID 29771928 DOI: 10.1371/Journal.Pone.0197272  0.775
2018 Norsigian CJ, Kavvas E, Seif Y, Palsson BO, Monk JM. iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of AYE. Frontiers in Genetics. 9: 121. PMID 29692801 DOI: 10.3389/Fgene.2018.00121  0.83
2018 Yurkovich JT, Bordbar A, Sigurjónsson ÓE, Palsson BO. Systems biology as an emerging paradigm in transfusion medicine. Bmc Systems Biology. 12: 31. PMID 29514691 DOI: 10.1186/S12918-018-0558-X  0.768
2018 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 Systems Biology. 12: 25. PMID 29499714 DOI: 10.1186/S12918-018-0557-Y  0.788
2018 Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, ... ... Palsson BO, et al. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nature Biotechnology. PMID 29457794 DOI: 10.1038/Nbt.4072  0.829
2018 Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z, Palsson BO, Valencia A. ssbio: A Python Framework for Structural Systems Biology. Bioinformatics (Oxford, England). PMID 29444205 DOI: 10.1093/Bioinformatics/Bty077  0.8
2018 Yurkovich JT, Palsson BO. Quantitative -omic data empowers bottom-up systems biology. Current Opinion in Biotechnology. 51: 130-136. PMID 29414439 DOI: 10.1016/J.Copbio.2018.01.009  0.705
2018 Choe D, Szubin R, Dahesh S, Cho S, Nizet V, Palsson B, Cho BK. Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance. Scientific Reports. 8: 2215. PMID 29396540 DOI: 10.1038/S41598-018-20661-1  0.331
2018 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 Research. PMID 29394395 DOI: 10.1093/Nar/Gky069  0.836
2018 Yang L, Yurkovich JT, King ZA, Palsson BO. Modeling the multi-scale mechanisms of macromolecular resource allocation. Current Opinion in Microbiology. 45: 8-15. PMID 29367175 DOI: 10.1016/J.Mib.2018.01.002  0.807
2018 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 Computational Biology. 14: e1005895. PMID 29300748 DOI: 10.1371/Journal.Pcbi.1005895  0.793
2018 Yurkovich JT, Yang L, Palsson BO. Toward a Proteome-Complete Computational Model of the Human Red Blood Cell Blood. 132: 4888-4888. DOI: 10.1182/Blood-2018-99-114969  0.738
2017 Nilsson A, Nielsen J, Palsson BO. Metabolic Models of Protein Allocation Call for the Kinetome. Cell Systems. 5: 538-541. PMID 29284126 DOI: 10.1016/J.Cels.2017.11.013  0.474
2017 Du B, Zielinski DC, Palsson BO. Topological and kinetic determinants of the modal matrices of dynamic models of metabolism. Plos One. 12: e0189880. PMID 29267329 DOI: 10.1371/Journal.Pone.0189880  0.691
2017 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 29255023 DOI: 10.1073/Pnas.1716056115  0.704
2017 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. 22: 757-765.e3. PMID 29199098 DOI: 10.1016/J.Chom.2017.10.020  0.796
2017 Chen K, Gao Y, Mih N, O'Brien EJ, Yang L, Palsson BO. Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation. Proceedings of the National Academy of Sciences of the United States of America. 114: 11548-11553. PMID 29073085 DOI: 10.1073/Pnas.1705524114  0.815
2017 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. The Journal of Biological Chemistry. PMID 29030425 DOI: 10.1074/Jbc.M117.804914  0.817
2017 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. Nature Biotechnology. 35: 904-908. PMID 29020004 DOI: 10.1038/Nbt.3956  0.77
2017 Yurkovich JT, Yurkovich BJ, Dräger A, Palsson BO, King ZA. A Padawan Programmer's Guide to Developing Software Libraries. Cell Systems. PMID 28988801 DOI: 10.1016/J.Cels.2017.08.003  0.657
2017 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. Metabolic Engineering. PMID 28951266 DOI: 10.1016/J.Ymben.2017.09.012  0.674
2017 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 28874552 DOI: 10.1073/Pnas.1702581114  0.795
2017 Rolfsson Ó, Johannsson F, Magnusdottir M, Paglia G, Sigurjonsson ÓE, Bordbar A, Palsson S, Brynjólfsson S, Guðmundsson S, Palsson B. Mannose and fructose metabolism in red blood cells during cold storage in SAGM. Transfusion. PMID 28833234 DOI: 10.1111/Trf.14266  0.605
2017 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. Scientific Reports. 7: 2181. PMID 28526842 DOI: 10.1038/S41598-017-02110-7  0.808
2017 Sandberg TE, Lloyd CJ, Palsson BO, Feist AM. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies. Applied and Environmental Microbiology. PMID 28455337 DOI: 10.1128/Aem.00410-17  0.817
2017 Sastry A, Monk J, Tegel H, Uhlén M, Palsson BO, Rockberg J, Brunk E. Machine Learning in Computational Biology to Accelerate High-Throughput Protein Expression. Bioinformatics (Oxford, England). PMID 28398465 DOI: 10.1093/Bioinformatics/Btx207  0.787
2017 Bordbar A, Yurkovich JT, Paglia G, Rolfsson O, Sigurjónsson ÓE, Palsson BO. Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics. Scientific Reports. 7: 46249. PMID 28387366 DOI: 10.1038/Srep46249  0.8
2017 Rolfsson Ó, Sigurjonsson ÓE, Magnusdottir M, Johannsson F, Paglia G, Guðmundsson S, Bordbar A, Palsson S, Brynjólfsson S, Guðmundsson S, Palsson B. Metabolomics comparison of red cells stored in four additive solutions reveals differences in citrate anticoagulant permeability and metabolism. Vox Sanguinis. PMID 28370161 DOI: 10.1111/Vox.12506  0.61
2017 Yurkovich JT, Yang L, Palsson BO. Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells. Plos Computational Biology. 13: e1005424. PMID 28264007 DOI: 10.1371/Journal.Pcbi.1005424  0.809
2017 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. 2. PMID 28217746 DOI: 10.1128/mSystems.00142-16  0.336
2017 LaCroix RA, Palsson BO, Feist AM. A Model for Designing Adaptive Laboratory Evolution Experiments. Applied and Environmental Microbiology. PMID 28159796 DOI: 10.1128/Aem.03115-16  0.725
2017 Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson BO. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism. Scientific Reports. 7: 41241. PMID 28120890 DOI: 10.1038/Srep41241  0.824
2017 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. Scientific Reports. 7: 40863. PMID 28098205 DOI: 10.1038/Srep40863  0.784
2017 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 α2 as a Host Factor for Bacterial Invasion. Mbio. 8. PMID 28074024 DOI: 10.1128/Mbio.02128-16  0.789
2017 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. Microbiological Research. 194: 47-52. PMID 27938862 DOI: 10.1016/J.Micres.2016.10.006  0.64
2017 Dräger A, King ZA, Yurkovich JT, Blessing C, Khandelwa D, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO. Visualization and creation of biochemical networks with Escher F1000research. 6. DOI: 10.7490/F1000Research.1114756.1  0.77
2016 King ZA, O'Brien EJ, Feist AM, Palsson BO. Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion. Metabolic Engineering. PMID 27986597 DOI: 10.1016/J.Ymben.2016.12.004  0.818
2016 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 27911809 DOI: 10.1073/Pnas.1613446113  0.843
2016 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, ... ... Palsson BO, et al. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Systems. 3: 434-443.e8. PMID 27883890 DOI: 10.1016/J.Cels.2016.10.020  0.824
2016 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. Scientific Reports. 6: 36734. PMID 27857205 DOI: 10.1038/Srep36734  0.831
2016 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. PMID 27813142 DOI: 10.1111/Trf.13892  0.627
2016 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. Nature Communications. 7: 13091. PMID 27782110 DOI: 10.1038/Ncomms13091  0.812
2016 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 Systems. PMID 27667363 DOI: 10.1016/J.Cels.2016.08.013  0.818
2016 Yang L, Ma D, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO. solveME: fast and reliable solution of nonlinear ME models. Bmc Bioinformatics. 17: 391. PMID 27659412 DOI: 10.1186/S12859-016-1240-1  0.818
2016 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. PMID 27554084 DOI: 10.1182/Blood-2016-06-721688  0.615
2016 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. PMID 27491795 DOI: 10.1111/Trf.13740  0.614
2016 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 Computational Biology. 12: e1005039. PMID 27467583 DOI: 10.1371/Journal.Pcbi.1005039  0.824
2016 Liu HC, Jamshidi N, Chen Y, Eraly SA, Cho SY, Bhatnagar V, Wu W, Bush KT, Abagyan R, Palsson BO, Nigam SK. Construction and Evaluation of an Organic Anion Transporter 1 (OAT1)-Centered Metabolic Network. The Journal of Biological Chemistry. PMID 27440044 DOI: 10.1074/Jbc.M116.745216  0.627
2016 O'Brien EJ, Utrilla J, Palsson BO. Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. Plos Computational Biology. 12: e1004998. PMID 27351952 DOI: 10.1371/Journal.Pcbi.1004998  0.694
2016 Bosi E, Monk JM, Aziz RK, Fondi M, Nizet V, Palsson BØ. Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. Proceedings of the National Academy of Sciences of the United States of America. PMID 27286824 DOI: 10.1073/Pnas.1523199113  0.661
2016 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 Systems Biology. 10: 40. PMID 27266508 DOI: 10.1186/S12918-016-0283-2  0.776
2016 Feist AM, Palsson BO. What do cells actually want? Genome Biology. 17: 110. PMID 27215675 DOI: 10.1186/S13059-016-0983-3  0.638
2016 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, ... ... Palsson BO, et al. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Systems. PMID 27211860 DOI: 10.1016/J.Cels.2016.04.004  0.822
2016 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. 11: e0155038. PMID 27152931 DOI: 10.1371/Journal.Pone.0155038  0.842
2016 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 Systems. 2: 260-271. PMID 27135538 DOI: 10.1016/J.Cels.2016.04.003  0.8
2016 McCloskey D, Young JD, Xu S, Palsson BØ, Feist AM. A modeling method for increased precision and scope of directly measurable fluxes at a genome-scale. Analytical Chemistry. PMID 26981784 DOI: 10.1021/Acs.Analchem.5B04914  0.839
2016 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 Systems Biology. 10: 26. PMID 26969117 DOI: 10.1186/S12918-016-0271-6  0.817
2016 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. 11: e0151130. PMID 26964043 DOI: 10.1371/Journal.Pone.0151130  0.628
2016 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. Biotechnology Advances. PMID 26948029 DOI: 10.1016/J.Biotechadv.2016.02.011  0.791
2016 Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, ... ... Palsson B, et al. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. Plos Neglected Tropical Diseases. 10: e0004403. PMID 26890609 DOI: 10.1371/Journal.Pntd.0004403  0.66
2016 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. PMID 26749434 DOI: 10.1111/Trf.13460  0.533
2016 Dräger A, King ZA, Lu JS, Ebrahim A, Sonnenschein N, Miller PC, Lerman JA, Palsson BO, Lewis NE. New standard resources for systems biology: BiGG Models database and the visual pathway editor Escher F1000research. 5. DOI: 10.7490/F1000Research.1112788.1  0.788
2016 Yurkovich JT, Zielinski DC, Paglia G, Rolfsson O, Sigurjónsson OE, Bordbar A, Palsson B. Metabolic Analysis of Red Blood Cells Stored at High Temperature Blood. 128: 3848-3848. DOI: 10.1182/Blood.V128.22.3848.3848  0.556
2016 Bordbar A, Palsson BO. Unravelling why some people have drug side effects The Biochemist. 38: 31-34. DOI: 10.1042/bio03801031  0.483
2015 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 Systems. 1: 283-292. PMID 27136057 DOI: 10.1016/J.Cels.2015.10.003  0.814
2015 McCloskey D, Young JD, Xu S, Palsson BØ, Feist AM. MID Max: A LC-MS/MS method for measuring the precursor and product mass isotopomer distributions (MIDs) of metabolic intermediates and cofactors for metabolic flux analysis (MFA) applications. Analytical Chemistry. PMID 26666286 DOI: 10.1021/Acs.Analchem.5B03887  0.809
2015 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. Scientific Reports. 5: 16025. PMID 26531810 DOI: 10.1038/Srep16025  0.686
2015 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 Research. PMID 26476456 DOI: 10.1093/Nar/Gkv1049  0.825
2015 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, ... ... Palsson BO, et al. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11: 831. PMID 26467284 DOI: 10.15252/Msb.20156157  0.783
2015 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 Systems Biology. 9: 68. PMID 26452770 DOI: 10.1186/S12918-015-0212-9  0.614
2015 Aziz RK, Khaw VL, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Palsson BØ, Charusanti P. Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC. Frontiers in Microbiology. 6: 958. PMID 26441892 DOI: 10.3389/Fmicb.2015.00958  0.82
2015 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 Computational Biology. 11: e1004321. PMID 26313928 DOI: 10.1371/Journal.Pcbi.1004321  0.804
2015 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 Reports. PMID 26279566 DOI: 10.1016/J.Celrep.2015.07.043  0.778
2015 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, et al. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proceedings of the National Academy of Sciences of the United States of America. PMID 26261351 DOI: 10.1073/Pnas.1501384112  0.823
2015 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. Nature Communications. 6: 7970. PMID 26258987 DOI: 10.1038/Ncomms8970  0.808
2015 Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F, Netz E, Diamantikos A, Eichner J, Keller R, Wrzodek C, ... ... Palsson BØ, et al. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics (Oxford, England). PMID 26079347 DOI: 10.1093/Bioinformatics/Btv341  0.68
2015 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. Nature Communications. 6: 7101. PMID 26055627 DOI: 10.1038/Ncomms8101  0.801
2015 O'Brien EJ, Monk JM, Palsson BO. Using Genome-scale Models to Predict Biological Capabilities. Cell. 161: 971-987. PMID 26000478 DOI: 10.1016/J.Cell.2015.05.019  0.812
2015 Aurich MK, Paglia G, Rolfsson Ó, Hrafnsdóttir S, Magnúsdóttir M, Stefaniak MM, Palsson BØ, Fleming RM, Thiele I. Prediction of intracellular metabolic states from extracellular metabolomic data. Metabolomics : Official Journal of the Metabolomic Society. 11: 603-619. PMID 25972769 DOI: 10.1007/S11306-014-0721-3  0.836
2015 Rolfsson Ó, Palsson BO. Decoding the jargon of bottom-up metabolic systems biology. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 37: 588-91. PMID 25761171 DOI: 10.1002/Bies.201400187  0.352
2015 Pronk JT, Lee SY, Lievense J, Pierce J, Palsson B, Uhlen M, Nielsen J. How to set up collaborations between academia and industrial biotech companies. Nature Biotechnology. 33: 237-40. PMID 25748909 DOI: 10.1038/Nbt.3171  0.328
2015 O'Brien EJ, Palsson BO. Computing the functional proteome: recent progress and future prospects for genome-scale models. Current Opinion in Biotechnology. 34: 125-134. PMID 25576845 DOI: 10.1016/J.Copbio.2014.12.017  0.752
2015 King ZA, Lloyd CJ, Feist AM, Palsson BO. Next-generation genome-scale models for metabolic engineering. Current Opinion in Biotechnology. 35: 23-29. PMID 25575024 DOI: 10.1016/J.Copbio.2014.12.016  0.836
2015 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. Proceedings of the National Academy of Sciences of the United States of America. 112: 929-34. PMID 25564669 DOI: 10.1073/Pnas.1414218112  0.842
2015 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. Applied and Environmental Microbiology. 81: 17-30. PMID 25304508 DOI: 10.1128/Aem.02246-14  0.812
2015 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 Systems. 1: 283-292. DOI: 10.1016/j.cels.2015.10.003  0.827
2015 McCloskey D, Gangoiti JA, Palsson BO, Feist AM. A pH and solvent optimized reverse-phase ion-paring-LC–MS/MS method that leverages multiple scan-types for targeted absolute quantification of intracellular metabolites Metabolomics. 11: 1338-1350. DOI: 10.1007/S11306-015-0790-Y  0.632
2014 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. 58: 329-32. PMID 26054770 DOI: 10.2144/000114302  0.807
2014 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 Computational Biology. 10: e1003837. PMID 25232952 DOI: 10.1371/Journal.Pcbi.1003837  0.756
2014 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 Systems Biology. 8: 110. PMID 25227965 DOI: 10.1186/S12918-014-0110-6  0.812
2014 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. Nature Communications. 5: 4910. PMID 25222563 DOI: 10.1038/Ncomms5910  0.804
2014 Latif H, Li HJ, Charusanti P, Palsson BØ, Aziz RK. A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933. Genome Announcements. 2. PMID 25125650 DOI: 10.1128/Genomea.00821-14  0.617
2014 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. Metabolic Engineering. 25: 140-58. PMID 25080239 DOI: 10.1016/J.Ymben.2014.07.009  0.673
2014 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. Molecular Biology and Evolution. 31: 2647-62. PMID 25015645 DOI: 10.1093/Molbev/Msu209  0.809
2014 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. Molecular Systems Biology. 10: 737. PMID 24987116 DOI: 10.15252/Msb.20145243  0.825
2014 Monk J, Palsson BO. Genetics. Predicting microbial growth. Science (New York, N.Y.). 344: 1448-9. PMID 24970063 DOI: 10.1126/Science.1253388  0.671
2014 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. 9: e98760. PMID 24896608 DOI: 10.1371/Journal.Pone.0098760  0.407
2014 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. 54: 2911-23. PMID 24840017 DOI: 10.1111/Trf.12710  0.316
2014 Monk J, Nogales J, Palsson BO. Optimizing genome-scale network reconstructions. Nature Biotechnology. 32: 447-52. PMID 24811519 DOI: 10.1038/Nbt.2870  0.664
2014 Nielsen J, Fussenegger M, Keasling J, Lee SY, Liao JC, Prather K, Palsson B. Engineering synergy in biotechnology. Nature Chemical Biology. 10: 319-22. PMID 24743245 DOI: 10.1038/Nchembio.1519  0.791
2014 Federowicz S, Kim D, Ebrahim A, Lerman J, Nagarajan H, Cho BK, Zengler K, Palsson B. Determining the control circuitry of redox metabolism at the genome-scale. Plos Genetics. 10: e1004264. PMID 24699140 DOI: 10.1371/Journal.Pgen.1004264  0.838
2014 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. Nature Communications. 5: 3233. PMID 24481126 DOI: 10.1038/Ncomms4233  0.425
2014 Thomas A, Rahmanian S, Bordbar A, Palsson BØ, Jamshidi N. Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance. Scientific Reports. 4: 3925. PMID 24473230 DOI: 10.1038/Srep03925  0.805
2014 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 Biology. 12: 4. PMID 24461193 DOI: 10.1186/1741-7007-12-4  0.654
2014 Bordbar A, Monk JM, King ZA, Palsson BO. Constraint-based models predict metabolic and associated cellular functions. Nature Reviews. Genetics. 15: 107-20. PMID 24430943 DOI: 10.1038/Nrg3643  0.776
2014 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. Biotechnology and Bioengineering. 111: 803-15. PMID 24249002 DOI: 10.1002/Bit.25133  0.841
2014 McCloskey D, Utrilla J, Naviaux RK, Palsson BO, Feist AM. Fast Swinnex filtration (FSF): a fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media Metabolomics. 11: 198-209. DOI: 10.1007/S11306-014-0686-2  0.608
2014 Bordbar A, Palsson BO. Moving toward genome-scale kinetic models: The mass action stoichiometric simulation approach Functional Coherence of Molecular Networks in Bioinformatics. 201-220. DOI: 10.1007/978-1-4614-0320-3_8  0.551
2013 Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proceedings of the National Academy of Sciences of the United States of America. 110: 20338-43. PMID 24277855 DOI: 10.1073/Pnas.1307797110  0.828
2013 Chang RL, Xie L, Bourne PE, Palsson BO. Antibacterial mechanisms identified through structural systems pharmacology. Bmc Systems Biology. 7: 102. PMID 24112686 DOI: 10.1186/1752-0509-7-102  0.687
2013 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 Systems Biology. 7: 95. PMID 24074340 DOI: 10.1186/1752-0509-7-95  0.308
2013 Ebrahim A, Lerman JA, Palsson BO, Hyduke DR. COBRApy: COnstraints-Based Reconstruction and Analysis for Python. Bmc Systems Biology. 7: 74. PMID 23927696 DOI: 10.1186/1752-0509-7-74  0.832
2013 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 Metabolism and Disposition: the Biological Fate of Chemicals. 41: 1825-34. PMID 23920220 DOI: 10.1124/Dmd.113.052647  0.645
2013 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, ... ... Palsson BO, et al. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nature Biotechnology. 31: 759-65. PMID 23873082 DOI: 10.1038/Nbt.2624  0.805
2013 Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO. Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. Science (New York, N.Y.). 340: 1220-3. PMID 23744946 DOI: 10.1126/Science.1234012  0.784
2013 McCloskey D, Palsson BØ, Feist AM. Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Molecular Systems Biology. 9: 661. PMID 23632383 DOI: 10.1038/Msb.2013.18  0.847
2013 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. Nature Communications. 4: 1755. PMID 23612296 DOI: 10.1038/Ncomms2743  0.783
2013 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, et al. Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. Molecular Biosystems. 9: 1522-34. PMID 23559334 DOI: 10.1039/C3Mb25598K  0.827
2013 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 Microbiology Letters. 342: 62-9. PMID 23432746 DOI: 10.1111/1574-6968.12109  0.776
2013 Hyduke DR, Lewis NE, Palsson BØ. Analysis of omics data with genome-scale models of metabolism. Molecular Biosystems. 9: 167-74. PMID 23247105 DOI: 10.1039/C2Mb25453K  0.572
2013 Rolfsson Ó, Paglia G, Magnusdóttir M, Palsson BØ, Thiele I. Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity. The Biochemical Journal. 449: 427-35. PMID 23067238 DOI: 10.1042/Bj20120980  0.623
2013 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, ... ... Palsson BO, et al. Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling. Current Topics in Microbiology and Immunology. 363: 21-41. PMID 22886542 DOI: 10.1007/82_2012_247  0.775
2013 Hefzi H, Palsson BO, Lewis NE. Reconstruction of Genome-Scale Metabolic Networks Handbook of Systems Biology. 229-250. DOI: 10.1016/B978-0-12-385944-0.00012-5  0.827
2013 Zielinski DC, Palsson BO. Kinetic modeling of metabolic networks Systems Metabolic Engineering. 25-55. DOI: 10.1007/978-94-007-4534-6_2  0.612
2013 Lee SY, Sohn SB, Kim HU, Park JM, Kim TY, Orth JD, Palsson BO. Genome-scale network modeling Systems Metabolic Engineering. 1-23. DOI: 10.1007/978-94-007-4534-6_1  0.721
2013 Jamshidi N, Bordbar A, Palsson B. Modeling Mycobacterium tuberculosis H37Rv in silico Systems Biology of Tuberculosis. 1-19. DOI: 10.1007/978-1-4614-4966-9_1  0.65
2012 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. 13: 679. PMID 23194155 DOI: 10.1186/1471-2164-13-679  0.641
2012 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. 7: e45635. PMID 23029152 DOI: 10.1371/Journal.Pone.0045635  0.767
2012 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, et al. Proteomic analysis of Chinese hamster ovary cells. Journal of Proteome Research. 11: 5265-76. PMID 22971049 DOI: 10.1021/Pr300476W  0.762
2012 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 (New York, N.Y.). 337: 1101-4. PMID 22936779 DOI: 10.1126/Science.1216861  0.806
2012 Kim D, Hong JS, Qiu Y, Nagarajan H, Seo JH, Cho BK, Tsai SF, Palsson BØ. Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. Plos Genetics. 8: e1002867. PMID 22912590 DOI: 10.1371/Journal.Pgen.1002867  0.765
2012 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, ... ... Palsson BO, et al. Studying Salmonellae and Yersiniae Host–Pathogen Interactions Using Integrated ‘Omics and Modeling Current Topics in Microbiology and Immunology. 363: 21-41. PMID 22886542 DOI: 10.1007/82-2012-247  0.792
2012 Fu W, Gudmundsson O, Feist AM, Herjolfsson G, Brynjolfsson S, Palsson BØ. Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor. Journal of Biotechnology. 161: 242-9. PMID 22796827 DOI: 10.1016/J.Jbiotec.2012.07.004  0.55
2012 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. Nature Communications. 3: 929. PMID 22760628 DOI: 10.1038/Ncomms1928  0.841
2012 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. Molecular Systems Biology. 8: 558. PMID 22735334 DOI: 10.1038/Msb.2012.21  0.815
2012 Orth JD, Palsson B. Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions Bmc Systems Biology. 6. PMID 22548736 DOI: 10.1186/1752-0509-6-30  0.745
2012 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. 7: e33727. PMID 22470465 DOI: 10.1371/Journal.Pone.0033727  0.702
2012 Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nature Reviews. Microbiology. 10: 291-305. PMID 22367118 DOI: 10.1038/Nrmicro2737  0.798
2012 Nogales J, Gudmundsson S, Knight EM, Palsson BO, Thiele I. Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis. Proceedings of the National Academy of Sciences of the United States of America. 109: 2678-83. PMID 22308420 DOI: 10.1073/Pnas.1117907109  0.62
2012 Schellenberger J, Zielinski DC, Choi W, Madireddi S, Portnoy V, Scott DA, Reed JL, Osterman AL, Palsson B. Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling. Bmc Systems Biology. 6: 9. PMID 22289253 DOI: 10.1186/1752-0509-6-9  0.799
2012 Bordbar A, Palsson BO. Using the reconstructed genome-scale human metabolic network to study physiology and pathology. Journal of Internal Medicine. 271: 131-41. PMID 22142339 DOI: 10.1111/J.1365-2796.2011.02494.X  0.668
2012 Cho BK, Federowicz S, Park YS, Zengler K, Palsson BØ. Deciphering the transcriptional regulatory logic of amino acid metabolism. Nature Chemical Biology. 8: 65-71. PMID 22082910 DOI: 10.1038/Nchembio.710  0.812
2011 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 Systems Biology. 5: 180. PMID 22041191 DOI: 10.1186/1752-0509-5-180  0.829
2011 Lee DH, Feist AM, Barrett CL, Palsson BØ. Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli. Plos One. 6: e26172. PMID 22028828 DOI: 10.1371/Journal.Pone.0026172  0.585
2011 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 Systems Biology. 5: 163. PMID 21995956 DOI: 10.1186/1752-0509-5-163  0.793
2011 Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BØ. A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. Molecular Systems Biology. 7: 535. PMID 21988831 DOI: 10.1038/Msb.2011.65  0.845
2011 Rolfsson O, Palsson BØ, Thiele I. The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. Bmc Systems Biology. 5: 155. PMID 21962087 DOI: 10.1186/1752-0509-5-155  0.632
2011 Cho BK, Palsson B, Zengler K. Deciphering the regulatory codes in bacterial genomes. Biotechnology Journal. 6: 1052-63. PMID 21845736 DOI: 10.1002/Biot.201000349  0.364
2011 Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K, Papin JA. Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Molecular Systems Biology. 7: 518. PMID 21811229 DOI: 10.1038/Msb.2011.52  0.803
2011 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, ... ... Palsson BO, et al. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nature Biotechnology. 29: 735-41. PMID 21804562 DOI: 10.1038/Nbt.1932  0.81
2011 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 Systems Biology. 5: 110. PMID 21749716 DOI: 10.1186/1752-0509-5-110  0.768
2011 Conrad TM, Lewis NE, Palsson BØ. Microbial laboratory evolution in the era of genome-scale science. Molecular Systems Biology. 7: 509. PMID 21734648 DOI: 10.1038/Msb.2011.42  0.716
2011 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. Frontiers in Microbiology. 2: 121. PMID 21687430 DOI: 10.3389/Fmicb.2011.00121  0.798
2011 Applebee MK, Joyce AR, Conrad TM, Pettigrew DW, Palsson BØ. Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli. The Journal of Biological Chemistry. 286: 23150-9. PMID 21550976 DOI: 10.1074/Jbc.M110.195305  0.789
2011 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. Journal of Bacteriology. 193: 1710-7. PMID 21296962 DOI: 10.1128/Jb.01218-10  0.476
2011 Schellenberger J, Lewis NE, Palsson BØ. Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophysical Journal. 100: 544-53. PMID 21281568 DOI: 10.1016/J.Bpj.2010.12.3707  0.792
2011 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, ... ... Palsson BO, et al. A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. Bmc Systems Biology. 5: 8. PMID 21244678 DOI: 10.1186/1752-0509-5-8  0.797
2011 Mahadevan R, Palsson BØ, Lovley DR. In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling. Nature Reviews. Microbiology. 9: 39-50. PMID 21132020 DOI: 10.1038/Nrmicro2456  0.38
2011 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 Research. 39: 1656-65. PMID 21051353 DOI: 10.1093/Nar/Gkq848  0.321
2011 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. Environmental Microbiology. 13: 13-23. PMID 20636372 DOI: 10.1111/J.1462-2920.2010.02302.X  0.328
2011 Hyduke D, Schellenberger J, Que R, Fleming R, Thiele I, Orth J, Feist A, Zielinski D, Bordbar A, Lewis N, Rahmanian S, Kang J, Palsson B. COBRA Toolbox 2.0 Protocol Exchange. DOI: 10.1038/Protex.2011.234  0.751
2011 Thiele I, Fleming RMT, Que R, Bordbar A, Palsson BO. A Systems Biology Approach to the Evolution of Codon Use Pattern Nature Precedings. DOI: 10.1038/Npre.2011.6312.1  0.674
2011 Jamshidi N, Palsson BO. Metabolic network dynamics: Properties and principles Understanding the Dynamics of Biological Systems: Lessons Learned From Integrative Systems Biology. 19-37. DOI: 10.1007/978-1-4419-7964-3_2  0.582
2010 Orth JD, Fleming RM, Palsson BØ. Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide. Ecosal Plus. 4. PMID 26443778 DOI: 10.1128/ecosalplus.10.2.1  0.759
2010 Lerman J, Palsson BO. Microbiology. Topping off a multiscale balancing act. Science (New York, N.Y.). 330: 1058-9. PMID 21097927 DOI: 10.1126/Science.1199353  0.743
2010 Charusanti P, Conrad TM, Knight EM, Venkataraman K, Fong NL, Xie B, Gao Y, Palsson BØ. Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene. Plos Genetics. 6: e1001186. PMID 21079674 DOI: 10.1371/Journal.Pgen.1001186  0.603
2010 Conrad TM, Frazier M, Joyce AR, Cho BK, Knight EM, Lewis NE, Landick R, Palsson BØ. RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proceedings of the National Academy of Sciences of the United States of America. 107: 20500-5. PMID 21057108 DOI: 10.1073/Pnas.0911253107  0.804
2010 Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Molecular Systems Biology. 6: 422. PMID 20959820 DOI: 10.1038/Msb.2010.68  0.829
2010 Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BØ. A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. Bmc Systems Biology. 4: 140. PMID 20959003 DOI: 10.1186/1752-0509-4-140  0.752
2010 Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ. Drug off-target effects predicted using structural analysis in the context of a metabolic network model. Plos Computational Biology. 6: e1000938. PMID 20957118 DOI: 10.1371/Journal.Pcbi.1000938  0.663
2010 Portnoy VA, Scott DA, Lewis NE, Tarasova Y, Osterman AL, Palsson BØ. Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655. Applied and Environmental Microbiology. 76: 6529-40. PMID 20709841 DOI: 10.1128/Aem.01178-10  0.83
2010 Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, Polpitiya AD, Adkins JN, Schramm G, Purvine SO, Lopez-Ferrer D, Weitz KK, Eils R, König R, Smith RD, Palsson BØ. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Molecular Systems Biology. 6: 390. PMID 20664636 DOI: 10.1038/Msb.2010.47  0.819
2010 Orth JD, Palsson B. Systematizing the generation of missing metabolic knowledge Biotechnology and Bioengineering. 107: 403-412. PMID 20589842 DOI: 10.1002/Bit.22844  0.763
2010 Feist AM, Palsson BO. The biomass objective function. Current Opinion in Microbiology. 13: 344-9. PMID 20430689 DOI: 10.1016/J.Mib.2010.03.003  0.651
2010 Schellenberger J, Park JO, Conrad TM, Palsson BØ. BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. Bmc Bioinformatics. 11: 213. PMID 20426874 DOI: 10.1186/1471-2105-11-213  0.837
2010 Thiele I, Palsson BØ. Reconstruction annotation jamborees: a community approach to systems biology. Molecular Systems Biology. 6: 361. PMID 20393581 DOI: 10.1038/Msb.2010.15  0.595
2010 Jamshidi N, Palsson BØ. Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models. Biophysical Journal. 98: 175-85. PMID 20338839 DOI: 10.1016/J.Bpj.2009.09.064  0.582
2010 Orth JD, Thiele I, Palsson BO. What is flux balance analysis? Nature Biotechnology. 28: 245-248. PMID 20212490 DOI: 10.1038/Nbt.1614  0.78
2010 Thiele I, Palsson BØ. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature Protocols. 5: 93-121. PMID 20057383 DOI: 10.1038/Nprot.2009.203  0.618
2010 Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BO. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli Metabolic Engineering. 12: 173-186. PMID 19840862 DOI: 10.1016/J.Ymben.2009.10.003  0.803
2010 Palsson B. Metabolic systems biology. Febs Letters. 583: 3900-4. PMID 19769971 DOI: 10.1016/J.Febslet.2009.09.031  0.449
2010 Thiele I, Fleming R, Rolfsson O, Palsson B. A systems biology approach for human metabolism in health and disease New Biotechnology. 27: S80. DOI: 10.1016/J.Nbt.2010.01.224  0.588
2009 Oberhardt MA, Palsson BØ, Papin JA. Applications of genome-scale metabolic reconstructions. Molecular Systems Biology. 5: 320. PMID 19888215 DOI: 10.1038/Msb.2009.77  0.802
2009 Conrad TM, Joyce AR, Applebee MK, Barrett CL, Xie B, Gao Y, Palsson BØ. Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biology. 10: R118. PMID 19849850 DOI: 10.1186/Gb-2009-10-10-R118  0.801
2009 Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A. Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science (New York, N.Y.). 325: 1544-9. PMID 19762644 DOI: 10.1126/Science.1174671  0.637
2009 Jamshidi N, Palsson BØ. Flux-concentration duality in dynamic nonequilibrium biological networks. Biophysical Journal. 97: L11-3. PMID 19720010 DOI: 10.1016/J.Bpj.2009.06.049  0.555
2009 Gianchandani EP, Joyce AR, Palsson BØ, Papin JA. Functional states of the genome-scale Escherichia coli transcriptional regulatory system. Plos Computational Biology. 5: e1000403. PMID 19503608 DOI: 10.1371/Journal.Pcbi.1000403  0.824
2009 Jamshidi N, Palsson BO. Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes. Bmc Systems Biology. 3: 44. PMID 19405968 DOI: 10.1186/1752-0509-3-44  0.647
2009 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. Journal of Bacteriology. 191: 3437-44. PMID 19363119 DOI: 10.1128/Jb.00034-09  0.621
2009 Raghunathan A, Reed J, Shin S, Palsson B, Daefler S. Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction Bmc Systems Biology. 3. PMID 19356237 DOI: 10.1186/1752-0509-3-38  0.515
2009 Mo ML, Palsson BO, HerrgÃ¥rd MJ. Connecting extracellular metabolomic measurements to intracellular flux states in yeast. Bmc Systems Biology. 3: 37. PMID 19321003 DOI: 10.1186/1752-0509-3-37  0.829
2009 Barrett CL, Herrgard MJ, Palsson B. Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation. Bmc Systems Biology. 3: 30. PMID 19267928 DOI: 10.1186/1752-0509-3-30  0.651
2009 Li F, Thiele I, Jamshidi N, Palsson BØ. Identification of potential pathway mediation targets in Toll-like receptor signaling. Plos Computational Biology. 5: e1000292. PMID 19229310 DOI: 10.1371/Journal.Pcbi.1000292  0.692
2009 Sigurdsson MI, Jamshidi N, Jonsson JJ, Palsson BO. Genome-scale network analysis of imprinted human metabolic genes. Epigenetics. 4: 43-6. PMID 19218833 DOI: 10.4161/Epi.4.1.7603  0.688
2009 Schellenberger J, Palsson BØ. Use of randomized sampling for analysis of metabolic networks. The Journal of Biological Chemistry. 284: 5457-61. PMID 18940807 DOI: 10.1074/Jbc.R800048200  0.77
2009 Li F, Thiele I, Jamshidi N, Palsson BØ. Correction: Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling Plos Computational Biology. 5. DOI: 10.1371/Annotation/5Cc0D918-83B8-44E4-9778-B96A249D4099  0.661
2009 Hua Q, Fong S, Palsson B. Phenotypic and metabolic properties of experimentally evolved microbial cells Journal of Bioscience and Bioengineering. 108: S165-S166. DOI: 10.1016/J.Jbiosc.2009.08.449  0.617
2009 Feist AM, Thiele I, Palsson B. Genome-scale reconstruction, modeling, and simulation of E. coli's metabolic network Systems Biology and Biotechnology of Escherichia Coli. 149-176. DOI: 10.1007/978-1-4020-9394-4_9  0.749
2009 Applebee MK, Palsson B. Genome-scale models and the genetic basis for E. coli adaptation Systems Biology and Biotechnology of Escherichia Coli. 237-256. DOI: 10.1007/978-1-4020-9394-4_12  0.803
2009 Joyce AR, Palsson B. In Silico Genome-Scale Metabolic Models: The Constraint-Based Approach and Its Applications Systems Biology and Synthetic Biology. 193-233. DOI: 10.1002/9780470437988.ch6  0.701
2008 Portnoy VA, Herrgård MJ, Palsson BØ. Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain. Applied and Environmental Microbiology. 74: 7561-9. PMID 18952873 DOI: 10.1128/Aem.00880-08  0.8
2008 Nogales J, Palsson BØ, Thiele I. A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. Bmc Systems Biology. 2: 79. PMID 18793442 DOI: 10.1186/1752-0509-2-79  0.645
2008 Jamshidi N, Palsson BØ. Top-down analysis of temporal hierarchy in biochemical reaction networks. Plos Computational Biology. 4: e1000177. PMID 18787685 DOI: 10.1371/Journal.Pcbi.1000177  0.619
2008 Lee J, Yun H, Feist AM, Palsson BØ, Lee SY. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Applied Microbiology and Biotechnology. 80: 849-62. PMID 18758767 DOI: 10.1007/S00253-008-1654-4  0.696
2008 Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E. Network-based prediction of human tissue-specific metabolism. Nature Biotechnology. 26: 1003-10. PMID 18711341 DOI: 10.1038/Nbt.1487  0.642
2008 Feist AM, Palsson BØ. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nature Biotechnology. 26: 659-67. PMID 18536691 DOI: 10.1038/Nbt1401  0.675
2008 Applebee MK, Herrgård MJ, Palsson BØ. Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli. Journal of Bacteriology. 190: 5087-94. PMID 18487343 DOI: 10.1128/Jb.01976-07  0.783
2008 Becker SA, Palsson BO. Context-specific metabolic networks are consistent with experiments. Plos Computational Biology. 4: e1000082. PMID 18483554 DOI: 10.1371/Journal.Pcbi.1000082  0.715
2008 Joyce AR, Palsson BØ. Predicting gene essentiality using genome-scale in silico models. Methods in Molecular Biology (Clifton, N.J.). 416: 433-57. PMID 18392986 DOI: 10.1007/978-1-59745-321-9_30  0.725
2008 Jamshidi N, Palsson BØ. Formulating genome-scale kinetic models in the post-genome era. Molecular Systems Biology. 4: 171. PMID 18319723 DOI: 10.1038/Msb.2008.8  0.625
2008 Becker SA, Palsson BO. Three factors underlying incorrect in silico predictions of essential metabolic genes. Bmc Systems Biology. 2: 14. PMID 18248675 DOI: 10.1186/1752-0509-2-14  0.664
2008 Reed JL, Hua Q, Palsson BO. Determining metabolic fluxes using experimental measurements Aiche Annual Meeting, Conference Proceedings 0.496
2007 Yeung M, Thiele I, Palsson BO. Estimation of the number of extreme pathways for metabolic networks. Bmc Bioinformatics. 8: 363. PMID 17897474 DOI: 10.1186/1471-2105-8-363  0.604
2007 Shlomi T, Herrgard M, Portnoy V, Naim E, Palsson BØ, Sharan R, Ruppin E. Systematic condition-dependent annotation of metabolic genes. Genome Research. 17: 1626-33. PMID 17895423 DOI: 10.1101/Gr.6678707  0.831
2007 Cho BK, Charusanti P, Herrgård MJ, Palsson BO. Microbial regulatory and metabolic networks. Current Opinion in Biotechnology. 18: 360-4. PMID 17719767 DOI: 10.1016/J.Copbio.2007.07.002  0.672
2007 Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Systems Biology. 3: 121. PMID 17593909 DOI: 10.1038/Msb4100155  0.834
2007 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. The Journal of Biological Chemistry. 282: 28791-9. PMID 17573341 DOI: 10.1074/Jbc.M703759200  0.653
2007 Jamshidi N, Vo TD, Palsson BO. In silico analysis of SNPs and other high-throughput data. Methods in Molecular Biology (Clifton, N.J.). 366: 267-85. PMID 17568130 DOI: 10.1007/978-1-59745-030-0_15  0.766
2007 Jamshidi N, Palsson BØ. Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. Bmc Systems Biology. 1: 26. PMID 17555602 DOI: 10.1186/1752-0509-1-26  0.607
2007 Hua Q, Joyce AR, Palsson BØ, Fong SS. Metabolic characterization of Escherichia coli strains adapted to growth on lactate. Applied and Environmental Microbiology. 73: 4639-47. PMID 17513588 DOI: 10.1128/Aem.00527-07  0.769
2007 Vo TD, Paul Lee WN, Palsson BO. Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome. Molecular Genetics and Metabolism. 91: 15-22. PMID 17336115 DOI: 10.1016/J.Ymgme.2007.01.012  0.659
2007 Joyce AR, Palsson BO. Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach. Progress in Drug Research. Fortschritte Der Arzneimittelforschung. ProgrèS Des Recherches Pharmaceutiques. 64: 265, 267-309. PMID 17195479 DOI: 10.1007/978-3-7643-7567-6_11  0.706
2007 Vo TD, Palsson BO. Building the power house: recent advances in mitochondrial studies through proteomics and systems biology. American Journal of Physiology. Cell Physiology. 292: C164-77. PMID 16885397 DOI: 10.1152/Ajpcell.00193.2006  0.64
2007 Thiele I, Palsson BO. Bringing genomes to life: The use of genome-scale in silico models Introduction to Systems Biology. 14-36. DOI: 10.1007/978-1-59745-531-2_2  0.568
2006 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. Proceedings of the National Academy of Sciences of the United States of America. 103: 17480-4. PMID 17088549 DOI: 10.1073/Pnas.0603364103  0.826
2006 Herring CD, Raghunathan A, Honisch C, Patel T, Applebee MK, Joyce AR, Albert TJ, Blattner FR, van den Boom D, Cantor CR, Palsson BØ. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nature Genetics. 38: 1406-12. PMID 17086184 DOI: 10.1038/Ng1906  0.812
2006 Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO. Matrix formalism to describe functional states of transcriptional regulatory systems. Plos Computational Biology. 2: e101. PMID 16895435 DOI: 10.1371/Journal.Pcbi.0020101  0.8
2006 Vo TD, Palsson BO. Isotopomer analysis of myocardial substrate metabolism: a systems biology approach. Biotechnology and Bioengineering. 95: 972-83. PMID 16878330 DOI: 10.1002/Bit.21063  0.642
2006 Herrgård MJ, Fong SS, Palsson BØ. Identification of genome-scale metabolic network models using experimentally measured flux profiles. Plos Computational Biology. 2: e72. PMID 16839195 DOI: 10.1371/Journal.Pcbi.0020072  0.77
2006 Jamshidi N, Palsson BØ. Systems biology of SNPs. Molecular Systems Biology. 2: 38. PMID 16820779 DOI: 10.1038/Msb4100077  0.598
2006 Hua Q, Joyce AR, Fong SS, Palsson BØ. Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains. Biotechnology and Bioengineering. 95: 992-1002. PMID 16807925 DOI: 10.1002/Bit.21073  0.76
2006 Feist AM, Scholten JC, Palsson BØ, Brockman FJ, Ideker T. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Molecular Systems Biology. 2: 2006.0004. PMID 16738551 DOI: 10.1038/Msb4100046  0.69
2006 Barrett CL, Palsson BO. Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. Plos Computational Biology. 2: e52. PMID 16710450 DOI: 10.1371/Journal.Pcbi.0020052  0.352
2006 Herrgård MJ, Lee BS, Portnoy V, Palsson BØ. Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Research. 16: 627-35. PMID 16606697 DOI: 10.1101/Gr.4083206  0.841
2006 Price ND, Thiele I, Palsson BØ. Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. Biophysical Journal. 90: 3919-28. PMID 16533855 DOI: 10.1529/Biophysj.105.072645  0.683
2006 Jamshidi N, Palsson BØ. Systems biology of the human red blood cell. Blood Cells, Molecules & Diseases. 36: 239-47. PMID 16533612 DOI: 10.1016/J.Bcmd.2006.01.006  0.587
2006 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. 7: 132. PMID 16533395 DOI: 10.1186/1471-2105-7-132  0.615
2006 Becker SA, Price ND, Palsson BØ. Metabolite coupling in genome-scale metabolic networks. Bmc Bioinformatics. 7: 111. PMID 16519800 DOI: 10.1186/1471-2105-7-111  0.717
2006 Joyce AR, Palsson BØ. The model organism as a system: integrating 'omics' data sets. Nature Reviews. Molecular Cell Biology. 7: 198-210. PMID 16496022 DOI: 10.1038/Nrm1857  0.649
2006 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. Applied and Environmental Microbiology. 72: 1558-68. PMID 16461711 DOI: 10.1128/Aem.72.2.1558-1568.2006  0.621
2006 Reed JL, Famili I, Thiele I, Palsson BO. Towards multidimensional genome annotation. Nature Reviews. Genetics. 7: 130-41. PMID 16418748 DOI: 10.1038/Nrg1769  0.807
2006 Allen TE, Price ND, Joyce AR, Palsson BØ. Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization. Plos Computational Biology. 2: e2. PMID 16410829 DOI: 10.1371/Journal.Pcbi.0020002  0.786
2006 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. The Journal of Biological Chemistry. 281: 8024-33. PMID 16319065 DOI: 10.1074/Jbc.M510016200  0.647
2006 Vo TD, Lim SK, Lee WNP, Palsson BO. Isotopomer analysis of cellular metabolism in tissue culture: A comparative study between the pathway and network-based methods Metabolomics. 2: 243-256. DOI: 10.1007/S11306-006-0033-3  0.705
2005 Fong SS, Joyce AR, Palsson BØ. The econometrics of evolution. Nature Chemical Biology. 1: 191-2. PMID 16408032 DOI: 10.1038/Nchembio0905-191  0.711
2005 Barrett CL, Herring CD, Reed JL, Palsson BO. The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states. Proceedings of the National Academy of Sciences of the United States of America. 102: 19103-8. PMID 16357206 DOI: 10.1073/Pnas.0505231102  0.641
2005 Fong SS, Joyce AR, Palsson BØ. Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Research. 15: 1365-72. PMID 16204189 DOI: 10.1101/Gr.3832305  0.727
2005 Herring CD, Raffaelle M, Allen TE, Kanin EI, Landick R, Ansari AZ, Palsson BØ. Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. Journal of Bacteriology. 187: 6166-74. PMID 16109958 DOI: 10.1128/Jb.187.17.6166-6174.2005  0.539
2005 Thiele I, Vo TD, Price ND, Palsson BØ. Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. Journal of Bacteriology. 187: 5818-30. PMID 16077130 DOI: 10.1128/Jb.187.16.5818-5830.2005  0.802
2005 Herrgård MJ, Palsson BØ. Untangling the web of functional and physical interactions in yeast. Journal of Biology. 4: 5. PMID 15982410 DOI: 10.1186/Jbiol26  0.583
2005 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 Biotechnology and Bioengineering. 91: 643-648. PMID 15962337 DOI: 10.1002/Bit.20542  0.599
2005 Becker SA, Palsson BØ. Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. Bmc Microbiology. 5: 8. PMID 15752426 DOI: 10.1186/1471-2180-5-8  0.673
2005 Papin JA, Hunter T, Palsson BO, Subramaniam S. Reconstruction of cellular signalling networks and analysis of their properties. Nature Reviews. Molecular Cell Biology. 6: 99-111. PMID 15654321 DOI: 10.1038/Nrm1570  0.58
2005 Famili I, Mahadevan R, Palsson BO. k-Cone analysis: determining all candidate values for kinetic parameters on a network scale. Biophysical Journal. 88: 1616-25. PMID 15626710 DOI: 10.1529/Biophysj.104.050385  0.779
2005 Mahadevan R, Palsson BO. Properties of metabolic networks: structure versus function. Biophysical Journal. 88: L07-9. PMID 15574705 DOI: 10.1529/Biophysj.104.055723  0.411
2005 Thiele I, Price ND, Vo TD, Palsson BØ. Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. The Journal of Biological Chemistry. 280: 11683-95. PMID 15572364 DOI: 10.1074/Jbc.M409072200  0.785
2004 Papin JA, Reed JL, Palsson BO. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends in Biochemical Sciences. 29: 641-7. PMID 15544950 DOI: 10.1016/J.Tibs.2004.10.001  0.662
2004 Westerhoff HV, Palsson BO. The evolution of molecular biology into systems biology. Nature Biotechnology. 22: 1249-52. PMID 15470464 DOI: 10.1038/Nbt1020  0.307
2004 Palsson B. Two-dimensional annotation of genomes. Nature Biotechnology. 22: 1218-1219. PMID 15470454 DOI: 10.1038/Nbt1004-1218  0.322
2004 Price ND, Schellenberger J, Palsson BO. Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. Biophysical Journal. 87: 2172-86. PMID 15454420 DOI: 10.1529/Biophysj.104.043000  0.814
2004 Fong SS, Palsson BØ. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nature Genetics. 36: 1056-8. PMID 15448692 DOI: 10.1038/Ng1432  0.613
2004 Duarte NC, Palsson BØ, Fu P. Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae. Bmc Genomics. 5: 63. PMID 15355549 DOI: 10.1186/1471-2164-5-63  0.376
2004 Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO. Comparison of network-based pathway analysis methods. Trends in Biotechnology. 22: 400-5. PMID 15283984 DOI: 10.1016/J.Tibtech.2004.06.010  0.713
2004 Papin JA, Palsson BO. The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. Biophysical Journal. 87: 37-46. PMID 15240442 DOI: 10.1529/Biophysj.103.029884  0.583
2004 Vo TD, Greenberg HJ, Palsson BO. Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. The Journal of Biological Chemistry. 279: 39532-40. PMID 15205464 DOI: 10.1074/Jbc.M403782200  0.673
2004 Duarte NC, Herrgård MJ, Palsson BØ. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Research. 14: 1298-309. PMID 15197165 DOI: 10.1101/Gr.2250904  0.691
2004 Herrgård MJ, Palsson BØ. Flagellar biosynthesis in silico: building quantitative models of regulatory networks. Cell. 117: 689-90. PMID 15186769 DOI: 10.1016/J.Cell.2004.05.020  0.632
2004 Wiback SJ, Famili I, Greenberg HJ, Palsson BØ. Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space. Journal of Theoretical Biology. 228: 437-47. PMID 15178193 DOI: 10.1016/J.Jtbi.2004.02.006  0.798
2004 Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 429: 92-6. PMID 15129285 DOI: 10.1038/Nature02456  0.84
2004 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 : a Journal of Integrative Biology. 8: 25-41. PMID 15107235 DOI: 10.1089/153623104773547471  0.608
2004 Herrgård MJ, Covert MW, Palsson BØ. Reconstruction of microbial transcriptional regulatory networks. Current Opinion in Biotechnology. 15: 70-7. PMID 15102470 DOI: 10.1016/J.Copbio.2003.11.002  0.79
2004 Wiback SJ, Mahadevan R, Palsson BØ. Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum. Biotechnology and Bioengineering. 86: 317-31. PMID 15083512 DOI: 10.1002/Bit.20011  0.827
2004 Papin JA, Palsson BO. Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. Journal of Theoretical Biology. 227: 283-97. PMID 14990392 DOI: 10.1016/J.Jtbi.2003.11.016  0.599
2003 Ibarra RU, Fu P, Palsson BO, DiTonno JR, Edwards JS. Quantitative analysis of Escherichia coli metabolic phenotypes within the context of phenotypic phase planes. Journal of Molecular Microbiology and Biotechnology. 6: 101-8. PMID 15044828 DOI: 10.1159/000076740  0.63
2003 Covert MW, Famili I, Palsson BO. Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology? Biotechnology and Bioengineering. 84: 763-72. PMID 14708117 DOI: 10.1002/Bit.10849  0.802
2003 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. Proceedings of the National Academy of Sciences of the United States of America. 100: 13134-9. PMID 14578455 DOI: 10.1073/Pnas.2235812100  0.845
2003 Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BO. Network-based analysis of metabolic regulation in the human red blood cell. Journal of Theoretical Biology. 225: 185-94. PMID 14575652 DOI: 10.1016/S0022-5193(03)00237-6  0.823
2003 Fong SS, Marciniak JY, Palsson BØ. Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model. Journal of Bacteriology. 185: 6400-8. PMID 14563875 DOI: 10.1128/Jb.185.21.6400-6408.2003  0.609
2003 Allen TE, Herrgård MJ, Liu M, Qiu Y, Glasner JD, Blattner FR, Palsson BØ. Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets. Journal of Bacteriology. 185: 6392-9. PMID 14563874 DOI: 10.1128/Jb.185.21.6392-6399.2003  0.768
2003 Herrgård MJ, Covert MW, Palsson BØ. Reconciling gene expression data with known genome-scale regulatory network structures. Genome Research. 13: 2423-34. PMID 14559784 DOI: 10.1101/Gr.1330003  0.767
2003 Förster J, Famili I, Palsson BO, Nielsen J. Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. Omics : a Journal of Integrative Biology. 7: 193-202. PMID 14506848 DOI: 10.1089/153623103322246584  0.832
2003 Reed JL, Vo TD, Schilling CH, Palsson BO. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biology. 4: R54. PMID 12952533 DOI: 10.1186/Gb-2003-4-9-R54  0.811
2003 Wiback SJ, Mahadevan R, Palsson BØ. Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum. Journal of Theoretical Biology. 224: 313-24. PMID 12941590 DOI: 10.1016/S0022-5193(03)00168-1  0.817
2003 Famili I, Palsson BO. Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices. Journal of Theoretical Biology. 224: 87-96. PMID 12900206 DOI: 10.1016/S0022-5193(03)00146-2  0.807
2003 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, ... ... Palsson BO, et al. Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. Journal of Bacteriology. 185: 4593-602. PMID 12867470 DOI: 10.1128/Jb.185.15.4593-4602.2003  0.344
2003 Famili I, Palsson BO. The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools. Biophysical Journal. 85: 16-26. PMID 12829460 DOI: 10.1016/S0006-3495(03)74450-6  0.775
2003 Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO. Metabolic pathways in the post-genome era. Trends in Biochemical Sciences. 28: 250-8. PMID 12765837 DOI: 10.1016/S0968-0004(03)00064-1  0.838
2003 Palsson BO, Price ND, Papin JA. Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends in Biotechnology. 21: 195-8. PMID 12727379 DOI: 10.1016/S0167-7799(03)00080-5  0.691
2003 Price ND, Papin JA, Schilling CH, Palsson BO. Genome-scale microbial in silico models: the constraints-based approach. Trends in Biotechnology. 21: 162-9. PMID 12679064 DOI: 10.1016/S0167-7799(03)00030-1  0.807
2003 Covert MW, Palsson BO. Constraints-based models: regulation of gene expression reduces the steady-state solution space. Journal of Theoretical Biology. 221: 309-25. PMID 12642111 DOI: 10.1006/Jtbi.2003.3071  0.719
2003 Förster J, Famili I, Fu P, Palsson BØ, Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Research. 13: 244-53. PMID 12566402 DOI: 10.1101/Gr.234503  0.83
2003 Price ND, Reed JL, Papin JA, Famili I, Palsson BO. Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophysical Journal. 84: 794-804. PMID 12547764 DOI: 10.1016/S0006-3495(03)74899-1  0.824
2003 Allen TE, Palsson BØ. Sequence-based analysis of metabolic demands for protein synthesis in prokaryotes. Journal of Theoretical Biology. 220: 1-18. PMID 12453446 DOI: 10.1006/Jtbi.2003.3087  0.634
2002 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 : a Journal of Integrative Biology. 6: 341-8. PMID 12626093 DOI: 10.1089/153623102321112764  0.379
2002 Papin JA, Price ND, Palsson BØ. Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Research. 12: 1889-900. PMID 12466293 DOI: 10.1101/Gr.327702  0.686
2002 Ibarra RU, Edwards JS, Palsson BO. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature. 420: 186-9. PMID 12432395 DOI: 10.1038/Nature01149  0.627
2002 Price ND, Famili I, Beard DA, Palsson BØ. Extreme pathways and Kirchhoff's second law. Biophysical Journal. 83: 2879-82. PMID 12425318 DOI: 10.1016/S0006-3495(02)75297-1  0.809
2002 Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO. Genome-scale metabolic model of Helicobacter pylori 26695. Journal of Bacteriology. 184: 4582-93. PMID 12142428 DOI: 10.1128/Jb.184.16.4582-4593.2002  0.844
2002 Wiback SJ, Palsson BO. Extreme pathway analysis of human red blood cell metabolism. Biophysical Journal. 83: 808-18. PMID 12124266 DOI: 10.1016/S0006-3495(02)75210-7  0.828
2002 Kauffman KJ, Pajerowski JD, Jamshidi N, Palsson BO, Edwards JS. Description and analysis of metabolic connectivity and dynamics in the human red blood cell. Biophysical Journal. 83: 646-62. PMID 12124254 DOI: 10.1016/S0006-3495(02)75198-9  0.748
2002 Palsson B. In silico biology through "omics". Nature Biotechnology. 20: 649-650. PMID 12089538 DOI: 10.1038/Nbt0702-649  0.356
2002 Francis K, Palsson B, Donahue J, Fong S, Carrier E. Murine Sca-1(+)/Lin(-) cells and human KG1a cells exhibit multiple pseudopod morphologies during migration. Experimental Hematology. 30: 460-3. PMID 12031652 DOI: 10.1016/S0301-472X(02)00778-6  0.658
2002 Covert MW, Palsson BØ. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. The Journal of Biological Chemistry. 277: 28058-64. PMID 12006566 DOI: 10.1074/Jbc.M201691200  0.727
2002 Edwards JS, Covert M, Palsson B. Metabolic modelling of microbes: the flux-balance approach. Environmental Microbiology. 4: 133-40. PMID 12000313 DOI: 10.1046/J.1462-2920.2002.00282.X  0.762
2002 Price ND, Papin JA, Palsson BØ. Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Research. 12: 760-9. PMID 11997342 DOI: 10.1101/Gr.218002  0.707
2002 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 Cellular & Developmental Biology. Animal. 38: 90-6. PMID 11929001 DOI: 10.1290/1071-2690(2002)038<0090:Caeopa>2.0.Co;2  0.701
2002 Edwards JS, Ramakrishna R, Palsson BO. Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnology and Bioengineering. 77: 27-36. PMID 11745171 DOI: 10.1002/Bit.10047  0.647
2002 Francis K, Palsson B. Comment on "Time Dependent Concentration Profile of Secreted Molecules in the Intercellular Signaling" Journal of the Physical Society of Japan. 71: 1005-1006. DOI: 10.1143/Jpsj.71.1005  0.5
2002 Francis K, Lee GM, Palsson BO. Characterization of the KG1a cell line for use in a cell migration based screening assay Biotechnology and Bioprocess Engineering. 7: 178-184. DOI: 10.1007/Bf02932916  0.628
2002 Halberstadt CR, Palsson BO, Midgley AR, Curl RL. Optimization and mathematical modeling of the transtubular bioreactor for the production of monoclonal antibodies from a hybridoma cell line Biotechnology and Bioprocess Engineering. 7: 163-170. DOI: 10.1007/Bf02932914  0.677
2001 Covert MW, Schilling CH, Palsson B. Regulation of gene expression in flux balance models of metabolism. Journal of Theoretical Biology. 213: 73-88. PMID 11708855 DOI: 10.1006/Jtbi.2001.2405  0.798
2001 Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson BO. Dynamic simulation of the human red blood cell metabolic network. Bioinformatics (Oxford, England). 17: 286-7. PMID 11294796 DOI: 10.1093/Bioinformatics/17.3.286  0.762
2001 Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO. Metabolic modeling of microbial strains in silico. Trends in Biochemical Sciences. 26: 179-86. PMID 11246024 DOI: 10.1016/S0968-0004(00)01754-0  0.847
2001 Edwards JS, Ibarra RU, Palsson BO. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nature Biotechnology. 19: 125-30. PMID 11175725 DOI: 10.1038/84379  0.667
2001 Ramakrishna R, Edwards JS, McCulloch A, Palsson BO. Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. American Journal of Physiology. Regulatory, Integrative and Comparative Physiology. 280: R695-704. PMID 11171647 DOI: 10.1152/Ajpregu.2001.280.3.R695  0.593
2000 Schilling CH, Edwards JS, Letscher D, Palsson BØ. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnology and Bioengineering. 71: 286-306. PMID 11291038 DOI: 10.1002/1097-0290(2000)71:4<286::Aid-Bit1018>3.0.Co;2-R  0.716
2000 Edwards JS, Palsson BO. Robustness analysis of the Escherichia coli metabolic network. Biotechnology Progress. 16: 927-39. PMID 11101318 DOI: 10.1021/Bp0000712  0.65
2000 Edwards JS, Palsson BO. Multiple steady states in kinetic models of red cell metabolism. Journal of Theoretical Biology. 207: 125-7. PMID 11027485 DOI: 10.1006/Jtbi.2000.2165  0.592
2000 Edwards JS, Palsson BO. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. Bmc Bioinformatics. 1: 1. PMID 11001586 DOI: 10.1186/1471-2105-1-1  0.662
2000 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. 40: 119-25. PMID 10805931 DOI: 10.1002/(Sici)1097-0320(20000601)40:2<119::Aid-Cyto5>3.0.Co;2-P  0.618
2000 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. 40: 109-18. PMID 10805930 DOI: 10.1002/(Sici)1097-0320(20000601)40:2<109::Aid-Cyto4>3.0.Co;2-V  0.63
2000 Edwards JS, Palsson BO. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proceedings of the National Academy of Sciences of the United States of America. 97: 5528-33. PMID 10805808 DOI: 10.1073/Pnas.97.10.5528  0.655
2000 Schilling CH, Palsson BO. Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. Journal of Theoretical Biology. 203: 249-83. PMID 10716908 DOI: 10.1006/jtbi.2000.1088  0.64
2000 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. Journal of Theoretical Biology. 203: 229-48. PMID 10716907 DOI: 10.1006/jtbi.2000.1073  0.62
2000 Lee GM, Fong S, Francis K, Oh DJ, Palsson BO. In situ labeling of adherent cells with PKH26. In Vitro Cellular & Developmental Biology. Animal. 36: 4-6. PMID 10691033 DOI: 10.1290/1071-2690(2000)036<0004:Isloac>2.0.Co;2  0.693
1999 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. 37: 171-7. PMID 10520196 DOI: 10.1002/(Sici)1097-0320(19991101)37:3<171::Aid-Cyto2>3.0.Co;2-8  0.52
1999 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. 94: 2595-604. PMID 10515863 DOI: 10.1182/Blood.V94.8.2595.420K37_2595_2604  0.528
1999 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. 36: 312-8. PMID 10404146 DOI: 10.1002/(Sici)1097-0320(19990801)36:4<312::Aid-Cyto5>3.0.Co;2-V  0.616
1999 Edwards JS, Palsson BO. Systems properties of the Haemophilus influenzae Rd metabolic genotype. The Journal of Biological Chemistry. 274: 17410-6. PMID 10364169 DOI: 10.1074/Jbc.274.25.17410  0.614
1999 Schilling CH, Schuster S, Palsson BO, Heinrich R. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnology Progress. 15: 296-303. PMID 10356246 DOI: 10.1021/Bp990048K  0.648
1999 Schilling CH, Edwards JS, Palsson BO. Toward metabolic phenomics: analysis of genomic data using flux balances. Biotechnology Progress. 15: 288-95. PMID 10356245 DOI: 10.1021/Bp9900357  0.749
1998 Andreadis S, Fuller AO, Palsson BO. Cell cycle dependence of retroviral transduction: An issue of overlapping time scales. Biotechnology and Bioengineering. 58: 272-81. PMID 10191401 DOI: 10.1002/(Sici)1097-0290(19980420)58:2/3<272::Aid-Bit23>3.0.Co;2-D  0.533
1998 Edwards JS, Palsson BO. How will bioinformatics influence metabolic engineering? Biotechnology and Bioengineering. 58: 162-9. PMID 10191386 DOI: 10.1002/(Sici)1097-0290(19980420)58:2/3<162::Aid-Bit8>3.0.Co;2-J  0.655
1998 Mandalam RK, Palsson BO. Elemental balancing of biomass and medium composition enhances growth capacity in high-density Chlorella vulgaris cultures. Biotechnology and Bioengineering. 59: 605-11. PMID 10099378 DOI: 10.1002/(SICI)1097-0290(19980905)59:5<605::AID-BIT11>3.0.CO;2-8  0.697
1998 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. 92: 3616-23. PMID 9808555 DOI: 10.1182/Blood.V92.10.3616.422K19_3616_3623  0.513
1998 Schilling CH, Palsson BO. The underlying pathway structure of biochemical reaction networks. Proceedings of the National Academy of Sciences of the United States of America. 95: 4193-8. PMID 9539712 DOI: 10.1073/Pnas.95.8.4193  0.596
1998 Lee GM, Choi JH, Jun SC, Palsson BO. Temperature significantly affects retroviral vector production and deactivation rates, and thereby determines retroviral titers Bioprocess Engineering. 19: 343. DOI: 10.1007/S004490050530  0.473
1997 Francis K, Palsson BO. Effective intercellular communication distances are determined by the relative time constants for cyto/chemokine secretion and diffusion. Proceedings of the National Academy of Sciences of the United States of America. 94: 12258-62. PMID 9356436 DOI: 10.1073/Pnas.94.23.12258  0.535
1997 Andreadis ST, Brott D, Fuller AO, Palsson BO. Moloney murine leukemia virus-derived retroviral vectors decay intracellularly with a half-life in the range of 5.5 to 7.5 hours. Journal of Virology. 71: 7541-8. PMID 9311834 DOI: 10.1128/Jvi.71.10.7541-7548.1997  0.554
1997 Andreadis S, Palsson BO. Coupled effects of polybrene and calf serum on the efficiency of retroviral transduction and the stability of retroviral vectors. Human Gene Therapy. 8: 285-91. PMID 9048195 DOI: 10.1089/Hum.1997.8.3-285  0.535
1997 Mandalam RK, Palsson BØ. Cell cycle of Chlorella vulgaris can deviate from the synchronous binary division model Biotechnology Letters. 19: 587-591. DOI: 10.1023/A:1018310008826  0.708
1997 Palsson B. Bioinformatics for bioengineers Annals of Biomedical Engineering. 25. DOI: 10.1007/Bf02647383  0.32
1996 Peng CA, Koller MR, Palsson BØ. Unilineage model of hematopoiesis predicts self-renewal of stem and progenitor cells based on ex vivo growth data. Biotechnology and Bioengineering. 52: 24-33. PMID 18629849 DOI: 10.1002/(Sici)1097-0290(19961005)52:1<24::Aid-Bit3>3.0.Co;2-0  0.587
1996 Peng CA, Palsson BØ. Cell growth and differentiation on feeder layers is predicted to be influenced by bioreactor geometry. Biotechnology and Bioengineering. 50: 479-92. PMID 18627010 DOI: 10.1002/(Sici)1097-0290(19960605)50:5<479::Aid-Bit2>3.0.Co;2-C  0.593
1996 Chuck AS, Palsson BØ. Membrane adsorption characteristics determine the kinetics of flow-through transductions. Biotechnology and Bioengineering. 51: 260-70. PMID 18624359 DOI: 10.1002/(SICI)1097-0290(19960805)51:3<260::AID-BIT2>3.0.CO;2-B  0.577
1996 Chuck AS, Palsson BO. Consistent and high rates of gene transfer can be obtained using flow-through transduction over a wide range of retroviral titers. Human Gene Therapy. 7: 743-50. PMID 8919596 DOI: 10.1089/Hum.1996.7.6-743  0.627
1996 Andreadis ST, Palsson BO. Kinetics of retrovirus mediated gene transfer: the importance of intracellular half-life of retroviruses. Journal of Theoretical Biology. 182: 1-20. PMID 8917734 DOI: 10.1006/Jtbi.1996.0140  0.586
1996 Chuck AS, Clarke MF, Palsson BO. Retroviral infection is limited by Brownian motion. Human Gene Therapy. 7: 1527-34. PMID 8864753 DOI: 10.1089/hum.1996.7.13-1527  0.619
1996 Peng CA, Palsson BO. Determination of specific oxygen uptake rates in human hematopoietic cultures and implications for bioreactor design. Annals of Biomedical Engineering. 24: 373-81. PMID 8734058 DOI: 10.1007/Bf02660886  0.614
1995 Varma A, Palsson BO. Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism. Biotechnology and Bioengineering. 45: 69-79. PMID 18623053 DOI: 10.1002/Bit.260450110  0.622
1995 Mandalam RK, Palsson BO. Chlorella vulgaris (Chlorellaceae ) does not secrete autoinhibitors at high cell densities American Journal of Botany. 82: 955-963. DOI: 10.1002/J.1537-2197.1995.Tb11559.X  0.703
1994 Lee CG, Palsson BØ. High-density algal photobioreactors using light-emitting diodes. Biotechnology and Bioengineering. 44: 1161-7. PMID 18618541 DOI: 10.1002/bit.260441002  0.44
1994 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. Biotechnology and Bioengineering. 43: 734-9. PMID 18615796 DOI: 10.1002/Bit.260430807  0.414
1994 Varma A, Palsson BO. Predictions for oxygen supply control to enhance population stability of engineered production strains. Biotechnology and Bioengineering. 43: 275-85. PMID 18615690 DOI: 10.1002/Bit.260430403  0.542
1994 Varma A, Palsson BO. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Applied and Environmental Microbiology. 60: 3724-31. PMID 7986045 DOI: 10.1128/Aem.60.10.3724-3731.1994  0.591
1994 Lee GM, Kim SJ, Palsson BO. Enhanced specific antibody productivity of calcium alginate-entrapped hybridoma is cell line-specific. Cytotechnology. 16: 1-15. PMID 7765785 DOI: 10.1007/Bf00761774  0.449
1994 Lee GM, Palsson BO. Monoclonal antibody production using free-suspended and entrapped hybridoma cells. Biotechnology & Genetic Engineering Reviews. 12: 509-33. PMID 7727036 DOI: 10.1080/02648725.1994.10647920  0.443
1994 Varma A, Palsson BO. Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use Bio/Technology. 12: 994-998. DOI: 10.1038/Nbt1094-994  0.6
1993 Varma A, Palsson BO. Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors. Journal of Theoretical Biology. 165: 477-502. PMID 21322280 DOI: 10.1006/Jtbi.1993.1202  0.615
1993 Lee GM, Palsson BO. Stability of antibody productivity is improved when hybridoma cells are entrapped in calcium alginate beads. Biotechnology and Bioengineering. 42: 1131-5. PMID 18613244 DOI: 10.1002/Bit.260420917  0.468
1993 Varma A, Boesch BW, Palsson BO. Biochemical production capabilities of Escherichia coli. Biotechnology and Bioengineering. 42: 59-73. PMID 18609648 DOI: 10.1002/Bit.260420109  0.583
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