Search Results - "Phaneuf, Patrick V"

ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation by Phaneuf, Patrick V, Gosting, Dennis, Palsson, Bernhard O, Feist, Adam M

“…Abstract Adaptive Laboratory Evolution (ALE) has emerged as an experimental approach to discover causal mutations that confer desired phenotypic functions. ALE…”
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Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers by Heckmann, David, Campeau, Anaamika, Lloyd, Colton J., Phaneuf, Patrick V., Hefner, Ying, Carrillo-Terrazas, Marvic, Feist, Adam M., Gonzalez, David J., Palsson, Bernhard O.

“…Enzyme turnover numbers (k cats) are essential for a quantitative understanding of cells. Because k cats are traditionally measured in low-throughput assays,…”
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Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution by Mundhada, Hemanshu, Seoane, Jose M., Schneider, Konstantin, Koza, Anna, Christensen, Hanne B., Klein, Tobias, Phaneuf, Patrick V., Herrgard, Markus, Feist, Adam M., Nielsen, Alex T.

“…L-serine is a promising building block biochemical with a high theoretical production yield from glucose. Toxicity of L-serine is however prohibitive for…”
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Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity by Anand, Amitesh, Patel, Arjun, Chen, Ke, Olson, Connor A., Phaneuf, Patrick V., Lamoureux, Cameron, Hefner, Ying, Szubin, Richard, Feist, Adam M., Palsson, Bernhard O.

“…The bacterial respiratory electron transport system (ETS) is branched to allow condition-specific modulation of energy metabolism. There is a detailed…”
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Adaptive laboratory evolution of Escherichia coli under acid stress by Du, Bin, Olson, Connor A, Sastry, Anand V, Fang, Xin, Phaneuf, Patrick V, Chen, Ke, Wu, Muyao, Szubin, Richard, Xu, Sibei, Gao, Ye, Hefner, Ying, Feist, Adam M, Palsson, Bernhard O

“…The ability of to tolerate acid stress is important for its survival and colonization in the human digestive tract. Here, we performed adaptive laboratory…”
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Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity by Phaneuf, Patrick V, Yurkovich, James T, Heckmann, David, Wu, Muyao, Sandberg, Troy E, King, Zachary A, Tan, Justin, Palsson, Bernhard O, Feist, Adam M

“…Adaptive Laboratory Evolution (ALE) has emerged as an experimental approach to discover mutations that confer phenotypic functions of interest. However, the…”
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Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance by Rychel, Kevin, Tan, Justin, Patel, Arjun, Lamoureux, Cameron, Hefner, Ying, Szubin, Richard, Johnsen, Josefin, Mohamed, Elsayed Tharwat Tolba, Phaneuf, Patrick V., Anand, Amitesh, Olson, Connor A., Park, Joon Ho, Sastry, Anand V., Yang, Laurence, Feist, Adam M., Palsson, Bernhard O.

“…Relationships between the genome, transcriptome, and metabolome underlie all evolved phenotypes. However, it has proved difficult to elucidate these…”
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The genetic basis for adaptation of model-designed syntrophic co-cultures by Lloyd, Colton J, King, Zachary A, Sandberg, Troy E, Hefner, Ying, Olson, Connor A, Phaneuf, Patrick V, O'Brien, Edward J, Sanders, Jon G, Salido, Rodolfo A, Sanders, Karenina, Brennan, Caitriona, Humphrey, Gregory, Knight, Rob, Feist, Adam M

“…Understanding the fundamental characteristics of microbial communities could have far reaching implications for human health and applied biotechnology. Despite…”
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iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning by Rychel, Kevin, Decker, Katherine, Sastry, Anand V, Phaneuf, Patrick V, Poudel, Saugat, Palsson, Bernhard O

“…Abstract Independent component analysis (ICA) of bacterial transcriptomes has emerged as a powerful tool for obtaining co-regulated, independently-modulated…”
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BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets by Nuhamunada, Matin, Mohite, Omkar S, Phaneuf, Patrick V, Palsson, Bernhard O, Weber, Tilmann

“…Genome mining is revolutionizing natural products discovery efforts. The rapid increase in available genomes demands comprehensive computational platforms to…”
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Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration by Anand, Amitesh, Chen, Ke, Yang, Laurence, Sastry, Anand V., Olson, Connor A., Poudel, Saugat, Seif, Yara, Hefner, Ying, Phaneuf, Patrick V., Xu, Sibei, Szubin, Richard, Feist, Adam M., Palsson, Bernhard O.

“…Evolution fine-tunes biological pathways to achieve a robust cellular physiology. Two and a half billion years ago, rapidly rising levels of oxygen as a…”
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iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets by Catoiu, Edward A, Krishnan, Jayanth, Li, Gaoyuan, Lou, Xuwen A, Rychel, Kevin, Yuan, Yuan, Bajpe, Heera, Patel, Arjun, Choe, Donghui, Shin, Jongoh, Burrows, Joshua, Phaneuf, Patrick V, Zielinski, Daniel C, Palsson, Bernhard O

“…iModulons—sets of co-expressed genes identified through independent component analysis (ICA) of high-quality transcriptomic datasets—provide an unbiased,…”
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Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals by Lennen, Rebecca M., Lim, Hyun Gyu, Jensen, Kristian, Mohammed, Elsayed T., Phaneuf, Patrick V., Noh, Myung Hyun, Malla, Sailesh, Börner, Rosa A., Chekina, Ksenia, Özdemir, Emre, Bonde, Ida, Koza, Anna, Maury, Jérôme, Pedersen, Lasse E., Schöning, Lars Y., Sonnenschein, Nikolaus, Palsson, Bernhard O., Nielsen, Alex T., Sommer, Morten O.A., Herrgård, Markus J., Feist, Adam M.

“…Although strain tolerance to high product concentrations is a barrier to the economically viable biomanufacturing of industrial chemicals, chemical tolerance…”
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Pseudogene repair driven by selection pressure applied in experimental evolution by Anand, Amitesh, Olson, Connor A, Yang, Laurence, Sastry, Anand V, Catoiu, Edward, Choudhary, Kumari Sonal, Phaneuf, Patrick V, Sandberg, Troy E, Xu, Sibei, Hefner, Ying, Szubin, Richard, Feist, Adam M, Palsson, Bernhard O

“…Pseudogenes represent open reading frames that have been damaged by mutations, rendering the gene product non-functional. Pseudogenes are found in many genomes…”
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The Bitome: digitized genomic features reveal fundamental genome organization by Lamoureux, Cameron R, Choudhary, Kumari Sonal, King, Zachary A, Sandberg, Troy E, Gao, Ye, Sastry, Anand V, Phaneuf, Patrick V, Choe, Donghui, Cho, Byung-Kwan, Palsson, Bernhard O

“…A genome contains the information underlying an organism's form and function. Yet, we lack formal framework to represent and study this information. Here, we…”
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Synthetic cross-phyla gene replacement and evolutionary assimilation of major enzymes by Sandberg, Troy E., Szubin, Richard, Phaneuf, Patrick V., Palsson, Bernhard O.

“…The ability of DNA to produce a functional protein even after transfer to a foreign host is of fundamental importance in both evolutionary biology and…”
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Escherichia coli non-coding regulatory regions are highly conserved by Lamoureux, Cameron R, Phaneuf, Patrick V, Palsson, Bernhard O, Zielinski, Daniel C

“…Abstract Microbial genome sequences are rapidly accumulating, enabling large-scale studies of sequence variation. Existing studies primarily focus on coding…”
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Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data by Phaneuf, Patrick V, Zielinski, Daniel C, Yurkovich, James T, Johnsen, Josefin, Szubin, Richard, Yang, Lei, Kim, Se Hyeuk, Schulz, Sebastian, Wu, Muyao, Dalldorf, Christopher, Ozdemir, Emre, Lennen, Rebecca M, Palsson, Bernhard O, Feist, Adam M

“…Microbes are being engineered for an increasingly large and diverse set of applications. However, the designing of microbial genomes remains challenging due to…”
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Pseudogene repair driven by selection pressure applied in experimental evolution by Anand, Amitesh, Olson, Connor A., Yang, Laurence, Sastry, Anand V., Catoiu, Edward, Choudhary, Kumari Sonal, Phaneuf, Patrick V., Sandberg, Troy E., Xu, Sibei, Hefner, Ying, Szubin, Richard, Feist, Adam M., Palsson, Bernhard O.

“…Pseudogenes represent open reading frames that have been damaged by mutations, rendering the gene product non-functional. Pseudogenes are found in many genomes…”
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Reframing gene essentiality in terms of adaptive flexibility by Guzmán, Gabriela I, Olson, Connor A, Hefner, Ying, Phaneuf, Patrick V, Catoiu, Edward, Crepaldi, Lais B, Micas, Lucas Goldschmidt, Palsson, Bernhard O, Feist, Adam M

“…Essentiality assays are important tools commonly utilized for the discovery of gene functions. Growth/no growth screens of single gene knockout strain…”
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