A bacterial sensor taxonomy across earth ecosystems for machine learning applications.

Autor: Park H; Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.; EPSRC/BBSRC Future Biomanufacturing Research Hub, EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom.; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Joachimiak MP; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Jungbluth SP; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Yang Z; Computational Science Initiative, Brookhaven National Laboratory, Upton, New York, USA., Riehl WJ; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Canon RS; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.; National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Arkin AP; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.; Department of Bioengineering, University of California, Berkeley, California, USA., Dehal PS; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

Publikováno v: MSystems [mSystems] 2024 Jan 23; Vol. 9 (1), pp. e0002623. Date of Electronic Publication: 2023 Dec 11.

Metagenome-assembled genome extraction and analysis from microbiomes using KBase.

Autor: Chivian D; Lawrence Berkeley National Laboratory, Berkeley, CA, USA. DCChivian@lbl.gov., Jungbluth SP; Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Dehal PS; Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Wood-Charlson EM; Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Canon RS; Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Allen BH; Oak Ridge National Laboratory, Oak Ridge, TN, USA., Clark MM; Oak Ridge National Laboratory, Oak Ridge, TN, USA.; University of Tennessee, Knoxville, TN, USA., Gu T; Argonne National Laboratory, Lemont, IL, USA., Land ML; Oak Ridge National Laboratory, Oak Ridge, TN, USA., Price GA; Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Riehl WJ; Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Sneddon MW; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Predicine, Inc., Hayward, CA, USA., Sutormin R; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Google, Inc., San Francisco, CA, USA., Zhang Q; Argonne National Laboratory, Lemont, IL, USA., Cottingham RW; Oak Ridge National Laboratory, Oak Ridge, TN, USA., Henry CS; Argonne National Laboratory, Lemont, IL, USA., Arkin AP; Lawrence Berkeley National Laboratory, Berkeley, CA, USA. APArkin@lbl.gov.

Publikováno v: Nature protocols [Nat Protoc] 2023 Jan; Vol. 18 (1), pp. 208-238. Date of Electronic Publication: 2022 Nov 14.

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.

Autor: Novichkov PS; Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. psnovichkov@lbl.org, Brettin TS, Novichkova ES, Dehal PS, Arkin AP, Dubchak I, Rodionov DA

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2012 Jul; Vol. 40 (Web Server issue), pp. W604-8. Date of Electronic Publication: 2012 Jun 14.

A universal TagModule collection for parallel genetic analysis of microorganisms.

Autor: Oh J; Department of Genetics, Stanford University, Palo Alto, CA 94305, USA., Fung E, Price MN, Dehal PS, Davis RW, Giaever G, Nislow C, Arkin AP, Deutschbauer A

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2010 Aug; Vol. 38 (14), pp. e146. Date of Electronic Publication: 2010 May 21.

MicrobesOnline: an integrated portal for comparative and functional genomics.

Autor: Dehal PS; Virtual Institute for Microbial Stress and Survival, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. psdehal@lbl.gov, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2010 Jan; Vol. 38 (Database issue), pp. D396-400. Date of Electronic Publication: 2009 Nov 11.