Search Results - "Flamholz, Avi"

SARS-CoV-2 (COVID-19) by the numbers by Bar-On, Yinon M, Flamholz, Avi, Phillips, Rob, Milo, Ron

“…The COVID-19 pandemic is a harsh reminder of the fact that, whether in a single human host or a wave of infection across continents, viral dynamics is often a…”
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eQuilibrator 3.0: a database solution for thermodynamic constant estimation by Beber, Moritz E, Gollub, Mattia G, Mozaffari, Dana, Shebek, Kevin M, Flamholz, Avi I, Milo, Ron, Noor, Elad

“…Abstract eQuilibrator (equilibrator.weizmann.ac.il) is a database of biochemical equilibrium constants and Gibbs free energies, originally designed as a…”
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Revisiting Trade-offs between Rubisco Kinetic Parameters by Flamholz, Avi I, Prywes, Noam, Moran, Uri, Davidi, Dan, Bar-On, Yinon M, Oltrogge, Luke M, Alves, Rui, Savage, David, Milo, Ron

“…Rubisco is the primary carboxylase of the Calvin cycle, the most abundant enzyme in the biosphere, and one of the best-characterized enzymes. On the basis of…”
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Microbial communities: The metabolic rate is the trait by Flamholz, Avi I., Newman, Dianne K.

“…Making sense of the metabolism of microbial communities is a daunting task. Using denitrification as a model metabolism, a new paper shows that the rate of…”
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The total number and mass of SARS-CoV-2 virions by Sender, Ron, Bar-On, Yinon M., Gleizer, Shmuel, Bernshtein, Biana, Flamholz, Avi, Phillips, Rob, Milo, Ron

“…Quantitatively describing the time course of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection within an infected individual is…”
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Matching metabolic supply to demand optimizes microbial growth by Flamholz, Avi I., Goyal, Akshit

“…Recent research has strengthened the notion that microbes allocate their biosynthetic capacity to maximize the growth rate, λ. Yet many microbes can grow…”
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Functional reconstitution of a bacterial CO2 concentrating mechanism in Escherichia coli by Flamholz, Avi I, Dugan, Eli, Blikstad, Cecilia, Gleizer, Shmuel, Ben-Nissan, Roee, Amram, Shira, Antonovsky, Niv, Ravishankar, Sumedha, Noor, Elad, Bar-Even, Arren, Milo, Ron, Savage, David F

“…Many photosynthetic organisms employ a CO 2 concentrating mechanism (CCM) to increase the rate of CO 2 fixation via the Calvin cycle. CCMs catalyze ≈50% of…”
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Glycolytic strategy as a tradeoff between energy yield and protein cost by Flamholz, Avi, Noor, Elad, Bar-Even, Arren, Liebermeister, Wolfram, Milo, Ron

“…Contrary to the textbook portrayal of glycolysis as a single pathway conserved across all domains of life, not all sugar-consuming organisms use the canonical…”
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Visual account of protein investment in cellular functions by Liebermeister, Wolfram, Noor, Elad, Flamholz, Avi, Davidi, Dan, Bernhardt, Jörg, Milo, Ron

“…Proteomics techniques generate an avalanche of data and promise to satisfy biologists' long-held desire to measure absolute protein abundances on a genome-wide…”
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Closed ecosystems extract energy through self-organized nutrient cycles by Goyal, Akshit, Flamholz, Avi I, Petroff, Alexander P, Murugan, Arvind

“…Our planet is a self-sustaining ecosystem powered by light energy from the sun, but roughly closed to matter. Many ecosystems on Earth are also approximately…”
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The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization by Noor, Elad, Flamholz, Avi, Bar-Even, Arren, Davidi, Dan, Milo, Ron, Liebermeister, Wolfram

“…Bacterial growth depends crucially on metabolic fluxes, which are limited by the cell's capacity to maintain metabolic enzymes. The necessary enzyme amount per…”
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Optical O 2 Sensors Also Respond to Redox Active Molecules Commonly Secreted by Bacteria by Flamholz, Avi I, Saccomano, Samuel, Cash, Kevin, Newman, Dianne K

“…From a metabolic perspective, molecular oxygen (O ) is arguably the most significant constituent of Earth's atmosphere. Nearly every facet of microbial…”
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Pathway thermodynamics highlights kinetic obstacles in central metabolism by Noor, Elad, Bar-Even, Arren, Flamholz, Avi, Reznik, Ed, Liebermeister, Wolfram, Milo, Ron

“…In metabolism research, thermodynamics is usually used to determine the directionality of a reaction or the feasibility of a pathway. However, the relationship…”
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Rethinking glycolysis: on the biochemical logic of metabolic pathways by Bar-Even, Arren, Flamholz, Avi, Noor, Elad, Milo, Ron

“…Metabolic pathways may seem arbitrary and unnecessarily complex. In many cases, a chemist might devise a simpler route for the biochemical transformation, so…”
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Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants by Crits-Christoph, Alexander, Kantor, Rose S, Olm, Matthew R, Whitney, Oscar N, Al-Shayeb, Basem, Lou, Yue Clare, Flamholz, Avi, Kennedy, Lauren C, Greenwald, Hannah, Hinkle, Adrian, Hetzel, Jonathan, Spitzer, Sara, Koble, Jeffery, Tan, Asako, Hyde, Fred, Schroth, Gary, Kuersten, Scott, Banfield, Jillian F, Nelson, Kara L

“…Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral…”
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Uniform binding and negative catalysis at the origin of enzymes by Noor, Elad, Flamholz, Avi I., Jayaraman, Vijay, Ross, Brian L., Cohen, Yair, Patrick, Wayne M., Gruic‐Sovulj, Ita, Tawfik, Dan S.

“…Enzymes are well known for their catalytic abilities, some even reaching “catalytic perfection” in the sense that the reaction they catalyze has reached the…”
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Competing constraints shape the nonequilibrium limits of cellular decision-making by Lammers, Nicholas C, Flamholz, Avi I, Garcia, Hernan G

“…Gene regulation is central to cellular function. Yet, despite decades of work, we lack quantitative models that can predict how transcriptional control emerges…”
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Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle by Claassens, Nico J., Scarinci, Giovanni, Fischer, Axel, Flamholz, Avi I., Newell, William, Frielingsdorf, Stefan, Lenz, Oliver, Bar-Even, Arren

“…Carbon fixation via the Calvin cycle is constrained by the side activity of Rubisco with dioxygen, generating 2-phosphoglycolate. The metabolic recycling of…”
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Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements by Davidi, Dan, Noor, Elad, Liebermeister, Wolfram, Bar-Even, Arren, Flamholz, Avi, Tummler, Katja, Barenholz, Uri, Goldenfeld, Miki, Shlomi, Tomer, Milo, Ron

“…Turnover numbers, also known as kcat values, are fundamental properties of enzymes. However, kcat data are scarce and measured in vitro, thus may not…”
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Tools for interpretation of wastewater SARS-CoV-2 temporal and spatial trends demonstrated with data collected in the San Francisco Bay Area by Greenwald, Hannah D., Kennedy, Lauren C., Hinkle, Adrian, Whitney, Oscar N., Fan, Vinson B., Crits-Christoph, Alexander, Harris-Lovett, Sasha, Flamholz, Avi I., Al-Shayeb, Basem, Liao, Lauren D., Beyers, Matt, Brown, Daniel, Chakrabarti, Alicia R., Dow, Jason, Frost, Dan, Koekemoer, Mark, Lynch, Chris, Sarkar, Payal, White, Eileen, Kantor, Rose, Nelson, Kara L.

“…•WBE was evaluated at sewershed and facility scales as a pandemic-response strategy.•Wastewater SARS-CoV-2 N1 significantly correlated with COVID-19 cases in…”
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