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Bernhard Palsson

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

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Seif Y, Kavvas E, Lachance JC, Yurkovich JT, Nuccio SP, Fang X, Catoiu E, Raffatellu M, Palsson BO, Monk JM. Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. Nat Commun. 2018 Sep 14; 9(1):3771. PMID: 30218022.
      View in: PubMed
    2. Gao Y, Yurkovich JT, Seo SW, Kabimoldayev I, Dräger A, Chen K, Sastry AV, Fang X, Mih N, Yang L, Eichner J, Cho BK, Kim D, Palsson BO. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. Nucleic Acids Res. 2018 Aug 23. PMID: 30137486.
      View in: PubMed
    3. Santos-Zavaleta A, Sánchez-Pérez M, Salgado H, Velázquez-Ramírez DA, Gama-Castro S, Tierrafría VH, Busby SJW, Aquino P, Fang X, Palsson BO, Galagan JE, Collado-Vides J. A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0. BMC Biol. 2018 Aug 16; 16(1):91. PMID: 30115066.
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    4. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome. Front Microbiol. 2018; 9:1793. PMID: 30131786.
      View in: PubMed
    5. Yurkovich JT, Alcantar MA, Haiman ZB, Palsson BO. Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials. PLoS Comput Biol. 2018 Aug 07; 14(8):e1006356. PMID: 30086174.
      View in: PubMed
    6. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in Escherichia coli pgi knockout evolutions. Appl Environ Microbiol. 2018 Jul 27. PMID: 30054360.
      View in: PubMed
    7. Lloyd CJ, Ebrahim A, Yang L, King ZA, Catoiu E, O'Brien EJ, Liu JK, Palsson BO. COBRAme: A computational framework for genome-scale models of metabolism and gene expression. PLoS Comput Biol. 2018 Jul 05; 14(7):e1006302. PMID: 29975681.
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    8. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System. Metab Eng. 2018 Jun 12. PMID: 29906504.
      View in: PubMed
    9. Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L, Palsson BO. Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. BMC Syst Biol. 2018 Jun 11; 12(1):66. PMID: 29890970.
      View in: PubMed
    10. Du B, Zhang Z, Grubner S, Yurkovich JT, Palsson BO, Zielinski DC. Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method. Biophys J. 2018 Jun 05; 114(11):2691-2702. PMID: 29874618.
      View in: PubMed
    11. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes. Metab Eng. 2018 May 26. PMID: 29842925.
      View in: PubMed
    12. Choudhary KS, Mih N, Monk J, Kavvas E, Yurkovich JT, Sakoulas G, Palsson BO. The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures. Front Microbiol. 2018; 9:1082. PMID: 29887846.
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    13. Latif H, Federowicz S, Ebrahim A, Tarasova J, Szubin R, Utrilla J, Zengler K, Palsson BO. ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. PLoS One. 2018; 13(5):e0197272. PMID: 29771928.
      View in: PubMed
    14. Norsigian CJ, Kavvas E, Seif Y, Palsson BO, Monk JM. iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE. Front Genet. 2018; 9:121. PMID: 29692801.
      View in: PubMed
    15. Kim D, Seo SW, Gao Y, Nam H, Guzman GI, Cho BK, Palsson BO. Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP. Nucleic Acids Res. 2018 Apr 06; 46(6):2901-2917. PMID: 29394395.
      View in: PubMed
    16. Yurkovich JT, Bordbar A, Sigurjónsson ÓE, Palsson BO. Systems biology as an emerging paradigm in transfusion medicine. BMC Syst Biol. 2018 Mar 07; 12(1):31. PMID: 29514691.
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    17. Kavvas ES, Seif Y, Yurkovich JT, Norsigian C, Poudel S, Greenwald WW, Ghatak S, Palsson BO, Monk JM. Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. BMC Syst Biol. 2018 Mar 02; 12(1):25. PMID: 29499714.
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    18. Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlic A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 Mar; 36(3):272-281. PMID: 29457794.
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    19. 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. 2018 Feb 12. PMID: 29444205.
      View in: PubMed
    20. Yurkovich JT, Palsson BO. Quantitative -omic data empowers bottom-up systems biology. Curr Opin Biotechnol. 2018 Feb 03; 51:130-136. PMID: 29414439.
      View in: PubMed
    21. Yang L, Yurkovich JT, King ZA, Palsson BO. Modeling the multi-scale mechanisms of macromolecular resource allocation. Curr Opin Microbiol. 2018 Jan 20; 45:8-15. PMID: 29367175.
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    22. Abdel-Haleem AM, Hefzi H, Mineta K, Gao X, Gojobori T, Palsson BO, Lewis NE, Jamshidi N. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. PLoS Comput Biol. 2018 Jan; 14(1):e1005895. PMID: 29300748.
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    23. Nilsson A, Nielsen J, Palsson BO. Metabolic Models of Protein Allocation Call for the Kinetome. Cell Syst. 2017 Dec 27; 5(6):538-541. PMID: 29284126.
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    24. Du B, Zielinski DC, Palsson BO. Topological and kinetic determinants of the modal matrices of dynamic models of metabolism. PLoS One. 2017; 12(12):e0189880. PMID: 29267329.
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    25. Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR. Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli. Proc Natl Acad Sci U S A. 2018 Jan 02; 115(1):222-227. PMID: 29255023.
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    26. Yang JH, Bhargava P, McCloskey D, Mao N, Palsson BO, Collins JJ. Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function. Cell Host Microbe. 2017 Dec 13; 22(6):757-765.e3. PMID: 29199098.
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    27. Yurkovich JT, Zielinski DC, Yang L, Paglia G, Rolfsson O, Sigurjónsson ÓE, Broddrick JT, Bordbar A, Wichuk K, Brynjólfsson S, Palsson S, Gudmundsson S, Palsson BO. Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks. J Biol Chem. 2017 12 01; 292(48):19556-19564. PMID: 29030425.
      View in: PubMed
    28. Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist AM, Palsson BO. iML1515, a knowledgebase that computes Escherichia coli traits. Nat Biotechnol. 2017 Oct 11; 35(10):904-908. PMID: 29020004.
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    29. Chen K, Gao Y, Mih N, O'Brien EJ, Yang L, Palsson BO. Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation. Proc Natl Acad Sci U S A. 2017 Oct 24; 114(43):11548-11553. PMID: 29073085.
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    30. Yurkovich JT, Yurkovich BJ, Dräger A, Palsson BO, King ZA. A Padawan Programmer's Guide to Developing Software Libraries. Cell Syst. 2017 Nov 22; 5(5):431-437. PMID: 28988801.
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    31. Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR. Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring. Metab Eng. 2017 Nov; 44:100-107. PMID: 28951266.
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    32. Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, Palsson BO. Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities. Proc Natl Acad Sci U S A. 2017 Sep 19; 114(38):10286-10291. PMID: 28874552.
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    33. Sastry A, Monk J, Tegel H, Uhlen M, Palsson BO, Rockberg J, Brunk E. Machine learning in computational biology to accelerate high-throughput protein expression. Bioinformatics. 2017 Aug 15; 33(16):2487-2495. PMID: 28398465.
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    34. Sandberg TE, Lloyd CJ, Palsson BO, Feist AM. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies. Appl Environ Microbiol. 2017 07 01; 83(13). PMID: 28455337.
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    35. Seo SW, Gao Y, Kim D, Szubin R, Yang J, Cho BK, Palsson BO. Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655. Sci Rep. 2017 May 19; 7(1):2181. PMID: 28526842.
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    36. Bordbar A, Yurkovich JT, Paglia G, Rolfsson O, Sigurjónsson ÓE, Palsson BO. Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics. Sci Rep. 2017 Apr 07; 7:46249. PMID: 28387366.
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    37. LaCroix RA, Palsson BO, Feist AM. A Model for Designing Adaptive Laboratory Evolution Experiments. Appl Environ Microbiol. 2017 04 15; 83(8). PMID: 28159796.
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    38. Yurkovich JT, Yang L, Palsson BO. Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells. PLoS Comput Biol. 2017 Mar; 13(3):e1005424. PMID: 28264007.
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    39. Levering J, Dupont CL, Allen AE, Palsson BO, Zengler K. Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels. mSystems. 2017 Jan-Feb; 2(1). PMID: 28217746.
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    40. Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson BO. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism. Sci Rep. 2017 Jan 25; 7:41241. PMID: 28120890.
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    41. Ma D, Yang L, Fleming RM, Thiele I, Palsson BO, Saunders MA. Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression. Sci Rep. 2017 Jan 18; 7:40863. PMID: 28098205.
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    42. van Wijk XM, Döhrmann S, Hallström BM, Li S, Voldborg BG, Meng BX, McKee KK, van Kuppevelt TH, Yurchenco PD, Palsson BO, Lewis NE, Nizet V, Esko JD. Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin a2 as a Host Factor for Bacterial Invasion. MBio. 2017 01 10; 8(1). PMID: 28074024.
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    43. King ZA, O'Brien EJ, Feist AM, Palsson BO. Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion. Metab Eng. 2017 01; 39:220-227. PMID: 27986597.
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    44. Broddrick JT, Rubin BE, Welkie DG, Du N, Mih N, Diamond S, Lee JJ, Golden SS, Palsson BO. Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis. Proc Natl Acad Sci U S A. 2016 12 20; 113(51):E8344-E8353. PMID: 27911809.
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    45. Hefzi H, Ang KS, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D, Martinez VS, Kyriakopoulos S, Jiménez NE, Zielinski DC, Quek LE, Wulff T, Arnsdorf J, Li S, Lee JS, Paglia G, Loira N, Spahn PN, Pedersen LE, Gutierrez JM, King ZA, Lund AM, Nagarajan H, Thomas A, Abdel-Haleem AM, Zanghellini J, Kildegaard HF, Voldborg BG, Gerdtzen ZP, Betenbaugh MJ, Palsson BO, Andersen MR, Nielsen LK, Borth N, Lee DY, Lewis NE. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Syst. 2016 Nov 23; 3(5):434-443.e8. PMID: 27883890.
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    46. Yang L, Yurkovich JT, Lloyd CJ, Ebrahim A, Saunders MA, Palsson BO. Principles of proteome allocation are revealed using proteomic data and genome-scale models. Sci Rep. 2016 11 18; 6:36734. PMID: 27857205.
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    47. D'Alessandro A, Nemkov T, Yoshida T, Bordbar A, Palsson BO, Hansen KC. Citrate metabolism in red blood cells stored in additive solution-3. Transfusion. 2017 02; 57(2):325-336. PMID: 27813142.
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    48. Aziz RK, Monk JM, Andrews KA, Nhan J, Khaw VL, Wong H, Palsson BO, Charusanti P. The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli. Microbiol Res. 2017 Jan; 194:47-52. PMID: 27938862.
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    49. Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM, Palsson BO. Multi-omic data integration enables discovery of hidden biological regularities. Nat Commun. 2016 Oct 26; 7:13091. PMID: 27782110.
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    50. Yang L, Ma D, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO. solveME: fast and reliable solution of nonlinear ME models. BMC Bioinformatics. 2016 Sep 22; 17(1):391. PMID: 27659412.
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    51. Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ, Feist AM. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Syst. 2016 Sep 28; 3(3):238-251.e12. PMID: 27667363.
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    52. Paglia G, D'Alessandro A, Rolfsson Ó, Sigurjónsson ÓE, Bordbar A, Palsson S, Nemkov T, Hansen KC, Gudmundsson S, Palsson BO. Biomarkers defining the metabolic age of red blood cells during cold storage. Blood. 2016 09 29; 128(13):e43-50. PMID: 27554084.
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    53. Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 2016 08 09; 34(8):828-837. PMID: 27504778.
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    54. Paglia G, Sigurjónsson ÓE, Bordbar A, Rolfsson Ó, Magnusdottir M, Palsson S, Wichuk K, Gudmundsson S, Palsson BO. Metabolic fate of adenine in red blood cells during storage in SAGM solution. Transfusion. 2016 Oct; 56(10):2538-2547. PMID: 27491795.
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    55. Mih N, Brunk E, Bordbar A, Palsson BO. A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PLoS Comput Biol. 2016 Jul; 12(7):e1005039. PMID: 27467583; PMCID: PMC4965186.
    56. O'Brien EJ, Utrilla J, Palsson BO. Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. PLoS Comput Biol. 2016 06; 12(6):e1004998. PMID: 27351952.
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    57. Du B, Zielinski DC, Kavvas ES, Dräger A, Tan J, Zhang Z, Ruggiero KE, Arzumanyan GA, Palsson BO. Evaluation of rate law approximations in bottom-up kinetic models of metabolism. BMC Syst Biol. 2016 06 06; 10(1):40. PMID: 27266508; PMCID: PMC4895898.
    58. Feist AM, Palsson BO. What do cells actually want? Genome Biol. 2016 05 23; 17(1):110. PMID: 27215675.
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    59. Brunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L, O'Brien EJ, Batth TS, Martin HG, Feist A, Adams PD, Keasling JD, Palsson BO, Lee TS. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Syst. 2016 May 25; 2(5):335-46. PMID: 27211860; PMCID: PMC4882250 [Available on 05/25/17].
    60. Levering J, Broddrick J, Dupont CL, Peers G, Beeri K, Mayers J, Gallina AA, Allen AE, Palsson BO, Zengler K. Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. PLoS One. 2016; 11(5):e0155038. PMID: 27152931; PMCID: PMC4859558.
    61. Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO. Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. Cell Syst. 2016 Apr 27; 2(4):260-71. PMID: 27135538; PMCID: PMC4853925 [Available on 04/27/17].
    62. McCloskey D, Young JD, Xu S, Palsson BO, Feist AM. Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale. Anal Chem. 2016 Apr 05; 88(7):3844-52. PMID: 26981784.
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    63. Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO. Systems biology of the structural proteome. BMC Syst Biol. 2016 Mar 11; 10:26. PMID: 26969117; PMCID: PMC4787049.
    64. Sandberg TE, Long CP, Gonzalez JE, Feist AM, Antoniewicz MR, Palsson BO. Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology. PLoS One. 2016; 11(3):e0151130. PMID: 26964043; PMCID: PMC4786092.
    65. Golabgir A, Gutierrez JM, Hefzi H, Li S, Palsson BO, Herwig C, Lewis NE. Quantitative feature extraction from the Chinese hamster ovary bioprocess bibliome using a novel meta-analysis workflow. Biotechnol Adv. 2016 Sep-Oct; 34(5):621-633. PMID: 26948029.
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    66. Bordbar A, Johansson PI, Paglia G, Harrison SJ, Wichuk K, Magnusdottir M, Valgeirsdottir S, Gybel-Brask M, Ostrowski SR, Palsson S, Rolfsson O, Sigurjónsson OE, Hansen MB, Gudmundsson S, Palsson BO. Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomes. Transfusion. 2016 Apr; 56(4):852-62. PMID: 26749434.
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    67. McCloskey D, Young JD, Xu S, Palsson BO, Feist AM. MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications. Anal Chem. 2016 Jan 19; 88(2):1362-70. PMID: 26666286.
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    68. Aziz RK, Monk JM, Lewis RM, In Loh S, Mishra A, Abhay Nagle A, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Fong NL, Li HJ, Palsson BO, Charusanti P. Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations. Sci Rep. 2015 Nov 04; 5:16025. PMID: 26531810; PMCID: PMC4631998.
    69. Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson BO. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Syst. 2015 Oct 28; 1(4):283-92. PMID: 27136057.
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    70. King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res. 2016 Jan 04; 44(D1):D515-22. PMID: 26476456; PMCID: PMC4702785.
    71. Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I. Do genome-scale models need exact solvers or clearer standards? Mol Syst Biol. 2015 Oct 14; 11(10):831. PMID: 26467284; PMCID: PMC4631202.
    72. Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. BMC Syst Biol. 2015 Oct 09; 9:68. PMID: 26452770; PMCID: PMC4600286.
    73. King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput Biol. 2015 Aug; 11(8):e1004321. PMID: 26313928; PMCID: PMC4552468.
    74. Seo SW, Kim D, Szubin R, Palsson BO. Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655. Cell Rep. 2015 Aug 25; 12(8):1289-99. PMID: 26279566.
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    77. Zielinski DC, Filipp FV, Bordbar A, Jensen K, Smith JW, Herrgard MJ, Mo ML, Palsson BO. Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis. Nat Commun. 2015 Jun 09; 6:7101. PMID: 26055627; PMCID: PMC4468904.
    78. Latif H, Szubin R, Tan J, Brunk E, Lechner A, Zengler K, Palsson BO. A streamlined ribosome profiling protocol for the characterization of microorganisms. Biotechniques. 2015 Jun; 58(6):329-32. PMID: 26054770.
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    79. O'Brien EJ, Monk JM, Palsson BO. Using Genome-scale Models to Predict Biological Capabilities. Cell. 2015 May 21; 161(5):971-987. PMID: 26000478; PMCID: PMC4451052.
    80. Rolfsson Ó, Palsson BO. Decoding the jargon of bottom-up metabolic systems biology. Bioessays. 2015 Jun; 37(6):588-91. PMID: 25761171.
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    81. Pacini T, Fu W, Gudmundsson S, Chiaravalle AE, Brynjolfson S, Palsson BO, Astarita G, Paglia G. Multidimensional analytical approach based on UHPLC-UV-ion mobility-MS for the screening of natural pigments. Anal Chem. 2015 Mar 03; 87(5):2593-9. PMID: 25647265.
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    83. King ZA, Lloyd CJ, Feist AM, Palsson BO. Next-generation genome-scale models for metabolic engineering. Curr Opin Biotechnol. 2015 Dec; 35:23-9. PMID: 25575024.
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    84. Guzmán GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson BO, Feist AM. Model-driven discovery of underground metabolic functions in Escherichia coli. Proc Natl Acad Sci U S A. 2015 Jan 20; 112(3):929-34. PMID: 25564669; PMCID: PMC4311852.
    85. Paglia G, Angel P, Williams JP, Richardson K, Olivos HJ, Thompson JW, Menikarachchi L, Lai S, Walsh C, Moseley A, Plumb RS, Grant DF, Palsson BO, Langridge J, Geromanos S, Astarita G. Ion mobility-derived collision cross section as an additional measure for lipid fingerprinting and identification. Anal Chem. 2015 Jan 20; 87(2):1137-44. PMID: 25495617; PMCID: PMC4302848.
    86. LaCroix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, Szubin R, Palsson BO, Feist AM. Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium. Appl Environ Microbiol. 2015 Jan; 81(1):17-30. PMID: 25304508; PMCID: PMC4272732.
    87. Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson BO, Feist AM. Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. BMC Syst Biol. 2014 Sep 18; 8:110. PMID: 25227965; PMCID: PMC4177180.
    88. Nam H, Campodonico M, Bordbar A, Hyduke DR, Kim S, Zielinski DC, Palsson BO. A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks. PLoS Comput Biol. 2014 Sep; 10(9):e1003837. PMID: 25232952; PMCID: PMC4168981.
    89. Seo SW, Kim D, Latif H, O'Brien EJ, Szubin R, Palsson BO. Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. Nat Commun. 2014 Sep 15; 5:4910. PMID: 25222563; PMCID: PMC4167408.
    90. Paglia G, Sigurjónsson ÓE, Rolfsson Ó, Hansen MB, Brynjólfsson S, Gudmundsson S, Palsson BO. Metabolomic analysis of platelets during storage: a comparison between apheresis- and buffy coat-derived platelet concentrates. Transfusion. 2015 Feb; 55(2):301-13. PMID: 25156572.
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    92. Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson BO, Sommer M, Feist AM. Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations. Mol Biol Evol. 2014 Oct; 31(10):2647-62. PMID: 25015645; PMCID: PMC4166923.
    93. Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Mol Syst Biol. 2014 Jul 01; 10:737. PMID: 24987116; PMCID: PMC4299494.
    94. Monk J, Palsson BO. Genetics. Predicting microbial growth. Science. 2014 Jun 27; 344(6191):1448-9. PMID: 24970063.
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    95. Rohatgi N, Nielsen TK, Bjørn SP, Axelsson I, Paglia G, Voldborg BG, Palsson BO, Rolfsson Ó. Biochemical characterization of human gluconokinase and the proposed metabolic impact of gluconic acid as determined by constraint based metabolic network analysis. PLoS One. 2014; 9(6):e98760. PMID: 24896608; PMCID: PMC4045858.
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    97. Monk J, Nogales J, Palsson BO. Optimizing genome-scale network reconstructions. Nat Biotechnol. 2014 May; 32(5):447-52. PMID: 24811519.
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    99. Cho BK, Kim D, Knight EM, Zengler K, Palsson BO. Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states. BMC Biol. 2014 Jan 24; 12:4. PMID: 24461193; PMCID: PMC3923258.
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    102. Cheng KK, Lee BS, Masuda T, Ito T, Ikeda K, Hirayama A, Deng L, Dong J, Shimizu K, Soga T, Tomita M, Palsson BO, Robert M. Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol. Nat Commun. 2014; 5:3233. PMID: 24481126.
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    103. McCloskey D, Gangoiti JA, King ZA, Naviaux RK, Barshop BA, Palsson BO, Feist AM. A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent. Biotechnol Bioeng. 2014 Apr; 111(4):803-15. PMID: 24249002.
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    104. Chang RL, Xie L, Bourne PE, Palsson BO. Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst Biol. 2013 Oct 10; 7:102. PMID: 24112686; PMCID: PMC3853765.
    105. Palsson S, Hickling TP, Bradshaw-Pierce EL, Zager M, Jooss K, O'Brien PJ, Spilker ME, Palsson BO, Vicini P. The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models. BMC Syst Biol. 2013 Sep 28; 7:95. PMID: 24074340; PMCID: PMC3853972.
    106. Ebrahim A, Lerman JA, Palsson BO, Hyduke DR. COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst Biol. 2013 Aug 08; 7:74. PMID: 23927696; PMCID: PMC3751080.
    107. Wu W, Jamshidi N, Eraly SA, Liu HC, Bush KT, Palsson BO, Nigam SK. Multispecific drug transporter Slc22a8 (Oat3) regulates multiple metabolic and signaling pathways. Drug Metab Dispos. 2013 Oct; 41(10):1825-34. PMID: 23920220; PMCID: PMC3781372.
    108. Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C, Xie M, Chen W, Li N, Baycin-Hizal D, Latif H, Forster J, Betenbaugh MJ, Famili I, Xu X, Wang J, Palsson BO. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nat Biotechnol. 2013 Aug; 31(8):759-65. PMID: 23873082.
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    110. Kim YM, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson BO, McDermott JE, Heffron F, Smith RD, Peterson SN, Ansong C, Hyduke DR, Metz TO, Adkins JN. Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. Mol Biosyst. 2013 Jun; 9(6):1522-34. PMID: 23559334; PMCID: PMC3665296.
    111. Fong NL, Lerman JA, Lam I, Palsson BO, Charusanti P. Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant. FEMS Microbiol Lett. 2013 May; 342(1):62-9. PMID: 23432746; PMCID: PMC3625468.
    112. Qiu Y, Nagarajan H, Embree M, Shieu W, Abate E, Juárez K, Cho BK, Elkins JG, Nevin KP, Barrett CL, Lovley DR, Palsson BO, Zengler K. Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks. Nat Commun. 2013; 4:1755. PMID: 23612296.
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    113. Ansong C, Deatherage BL, Hyduke D, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P, Kim YM, Nakayasu ES, Li J, Kidwai A, Niemann G, Brown RN, Metz TO, McAteer K, Heffron F, Peterson SN, Motin V, Palsson BO, Smith RD, Adkins JN. Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling. Curr Top Microbiol Immunol. 2013; 363:21-41. PMID: 22886542.
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    115. Fu W, Guðmundsson O, Paglia G, Herjólfsson G, Andrésson OS, Palsson BO, Brynjólfsson S. Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution. Appl Microbiol Biotechnol. 2013 Mar; 97(6):2395-403. PMID: 23095941; PMCID: PMC3586100.
    116. Baycin-Hizal D, Tabb DL, Chaerkady R, Chen L, Lewis NE, Nagarajan H, Sarkaria V, Kumar A, Wolozny D, Colao J, Jacobson E, Tian Y, O'Meally RN, Krag SS, Cole RN, Palsson BO, Zhang H, Betenbaugh M. Proteomic analysis of Chinese hamster ovary cells. J Proteome Res. 2012 Nov 02; 11(11):5265-76. PMID: 22971049; PMCID: PMC3772721.
    117. Thiele I, Fleming RM, Que R, Bordbar A, Diep D, Palsson BO. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PLoS One. 2012; 7(9):e45635. PMID: 23029152; PMCID: PMC3461016.
    118. Nam H, Lewis NE, Lerman JA, Lee DH, Chang RL, Kim D, Palsson BO. Network context and selection in the evolution to enzyme specificity. Science. 2012 Aug 31; 337(6098):1101-4. PMID: 22936779; PMCID: PMC3536066.
    119. Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun. 2012 Jul 03; 3:929. PMID: 22760628; PMCID: PMC3827721.
    120. Bordbar A, Mo ML, Nakayasu ES, Schrimpe-Rutledge AC, Kim YM, Metz TO, Jones MB, Frank BC, Smith RD, Peterson SN, Hyduke DR, Adkins JN, Palsson BO. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol Syst Biol. 2012 Jun 26; 8:558. PMID: 22735334; PMCID: PMC3397418.
    121. Orth JD, Palsson B. Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. BMC Syst Biol. 2012 May 01; 6:30. PMID: 22548736; PMCID: PMC3423039.
    122. Zengler K, Palsson BO. A road map for the development of community systems (CoSy) biology. Nat Rev Microbiol. 2012 03 27; 10(5):366-72. PMID: 22450377.
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    123. Charusanti P, Fong NL, Nagarajan H, Pereira AR, Li HJ, Abate EA, Su Y, Gerwick WH, Palsson BO. Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction. PLoS One. 2012; 7(3):e33727. PMID: 22470465; PMCID: PMC3312335.
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    125. Nogales J, Gudmundsson S, Knight EM, Palsson BO, Thiele I. Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis. Proc Natl Acad Sci U S A. 2012 Feb 14; 109(7):2678-83. PMID: 22308420; PMCID: PMC3289291.
    126. Bordbar A, Feist AM, Usaite-Black R, Woodcock J, Palsson BO, Famili I. A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst Biol. 2011 Oct 31; 5:180. PMID: 22041191; PMCID: PMC3219569.
    127. Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson BO. An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. BMC Syst Biol. 2011 Oct 13; 5:163. PMID: 21995956; PMCID: PMC3220653.
    128. Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S, Andersen MR, Neff N, Passarelli B, Koh W, Fan HC, Wang J, Gui Y, Lee KH, Betenbaugh MJ, Quake SR, Famili I, Palsson BO, Wang J. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nat Biotechnol. 2011 Jul 31; 29(8):735-41. PMID: 21804562; PMCID: PMC3164356.
    129. Bordbar A, Jamshidi N, Palsson BO. iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. BMC Syst Biol. 2011 Jul 12; 5:110. PMID: 21749716; PMCID: PMC3158119.
    130. McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F. Technologies and approaches to elucidate and model the virulence program of salmonella. Front Microbiol. 2011; 2:121. PMID: 21687430; PMCID: PMC3108385.
    131. Liao YC, Huang TW, Chen FC, Charusanti P, Hong JS, Chang HY, Tsai SF, Palsson BO, Hsiung CA. An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. J Bacteriol. 2011 Apr; 193(7):1710-7. PMID: 21296962; PMCID: PMC3067640.
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    133. Tremblay PL, Summers ZM, Glaven RH, Nevin KP, Zengler K, Barrett CL, Qiu Y, Palsson BO, Lovley DR. A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution. Environ Microbiol. 2011 Jan; 13(1):13-23. PMID: 20636372.
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    136. Feist AM, Palsson BO. The biomass objective function. Curr Opin Microbiol. 2010 Jun; 13(3):344-9. PMID: 20430689; PMCID: PMC2912156.
    137. Jamshidi N, Palsson BO. Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes. BMC Syst Biol. 2009 Apr 30; 3:44. PMID: 19405968; PMCID: PMC2689188.
    138. Lewis NE, Cho BK, Knight EM, Palsson BO. Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content. J Bacteriol. 2009 Jun; 191(11):3437-44. PMID: 19363119; PMCID: PMC2681886.
    139. Mo ML, Palsson BO, Herrgård MJ. Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst Biol. 2009 Mar 25; 3:37. PMID: 19321003; PMCID: PMC2679711.
    140. Sigurdsson MI, Jamshidi N, Jonsson JJ, Palsson BO. Genome-scale network analysis of imprinted human metabolic genes. Epigenetics. 2009 Jan; 4(1):43-6. PMID: 19218833.
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    142. Becker SA, Palsson BO. Three factors underlying incorrect in silico predictions of essential metabolic genes. BMC Syst Biol. 2008 Feb 04; 2:14. PMID: 18248675; PMCID: PMC2248557.
    143. Cho BK, Charusanti P, Herrgård MJ, Palsson BO. Microbial regulatory and metabolic networks. Curr Opin Biotechnol. 2007 Aug; 18(4):360-4. PMID: 17719767.
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    144. Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R. Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem. 2007 Sep 28; 282(39):28791-9. PMID: 17573341.
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    145. Anderson MJ, DeLabarre B, Raghunathan A, Palsson BO, Brunger AT, Quake SR. Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices. Biochemistry. 2007 May 15; 46(19):5722-31. PMID: 17441732.
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    146. Vo TD, Paul Lee WN, Palsson BO. Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome. Mol Genet Metab. 2007 May; 91(1):15-22. PMID: 17336115.
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    147. Jamshidi N, Vo TD, Palsson BO. In silico analysis of SNPs and other high-throughput data. Methods Mol Biol. 2007; 366:267-85. PMID: 17568130.
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    148. Joyce AR, Palsson BO. Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach. Prog Drug Res. 2007; 64:265, 267-309. PMID: 17195479.
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    149. Vo TD, Palsson BO. Isotopomer analysis of myocardial substrate metabolism: a systems biology approach. Biotechnol Bioeng. 2006 Dec 05; 95(5):972-83. PMID: 16878330.
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    150. Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO. Systems approach to refining genome annotation. Proc Natl Acad Sci U S A. 2006 Nov 14; 103(46):17480-4. PMID: 17088549; PMCID: PMC1859954.
    151. Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO. Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput Biol. 2006 Aug 11; 2(8):e101. PMID: 16895435; PMCID: PMC1534074.
    152. Vo TD, Palsson BO. Building the power house: recent advances in mitochondrial studies through proteomics and systems biology. Am J Physiol Cell Physiol. 2007 Jan; 292(1):C164-77. PMID: 16885397.
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    153. Barrett CL, Palsson BO. Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PLoS Comput Biol. 2006 May; 2(5):e52. PMID: 16710450; PMCID: PMC1463018.
    154. Barrett CL, Price ND, Palsson BO. Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition. BMC Bioinformatics. 2006 Mar 13; 7:132. PMID: 16533395; PMCID: PMC1421444.
    155. Reed JL, Famili I, Thiele I, Palsson BO. Towards multidimensional genome annotation. Nat Rev Genet. 2006 Feb; 7(2):130-41. PMID: 16418748.
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    156. Cho BK, Knight EM, Palsson BO. PCR-based tandem epitope tagging system for Escherichia coli genome engineering. Biotechniques. 2006 Jan; 40(1):67-72. PMID: 16454042.
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    157. Barrett CL, Herring CD, Reed JL, Palsson BO. The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states. Proc Natl Acad Sci U S A. 2005 Dec 27; 102(52):19103-8. PMID: 16357206; PMCID: PMC1323155.
    158. Fong SS, Nanchen A, Palsson BO, Sauer U. Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes. J Biol Chem. 2006 Mar 24; 281(12):8024-33. PMID: 16319065.
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    159. Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BO. In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng. 2005 Sep 05; 91(5):643-8. PMID: 15962337.
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    160. Papin JA, Hunter T, Palsson BO, Subramaniam S. Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol. 2005 Feb; 6(2):99-111. PMID: 15654321.
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    161. Famili I, Mahadevan R, Palsson BO. k-Cone analysis: determining all candidate values for kinetic parameters on a network scale. Biophys J. 2005 Mar; 88(3):1616-25. PMID: 15626710; PMCID: PMC1305218.
    162. Papin JA, Reed JL, Palsson BO. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends Biochem Sci. 2004 Dec; 29(12):641-7. PMID: 15544950.
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    163. Price ND, Schellenberger J, Palsson BO. Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. Biophys J. 2004 Oct; 87(4):2172-86. PMID: 15454420; PMCID: PMC1304643.
    164. Westerhoff HV, Palsson BO. The evolution of molecular biology into systems biology. Nat Biotechnol. 2004 Oct; 22(10):1249-52. PMID: 15470464.
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    165. Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO. Comparison of network-based pathway analysis methods. Trends Biotechnol. 2004 Aug; 22(8):400-5. PMID: 15283984.
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    166. Papin JA, Palsson BO. The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. Biophys J. 2004 Jul; 87(1):37-46. PMID: 15240442; PMCID: PMC1304358.
    167. Vo TD, Greenberg HJ, Palsson BO. Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J Biol Chem. 2004 Sep 17; 279(38):39532-40. PMID: 15205464.
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    168. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004 May 06; 429(6987):92-6. PMID: 15129285.
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    169. Papin JA, Palsson BO. Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. J Theor Biol. 2004 Mar 21; 227(2):283-97. PMID: 14990392.
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    170. Raghunathan A, Price ND, Galperin MY, Makarova KS, Purvine S, Picone AF, Cherny T, Xie T, Reilly TJ, Munson R, Tyler RE, Akerley BJ, Smith AL, Palsson BO, Kolker E. In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium. OMICS. 2004; 8(1):25-41. PMID: 15107235.
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    171. Covert MW, Famili I, Palsson BO. Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology? Biotechnol Bioeng. 2003 Dec 30; 84(7):763-72. PMID: 14708117.
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    172. Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BO. Network-based analysis of metabolic regulation in the human red blood cell. J Theor Biol. 2003 Nov 21; 225(2):185-94. PMID: 14575652.
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    173. Famili I, Forster J, Nielsen J, Palsson BO. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc Natl Acad Sci U S A. 2003 Nov 11; 100(23):13134-9. PMID: 14578455; PMCID: PMC263729.
    174. Famili I, Palsson BO. Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices. J Theor Biol. 2003 Sep 07; 224(1):87-96. PMID: 12900206.
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    175. Reed JL, Vo TD, Schilling CH, Palsson BO. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 2003; 4(9):R54. PMID: 12952533; PMCID: PMC193654.
    176. Kolker E, Purvine S, Galperin MY, Stolyar S, Goodlett DR, Nesvizhskii AI, Keller A, Xie T, Eng JK, Yi E, Hood L, Picone AF, Cherny T, Tjaden BC, Siegel AF, Reilly TJ, Makarova KS, Palsson BO, Smith AL. Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol. 2003 Aug; 185(15):4593-602. PMID: 12867470.
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    177. Famili I, Palsson BO. The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools. Biophys J. 2003 Jul; 85(1):16-26. PMID: 12829460; PMCID: PMC1303061.
    178. Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO. Metabolic pathways in the post-genome era. Trends Biochem Sci. 2003 May; 28(5):250-8. PMID: 12765837.
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    179. Palsson BO, Price ND, Papin JA. Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends Biotechnol. 2003 May; 21(5):195-8. PMID: 12727379.
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    180. Covert MW, Palsson BO. Constraints-based models: regulation of gene expression reduces the steady-state solution space. J Theor Biol. 2003 Apr 07; 221(3):309-25. PMID: 12642111.
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    181. Price ND, Papin JA, Schilling CH, Palsson BO. Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol. 2003 Apr; 21(4):162-9. PMID: 12679064.
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    182. Raghunathan A, Palsson BO. Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli. Biotechnol Lett. 2003 Mar; 25(5):435-41. PMID: 12882568.
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    183. Price ND, Reed JL, Papin JA, Famili I, Palsson BO. Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophys J. 2003 Feb; 84(2 Pt 1):794-804. PMID: 12547764; PMCID: PMC1302660.
    184. Förster J, Famili I, Palsson BO, Nielsen J. Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS. 2003; 7(2):193-202. PMID: 14506848.
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    185. Ibarra RU, Edwards JS, Palsson BO. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature. 2002 Nov 14; 420(6912):186-9. PMID: 12432395.
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    186. Kauffman KJ, Pajerowski JD, Jamshidi N, Palsson BO, Edwards JS. Description and analysis of metabolic connectivity and dynamics in the human red blood cell. Biophys J. 2002 Aug; 83(2):646-62. PMID: 12124254; PMCID: PMC1302176.
    187. Wiback SJ, Palsson BO. Extreme pathway analysis of human red blood cell metabolism. Biophys J. 2002 Aug; 83(2):808-18. PMID: 12124266; PMCID: PMC1302188.
    188. Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO. Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol. 2002 Aug; 184(16):4582-93. PMID: 12142428; PMCID: PMC135230.
    189. Lee GM, Fong SS, Oh DJ, Francis K, Palsson BO. Characterization and efficacy of PKH26 as a probe to study the replication history of the human hematopoietic KG1a progenitor cell line. In Vitro Cell Dev Biol Anim. 2002 Feb; 38(2):90-6. PMID: 11929001.
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    190. Edwards JS, Ramakrishna R, Palsson BO. Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol Bioeng. 2002 Jan 05; 77(1):27-36. PMID: 11745171.
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    191. Kolker E, Purvine S, Picone A, Cherny T, Akerley BJ, Munson RS, Palsson BO, Daines DA, Smith AL. H. influenzae Consortium: integrative study of H. influenzae-human interactions. OMICS. 2002; 6(4):341-8. PMID: 12626093.
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