Publications

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2010
Lee D-H, Palsson BØ.  2010.  Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol.. Applied and environmental microbiology. 76(13):4158-68.
Schellenberger J, Park JO, Conrad TM, Palsson BØ.  2010.  BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.. BMC bioinformatics. 11:213.
Feist AM, Palsson BØ.  2010.  The biomass objective function.. Current opinion in microbiology. 13(3):344-9.
Palsson BØ, Zengler K.  2010.  The challenges of integrating multi-omic data sets.. Nature chemical biology. 6(11):787-9.
Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methé BA, Palsson BØ, Lovley DR et al..  2010.  De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.. PloS one. 5(6):e10922.
Portnoy VA, Scott DA, Lewis NE, Tarasova Y, Osterman AL, Palsson BØ.  2010.  Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655.. Applied and environmental microbiology. 76(19):6529-40.
Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BØ.  2010.  A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.. BMC systems biology. 4:140.
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.
Thiele I, Fleming RMT, Bordbar A, Schellenberger J, Palsson BØ.  2010.  Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.. Biophysical journal. 98(10):2072-81.
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.
Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N.  2010.  Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.. Molecular systems biology. 6:422.
Lewis NE, Schramm G, Bordbar A, Schellenberger J, Andersen MP, Cheng JK, Patel N, Yee A, Lewis RA, Eils R et al..  2010.  Large-scale in silico modeling of metabolic interactions between cell types in the human brain.. Nature biotechnology. 28(12):1279-85.
Jamshidi N, Palsson BØ.  2010.  Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models.. Biophysical journal. 98(2):175-85.
Lerman JA, Palsson BØ.  2010.  Microbiology. Topping off a multiscale balancing act.. Science (New York, N.Y.). 330(6007):1058-9.
Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ.  2010.  Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.. Metabolic engineering. 12(3):173-86.
Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, Polpitiya AD, Adkins JN, Schramm G, Purvine SO, Lopez-Ferrer D et al..  2010.  Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.. Molecular systems biology. 6:390.
Thiele I, Palsson BØ.  2010.  A protocol for generating a high-quality genome-scale metabolic reconstruction.. Nature protocols. 5(1):93-121.
Thiele I, Palsson BØ.  2010.  Reconstruction annotation jamborees: a community approach to systems biology.. Molecular systems biology. 6:361.
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.
Qiu Y, Cho B-K, Park Y S, Lovley DR, Palsson BØ, Zengler K.  2010.  Structural and operational complexity of the Geobacter sulfurreducens genome.. Genome research. 20(9):1304-11.
Orth JD, Palsson BØ.  2010.  Systematizing the generation of missing metabolic knowledge.. Biotechnology and bioengineering. 107(3):403-12.
Hyduke DR, Palsson BØ.  2010.  Towards genome-scale signalling network reconstructions.. Nature reviews. Genetics. 11(4):297-307.
Orth JD, Thiele I, Palsson BØ.  2010.  What is flux balance analysis? Nature biotechnology. 28(3):245-8.
2009
Oberhardt MA, Palsson BØ, Papin JA.  2009.  Applications of genome-scale metabolic reconstructions.. Molecular systems biology. 5:320.
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.
Mo ML, Palsson BØ, Herrgard MJ.  2009.  Connecting extracellular metabolomic measurements to intracellular flux states in yeast.. BMC systems biology. 3:37.
Raghunathan A, Reed JL, Shin S, Palsson BØ, Daefler S.  2009.  Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction.. BMC systems biology. 3:38.
Barrett CL, Herrgard MJ, Palsson BØ.  2009.  Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation.. BMC systems biology. 3:30.
Jamshidi N, Palsson BØ.  2009.  Flux-concentration duality in dynamic nonequilibrium biological networks.. Biophysical journal. 97(5):L11-3.
Gianchandani EP, Joyce AR, Palsson BØ, Papin JA.  2009.  Functional states of the genome-scale Escherichia coli transcriptional regulatory system.. PLoS computational biology. 5(6):e1000403.
Lewis NE, Cho B-K, Knight EM, Palsson BØ.  2009.  Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content.. Journal of bacteriology. 191(11):3437-44.
Sigurdsson MI, Jamshidi N, Jonsson JJ, Palsson BØ.  2009.  Genome-scale network analysis of imprinted human metabolic genes.. Epigenetics : official journal of the DNA Methylation Society. 4(1):43-6.
Thiele I, Jamshidi N, Fleming RMT, Palsson BØ.  2009.  Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.. PLoS computational biology. 5(3):e1000312.
Li F, Thiele I, Jamshidi N, Palsson BØ.  2009.  Identification of potential pathway mediation targets in Toll-like receptor signaling.. PLoS computational biology. 5(2):e1000292.
Palsson BØ.  2009.  Metabolic systems biology.. FEBS letters. 583(24):3900-4.
Cho B-K, Palsson BØ.  2009.  Probing the basis for genotype-phenotype relationships.. Nature methods. 6(8):565-6.
Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BØ.  2009.  Reconstruction of biochemical networks in microorganisms.. Nature reviews. Microbiology. 7(2):129-43.
Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA et al..  2009.  Three-dimensional structural view of the central metabolic network of Thermotoga maritima.. Science (New York, N.Y.). 325(5947):1544-9.
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.
Mo ML, Palsson BØ.  2009.  Understanding human metabolic physiology: a genome-to-systems approach.. Trends in biotechnology. 27(1):37-44.
Schellenberger J, Palsson BØ.  2009.  Use of randomized sampling for analysis of metabolic networks.. The Journal of biological chemistry. 284(9):5457-61.
Jamshidi N, Palsson BØ.  2009.  Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes.. BMC systems biology. 3:44.
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.
2008
Portnoy VA, Herrgard MJ, Palsson BØ.  2008.  Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain.. Applied and environmental microbiology. 74(24):7561-9.
Herrgard MJ, Swainston N, Dobson P, Dunn WB, Arga YK, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M et al..  2008.  A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.. Nature biotechnology. 26(10):1155-60.
Becker SA, Palsson BØ.  2008.  Context-specific metabolic networks are consistent with experiments.. PLoS computational biology. 4(5):e1000082.
Jamshidi N, Palsson BØ.  2008.  Formulating genome-scale kinetic models in the post-genome era.. Molecular systems biology. 4:171.
Nogales J, Palsson BØ, Thiele I.  2008.  A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.. BMC systems biology. 2:79.
Lee J, Yun H, Feist AM, Palsson BØ, Lee S Y.  2008.  Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network.. Applied microbiology and biotechnology. 80(5):849-62.
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, 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, 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.
Feist AM, Palsson BØ.  2008.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.. Nature biotechnology. 26(6):659-67.
Applebee KM, Herrgard MJ, Palsson BØ.  2008.  Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli.. Journal of bacteriology. 190(14):5087-94.
Shlomi T, Cabili MN, Herrgard MJ, Palsson BØ, Ruppin E.  2008.  Network-based prediction of human tissue-specific metabolism.. Nature biotechnology. 26(9):1003-10.
Joyce AR, Palsson BØ.  2008.  Predicting gene essentiality using genome-scale in silico models.. Methods in molecular biology (Clifton, N.J.). 416:433-57.
Becker SA, Palsson BØ.  2008.  Three factors underlying incorrect in silico predictions of essential metabolic genes.. BMC systems biology. 2:14.
Jamshidi N, Palsson BØ.  2008.  Top-down analysis of temporal hierarchy in biochemical reaction networks.. PLoS computational biology. 4(9):e1000177.
2007
Vo TD, Palsson BØ.  2007.  Building the power house: recent advances in mitochondrial studies through proteomics and systems biology.. American journal of physiology. Cell physiology. 292(1):C164-77.
Anderson MJ, DeLabarre B, Raghunathan A, Palsson BØ, Brunger AT, Quake SR.  2007.  Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices.. Biochemistry. 46(19):5722-31.
Yeung M, Thiele I, Palsson BØ.  2007.  Estimation of the number of extreme pathways for metabolic networks.. BMC bioinformatics. 8(1):363.
Herring CD, Palsson BØ.  2007.  An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes.. BMC genomics. 8:274.
Mo ML, Jamshidi N, Palsson BØ.  2007.  A genome-scale, constraint-based approach to systems biology of human metabolism.. Molecular bioSystems. 3(9):598-603.
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ.  2007.  A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.. Molecular systems biology. 3:121.
Oh Y-K, Palsson BØ, Park SM, Schilling CH, Mahadevan R.  2007.  Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data.. The Journal of biological chemistry. 282(39):28791-9.
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BØ.  2007.  Global reconstruction of the human metabolic network based on genomic and bibliomic data.. Proceedings of the National Academy of Sciences of the United States of America. 104(6):1777-82.
Jamshidi N, Vo TD, Palsson BØ.  2007.  In silico analysis of SNPs and other high-throughput data.. Methods in molecular biology (Clifton, N.J.). 366:267-85.
Jamshidi N, Palsson BØ.  2007.  Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets.. BMC systems biology. 1:26.
Hua Q, Joyce AR, Palsson BØ, Fong S.  2007.  Metabolic characterization of Escherichia coli strains adapted to growth on lactate.. Applied and environmental microbiology. 73(14):4639-47.
Resendis-Antonio O, Reed JL, Encarnación S, Collado-Vides J, Palsson BØ.  2007.  Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli.. PLoS computational biology. 3(10):1887-95.
Cho B-K, Charusanti P, Herrgard MJ, Palsson BØ.  2007.  Microbial regulatory and metabolic networks.. Current opinion in biotechnology. 18(4):360-4.
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ.  2007.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.. Nature protocols. 2(3):727-38.
Shlomi T, Herrgard MJ, Portnoy VA, Naim E, Palsson BØ, Sharan R, Ruppin E.  2007.  Systematic condition-dependent annotation of metabolic genes.. Genome research. 17(11):1626-33.
Vo TD, Paul Lee WN, Palsson BØ.  2007.  Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome.. Molecular genetics and metabolism. 91(1):15-22.
Joyce AR, Palsson BØ.  2007.  Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach.. Progress in drug research. Fortschritte der Arzneimittelforschung. Progrès des recherches pharmaceutiques. 64:265,267-309.
2006
Price ND, Thiele I, Palsson BØ.  2006.  Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.. Biophysical journal. 90(11):3919-28.
Mahadevan R, Bond DR, Butler JE, Esteve-Nuñez A, Coppi MV, Palsson BØ, Schilling CH, Lovley DR.  2006.  Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling.. Applied and environmental microbiology. 72(2):1558-68.
Herring CD, Raghunathan A, Honisch C, Patel T, Applebee KM, Joyce AR, Albert TJ, Blattner FR, van den Boom D, Cantor CR et al..  2006.  Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale.. Nature genetics. 38(12):1406-12.
Joyce AR, Reed JL, White A, Edwards R, Osterman AL, Baba T, Mori H, Lesely SA, Palsson BØ, Agarwalla S.  2006.  Experimental and computational assessment of conditionally essential genes in Escherichia coli.. Journal of bacteriology. 188(23):8259-71.
Herrgard MJ, Fong S, Palsson BØ.  2006.  Identification of genome-scale metabolic network models using experimentally measured flux profiles.. PLoS computational biology. 2(7):e72.
Herrgard MJ, Lee B-S, Portnoy VA, Palsson BØ.  2006.  Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.. Genome research. 16(5):627-35.
Vo TD, Palsson BØ.  2006.  Isotopomer analysis of myocardial substrate metabolism: a systems biology approach.. Biotechnology and bioengineering. 95(5):972-83.
Barrett CL, Palsson BØ.  2006.  Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach.. PLoS computational biology. 2(5):e52.
Fong S, Nanchen A, Palsson BØ, Sauer U.  2006.  Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes.. The Journal of biological chemistry. 281(12):8024-33.
Allen TE, Price ND, Joyce AR, Palsson BØ.  2006.  Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.. PLoS computational biology. 2(1):e2.
Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BØ.  2006.  Matrix formalism to describe functional states of transcriptional regulatory systems.. PLoS computational biology. 2(8):e101.
Hua Q, Joyce AR, Fong S, Palsson BØ.  2006.  Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains.. Biotechnology and bioengineering. 95(5):992-1002.
Becker SA, Price ND, Palsson BØ.  2006.  Metabolite coupling in genome-scale metabolic networks.. BMC bioinformatics. 7:111.
Joyce AR, Palsson BØ.  2006.  The model organism as a system: integrating 'omics' data sets.. Nature reviews. Molecular cell biology. 7(3):198-210.
Feist AM, Scholten JCM, Palsson BØ, Brockman FJ, Ideker T.  2006.  Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri.. Molecular systems biology. 2:2006.0004.
Barrett CL, Price ND, Palsson BØ.  2006.  Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition.. BMC bioinformatics. 7:132.
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.
Cho B-K, Knight EM, Palsson BØ.  2006.  PCR-based tandem epitope tagging system for Escherichia coli genome engineering.. BioTechniques. 40(1):67-72.
Reed JL, Patel TR, Chen KH, Joyce AR, Applebee KM, Herring CD, Bui OT, Knight EM, Fong S, Palsson BØ.  2006.  Systems approach to refining genome annotation.. Proceedings of the National Academy of Sciences of the United States of America. 103(46):17480-4.
Barrett CL, Kim T Y, Kim H U, Palsson BØ, Lee S Y.  2006.  Systems biology as a foundation for genome-scale synthetic biology.. Current opinion in biotechnology. 17(5):488-92.
Jamshidi N, Palsson BØ.  2006.  Systems biology of SNPs.. Molecular systems biology. 2:38.
Jamshidi N, Palsson BØ.  2006.  Systems biology of the human red blood cell.. Blood cells, molecules & diseases. 36(2):239-47.
Reed JL, Famili I, Thiele I, Palsson BØ.  2006.  Towards multidimensional genome annotation.. Nature reviews. Genetics. 7(2):130-41.
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.
2005
Hanania EG, Fieck A, Stevens J, Bodzin LJ, Palsson BØ, Koller MR.  2005.  Automated in situ measurement of cell-specific antibody secretion and laser-mediated purification for rapid cloning of highly-secreting producers.. Biotechnology and bioengineering. 91(7):872-6.
Thiele I, Price ND, Vo TD, Palsson BØ.  2005.  Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.. The Journal of biological chemistry. 280(12):11683-95.
Fong S, Joyce AR, Palsson BØ.  2005.  The econometrics of evolution.. Nature chemical biology. 1(4):191-2.
Bell SL, Palsson BØ.  2005.  Expa: a program for calculating extreme pathways in biochemical reaction networks.. Bioinformatics (Oxford, England). 21(8):1739-40.
Thiele I, Vo TD, Price ND, Palsson BØ.  2005.  Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants.. Journal of bacteriology. 187(16):5818-30.
Becker SA, Palsson BØ.  2005.  Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation.. BMC microbiology. 5:8.
Barrett CL, Herring CD, Reed JL, Palsson BØ.  2005.  The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.. Proceedings of the National Academy of Sciences of the United States of America. 102(52):19103-8.
Herring CD, Raffaelle M, Allen TE, Kanin EI, Landick R, Ansari AZ, Palsson BØ.  2005.  Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays.. Journal of bacteriology. 187(17):6166-74.
Fong S, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BØ.  2005.  In silico design and adaptive evolution of Escherichia coli for production of lactic acid.. Biotechnology and bioengineering. 91(5):643-8.
Famili I, Mahadevan R, Palsson BØ.  2005.  k-Cone analysis: determining all candidate values for kinetic parameters on a network scale.. Biophysical journal. 88(3):1616-25.
Fong S, Joyce AR, Palsson BØ.  2005.  Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states.. Genome research. 15(10):1365-72.
Mahadevan R, Palsson BØ.  2005.  Properties of metabolic networks: structure versus function.. Biophysical journal. 88(1):L07-9.
Papin JA, Hunter T, Palsson BØ, Subramaniam S.  2005.  Reconstruction of cellular signalling networks and analysis of their properties.. Nature reviews. Molecular cell biology. 6(2):99-111.
Herrgard MJ, Palsson BØ.  2005.  Untangling the web of functional and physical interactions in yeast.. Journal of biology. 4(2):5.
2004
Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BØ.  2004.  Comparison of network-based pathway analysis methods.. Trends in biotechnology. 22(8):400-5.
Westerhoff HV, Palsson BØ.  2004.  The evolution of molecular biology into systems biology.. Nature biotechnology. 22(10):1249-52.
Herrgard MJ, Palsson BØ.  2004.  Flagellar biosynthesis in silico: building quantitative models of regulatory networks.. Cell. 117(6):689-90.
Reed JL, Palsson BØ.  2004.  Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states.. Genome research. 14(9):1797-805.
Price ND, Reed JL, Palsson BØ.  2004.  Genome-scale models of microbial cells: evaluating the consequences of constraints.. Nature reviews. Microbiology. 2(11):886-97.
Papin JA, Reed JL, Palsson BØ.  2004.  Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.. Trends in biochemical sciences. 29(12):641-7.
Koller MR, Hanania EG, Stevens J, Eisfeld TM, Sasaki GC, Fieck A, Palsson BØ.  2004.  High-throughput laser-mediated in situ cell purification with high purity and yield.. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 61(2):153-61.
Honisch C, Raghunathan A, Cantor CR, Palsson BØ, van den Boom D.  2004.  High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12.. Genome research. 14(12):2495-502.
Palsson BØ.  2004.  In silico biotechnology. Era of reconstruction and interrogation.. Current opinion in biotechnology. 15(1):50-1.
Raghunathan A, Price ND, Galperin MY, Makarova KS, Purvine S, Picone AF, Cherny T, Xie T, Reilly TJ, Munson R et al..  2004.  In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.. Omics : a journal of integrative biology. 8(1):25-41.
Duarte NC, Palsson BØ, Fu P.  2004.  Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae.. BMC genomics. 5:63.
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.
Papin JA, Palsson BØ.  2004.  The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis.. Biophysical journal. 87(1):37-46.
Fong S, Palsson BØ.  2004.  Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes.. Nature genetics. 36(10):1056-8.
Wiback SJ, Famili I, Greenberg HJ, Palsson BØ.  2004.  Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space.. Journal of theoretical biology. 228(4):437-47.
Vo TD, Greenberg HJ, Palsson BØ.  2004.  Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data.. The Journal of biological chemistry. 279(38):39532-40.
Duarte NC, Herrgard MJ, Palsson BØ.  2004.  Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model.. Genome research. 14(7):1298-309.
Herrgard MJ, Covert MW, Palsson BØ.  2004.  Reconstruction of microbial transcriptional regulatory networks.. Current opinion in biotechnology. 15(1):70-7.
Papin JA, Palsson BØ.  2004.  Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk.. Journal of theoretical biology. 227(2):283-97.
Price ND, Schellenberger J, Palsson BØ.  2004.  Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies.. Biophysical journal. 87(4):2172-86.
Wiback SJ, Mahadevan R, Palsson BØ.  2004.  Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum.. Biotechnology and bioengineering. 86(3):317-31.
2003
Price ND, Reed JL, Papin JA, Famili I, Palsson BØ.  2003.  Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices.. Biophysical journal. 84(2 Pt 1):794-804.
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.
Famili I, Palsson BØ.  2003.  The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools.. Biophysical journal. 85(1):16-26.
Fong S, Marciniak JY, Palsson BØ.  2003.  Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model.. Journal of bacteriology. 185(21):6400-8.
Palsson BØ, Price ND, Papin JA.  2003.  Development of network-based pathway definitions: the need to analyze real metabolic networks.. Trends in biotechnology. 21(5):195-8.
Reed JL, Vo TD, Schilling CH, Palsson BØ.  2003.  An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR).. Genome biology. 4(9):R54.
Allen TE, Herrgard MJ, Liu M, Qiu Y, Glasner JD, Blattner FR, Palsson BØ.  2003.  Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets.. Journal of bacteriology. 185(21):6392-9.
Price ND, Papin JA, Schilling CH, Palsson BØ.  2003.  Genome-scale microbial in silico models: the constraints-based approach.. Trends in biotechnology. 21(4):162-9.
Förster J, Famili I, Fu P, Palsson BØ, Nielsen J.  2003.  Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.. Genome research. 13(2):244-53.
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.
Kolker E, Purvine S, Galperin MY, Stolyar S, Goodlett DR, Nesvizhskii AI, Keller A, Xie T, Eng JK, Yi E et al..  2003.  Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.. Journal of bacteriology. 185(15):4593-602.
Förster J, Famili I, Palsson BØ, Nielsen J.  2003.  Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae.. Omics : a journal of integrative biology. 7(2):193-202.
Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BØ.  2003.  Metabolic pathways in the post-genome era.. Trends in biochemical sciences. 28(5):250-8.
Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BØ.  2003.  Network-based analysis of metabolic regulation in the human red blood cell.. Journal of theoretical biology. 225(2):185-94.
Ibarra RU, Fu P, Palsson BØ, DiTonno JR, Edwards JS.  2003.  Quantitative analysis of Escherichia coli metabolic phenotypes within the context of phenotypic phase planes.. Journal of molecular microbiology and biotechnology. 6(2):101-8.
Herrgard MJ, Covert MW, Palsson BØ.  2003.  Reconciling gene expression data with known genome-scale regulatory network structures.. Genome research. 13(11):2423-34.
Wiback SJ, Mahadevan R, Palsson BØ.  2003.  Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum.. Journal of theoretical biology. 224(3):313-24.
Famili I, Forster J, Nielsen J, Palsson BØ.  2003.  Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network.. Proceedings of the National Academy of Sciences of the United States of America. 100(23):13134-9.
Raghunathan A, Palsson BØ.  2003.  Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli.. Biotechnology letters. 25(5):435-41.
Allen TE, Palsson BØ.  2003.  Sequence-based analysis of metabolic demands for protein synthesis in prokaryotes.. Journal of theoretical biology. 220(1):1-18.
Famili I, Palsson BØ.  2003.  Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices.. Journal of theoretical biology. 224(1):87-96.
Reed JL, Palsson BØ.  2003.  Thirteen years of building constraint-based in silico models of Escherichia coli.. Journal of bacteriology. 185(9):2692-9.
2002
Lee G M, Fong S, Oh D J, Francis K, Palsson BØ.  2002.  Characterization and efficacy of PKH26 as a probe to study the replication history of the human hematopoietic KG1a progenitor cell line.. In vitro cellular & developmental biology. Animal. 38(2):90-6.
Edwards JS, Ramakrishna R, Palsson BØ.  2002.  Characterizing the metabolic phenotype: a phenotype phase plane analysis.. Biotechnology and bioengineering. 77(1):27-36.
Kauffman KJ, Pajerowski J D, Jamshidi N, Palsson BØ, Edwards JS.  2002.  Description and analysis of metabolic connectivity and dynamics in the human red blood cell.. Biophysical journal. 83(2):646-62.
Price ND, Papin JA, Palsson BØ.  2002.  Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis.. Genome research. 12(5):760-9.
Ibarra RU, Edwards JS, Palsson BØ.  2002.  Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth.. Nature. 420(6912):186-9.
Wiback SJ, Palsson BØ.  2002.  Extreme pathway analysis of human red blood cell metabolism.. Biophysical journal. 83(2):808-18.
Papin JA, Price ND, Palsson BØ.  2002.  Extreme pathway lengths and reaction participation in genome-scale metabolic networks.. Genome research. 12(12):1889-900.
Price ND, Famili I, Beard DA, Palsson BØ.  2002.  Extreme pathways and Kirchhoff's second law.. Biophysical journal. 83(5):2879-82.
Papin JA, Price ND, Edwards JS, Palsson BØ.  2002.  The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy.. Journal of theoretical biology. 215(1):67-82.
Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BØ.  2002.  Genome-scale metabolic model of Helicobacter pylori 26695.. Journal of bacteriology. 184(16):4582-93.
Kolker E, Purvine S, Picone A, Cherny T, Akerley BJ, Munson RS, Palsson BØ, Daines DA, Smith AL.  2002.  H. influenzae Consortium: integrative study of H. influenzae-human interactions.. Omics : a journal of integrative biology. 6(4):341-8.
Jamshidi N, Wiback SJ, Palsson BØ.  2002.  In silico model-driven assessment of the effects of single nucleotide polymorphisms (SNPs) on human red blood cell metabolism.. Genome research. 12(11):1687-92.
Edwards JS, Covert MW, Palsson BØ.  2002.  Metabolic modelling of microbes: the flux-balance approach.. Environmental microbiology. 4(3):133-40.
Francis K, Palsson BØ, Donahue J, Fong S, Carrier E.  2002.  Murine Sca-1(+)/Lin(-) cells and human KG1a cells exhibit multiple pseudopod morphologies during migration.. Experimental hematology. 30(5):460-3.
Covert MW, Palsson BØ.  2002.  Transcriptional regulation in constraints-based metabolic models of Escherichia coli.. The Journal of biological chemistry. 277(31):28058-64.
2000
Schilling CH, Palsson BØ.  2000.  Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis.. Journal of theoretical biology. 203(3):249-83.
Schilling CH, Edwards JS, Letscher D, Palsson BØ.  2000.  Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems.. Biotechnology and bioengineering. 71(4):286-306.
Edwards JS, Palsson BØ.  2000.  The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.. Proceedings of the National Academy of Sciences of the United States of America. 97(10):5528-33.
Oh DJ, Martinez AR, Lee GM, Francis K, Palsson BØ.  2000.  Extension of osmolality-induced podia is observed from fluorescently labeled hematopoietic cell lines in hyperosmotic medium.. Cytometry. 40(2):109-18.
Lee GM, Fong S, Francis K, Oh DJ, Palsson BØ.  2000.  In situ labeling of adherent cells with PKH26.. In vitro cellular & developmental biology. Animal. 36(1):4-6.
Oh DJ, Martinez AR, Lee GM, Francis K, Palsson BØ.  2000.  Intercellular adhesion can be visualized using fluorescently labeled fibrosarcoma HT1080 cells cocultured with hematopoietic cell lines or CD34(+) enriched human mobilized peripheral blood cells.. Cytometry. 40(2):119-25.
Edwards JS, Palsson BØ.  2000.  Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions.. BMC bioinformatics. 1:1.
Edwards JS, Palsson BØ.  2000.  Multiple steady states in kinetic models of red cell metabolism.. Journal of theoretical biology. 207(1):125-7.
Edwards JS, Palsson BØ.  2000.  Robustness analysis of the Escherichia coli metabolic network.. Biotechnology progress. 16(6):927-39.
Schilling CH, Letscher D, Palsson BØ.  2000.  Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective.. Journal of theoretical biology. 203(3):229-48.
1996
Peng CA, Palsson BØ.  1996.  Cell growth and differentiation on feeder layers is predicted to be influenced by bioreactor geometry.. Biotechnology and bioengineering. 50(5):479-92.
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.
Peng CA, Palsson BØ.  1996.  Determination of specific oxygen uptake rates in human hematopoietic cultures and implications for bioreactor design.. Annals of biomedical engineering. 24(3):373-81.
Koller MR, Manchel I, Palsson MA, Maher RJ, Palsson BØ.  1996.  Different measures of human hematopoietic cell culture performance are optimized under vastly different conditions.. Biotechnology and bioengineering. 50(5):505-13.
Rogers CE, Bradley MS, Palsson BØ, Koller MR.  1996.  Flow cytometric analysis of human bone marrow perfusion cultures: erythroid development and relationship with burst-forming units-erythroid.. Experimental hematology. 24(5):597-604.
Koller MR, Oxender M, Brott DA, Palsson BØ.  1996.  flt-3 ligand is more potent than c-kit ligand for the synergistic stimulation of ex vivo hematopoietic cell expansion.. Journal of hematotherapy. 5(5):449-59.
Andreadis ST, Palsson BØ.  1996.  Kinetics of retrovirus mediated gene transfer: the importance of intracellular half-life of retroviruses.. Journal of theoretical biology. 182(1):1-20.
Chuck AS, Palsson BØ.  1996.  Membrane adsorption characteristics determine the kinetics of flow-through transductions.. Biotechnology and bioengineering. 51(3):260-70.
Chuck AS, Clarke MF, Palsson BØ.  1996.  Retroviral infection is limited by Brownian motion.. Human gene therapy. 7(13):1527-34.
Peng CA, Koller MR, Palsson BØ.  1996.  Unilineage model of hematopoiesis predicts self-renewal of stem and progenitor cells based on ex vivo growth data.. Biotechnology and bioengineering. 52(1):24-33.
1994
Lee GM, Kim SJ, Palsson BØ.  1994.  Enhanced specific antibody productivity of calcium alginate-entrapped hybridoma is cell line-specific.. Cytotechnology. 16(1):1-15.
Oh DJ, Koller MR, Palsson BØ.  1994.  Frequent harvesting from perfused bone marrow cultures results in increased overall cell and progenitor expansion.. Biotechnology and bioengineering. 44(5):609-16.
Lee CG, Palsson BØ.  1994.  High-density algal photobioreactors using light-emitting diodes.. Biotechnology and bioengineering. 44(10):1161-7.
Levee MG, Lee GM, Paek SH, Palsson BØ.  1994.  Microencapsulated human bone marrow cultures: a potential culture system for the clonal outgrowth of hematopoietic progenitor cells.. Biotechnology and bioengineering. 43(8):734-9.
Lee GM, Palsson BØ.  1994.  Monoclonal antibody production using free-suspended and entrapped hybridoma cells.. Biotechnology & genetic engineering reviews. 12:509-33.
Varma A, Palsson BØ.  1994.  Predictions for oxygen supply control to enhance population stability of engineered production strains.. Biotechnology and bioengineering. 43(4):275-85.
Hubbell JA, Palsson BØ, Papoutsakis ET.  1994.  Preface. Tissue engineering and cell therapies.. Biotechnology and bioengineering. 43(7):541.
Hubbell JA, Palsson BØ, Papoutsakis ET.  1994.  Preface: Tissue engineering and cell therapies: II.. Biotechnology and bioengineering. 43(8):683.
Varma A, Palsson BØ.  1994.  Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.. Applied and environmental microbiology. 60(10):3724-31.
1993
Varma A, Boesch BW, Palsson BØ.  1993.  Biochemical production capabilities of Escherichia coli.. Biotechnology and bioengineering. 42(1):59-73.
Lee GM, Chuck AS, Palsson BØ.  1993.  Cell Culture conditions determine the enhancement of specific monoclonal antibody productivity of calcium alginate-entrapped S3H5/gamma2bA2 hybridoma cells.. Biotechnology and bioengineering. 41(3):330-40.
Palsson BØ, Paek SH, Schwartz RM, Palsson MA, Lee GM, Silver S, Emerson SG.  1993.  Expansion of human bone marrow progenitor cells in a high cell density continuous perfusion system.. Bio/technology (Nature Publishing Company). 11(3):368-72.
Koller MR, Emerson SG, Palsson BØ.  1993.  Large-scale expansion of human stem and progenitor cells from bone marrow mononuclear cells in continuous perfusion cultures.. Blood. 82(2):378-84.
Merritt SE, Palsson BØ.  1993.  Loss of antibody productivity is highly reproducible in multiple hybridoma subclones.. Biotechnology and bioengineering. 42(2):247-50.
Varma A, Palsson BØ.  1993.  Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors.. Journal of theoretical biology. 165(4):477-502.
Palsson BØ, Lee ID.  1993.  Model complexity has a significant effect on the numerical value and interpretation of metabolic sensitivity coefficients.. Journal of theoretical biology. 161(3):299-315.
Koller MR, Palsson BØ.  1993.  Review: tissue engineering: reconstitution of human hematopoiesis ex vivo.. Biotechnology and bioengineering. 42(8):909-30.
Palsson BØ, Shen BQ, Meyerhoff ME, Trojanowicz M.  1993.  Simultaneous determination of ammonia nitrogen and L-glutamine in bioreactor media using flow injection.. The Analyst. 118(11):1361-5.
Meyerhoff ME, Trojanowicz M, Palsson BØ.  1993.  Simultaneous enzymatic/electrochemical determination of glucose and L-glutamine in hybridoma media by flow-injection analysis.. Biotechnology and bioengineering. 41(10):964-9.
Lee GM, Palsson BØ.  1993.  Stability of antibody productivity is improved when hybridoma cells are entrapped in calcium alginate beads.. Biotechnology and bioengineering. 42(9):1131-5.
Varma A, Boesch BW, Palsson BØ.  1993.  Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates.. Applied and environmental microbiology. 59(8):2465-73.

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