Search Results - "Haiman, Zachary"

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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MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics by Haiman, Zachary B, Zielinski, Daniel C, Koike, Yuko, Yurkovich, James T, Palsson, Bernhard O

“…Mathematical models of metabolic networks utilize simulation to study system-level mechanisms and functions. Various approaches have been used to model the…”
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iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia by Sastry, Anand V, Yuan, Yuan, Poudel, Saugat, Rychel, Kevin, Yoo, Reo, Lamoureux, Cameron R, Li, Gaoyuan, Burrows, Joshua T, Chauhan, Siddharth, Haiman, Zachary B, Al Bulushi, Tahani, Seif, Yara, Palsson, Bernhard O, Zielinski, Daniel C

“…Public gene expression databases are a rapidly expanding resource of organism responses to diverse perturbations, presenting both an opportunity and a…”
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Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials by Yurkovich, James T, Alcantar, Miguel A, Haiman, Zachary B, Palsson, Bernhard O

“…Allosteric regulation has traditionally been described by mathematically-complex allosteric rate laws in the form of ratios of polynomials derived from the…”
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Biological and genetic determinants of glycolysis: Phosphofructokinase isoforms boost energy status of stored red blood cells and transfusion outcomes by Nemkov, Travis, Stephenson, Daniel, Earley, Eric J, Keele, Gregory R, Hay, Ariel, Key, Alicia, Haiman, Zachary B, Erickson, Christopher, Dzieciatkowska, Monika, Reisz, Julie A, Moore, Amy, Stone, Mars, Deng, Xutao, Kleinman, Steven, Spitalnik, Steven L, Hod, Eldad A, Hudson, Krystalyn E, Hansen, Kirk C, Palsson, Bernhard O, Churchill, Gary A, Roubinian, Nareg, Norris, Philip J, Busch, Michael P, Zimring, James C, Page, Grier P, D'Alessandro, Angelo

“…Mature red blood cells (RBCs) lack mitochondria and thus exclusively rely on glycolysis to generate adenosine triphosphate (ATP) during aging in vivo or…”
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A data-driven approach for timescale decomposition of biochemical reaction networks by Akbari, Amir, Haiman, Zachary B, Palsson, Bernhard O

“…Understanding the dynamics of biological systems in evolving environments is a challenge due to their scale and complexity. Here, we present a computational…”
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Modeling Red Blood Cell Metabolism in the Omics Era by Key, Alicia, Haiman, Zachary, Palsson, Bernhard O, D'Alessandro, Angelo

“…Red blood cells (RBCs) are abundant (more than 80% of the total cells in the human body), yet relatively simple, as they lack nuclei and organelles, including…”
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BioSimulators: a central registry of simulation engines and services for recommending specific tools by Shaikh, Bilal, Smith, Lucian P, Vasilescu, Dan, Marupilla, Gnaneswara, Wilson, Michael, Agmon, Eran, Agnew, Henry, Andrews, Steven S, Anwar, Azraf, Beber, Moritz E, Bergmann, Frank T, Brooks, David, Brusch, Lutz, Calzone, Laurence, Choi, Kiri, Cooper, Joshua, Detloff, John, Drawert, Brian, Dumontier, Michel, Ermentrout, G Bard, Faeder, James R, Freiburger, Andrew P, Fröhlich, Fabian, Funahashi, Akira, Garny, Alan, Gennari, John H, Gleeson, Padraig, Goelzer, Anne, Haiman, Zachary, Hasenauer, Jan, Hellerstein, Joseph L, Hermjakob, Henning, Hoops, Stefan, Ison, Jon C, Jahn, Diego, Jakubowski, Henry V, Jordan, Ryann, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, Sheriff, Rahuman S Malik, Mandal, Synchon, McDougal, Robert, Medley, J Kyle, Mendes, Pedro, Müller, Robert, Myers, Chris J, Naldi, Aurelien, Nguyen, Tung V N, Nickerson, David P, Olivier, Brett G, Patoliya, Drashti, Paulevé, Loïc, Petzold, Linda R, Priya, Ankita, Rampadarath, Anand K, Rohwer, Johann M, Saglam, Ali S, Singh, Dilawar, Sinha, Ankur, Snoep, Jacky, Sorby, Hugh, Spangler, Ryan, Starruß, Jörn, Thomas, Payton J, van Niekerk, David, Weindl, Daniel, Zhang, Fengkai, Zhukova, Anna, Goldberg, Arthur P, Schaff, James C, Blinov, Michael L, Sauro, Herbert M, Moraru, Ion I, Karr, Jonathan R

“…Abstract Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and…”
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BioSimulators: a central registry of simulation engines and services for recommending specific tools by Shaikh, Bilal, Smith, Lucian P, Vasilescu, Dan, Marupilla, Gnaneswara, Wilson, Michael, Agmon, Eran, Agnew, Henry, Andrews, Steven S, Anwar, Azraf, Beber, Moritz E, Bergmann, Frank T, Brooks, David, Brusch, Lutz, Calzone, Laurence, Choi, Kiri, Cooper, Joshua, Detloff, John, Drawert, Brian, Dumontier, Michel, Ermentrout, G. Bard, Faeder, James R, Freiburger, Andrew P, Fröhlich, Fabian, Funahashi, Akira, Garny, Alan, Gennari, John H, Gleeson, Padraig, Goelzer, Anne, Haiman, Zachary, Hellerstein, Joseph L, Hoops, Stefan, Ison, Jon C, Jahn, Diego, Jakubowski, Henry V, Jordan, Ryann, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, Mandal, Synchon, McDougal, Robert, Medley, J. Kyle, Mendes, Pedro, Müller, Robert, Myers, Chris J, Naldi, Aurelien, Nguyen, Tung V. N, Nickerson, David P, Olivier, Brett G, Patoliya, Drashti, Paulevé, Loïc, Petzold, Linda R, Priya, Ankita, Rampadarath, Anand K, Rohwer, Johann M, Saglam, Ali S, Singh, Dilawar, Sinha, Ankur, Snoep, Jacky, Sorby, Hugh, Spangler, Ryan, Starruß, Jörn, Thomas, Payton J, van Niekerk, David, Weindl, Daniel, Zhang, Fengkai, Zhukova, Anna, Goldberg, Arthur P, Blinov, Michael L, Sauro, Herbert M, Moraru, Ion I, Karr, Jonathan R

“…Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse…”
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