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检索条件"机构=Bioinformatics Program and Biological Design Center"
13 条 记 录,以下是1-10 订阅
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Interplay between morphology and competition in two-dimensional colony expansion
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Physical Review E 2023年 第3期108卷 L032301-L032301页
作者: Daniel W. Swartz Hyunseok Lee Mehran Kardar Kirill S. Korolev Department of Physics Graduate Program in Bioinformatics and Biological Design Center Boston University Boston Massachusetts 02215 USA
In growing populations, the fate of mutations depends on their competitive ability against the ancestor and their ability to colonize new territory. Here we present a theory that integrates both aspects of mutant fitn... 详细信息
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Mechanically-driven growth and competition in a Voronoi model of tissues
arXiv
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arXiv 2024年
作者: Brézin, Louis Korolev, Kirill S. Department of Physics Graduate Program in Bioinformatics Biological Design Center Boston University BostonMA02215 United States
The mechanisms leading cells to acquire a fitness advantage and establish themselves in a population are paramount to understanding the development and growth of cancer. Although there are many works that study separa... 详细信息
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Modern views of ancient metabolic networks
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Current Opinion in Systems Biology 2018年 8卷 117-124页
作者: Goldford, Joshua E. Segrè, Daniel Bioinformatics Program and Biological Design Center Boston University Boston 02215 MA United States Department of Biology Boston University Boston 02215 MA United States Department of Biomedical Engineering Boston University Boston 02215 MA United States Department of Physics Boston University Boston 02215 MA United States
Metabolism is a molecular, cellular, ecological and planetary phenomenon, whose fundamental principles are likely at the heart of what makes living matter different from inanimate one. Systems biology approaches devel... 详细信息
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Competition on the edge of an expanding population
arXiv
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arXiv 2023年
作者: Swartz, Daniel W. Lee, Hyunseok Kardar, Mehran Korolev, Kirill S. Department of Physics Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics Graduate Program in Bioinformatics and Biological Design Center Boston University BostonMA02215 United States
In growing populations, the fate of mutations depends on their competitive ability against the ancestor and their ability to colonize new territory. Here we present a theory that integrates both aspects of mutant fitn...
来源: 评论
New sector morphologies emerge from anisotropic colony growth
arXiv
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arXiv 2024年
作者: Swartz, Daniel W. Lee, Hyunseok Kardar, Mehran Korolev, Kirill S. Department of Physics Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics Graduate Program in Bioinformatics and Biological Design Center Boston University BostonMA02215 United States
Competition during range expansions is of great interest from both practical and theoretical view points. Experimentally, range expansions are often studied in homogeneous Petri dishes, which lack spatial anisotropy t... 详细信息
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1 Slow expanders invade by forming dented fronts in microbial 2 colonies
arXiv
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arXiv 2021年
作者: Lee, Hyunseok Gore, Jeff Korolev, Kirill S. Physics of Living Systems Group Department of Physics Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics Graduate Program in Bioinformatics Biological Design Center Boston University BostonMA02215 United States
Most organisms grow in space, whether they are viruses spreading within a host tissue or invasive species colonizing a new continent. Evolution typically selects for higher expansion rates during spatial growth, but i... 详细信息
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Data-driven modeling reveals a universal dynamic underlying the COVID-19 pandemic under social distancing
arXiv
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arXiv 2020年
作者: Marsland, Robert Mehta, Pankaj Department of Physics Boston University BostonMA02215 United States Biological Design Center Boston University BostonMA02215 United States Microbiome Initiative Boston University BostonMA02215 United States Bioinformatics Program Boston University BostonMA02215 United States College of Data Science Boston University BostonMA02215 United States
We show that the COVID-19 pandemic under social distancing exhibits universal dynamics. The cumulative numbers of both infections and deaths quickly cross over from exponential growth at early times to a longer period... 详细信息
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Ecological landscapes guide the assembly of optimal microbial communities
arXiv
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arXiv 2021年
作者: George, Ashish B. Korolev, Kirill S. Department of Physics Boston University BostonMA02215 United States Biological Design Center Boston University BostonMA02215 United States Carl R. Woese Institute for Genomic Biology Department of Plant Biology University of Illinois at Urbana-Champaign UrbanaIL61801 United States Graduate Program in Bioinformatics Boston University BostonMA02215 United States
Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities gr... 详细信息
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Custom CRISPR-Cas9 PAM variants via scalable engineering and machine learning
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Nature 2025年 2025 Apr 22页
作者: Rachel A Silverstein Nahye Kim Ann-Sophie Kroell Russell T Walton Justin Delano Rossano M Butcher Martin Pacesa Blaire K Smith Kathleen A Christie Leillani L Ha Ronald J Meis Aaron B Clark Aviv D Spinner Cicera R Lazzarotto Yichao Li Azusa Matsubara Elizabeth O Urbina Gary A Dahl Bruno E Correia Debora S Marks Shengdar Q Tsai Luca Pinello Suk See De Ravin Qin Liu Benjamin P Kleinstiver PhD Program in Biological and Biomedical Sciences Harvard Medical School Boston MA USA. Center for Genomic Medicine Massachusetts General Hospital Boston MA USA. Department of Pathology Massachusetts General Hospital Boston MA USA. Department of Pathology Harvard Medical School Boston MA USA. Institute of Pharmacy and Molecular Biotechnology (IPMB) Faculty of Engineering Sciences Heidelberg University Heidelberg Germany. Department of Biomedical Informatics Harvard Medical School Boston MA USA. Molecular Pathology Unit Massachusetts General Hospital Charlestown MA USA. Krantz Family Center for Cancer Research Massachusetts General Hospital Charlestown Charlestown MA USA. Broad Institute of Harvard and MIT Cambridge MA USA. Ocular Genomics Institute Massachusetts Eye and Ear Boston MA USA. Department of Ophthalmology Harvard Medical School Boston MA USA. Laboratory of Protein Design and Immunoengineering École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics Lausanne Switzerland. CELLSCRIPTTM Madison WI USA. Department of Systems Biology Harvard Medical School Boston MA USA. Department of Hematology St. Jude Children's Research Hospital Memphis TN USA. Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda MD USA. Center for Genomic Medicine Massachusetts General Hospital Boston MA USA. bkleinstiver@mgh.harvard.edu. Department of Pathology Massachusetts General Hospital Boston MA USA. bkleinstiver@mgh.harvard.edu. Department of Pathology Harvard Medical School Boston MA USA. bkleinstiver@mgh.harvard.edu.
Engineering and characterizing proteins can be time-consuming and cumbersome, motivating the development of generalist CRISPR-Cas enzymes to enable diverse genome editing applications. However, such enzymes have cavea...
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Computation of Microbial Ecosystems in Time and Space (COMETS): An open source collaborative platform for modeling ecosystems metabolism
arXiv
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arXiv 2020年
作者: Dukovski, Ilija Bajić, Djordje Chacón, Jeremy M. Quintin, Michael Vila, Jean C.C. Sulheim, Snorre Pacheco, Alan R. Bernstein, David B. Riehl, William J. Korolev, Kirill S. Sanchez, Alvaro Harcombe, William R. Segrè, Daniel Bioinformatics Program Boston University BostonMA United States Biological Design Center Boston University BostonMA United States Department of Ecology and Evolutionary Biology Yale University New HavenCT United States Microbial Sciences Institute Yale University West HavenCT United States Department of Ecology Evolution and Behavior University of Minnesota St. PaulMN United States BioTechnology Institute University of Minnesota St. PaulMN United States Department of Biotechnology and Food Science Norwegian University of Science and Technology Trondheim Norway Department of Biotechnology and Nanomedicine SINTEF Industry Trondheim Norway Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory BerkeleyCA United States Department of Biomedical Engineering Boston University BostonMA United States Department of Physics Boston University BostonMA United States Department of Biology Boston University BostonMA United States
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predict... 详细信息
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