Analysis of the first genetic engineering attribution challenge.

Autor: Crook OM; Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK., Warmbrod KL; Johns Hopkins Center for Health Security, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.; Institute of Public Health Genetics, University of Washington, Seattle, WA, USA., Lipstein G; DrivenData Inc, Denver, CO, USA., Chung C; DrivenData Inc, Denver, CO, USA., Bakerlee CW; altLabs Inc, Berkeley, CA, USA., McKelvey TG Jr; altLabs Inc, Berkeley, CA, USA., Holland SR; altLabs Inc, Berkeley, CA, USA., Swett JL; altLabs Inc, Berkeley, CA, USA., Esvelt KM; altLabs Inc, Berkeley, CA, USA.; Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA., Alley EC; altLabs Inc, Berkeley, CA, USA. ethan@altlabs.tech.; Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA. ethan@altlabs.tech., Bradshaw WJ; altLabs Inc, Berkeley, CA, USA. wjbrad@mit.edu.; Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA. wjbrad@mit.edu.

Publikováno v: Nature communications [Nat Commun] 2022 Nov 30; Vol. 13 (1), pp. 7374. Date of Electronic Publication: 2022 Nov 30.

Increased energy demand from anabolic-catabolic processes drives β-lactam antibiotic lethality.

Autor: Lobritz MA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA., Andrews IW; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA., Braff D; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA., Porter CBM; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA., Gutierrez A; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA., Furuta Y; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA., Cortes LBG; School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA., Ferrante T; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA., Bening SC; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA., Wong F; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA., Gruber C; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA., Bakerlee CW; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA., Lambert G; School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA., Walker GC; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA., Dwyer DJ; Department of Cell Biology and Molecular Genetics, Institute for Physical Science and Technology, Department of Biomedical Engineering, and Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA. Electronic address: djdwyer@umd.edu., Collins JJ; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA. Electronic address: jimjc@mit.edu.

Publikováno v: Cell chemical biology [Cell Chem Biol] 2022 Feb 17; Vol. 29 (2), pp. 276-286.e4. Date of Electronic Publication: 2022 Jan 05.

The genetic basis of differential autodiploidization in evolving yeast populations.

Autor: Tung S; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.; The Lakshmi Mittal And Family South Asia Institute, Harvard University, Cambridge, MA 02138, USA., Bakerlee CW; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.; Quantitative Biology Initiative, Harvard University, Cambridge, MA 02138, USA.; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA.; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA., Phillips AM; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA., Nguyen Ba AN; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.; Quantitative Biology Initiative, Harvard University, Cambridge, MA 02138, USA.; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA., Desai MM; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.; Quantitative Biology Initiative, Harvard University, Cambridge, MA 02138, USA.; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA.; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.; Department of Physics, Harvard University, Cambridge, MA 02138, USA.

Publikováno v: G3 (Bethesda, Md.) [G3 (Bethesda)] 2021 Aug 07; Vol. 11 (8).

Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations.

Autor: Johnson MS; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; Quantitative Biology Initiative, Harvard University, Cambridge, United States.; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, United States., Gopalakrishnan S; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; Quantitative Biology Initiative, Harvard University, Cambridge, United States.; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, United States.; Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States., Goyal J; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; John A Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, United States., Dillingham ME; Quantitative Biology Initiative, Harvard University, Cambridge, United States.; Graduate Program in Systems, Synthetic, and Quantitative Biology, Harvard University, Cambridge, United States., Bakerlee CW; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; Quantitative Biology Initiative, Harvard University, Cambridge, United States.; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, United States.; Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States., Humphrey PT; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; Quantitative Biology Initiative, Harvard University, Cambridge, United States.; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, United States., Jagdish T; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; Quantitative Biology Initiative, Harvard University, Cambridge, United States.; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, United States.; Graduate Program in Systems, Synthetic, and Quantitative Biology, Harvard University, Cambridge, United States., Jerison ER; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; Department of Physics, Harvard University, Cambridge, United States.; Department of Applied Physics, Stanford University, Stanford, United States., Kosheleva K; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; Department of Physics, Harvard University, Cambridge, United States., Lawrence KR; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; Quantitative Biology Initiative, Harvard University, Cambridge, United States.; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, United States.; Department of Physics, Massachusetts Institute of Technology, Cambridge, United States., Min J; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; Quantitative Biology Initiative, Harvard University, Cambridge, United States.; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, United States.; Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.; John A Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, United States., Moulana A; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States., Phillips AM; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States., Piper JC; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; AeroLabs, Aeronaut Brewing Co, Somerville, United States., Purkanti R; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; The Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany., Rego-Costa A; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States., McDonald MJ; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; School of Biological Sciences, Monash University, Victoria, Monash, Australia., Nguyen Ba AN; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; Quantitative Biology Initiative, Harvard University, Cambridge, United States.; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, United States.; Department of Physics, Harvard University, Cambridge, United States.; Department of Cell and Systems Biology, University of Toronto, Toronto, Canada., Desai MM; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.; Quantitative Biology Initiative, Harvard University, Cambridge, United States.; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, United States.; Department of Physics, Harvard University, Cambridge, United States.

Publikováno v: ELife [Elife] 2021 Jan 19; Vol. 10. Date of Electronic Publication: 2021 Jan 19.