Search Results - "Palsson, Bernhard O."

Using Genome-scale Models to Predict Biological Capabilities by O’Brien, Edward J., Monk, Jonathan M., Palsson, Bernhard O.

“…Constraint-based reconstruction and analysis (COBRA) methods at the genome scale have been under development since the first whole-genome sequences appeared in…”
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Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods by Lewis, Nathan E., Nagarajan, Harish, Palsson, Bernhard O.

“…Key Points Our understanding of genotype–phenotype relationships has classically been qualitative, but recent advances are enabling us to overcome conceptual…”
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Constraint-based models predict metabolic and associated cellular functions by Bordbar, Aarash, Monk, Jonathan M., King, Zachary A., Palsson, Bernhard O.

“…Key Points Understanding the genotype–phenotype relationship of a cell has been a long-standing goal in biology. The availability of genome sequencing and of…”
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Reconstruction of biochemical networks in microorganisms by Palsson, Bernhard Ø, Feist, Adam M, Herrgård, Markus J, Thiele, Ines, Reed, Jennie L

“…Key Points Our ability to reconstruct genome-scale metabolic networks in microbial cells from genomic and high-throughput data has grown substantially in…”
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Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways by King, Zachary A, Dräger, Andreas, Ebrahim, Ali, Sonnenschein, Nikolaus, Lewis, Nathan E, Palsson, Bernhard O

“…Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization…”
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The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology by Sandberg, Troy E., Salazar, Michael J., Weng, Liam L., Palsson, Bernhard O., Feist, Adam M.

“…Harnessing the process of natural selection to obtain and understand new microbial phenotypes has become increasingly possible due to advances in culturing…”
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The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli by Palsson, Bernhard Ø, Feist, Adam M

“…The number and scope of methods developed to interrogate and use metabolic network reconstructions has significantly expanded over the past 15 years. In…”
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Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 by Schellenberger, Jan, Que, Richard, Fleming, Ronan M T, Thiele, Ines, Orth, Jeffrey D, Feist, Adam M, Zielinski, Daniel C, Bordbar, Aarash, Lewis, Nathan E, Rahmanian, Sorena, Kang, Joseph, Hyduke, Daniel R, Palsson, Bernhard Ø

“…Over the past decade, a growing community of researchers has emerged around the use of constraint-based reconstruction and analysis (COBRA) methods to…”
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Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism by Akbari, Amir, Palsson, Bernhard O

“…Identifying plausible mechanisms for compartmentalization and accumulation of the organic intermediates of early metabolic cycles in primitive cells has been a…”
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Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function by Yang, Jason H., Bhargava, Prerna, McCloskey, Douglas, Mao, Ning, Palsson, Bernhard O., Collins, James J.

“…Bactericidal antibiotics alter microbial metabolism as part of their lethality and can damage mitochondria in mammalian cells. In addition, antibiotic…”
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Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome by Rychel, Kevin, Sastry, Anand V., Palsson, Bernhard O.

“…The transcriptional regulatory network (TRN) of Bacillus subtilis coordinates cellular functions of fundamental interest, including metabolism, biofilm…”
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The Escherichia coli transcriptome mostly consists of independently regulated modules by Sastry, Anand V., Gao, Ye, Szubin, Richard, Hefner, Ying, Xu, Sibei, Kim, Donghyuk, Choudhary, Kumari Sonal, Yang, Laurence, King, Zachary A., Palsson, Bernhard O.

“…Underlying cellular responses is a transcriptional regulatory network (TRN) that modulates gene expression. A useful description of the TRN would decompose the…”
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Drug off-target effects predicted using structural analysis in the context of a metabolic network model by Chang, Roger L, Xie, Li, Xie, Lei, Bourne, Philip E, Palsson, Bernhard Ø

“…Recent advances in structural bioinformatics have enabled the prediction of protein-drug off-targets based on their ligand binding sites. Concurrent…”
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COBRApy: COnstraints-Based Reconstruction and Analysis for Python by Ebrahim, Ali, Lerman, Joshua A, Palsson, Bernhard O, Hyduke, Daniel R

“…COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and…”
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Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments by O'Brien, Edward J, Utrilla, Jose, Palsson, Bernhard O

“…The costs and benefits of protein expression are balanced through evolution. Expression of un-utilized protein (that have no benefits in the current…”
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Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655 by Seo, Sang Woo, Kim, Donghyuk, Szubin, Richard, Palsson, Bernhard O.

“…Three transcription factors (TFs), OxyR, SoxR, and SoxS, play a critical role in transcriptional regulation of the defense system for oxidative stress in…”
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Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, L-1,2-Propanediol by Lee, Dae-Hee, Palsson, Bernhard Ø

“…Laboratory adaptive evolution studies can provide key information to address a wide range of issues in evolutionary biology. Such studies have been limited…”
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Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks by Catoiu, Edward Alexander, Phaneuf, Patrick, Monk, Jonathan, Palsson, Bernhard O

“…The genomic diversity across strains of a species forms the genetic basis for differences in their behavior. A large-scale assessment of sequence variation has…”
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Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules by Shin, Jongoh, Zielinski, Daniel C, Palsson, Bernhard O

“…Abstract Synthetic biology enables the reprogramming of cellular functions for various applications. However, challenges in scalability and predictability…”
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Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models by Heckmann, David, Lloyd, Colton J., Mih, Nathan, Ha, Yuanchi, Zielinski, Daniel C., Haiman, Zachary B., Desouki, Abdelmoneim Amer, Lercher, Martin J., Palsson, Bernhard O.

“…Knowing the catalytic turnover numbers of enzymes is essential for understanding the growth rate, proteome composition, and physiology of organisms, but…”
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