Publications

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C
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BØ.  2004.  Integrating high-throughput and computational data elucidates bacterial networks.. Nature. 429(6987):92-6.
Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BØ.  2001.  Metabolic modeling of microbial strains in silico.. Trends in biochemical sciences. 26(3):179-86.
Covert MW, Schilling CH, Palsson BØ.  2001.  Regulation of gene expression in flux balance models of metabolism.. Journal of theoretical biology. 213(1):73-88.
Covert MW, Palsson BØ.  2002.  Transcriptional regulation in constraints-based metabolic models of Escherichia coli.. The Journal of biological chemistry. 277(31):28058-64.
Covert MW, Palsson BØ.  2003.  Constraints-based models: regulation of gene expression reduces the steady-state solution space.. Journal of theoretical biology. 221(3):309-25.
Covert MW, Famili I, Palsson BØ.  2003.  Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology? Biotechnology and bioengineering. 84(7):763-72.
Conrad TM, Joyce AR, Applebee KM, Barrett CL, Xie B, Gao Y, Palsson BØ.  2009.  Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations.. Genome biology. 10(10):R118.
Conrad TM, Lewis NE, Palsson BØ.  2011.  Microbial laboratory evolution in the era of genome-scale science.. Mol Syst Biol. 7:509.
Conrad TM, Frazier M, Joyce AR, Cho B-K, Knight EM, Lewis NE, Landick R, Palsson BØ.  2010.  RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media.. Proceedings of the National Academy of Sciences of the United States of America. 107(47):20500-5.
Clark IB, Hanania EG, Stevens J, Gallina M, Fieck A, Brandes R, Palsson BØ, Koller MR.  2006.  Optoinjection for efficient targeted delivery of a broad range of compounds and macromolecules into diverse cell types.. Journal of biomedical optics. 11(1):014034.
Chuck AS, Clarke MF, Palsson BØ.  1996.  Retroviral infection is limited by Brownian motion.. Human gene therapy. 7(13):1527-34.
Chuck AS, Palsson BØ.  1996.  Consistent and high rates of gene transfer can be obtained using flow-through transduction over a wide range of retroviral titers.. Human gene therapy. 7(6):743-50.
Chuck AS, Palsson BØ.  1996.  Membrane adsorption characteristics determine the kinetics of flow-through transductions.. Biotechnology and bioengineering. 51(3):260-70.
Choudhary KS, Mih N, Monk J, Kavvas E, Yurkovich JT, Sakoulas G, Palsson BO.  2018.  The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures. Frontiers in Microbiology. 9
Choe D, Szubin R, Dahesh S, Cho S, Nizet V, Palsson B, Cho B-K.  2018.  Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance.. Sci Rep. 8(1):2215.
Cho B-K, Charusanti P, Herrgard MJ, Palsson BØ.  2007.  Microbial regulatory and metabolic networks.. Current opinion in biotechnology. 18(4):360-4.
Cho B-K, Federowicz S, Park Y-S, Zengler K, Palsson BØ.  2011.  Deciphering the transcriptional regulatory logic of amino acid metabolism.. Nat Chem Biol. 8(1):65-71.
Cho B-K, Palsson BØ.  2009.  Can the protein occupancy landscape show the topologically isolated chromosomal domains in the E. coli genome?: An exciting prospect. Molecular cell. 35(3):255-6.
Cho B-K, Knight EM, Barrett CL, Palsson BØ.  2008.  Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts.. Genome research. 18(6):900-10.
Cho B-K, Federowicz SA, Embree M, Park Y-S, Kim D, Palsson BØ.  2011.  The PurR regulon in Escherichia coli K-12 MG1655.. Nucleic Acids Res. 39(15):6456-64.
Cho B-K, Knight EM, Palsson BØ.  2006.  PCR-based tandem epitope tagging system for Escherichia coli genome engineering.. BioTechniques. 40(1):67-72.
Cho B-K, Knight EM, Palsson BØ.  2008.  Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray.. Methods in molecular biology (Clifton, N.J.). 439:131-45.
Cho S, Choe D, Lee E, Kim SChang, Palsson B, Cho B-K.  2018.  High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli.. ACS Synth Biol. 7(4):1085-1094.
Cho B-K, Zengler K, Qiu Y, Park Y S, Knight EM, Barrett CL, Gao Y, Palsson BØ.  2009.  The transcription unit architecture of the Escherichia coli genome.. Nature biotechnology. 27(11):1043-9.
Cho S, Cho Y-B, Kang TJin, Kim SChang, Palsson B, Cho B-K.  2015.  The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli.. Nucleic Acids Res.
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.
Cho B-K, Barrett CL, Knight EM, Park Y S, Palsson BØ.  2008.  Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli.. Proceedings of the National Academy of Sciences of the United States of America. 105(49):19462-7.
Cho B-K, Knight EM, Palsson BØ.  2006.  Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA.. Microbiology (Reading, England). 152(Pt 8):2207-19.
Cho B-K, Palsson BØ.  2009.  Probing the basis for genotype-phenotype relationships.. Nature methods. 6(8):565-6.
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.
Chen P, Torralba M, Tan J, Embree M, Zengler K, Stärkel P, van Pijkeren J-P, DePew J, Loomba R, Ho SB et al..  2014.  Supplementation of Saturated Long-chain Fatty Acids Maintains Intestinal Eubiosis and Reduces Ethanol-induced Liver Injury in Mice.. Gastroenterology.
Chen K, Gao Y, Mih N, Brien EJ ’, Yang L, Palsson BO.  2017.  Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation. Proceedings of the National Academy of Sciences. 377121391183:201705524.
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.
Charusanti P, Conrad TM, Knight EM, Venkataraman K, Fong NL, Xie B, Gao Y, Palsson BØ.  2010.  Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene.. PLoS genetics. 6(11):e1001186.
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.
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B et al..  2013.  SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.. BMC Syst Biol. 7:135.
Chang RL, Xie L, Bourne PE, Palsson BO.  2013.  Antibacterial mechanisms identified through structural systems pharmacology.. BMC Syst Biol. 7(1):102.
Chang RL, Ghamsari L, Manichaikul A, Hom EFY, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K et al..  2011.  Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.. Mol Syst Biol. 7:518.
Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ.  2010.  Drug off-target effects predicted using structural analysis in the context of a metabolic network model.. PLoS computational biology. 6(9):e1000938.
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.
Campodonico MA, Vaisman D, Castro JF, Razmilic V, Mercado F, Andrews BA, Feist AM, Asenjo JA.  2016.  Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications. Metabolic Engineering Communications. 3
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.

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