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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. Lloyd CJ, Ebrahim A, Yang L, King ZA, Catoiu E, O'Brien EJ, Liu JK, Palsson B. COBRAme: A computational framework for genome-scale models of metabolism and gene expression. PLoS Comput Biol. 2018 Jul 05; 14(7):e1006302. PMID: 29975681.
      View in: PubMed
    2. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson B. 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
    3. Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L, Palsson B. 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
    4. Du B, Zhang Z, Grubner S, Yurkovich JT, Palsson B, 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
    5. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson B. 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
    6. Choudhary KS, Mih N, Monk J, Kavvas E, Yurkovich JT, Sakoulas G, Palsson B. The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures. Front Microbiol. 2018; 9:1082. PMID: 29887846.
      View in: PubMed
    7. Latif H, Federowicz S, Ebrahim A, Tarasova J, Szubin R, Utrilla J, Zengler K, Palsson B. ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. PLoS One. 2018; 13(5):e0197272. PMID: 29771928.
      View in: PubMed
    8. Norsigian CJ, Kavvas E, Seif Y, Palsson B, 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
    9. Kim D, Seo SW, Gao Y, Nam H, Guzman GI, Cho BK, Palsson B. 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
    10. Yurkovich JT, Bordbar A, Sigurjónsson ÓE, Palsson B. Systems biology as an emerging paradigm in transfusion medicine. BMC Syst Biol. 2018 Mar 07; 12(1):31. PMID: 29514691.
      View in: PubMed
    11. Kavvas ES, Seif Y, Yurkovich JT, Norsigian C, Poudel S, Greenwald WW, Ghatak S, Palsson B, 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.
      View in: PubMed
    12. 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 B. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 Mar; 36(3):272-281. PMID: 29457794.
      View in: PubMed
    13. Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z, Palsson B, Valencia A. ssbio: A Python Framework for Structural Systems Biology. Bioinformatics. 2018 Feb 12. PMID: 29444205.
      View in: PubMed
    14. Yurkovich JT, Palsson B. Quantitative -omic data empowers bottom-up systems biology. Curr Opin Biotechnol. 2018 Feb 03; 51:130-136. PMID: 29414439.
      View in: PubMed
    15. Yang L, Yurkovich JT, King ZA, Palsson B. Modeling the multi-scale mechanisms of macromolecular resource allocation. Curr Opin Microbiol. 2018 Jan 20; 45:8-15. PMID: 29367175.
      View in: PubMed
    16. Abdel-Haleem AM, Hefzi H, Mineta K, Gao X, Gojobori T, Palsson B, 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.
      View in: PubMed
    17. Nilsson A, Nielsen J, Palsson B. Metabolic Models of Protein Allocation Call for the Kinetome. Cell Syst. 2017 Dec 27; 5(6):538-541. PMID: 29284126.
      View in: PubMed
    18. Du B, Zielinski DC, Palsson B. Topological and kinetic determinants of the modal matrices of dynamic models of metabolism. PLoS One. 2017; 12(12):e0189880. PMID: 29267329.
      View in: PubMed
    19. Long CP, Gonzalez JE, Feist AM, Palsson B, 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.
      View in: PubMed
    20. Yang JH, Bhargava P, McCloskey D, Mao N, Palsson B, Collins JJ. Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function. Cell Host Microbe. 2017 Dec 13; 22(6):757-765.e3. PMID: 29199098.
      View in: PubMed
    21. 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 B. 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
    22. Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist AM, Palsson B. iML1515, a knowledgebase that computes Escherichia coli traits. Nat Biotechnol. 2017 Oct 11; 35(10):904-908. PMID: 29020004.
      View in: PubMed
    23. Chen K, Gao Y, Mih N, O'Brien EJ, Yang L, Palsson B. 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.
      View in: PubMed
    24. Yurkovich JT, Yurkovich BJ, Dräger A, Palsson B, King ZA. A Padawan Programmer's Guide to Developing Software Libraries. Cell Syst. 2017 Nov 22; 5(5):431-437. PMID: 28988801.
      View in: PubMed
    25. Long CP, Gonzalez JE, Feist AM, Palsson B, 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.
      View in: PubMed
    26. Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, Palsson B. 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.
      View in: PubMed
    27. Sastry A, Monk J, Tegel H, Uhlen M, Palsson B, Rockberg J, Brunk E. Machine learning in computational biology to accelerate high-throughput protein expression. Bioinformatics. 2017 Aug 15; 33(16):2487-2495. PMID: 28398465.
      View in: PubMed
    28. Sandberg TE, Lloyd CJ, Palsson B, Feist AM. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies. Appl Environ Microbiol. 2017 07 01; 83(13). PMID: 28455337.
      View in: PubMed
    29. Seo SW, Gao Y, Kim D, Szubin R, Yang J, Cho BK, Palsson B. 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.
      View in: PubMed
    30. Bordbar A, Yurkovich JT, Paglia G, Rolfsson O, Sigurjónsson ÓE, Palsson B. Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics. Sci Rep. 2017 Apr 07; 7:46249. PMID: 28387366.
      View in: PubMed
    31. LaCroix RA, Palsson B, Feist AM. A Model for Designing Adaptive Laboratory Evolution Experiments. Appl Environ Microbiol. 2017 04 15; 83(8). PMID: 28159796.
      View in: PubMed
    32. Yurkovich JT, Yang L, Palsson B. Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells. PLoS Comput Biol. 2017 Mar; 13(3):e1005424. PMID: 28264007.
      View in: PubMed
    33. Levering J, Dupont CL, Allen AE, Palsson B, Zengler K. Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels. mSystems. 2017 Jan-Feb; 2(1). PMID: 28217746.
      View in: PubMed
    34. Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson B. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism. Sci Rep. 2017 Jan 25; 7:41241. PMID: 28120890.
      View in: PubMed
    35. Ma D, Yang L, Fleming RM, Thiele I, Palsson B, Saunders MA. Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression. Sci Rep. 2017 Jan 18; 7:40863. PMID: 28098205.
      View in: PubMed
    36. van Wijk XM, Döhrmann S, Hallström BM, Li S, Voldborg BG, Meng BX, McKee KK, van Kuppevelt TH, Yurchenco PD, Palsson B, Lewis NE, Nizet V, Esko JD. Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin a2 as a Host Factor for Bacterial Invasion. MBio. 2017 01 10; 8(1). PMID: 28074024.
      View in: PubMed
    37. King ZA, O'Brien EJ, Feist AM, Palsson B. Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion. Metab Eng. 2017 01; 39:220-227. PMID: 27986597.
      View in: PubMed
    38. Broddrick JT, Rubin BE, Welkie DG, Du N, Mih N, Diamond S, Lee JJ, Golden SS, Palsson B. Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis. Proc Natl Acad Sci U S A. 2016 12 20; 113(51):E8344-E8353. PMID: 27911809.
      View in: PubMed
    39. 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 B, 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.
      View in: PubMed
    40. Yang L, Yurkovich JT, Lloyd CJ, Ebrahim A, Saunders MA, Palsson B. Principles of proteome allocation are revealed using proteomic data and genome-scale models. Sci Rep. 2016 11 18; 6:36734. PMID: 27857205.
      View in: PubMed
    41. D'Alessandro A, Nemkov T, Yoshida T, Bordbar A, Palsson B, Hansen KC. Citrate metabolism in red blood cells stored in additive solution-3. Transfusion. 2017 02; 57(2):325-336. PMID: 27813142.
      View in: PubMed
    42. Aziz RK, Monk JM, Andrews KA, Nhan J, Khaw VL, Wong H, Palsson B, Charusanti P. The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli. Microbiol Res. 2017 Jan; 194:47-52. PMID: 27938862.
      View in: PubMed
    43. Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM, Palsson B. Multi-omic data integration enables discovery of hidden biological regularities. Nat Commun. 2016 Oct 26; 7:13091. PMID: 27782110.
      View in: PubMed
    44. Yang L, Ma D, Ebrahim A, Lloyd CJ, Saunders MA, Palsson B. solveME: fast and reliable solution of nonlinear ME models. BMC Bioinformatics. 2016 Sep 22; 17(1):391. PMID: 27659412.
      View in: PubMed
    45. Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson B, 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.
      View in: PubMed
    46. Paglia G, D'Alessandro A, Rolfsson Ó, Sigurjónsson ÓE, Bordbar A, Palsson S, Nemkov T, Hansen KC, Gudmundsson S, Palsson B. Biomarkers defining the metabolic age of red blood cells during cold storage. Blood. 2016 09 29; 128(13):e43-50. PMID: 27554084.
      View in: PubMed
    47. 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 B, 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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    48. Paglia G, Sigurjónsson ÓE, Bordbar A, Rolfsson Ó, Magnusdottir M, Palsson S, Wichuk K, Gudmundsson S, Palsson B. Metabolic fate of adenine in red blood cells during storage in SAGM solution. Transfusion. 2016 Oct; 56(10):2538-2547. PMID: 27491795.
      View in: PubMed
    49. Mih N, Brunk E, Bordbar A, Palsson B. 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.
    50. O'Brien EJ, Utrilla J, Palsson B. Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. PLoS Comput Biol. 2016 06; 12(6):e1004998. PMID: 27351952.
      View in: PubMed
    51. Du B, Zielinski DC, Kavvas ES, Dräger A, Tan J, Zhang Z, Ruggiero KE, Arzumanyan GA, Palsson B. 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.
    52. Feist AM, Palsson B. What do cells actually want? Genome Biol. 2016 05 23; 17(1):110. PMID: 27215675.
      View in: PubMed
    53. 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 B, 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].
    54. Levering J, Broddrick J, Dupont CL, Peers G, Beeri K, Mayers J, Gallina AA, Allen AE, Palsson B, 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.
    55. Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson B. 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].
    56. McCloskey D, Young JD, Xu S, Palsson B, Feist AM. Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale. Anal Chem. 2016 Apr 05; 88(7):3844-52. PMID: 26981784.
      View in: PubMed
    57. Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson B. Systems biology of the structural proteome. BMC Syst Biol. 2016 Mar 11; 10:26. PMID: 26969117; PMCID: PMC4787049.
    58. Sandberg TE, Long CP, Gonzalez JE, Feist AM, Antoniewicz MR, Palsson B. 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.
    59. Golabgir A, Gutierrez JM, Hefzi H, Li S, Palsson B, 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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    60. 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 B. 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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    61. McCloskey D, Young JD, Xu S, Palsson B, Feist AM. MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications. Anal Chem. 2016 Jan 19; 88(2):1362-70. PMID: 26666286.
      View in: PubMed
    62. 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 B, 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.
    63. Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson B. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Syst. 2015 Oct 28; 1(4):283-92. PMID: 27136057.
      View in: PubMed
    64. King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson B, 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.
    65. 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 B, 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.
    66. Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson B, 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.
    67. King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson B. 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.
    68. Seo SW, Kim D, Szubin R, Palsson B. 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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    69. 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 B. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proc Natl Acad Sci U S A. 2015 Aug 25; 112(34):10810-5. PMID: 26261351; PMCID: PMC4553782.
    70. Seo SW, Kim D, O'Brien EJ, Szubin R, Palsson B. Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli. Nat Commun. 2015 Aug 10; 6:7970. PMID: 26258987; PMCID: PMC4918353.
    71. Zielinski DC, Filipp FV, Bordbar A, Jensen K, Smith JW, Herrgard MJ, Mo ML, Palsson B. 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.
    72. Latif H, Szubin R, Tan J, Brunk E, Lechner A, Zengler K, Palsson B. A streamlined ribosome profiling protocol for the characterization of microorganisms. Biotechniques. 2015 Jun; 58(6):329-32. PMID: 26054770.
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    73. O'Brien EJ, Monk JM, Palsson B. Using Genome-scale Models to Predict Biological Capabilities. Cell. 2015 May 21; 161(5):971-987. PMID: 26000478; PMCID: PMC4451052.
    74. Rolfsson Ó, Palsson B. Decoding the jargon of bottom-up metabolic systems biology. Bioessays. 2015 Jun; 37(6):588-91. PMID: 25761171.
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    75. Pacini T, Fu W, Gudmundsson S, Chiaravalle AE, Brynjolfson S, Palsson B, 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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    76. O'Brien EJ, Palsson B. Computing the functional proteome: recent progress and future prospects for genome-scale models. Curr Opin Biotechnol. 2015 Aug; 34:125-34. PMID: 25576845; PMCID: PMC4495013.
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    78. Guzmán GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson B, 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.
    79. 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 B, 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.
    80. LaCroix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, Szubin R, Palsson B, 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.
    81. Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson B, 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.
    82. Nam H, Campodonico M, Bordbar A, Hyduke DR, Kim S, Zielinski DC, Palsson B. 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.
    83. Seo SW, Kim D, Latif H, O'Brien EJ, Szubin R, Palsson B. 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.
    84. Paglia G, Sigurjónsson ÓE, Rolfsson Ó, Hansen MB, Brynjólfsson S, Gudmundsson S, Palsson B. 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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    86. Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson B, 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.
    87. Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson B. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Mol Syst Biol. 2014 Jul 01; 10:737. PMID: 24987116; PMCID: PMC4299494.
    88. Monk J, Palsson B. Genetics. Predicting microbial growth. Science. 2014 Jun 27; 344(6191):1448-9. PMID: 24970063.
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    89. Rohatgi N, Nielsen TK, Bjørn SP, Axelsson I, Paglia G, Voldborg BG, Palsson B, 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.
    90. Paglia G, Sigurjónsson ÓE, Rolfsson Ó, Valgeirsdottir S, Hansen MB, Brynjólfsson S, Gudmundsson S, Palsson B. Comprehensive metabolomic study of platelets reveals the expression of discrete metabolic phenotypes during storage. Transfusion. 2014 Nov; 54(11):2911-23. PMID: 24840017.
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    91. Monk J, Nogales J, Palsson B. Optimizing genome-scale network reconstructions. Nat Biotechnol. 2014 May; 32(5):447-52. PMID: 24811519.
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    92. Paglia G, Williams JP, Menikarachchi L, Thompson JW, Tyldesley-Worster R, Halldórsson S, Rolfsson O, Moseley A, Grant D, Langridge J, Palsson B, Astarita G. Ion mobility derived collision cross sections to support metabolomics applications. Anal Chem. 2014 Apr 15; 86(8):3985-93. PMID: 24640936; PMCID: PMC4004193.
    93. Cho BK, Kim D, Knight EM, Zengler K, Palsson B. 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.
    94. Bordbar A, Monk JM, King ZA, Palsson B. Constraint-based models predict metabolic and associated cellular functions. Nat Rev Genet. 2014 Feb; 15(2):107-20. PMID: 24430943.
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    95. Huang TW, Lam I, Chang HY, Tsai SF, Palsson B, Charusanti P. Capsule deletion via a ?-Red knockout system perturbs biofilm formation and fimbriae expression in Klebsiella pneumoniae MGH 78578. BMC Res Notes. 2014 Jan 08; 7:13. PMID: 24398052; PMCID: PMC3892127.
    96. Cheng KK, Lee BS, Masuda T, Ito T, Ikeda K, Hirayama A, Deng L, Dong J, Shimizu K, Soga T, Tomita M, Palsson B, 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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    97. McCloskey D, Gangoiti JA, King ZA, Naviaux RK, Barshop BA, Palsson B, 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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    98. Chang RL, Xie L, Bourne PE, Palsson B. Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst Biol. 2013 Oct 10; 7:102. PMID: 24112686; PMCID: PMC3853765.
    99. Palsson S, Hickling TP, Bradshaw-Pierce EL, Zager M, Jooss K, O'Brien PJ, Spilker ME, Palsson B, 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.
    100. Ebrahim A, Lerman JA, Palsson B, Hyduke DR. COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst Biol. 2013 Aug 08; 7:74. PMID: 23927696; PMCID: PMC3751080.
    101. Wu W, Jamshidi N, Eraly SA, Liu HC, Bush KT, Palsson B, 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.
    102. 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 B. 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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    103. Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson B. Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. Science. 2013 Jun 07; 340(6137):1220-3. PMID: 23744946; PMCID: PMC3777776.
    104. Kim YM, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson B, 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.
    105. Fong NL, Lerman JA, Lam I, Palsson B, 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.
    106. Qiu Y, Nagarajan H, Embree M, Shieu W, Abate E, Juárez K, Cho BK, Elkins JG, Nevin KP, Barrett CL, Lovley DR, Palsson B, 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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    107. 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 B, 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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    108. Seo JH, Hong JS, Kim D, Cho BK, Huang TW, Tsai SF, Palsson B, Charusanti P. Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features. BMC Genomics. 2012 Nov 29; 13:679. PMID: 23194155; PMCID: PMC3536570.
    109. Fu W, Guðmundsson O, Paglia G, Herjólfsson G, Andrésson OS, Palsson B, 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.
    110. 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 B, 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.
    111. Thiele I, Fleming RM, Que R, Bordbar A, Diep D, Palsson B. 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.
    112. Nam H, Lewis NE, Lerman JA, Lee DH, Chang RL, Kim D, Palsson B. Network context and selection in the evolution to enzyme specificity. Science. 2012 Aug 31; 337(6098):1101-4. PMID: 22936779; PMCID: PMC3536066.
    113. Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson B. In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun. 2012 Jul 03; 3:929. PMID: 22760628; PMCID: PMC3827721.
    114. 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 B. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol Syst Biol. 2012 Jun 26; 8:558. PMID: 22735334; PMCID: PMC3397418.
    115. 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.
    116. Zengler K, Palsson B. 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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    117. Charusanti P, Fong NL, Nagarajan H, Pereira AR, Li HJ, Abate EA, Su Y, Gerwick WH, Palsson B. 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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    119. Nogales J, Gudmundsson S, Knight EM, Palsson B, 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.
    120. Bordbar A, Feist AM, Usaite-Black R, Woodcock J, Palsson B, 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.
    121. Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson B. An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. BMC Syst Biol. 2011 Oct 13; 5:163. PMID: 21995956; PMCID: PMC3220653.
    122. 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 B, 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.
    123. Bordbar A, Jamshidi N, Palsson B. 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.
    124. McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson B, 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.
    125. Liao YC, Huang TW, Chen FC, Charusanti P, Hong JS, Chang HY, Tsai SF, Palsson B, 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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    127. Tremblay PL, Summers ZM, Glaven RH, Nevin KP, Zengler K, Barrett CL, Qiu Y, Palsson B, 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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    128. Lerman J, Palsson B. Microbiology. Topping off a multiscale balancing act. Science. 2010 Nov 19; 330(6007):1058-9. PMID: 21097927.
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    129. Barrett CL, Cho BK, Palsson B. Sensitive and accurate identification of protein-DNA binding events in ChIP-chip assays using higher order derivative analysis. Nucleic Acids Res. 2011 Mar; 39(5):1656-65. PMID: 21051353; PMCID: PMC3061075.
    130. Feist AM, Palsson B. The biomass objective function. Curr Opin Microbiol. 2010 Jun; 13(3):344-9. PMID: 20430689; PMCID: PMC2912156.
    131. Jamshidi N, Palsson B. 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.
    132. Lewis NE, Cho BK, Knight EM, Palsson B. 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.
    133. Mo ML, Palsson B, Herrgård MJ. Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst Biol. 2009 Mar 25; 3:37. PMID: 19321003; PMCID: PMC2679711.
    134. Sigurdsson MI, Jamshidi N, Jonsson JJ, Palsson B. Genome-scale network analysis of imprinted human metabolic genes. Epigenetics. 2009 Jan; 4(1):43-6. PMID: 19218833.
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    135. Becker SA, Palsson B. Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol. 2008 May 16; 4(5):e1000082. PMID: 18483554; PMCID: PMC2366062.
    136. Becker SA, Palsson B. Three factors underlying incorrect in silico predictions of essential metabolic genes. BMC Syst Biol. 2008 Feb 04; 2:14. PMID: 18248675; PMCID: PMC2248557.
    137. Cho BK, Charusanti P, Herrgård MJ, Palsson B. Microbial regulatory and metabolic networks. Curr Opin Biotechnol. 2007 Aug; 18(4):360-4. PMID: 17719767.
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    138. Oh YK, Palsson B, 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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    139. Anderson MJ, DeLabarre B, Raghunathan A, Palsson B, 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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    140. Vo TD, Paul Lee WN, Palsson B. 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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    141. Jamshidi N, Vo TD, Palsson B. In silico analysis of SNPs and other high-throughput data. Methods Mol Biol. 2007; 366:267-85. PMID: 17568130.
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    142. Joyce AR, Palsson B. 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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    143. Vo TD, Palsson B. 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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    144. Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson B. Systems approach to refining genome annotation. Proc Natl Acad Sci U S A. 2006 Nov 14; 103(46):17480-4. PMID: 17088549; PMCID: PMC1859954.
    145. Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson B. Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput Biol. 2006 Aug 11; 2(8):e101. PMID: 16895435; PMCID: PMC1534074.
    146. Vo TD, Palsson B. 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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    148. Barrett CL, Price ND, Palsson B. 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.
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    150. Cho BK, Knight EM, Palsson B. PCR-based tandem epitope tagging system for Escherichia coli genome engineering. Biotechniques. 2006 Jan; 40(1):67-72. PMID: 16454042.
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    151. Barrett CL, Herring CD, Reed JL, Palsson B. 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.
    152. Fong SS, Nanchen A, Palsson B, 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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    153. Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson B. 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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    154. Papin JA, Hunter T, Palsson B, 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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    155. Famili I, Mahadevan R, Palsson B. 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.
    156. Papin JA, Reed JL, Palsson B. 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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    157. Price ND, Schellenberger J, Palsson B. 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.
    158. Westerhoff HV, Palsson B. The evolution of molecular biology into systems biology. Nat Biotechnol. 2004 Oct; 22(10):1249-52. PMID: 15470464.
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    159. Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson B. Comparison of network-based pathway analysis methods. Trends Biotechnol. 2004 Aug; 22(8):400-5. PMID: 15283984.
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    160. Papin JA, Palsson B. 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.
    161. Vo TD, Greenberg HJ, Palsson B. 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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    162. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson B. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004 May 06; 429(6987):92-6. PMID: 15129285.
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    163. Papin JA, Palsson B. 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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    164. 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 B, 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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    165. Covert MW, Famili I, Palsson B. 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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    166. Price ND, Reed JL, Papin JA, Wiback SJ, Palsson B. 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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    167. Famili I, Forster J, Nielsen J, Palsson B. 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.
    168. Famili I, Palsson B. 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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    169. Reed JL, Vo TD, Schilling CH, Palsson B. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 2003; 4(9):R54. PMID: 12952533; PMCID: PMC193654.
    170. 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 B, 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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    171. Famili I, Palsson B. 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.
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    174. Covert MW, Palsson B. 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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    175. Price ND, Papin JA, Schilling CH, Palsson B. Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol. 2003 Apr; 21(4):162-9. PMID: 12679064.
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    176. Raghunathan A, Palsson B. 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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    177. Price ND, Reed JL, Papin JA, Famili I, Palsson B. 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.
    178. Förster J, Famili I, Palsson B, 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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    179. Ibarra RU, Edwards JS, Palsson B. 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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    180. Kauffman KJ, Pajerowski JD, Jamshidi N, Palsson B, 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.
    181. Wiback SJ, Palsson B. Extreme pathway analysis of human red blood cell metabolism. Biophys J. 2002 Aug; 83(2):808-18. PMID: 12124266; PMCID: PMC1302188.
    182. Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson B. Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol. 2002 Aug; 184(16):4582-93. PMID: 12142428; PMCID: PMC135230.
    183. Lee GM, Fong SS, Oh DJ, Francis K, Palsson B. 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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    184. Edwards JS, Ramakrishna R, Palsson B. Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol Bioeng. 2002 Jan 05; 77(1):27-36. PMID: 11745171.
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    185. Kolker E, Purvine S, Picone A, Cherny T, Akerley BJ, Munson RS, Palsson B, 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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