Publications

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Huang T-W, Lam I, Chang H-Y, Tsai S-F, Palsson BO, Charusanti P.  2014.  Capsule deletion via a lamda-Red knockout system perturbs biofilm formation and fimbriae expression in Klebsiella pneumoniae MGH 78578.. BMC Res Notes. 7(1):13.
Brunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L et al..  2016.  Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.. Cell Syst.
Qiu Y, Nagarajan H, Embree M, Shieu W, Abate E, Juárez K, Cho B-K, Elkins JG, Nevin KP, Barrett CL et al..  2013.  Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks.. Nat Commun. 4:1755.
Latif H, Federowicz S, Ebrahim A, Tarasova J, Szubin R, Utrilla J, Zengler K, Palsson BO.  2016.  ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. bioRxiv.
Latif H, Federowicz S, Ebrahim A, Tarasova J, Szubin R, Utrilla J, Zengler K, Palsson BO.  2018.  ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions.. PLoS One. 13(5):e0197272.
D'Alessandro A, Nemkov T, Yoshida T, Bordbar A, Palsson BO, Hansen KC.  2016.  Citrate metabolism in red blood cells stored in additive solution-3.. Transfusion. 57(2):325-336.
Lloyd CJ, Ebrahim A, Yang L, King ZA, Catoiu E, O'Brien EJ, Liu JK, Palsson BO.  2017.  COBRAme: A Computational Framework for Building and Manipulating Models of Metabolism and Gene Expression. bioRxiv.
Lloyd CJ, Ebrahim A, Yang L, King ZA, Catoiu E, O'Brien EJ, Liu JK, Palsson BO.  2018.  COBRAme: A computational framework for genome-scale models of metabolism and gene expression.. PLoS Comput Biol. 14(7):e1006302.
Ebrahim A, Lerman JA, Palsson BO, Hyduke DR.  2013.  COBRApy: COnstraints-Based Reconstruction and Analysis for Python.. BMC Syst Biol. 7(1):74.
Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen F-C, Fleming RMT, Hsiung CA et al..  2011.  A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.. BMC Syst Biol. 5:8.
Paglia G, Sigurjónsson OE, Rolfsson O, Valgeirsdottir S, Hansen MBagge, Brynjólfsson S, Gudmundsson S, Palsson BO.  2014.  Comprehensive metabolomic study of platelets reveals the expression of discrete metabolic phenotypes during storage.. Transfusion.
Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO.  2019.  A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.. PLoS Comput Biol. 15(1):e1006644.
O'Brien EJ, Palsson BO.  2015.  Computing the functional proteome: recent progress and future prospects for genome-scale models.. Curr Opin Biotechnol. 34C:125-134.
Hefzi H, Ang KSiong, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D et al..  2016.  A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.. Cell Syst. 3(5):434-443.e8.
Lewis NE, Nagarajan H, Palsson BO.  2012.  Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.. Nat Rev Microbiol. 10(4):291-305.
Bordbar A, Monk JM, King ZA, Palsson BO.  2014.  Constraint-based models predict metabolic and associated cellular functions.. Nat Rev Genet. 15(2):107-20.
Liu HC, Jamshidi N, Chen Y, Eraly SA, Cho SYee, Bhatnagar V, Wu W, Bush KT, Abagyan R, Palsson BO et al..  2016.  Construction and Evaluation of an Organic Anion Transporter 1 (OAT1)-Centered Metabolic Network.. J Biol Chem.
Tremblay P-L, Summers ZM, Glaven RH, Nevin KP, Zengler K, Barrett CL, Qiu Y, Palsson BO, Lovley DR.  2011.  A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution.. Environ Microbiol. 13(1):13-23.
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Fu W, Gudmundsson S, Wichuk K, Palsson S, Palsson BO, Salehi-Ashtiani K, Brynjólfsson S.  2018.  Dataset on economic analysis of mass production of algae in LED-based photobioreactors.. Data Brief. 22:137-139.
Seo SWoo, Kim D, Latif H, O'Brien EJ, Szubin R, Palsson BO.  2014.  Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli.. Nat Commun. 5:4910.
Seo SWoo, Kim D, O'Brien EJ, Szubin R, Palsson BO.  2015.  Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli.. Nat Commun. 6:7970.
Rolfsson O, Palsson BO.  2015.  Decoding the jargon of bottom-up metabolic systems biology.. Bioessays.
Nogales J, Gudmundsson S, Knight EM, Palsson BO, Thiele I.  2012.  Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis.. Proc Natl Acad Sci U S A. 109(7):2678-83.
Palsson S, Hickling TP, Bradshaw-Pierce EL, Zager M, Jooss K, Brien PJO, Spilker ME, Palsson BO, Vicini P.  2013.  The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models.. BMC Syst Biol. 7(1):95.
LaCroix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, Szubin R, Palsson BO, Feist AM.  2014.  Discovery of key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal media using adaptive laboratory evolution.. Appl Environ Microbiol.
Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR.  2017.  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.
Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RMt et al..  2015.  Do genome-scale models need exact solvers or clearer standards? Mol Syst Biol. 11(10):831.
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Fu W, Paglia G, Magnúsdóttir M, Steinarsdóttir EA, Gudmundsson S, Palsson BO, Andrésson OS, Brynjólfsson S.  2014.  Effects of abiotic stressors on lutein production in the green microalga Dunaliella salina.. Microb Cell Fact. 13(1):3.
Bordbar A, Yurkovich JT, Paglia G, Rolfsson O, Sigurjónsson OE, Palsson BO.  2017.  Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics.. Sci Rep. 7:46249.
Fu W, Guðmundsson O, Paglia G, Herjólfsson G, Andrésson OS, Palsson BO, Brynjólfsson S.  2013.  Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution.. Appl Microbiol Biotechnol. 97(6):2395-403.
King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO.  2015.  Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.. PLoS Comput Biol. 11(8):e1004321.
Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L, Palsson BO.  2018.  Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.. BMC Syst Biol. 12(1):66.
Du B, Zielinski DC, Kavvas ES, Dräger A, Tan J, Zhang Z, Ruggiero KE, Arzumanyan GA, Palsson BO.  2016.  Evaluation of rate law approximations in bottom-up kinetic models of metabolism.. BMC Syst Biol. 10(1):40.
Sandberg TE, Long CP, Gonzalez JE, Feist AM, Antoniewicz MR, Palsson BO.  2016.  Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology.. PLoS One. 11(3):e0151130.
Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson BO, Sommer M, Feist AM.  2014.  Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations.. Mol Biol Evol.
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.  2018.  Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism.. Nat Commun. 9(1):3796.
Nogales J, Gudmundsson S, Duque E., Ramos JLewis, Palsson BO.  2017.  Expanding The Computable Reactome In Pseudomonas putida Reveals Metabolic Cycles Providing Robustness. bioRxiv.
Liao Y-C, Huang T-W, Chen F-C, Charusanti P, Hong JSJ, Chang H-Y, Tsai S-F, Palsson BO, Hsiung CA.  2011.  An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228.. J Bacteriol. 193(7):1710-7.
Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson BO.  2011.  An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.. BMC Syst Biol. 5:163.
Charusanti P, Fong NL, Nagarajan H, Pereira AR, Li HJ, Abate EA, Su Y, Gerwick WH, Palsson BO.  2012.  Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction.. PLoS One. 7(3):e33727.
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Orth JD, Palsson BO.  2012.  Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions.. BMC Syst Biol. 6(1):30.
Campodonico MA, Andrews BA, Asenjo JA, Palsson BO, Feist AM.  2014.  Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path.. Metab Eng. 25C:140-158.
Seif Y, Kavvas E, Lachance J-C, Yurkovich JT, Nuccio S-P, Fang X, Catoiu E, Raffatellu M, Palsson BO, Monk JM.  2018.  Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits.. Nat Commun. 9(1):3771.
Levering J, Broddrick J, Dupont CL, Peers G, Beeri K, Mayers J, Gallina AA, Allen AE, Palsson BO, Zengler K.  2016.  Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom.. PLoS One. 11(5):e0155038.
Cho B-K, Kim D, Knight EM, Zengler K, Palsson BO.  2014.  Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states.. BMC Biol. 12(1):4.
Seo SWoo, Kim D, Szubin R, Palsson BO.  2015.  Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655.. Cell Rep.
Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C et al..  2013.  Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome.. Nat Biotechnol.
Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S et al..  2011.  The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line.. Nat Biotechnol. 29(8):735-41.
Cheng K-K, Lee B-S, Masuda T, Ito T, Ikeda K, Hirayama A, Deng L, Dong J, Shimizu K, Soga T et al..  2014.  Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol.. Nat Commun. 5:3233.
Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO.  2016.  Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution.. Cell Syst. 2(4):260-71.
Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, Palsson BO.  2017.  Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities.. Proc Natl Acad Sci U S A.
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Bordbar A, Jamshidi N, Palsson BO.  2011.  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. 5:110.
Bordbar A, Johansson PI, Paglia G, Harrison SJ, Wichuk K, Magnúsdóttir M, Valgeirsdottir S, Gybel-Brask M, Ostrowski SR, Palsson S et al..  2016.  Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomes.. Transfusion.
Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H et al..  2017.  iML1515, a knowledgebase that computes Escherichia coli traits.. Nat Biotechnol. 35(10):904-908.
Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K et al..  2012.  In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun. 3:929.
Levering J, Dupont CL, Allen AE, Palsson BO, Zengler K.  2017.  Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels.. mSystems. 2(1)
Paglia G, Williams JP, Menikarachchi L, J Thompson W, Tyldesley-Worster R, Halldórsson S, Rolfsson O, Moseley A, Grant D, Langridge J et al..  2014.  Ion mobility derived collision cross sections to support metabolomics applications.. Anal Chem. 86(8):3985-93.
Paglia G, Angel P, Williams JP, Richardson K, Olivos HJ, J Thompson W, Menikarachchi L, Lai S, Walsh C, Moseley A et al..  2014.  Ion Mobility-Derived Collision Cross Section As an Additional Measure for Lipid Fingerprinting and Identification.. Anal Chem.
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Sastry A, Monk J, Tegel H, Uhlen M, Palsson BO, Rockberg J, Brunk E.  2017.  Machine Learning in Computational Biology to Accelerate High-Throughput Protein Expression.. Bioinformatics.
Fu W, Gudmundsson O, Feist AM, Herjolfsson G, Brynjolfsson S, Palsson BO.  2012.  Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor.. J Biotechnol.
Paglia G, Sigurjónsson OE, Bordbar A, Rolfsson O, Magnúsdóttir M, Palsson S, Wichuk K, Gudmundsson S, Palsson BO.  2016.  Metabolic fate of adenine in red blood cells during storage in SAGM solution.. Transfusion.
Nilsson A, Nielsen J, Palsson BO.  2017.  Metabolic Models of Protein Allocation Call for the Kinetome.. Cell Syst. 5(6):538-541.
Paglia G, Sigurjónsson OE, Rolfsson O, Hansen MBagge, Brynjólfsson S, Gudmundsson S, Palsson BO.  2014.  Metabolomic analysis of platelets during storage: a comparison between apheresis- and buffy coat-derived platelet concentrates.. Transfusion.
McCloskey D, Young JD, Xu S, Palsson BO, Feist AM.  2015.  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.
Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO.  2014.  Minimal metabolic pathway structure is consistent with associated biomolecular interactions.. Mol Syst Biol. 10(7):737.
LaCroix RA, Palsson BO, Feist AM.  2017.  A Model for Designing Adaptive Laboratory Evolution Experiments.. Appl Environ Microbiol.
Guzman GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson BO, Feist AM.  2015.  Model-driven discovery of underground metabolic functions in Escherichia coli.. Proc Natl Acad Sci U S A.
Bordbar A, Mo ML, Nakayasu ES, Schrimpe-Rutledge AC, Kim Y-M, Metz TO, Jones MB, Frank BC, Smith RD, Peterson SN et al..  2012.  Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation.. Mol Syst Biol. 8:558.
McCloskey D, Gangoiti JA, King ZA, Naviaux RK, Barshop BA, Palsson BO, Feist AM.  2013.  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.
Yang L, Yurkovich JT, King ZA, Palsson BO.  2018.  Modeling the multi-scale mechanisms of macromolecular resource allocation. Current Opinion in Microbiology. 45:8-15.
Pacini T, Fu W, Gudmundsson S, A Chiaravalle E, Brynjolfson S, Palsson BO, Astarita G, Paglia G.  2015.  Multidimensional Analytical Approach Based on UHPLC-UV-Ion Mobility-MS for the Screening of Natural Pigments.. Anal Chem. 87(5):2593-9.
Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A et al..  2016.  Multi-omic data integration enables discovery of hidden biological regularities.. Nat Commun. 7:13091.
Monk JM, Koza A, Campodonico MA, Machado D, Seoane JMiguel, Palsson BO, Herrgard MJ, Feist AM.  2016.  Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes.. Cell Syst.
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.  2018.  Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in knockout evolutions.. Appl Environ Microbiol.
Seo J-H, Hong J S-J, Kim D, Cho B-K, Huang T-W, Tsai S-F, Palsson BO, Charusanti P.  2012.  Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features.. BMC Genomics. 13(1):679.
Mih N, Brunk E, Bordbar A, Palsson BO.  2016.  A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism.. PLoS Comput Biol. 12(7):e1005039.
Thiele I, Fleming RMT, Que R, Bordbar A, Diep D, Palsson BO.  2012.  Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage.. PLoS One. 7(9):e45635.
Wu W, Jamshidi N, Eraly SA, Liu HC, Bush KT, Palsson BO, Nigam SK.  2013.  Multispecific Drug Transporter Oat3 (Slc22a8) Regulates Multiple Metabolic Pathways.. Drug Metab Dispos.
Bordbar A, Feist AM, Usaite-Black R, Woodcock J, Palsson BO, Famili I.  2011.  A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology.. BMC Syst Biol. 5:180.
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Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Gonzalez GAndres Pre, Aurich MKathrin et al..  2018.  Recon3D enables a three-dimensional view of gene variation in human metabolism.. Nat Biotechnol.
Fong NL, Lerman JA, Lam I, Palsson BO, Charusanti P.  2013.  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. 342(1):62-9.
Liu JK, Brien EJO, Lerman JA, Zengler K, Palsson BO, Feist AM.  2014.  Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale.. BMC Syst Biol. 8(1):110.
Guzman GI, Olson CA, Hefner Y, Phaneuf PV, Catoiu E, Crepaldi LB, Micas LGoldschmid, Palsson BO, Feist AM.  2018.  Reframing gene essentiality in terms of adaptive flexibility.. BMC Syst Biol. 12(1):143.
Ma D, Yang L, Fleming RMT, Thiele I, Palsson BO, Saunders MA.  2016.  Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression.. Sci Rep. 7:40863.
Seo SWoo, Gao Y, Kim D, Szubin R, Yang J, Cho B-K, Palsson BO.  2017.  Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655.. Sci Rep. 7(1):2181.
Lee JSeong, Park JHyoung, Ha TKwang, Samoudi M, Lewis NE, Palsson BO, Kildegaard HFaustrup, Lee G M.  2018.  Revealing Key Determinants of Clonal Variation in Transgene Expression in Recombinant CHO Cells Using Targeted Genome Editing.. ACS Synth Biol.
Zengler K, Palsson BO.  2012.  A road map for the development of community systems (CoSy) biology.. Nat Rev Microbiol. 10(5):366-72.
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Kim Y-M, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson BO, McDermott JE, Heffron F et al..  2013.  Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes.. Mol Biosyst.
Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A.  2015.  SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.. BMC Syst Biol. 9(1):68.
Barrett CL, Cho B-K, Palsson BO.  2011.  Sensitive and accurate identification of protein-DNA binding events in ChIP-chip assays using higher order derivative analysis.. Nucleic Acids Res. 39(5):1656-65.
Yang L, Ma D, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO.  2016.  solveME: fast and reliable solution of nonlinear ME models.. BMC Bioinformatics. 17(1):391.
Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z, Palsson BO.  2018.  ssbio: A Python Framework for Structural Systems Biology. Bioinformatics.
Latif H, Szubin R, Tan J, Brunk E, Lechner A, Zengler K, Palsson BO.  2015.  A streamlined ribosome profiling protocol for the characterization of microorganisms.. Biotechniques. 58(6):329-32.
Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO.  2013.  Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli.. Science. 340(6137):1220-3.
Ansong C, Deatherage BL, Hyduke D, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P, Kim Y-M, Nakayasu ES et al..  2013.  Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling.. Curr Top Microbiol Immunol. 363:21-41.
Gao Y, Yurkovich JT, Seo SWoo, Kabimoldayev I, Dräger A, Chen K, Sastry AV, Fang X, Mih N, Yang L et al..  2018.  Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.. Nucleic Acids Res.
Nam H, Campodonico M, Bordbar A, Hyduke DR, Kim S, Zielinski DC, Palsson BO.  2014.  A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks.. PLoS Comput Biol. 10(9):e1003837.
Kim D, Seo SWoo, Nam H, Guzman GI, Gao Y, Palsson BO.  2016.  Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP. bioRxiv.
Kim D, Seo SWoo, Gao Y, Nam H, Guzman GI, Cho B-K, Palsson BO.  2018.  Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP.. Nucleic Acids Res.
Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson BO.  2017.  Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism.. Sci Rep. 7:41241.
Yurkovich JT, Bordbar A, Sigurjónsson OE, Palsson BO.  2018.  Systems biology as an emerging paradigm in transfusion medicine.. BMC Syst Biol. 12(1):31.
Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT et al..  2015.  Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.. Proc Natl Acad Sci U S A.
Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO.  2016.  Systems biology of the structural proteome.. BMC Syst Biol. 10(1):26.

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