Now showing items 1-7 of 7

    • Compressive genomics for protein databases 

      Daniels, Noah M.; Gallant, Andrew; Peng, Jian; Cowen, Lenore J.; Baym, Michael; Berger, Bonnie (Oxford University Press, 2013)
      Motivation: The exponential growth of protein sequence databases has increasingly made the fundamental question of searching for homologs a computational bottleneck. The amount of unique data, however, is not growing nearly ...
    • Decreased thermal niche breadth as a trade-off of antibiotic resistance 

      Herren, Cristina; Baym, Michael (Springer Science and Business Media LLC, 2022-04-14)
      Evolutionary theory predicts that adaptations, including antibiotic resistance, should come with associated fitness costs; yet, many resistance mutations seemingly contradict this prediction by inducing no growth rate ...
    • Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes 

      Baym, Michael; Kryazhimskiy, Sergey; Lieberman, Tami D.; Chung, Hattie; Desai, Michael M.; Kishony, Roy (Public Library of Science, 2015)
      Whole-genome sequencing has become an indispensible tool of modern biology. However, the cost of sample preparation relative to the cost of sequencing remains high, especially for small genomes where the former is dominant. ...
    • Large-scale identification of genetic design strategies using local search 

      Lun, Desmond S; Rockwell, Graham; Guido, Nicholas; Baym, Michael Hartmann; Kelner, Jonathan A; Berger, Bonnie; Galagan, James E; Church, George McDonald (Nature Publishing Group, 2009)
      In the past decade, computational methods have been shown to be well suited to unraveling the complex web of metabolic reactions in biological systems. Methods based on flux–balance analysis (FBA) and bi-level optimization ...
    • Perfect as the Enemy of the Good: Using Low-Sensitivity Tests to Mitigate SARS-CoV-2 Outbreaks 

      Kennedy-Shaffer, Lee; Baym, Michael; Hanage, William (2020)
      Preventing future infection waves of COVID-19 will depend on effective and efficient contact tracing. SARS-CoV-2 transmission appears to be characterized by high individual variation and a large role of superspreading ...
    • Rapid construction of a whole-genome transposon insertion collection for Shewanella oneidensis by Knockout Sudoku 

      Baym, Michael; Shaket, Lev; Anzai, Isao A.; Adesina, Oluwakemi; Barstow, Buz (Nature Publishing Group, 2016)
      Whole-genome knockout collections are invaluable for connecting gene sequence to function, yet traditionally, their construction has required an extraordinary technical effort. Here we report a method for the construction ...
    • The Separatrix Algorithm for Synthesis and Analysis of Stochastic Simulations with Applications in Disease Modeling 

      Klein, Daniel J.; Baym, Michael; Eckhoff, Philip (Public Library of Science, 2014)
      Decision makers in epidemiology and other disciplines are faced with the daunting challenge of designing interventions that will be successful with high probability and robust against a multitude of uncertainties. To ...