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Lawrence Berkeley National Laboratory's Articles

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Page 3 of 43

Engineering isoprenoids production in metabolically versatile microbial host Pseudomonas putida

Authors: Xi Wang, Edward E. K. Baidoo, Ramu Kakumanu, Silvia Xie, Aindrila Mukhopadhyay and Taek Soon Lee

Citation: Biotechnology for Biofuels and Bioproducts 2022 15:137

Content type: Research Published on: 12 December 2022
Advanced one-pot deconstruction and valorization of lignocellulosic biomass into triacetic acid lactone using Rhodosporidium toruloides

Authors: Peter B. Otoupal, Gina M. Geiselman, Asun M. Oka, Carolina A. Barcelos, Hemant Choudhary, Duy Dinh, Wenqing Zhong, HeeJin Hwang, Jay D. Keasling, Aindrila Mukhopadhyay, Eric Sundstrom, Robert W. Haushalter, Ning Sun, Blake A. Simmons and John M. Gladden

Citation: Microbial Cell Factories 2022 21:254

Content type: Research Published on: 8 December 2022
Persistent memory as an effective alternative to random access memory in metagenome assembly

Authors: Jingchao Sun, Zhining Qiu, Rob Egan, Harrison Ho, Yue Li and Zhong Wang

Citation: BMC Bioinformatics 2022 23:513

Content type: Research article Published on: 30 November 2022
HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Authors: Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone and Jennifer Pett-Ridge

Citation: Microbiome 2022 10:199

Content type: Research Published on: 25 November 2022
Precursor prioritization for p-cymene production through synergistic integration of biology and chemistry

Authors: Hsi-Hsin Lin, Daniel Mendez‐Perez, Jimin Park, Xi Wang, Yan Cheng, Jiajie Huo, Aindrila Mukhopadhyay, Taek Soon Lee and Brent H. Shanks

Citation: Biotechnology for Biofuels and Bioproducts 2022 15:126

Content type: Research Published on: 17 November 2022
Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Authors: Lauren M. Tom, Martina Aulitto, Yu-Wei Wu, Kai Deng, Yu Gao, Naijia Xiao, Beatrice Garcia Rodriguez, Clifford Louime, Trent R. Northen, Aymerick Eudes, Jenny C. Mortimer, Paul D. Adams, Henrik V. Scheller, Blake A. Simmons, Javier A. Ceja-Navarro and Steven W. Singer

Citation: Microbiome 2022 10:183

Content type: Research Published on: 25 October 2022
Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

Authors: Hoon Je Seong, Simon Roux, Chung Yeon Hwang and Woo Jun Sul

Citation: Microbiome 2022 10:157

Content type: Research Published on: 28 September 2022
Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome

Authors: Tina Keller-Costa, Lydia Kozma, Sandra G. Silva, Rodolfo Toscan, Jorge Gonçalves, Asunción Lago-Lestón, Nikos C. Kyrpides, Ulisses Nunes da Rocha and Rodrigo Costa

Citation: Microbiome 2022 10:151

Content type: Research Published on: 22 September 2022
NSAID use and clinical outcomes in COVID-19 patients: a 38-center retrospective cohort study

Authors: Justin T. Reese, Ben Coleman, Lauren Chan, Hannah Blau, Tiffany J. Callahan, Luca Cappelletti, Tommaso Fontana, Katie R. Bradwell, Nomi L. Harris, Elena Casiraghi, Giorgio Valentini, Guy Karlebach, Rachel Deer, Julie A. McMurry, Melissa A. Haendel, Christopher G. Chute…

Citation: Virology Journal 2022 19:84

Content type: Research Published on: 15 May 2022
SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing

Authors: Daniel Danis, Julius O. B. Jacobsen, Parithi Balachandran, Qihui Zhu, Feyza Yilmaz, Justin Reese, Matthias Haimel, Gholson J. Lyon, Ingo Helbig, Christopher J. Mungall, Christine R. Beck, Charles Lee, Damian Smedley and Peter N. Robinson

Citation: Genome Medicine 2022 14:44

Content type: Method Published on: 28 April 2022
BMC Caller: a webtool to identify and analyze bacterial microcompartment types in sequence data

Authors: Markus Sutter and Cheryl A. Kerfeld

Citation: Biology Direct 2022 17:9

Content type: Research Published on: 28 April 2022
Adapted laboratory evolution of Thermotoga sp. strain RQ7 under carbon starvation

Authors: Jyotshana Gautam, Hui Xu, Junxi Hu, Christa Pennacchio, Anna Lipzen, Joel Martin and Zhaohui Xu

Citation: BMC Research Notes 2022 15:99

Content type: Research note Published on: 10 March 2022
Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates

Authors: Jennifer L. Brown, Candice L. Swift, Stephen J. Mondo, Susanna Seppala, Asaf Salamov, Vasanth Singan, Bernard Henrissat, Elodie Drula, John K. Henske, Samantha Lee, Kurt LaButti, Guifen He, Mi Yan, Kerrie Barry, Igor V. Grigoriev and Michelle A. O’Malley

Citation: Biotechnology for Biofuels 2021 14:234

Content type: Research Published on: 10 December 2021
Overexpression of the rice BAHD acyltransferase AT10 increases xylan-bound p-coumarate and reduces lignin in Sorghum bicolor

Authors: Yang Tian, Chien-Yuan Lin, Joon-Hyun Park, Chuan-Yin Wu, Ramu Kakumanu, Venkataramana R. Pidatala, Khanh M. Vuu, Alberto Rodriguez, Patrick M. Shih, Edward E. K. Baidoo, Stephen Temple, Blake A. Simmons, John M. Gladden, Henrik V. Scheller and Aymerick Eudes

Citation: Biotechnology for Biofuels 2021 14:217

Content type: Research Published on: 20 November 2021
A synthetic promoter system for well-controlled protein expression with different carbon sources in Saccharomyces cerevisiae

Authors: Jiliang Deng, Yanling Wu, Zhaohui Zheng, Nanzhu Chen, Xiaozhou Luo, Hongting Tang and Jay D. Keasling

Citation: Microbial Cell Factories 2021 20:202

Content type: Research Published on: 18 October 2021
Age, vascular disease, and Alzheimer’s disease pathologies in amyloid negative elderly adults

Authors: Tengfei Guo, Susan M. Landau and William J. Jagust

Citation: Alzheimer's Research & Therapy 2021 13:174

Content type: Research Published on: 15 October 2021
Evaluation of bacterial hosts for conversion of lignin-derived p-coumaric acid to 4-vinylphenol

Authors: Alberto Rodriguez, Jamie A. Meadows, Ning Sun, Blake A. Simmons and John M. Gladden

Citation: Microbial Cell Factories 2021 20:181

Content type: Research Published on: 15 September 2021
Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage

Authors: Dominique Boeuf, John M. Eppley, Daniel R. Mende, Rex R. Malmstrom, Tanja Woyke and Edward F. DeLong

Citation: Microbiome 2021 9:172

Content type: Research Published on: 13 August 2021
CAZymes from the thermophilic fungus Thermoascus aurantiacus are induced by C5 and C6 sugars

Authors: Raphael Gabriel, Rebecca Mueller, Lena Floerl, Cynthia Hopson, Simon Harth, Timo Schuerg, Andre Fleissner and Steven W. Singer

Citation: Biotechnology for Biofuels 2021 14:169

Content type: Research Published on: 12 August 2021
Glacier ice archives nearly 15,000-year-old microbes and phages

Authors: Zhi-Ping Zhong, Funing Tian, Simon Roux, M. Consuelo Gazitúa, Natalie E. Solonenko, Yueh-Fen Li, Mary E. Davis, James L. Van Etten, Ellen Mosley-Thompson, Virginia I. Rich, Matthew B. Sullivan and Lonnie G. Thompson

Citation: Microbiome 2021 9:160

Content type: Research Published on: 20 July 2021

Lawrence Berkeley National Laboratory

Lawrence Berkeley National Laboratory's Articles

Engineering isoprenoids production in metabolically versatile microbial host Pseudomonas putida

Advanced one-pot deconstruction and valorization of lignocellulosic biomass into triacetic acid lactone using Rhodosporidium toruloides

Persistent memory as an effective alternative to random access memory in metagenome assembly

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Precursor prioritization for p-cymene production through synergistic integration of biology and chemistry

Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome

NSAID use and clinical outcomes in COVID-19 patients: a 38-center retrospective cohort study

SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing

BMC Caller: a webtool to identify and analyze bacterial microcompartment types in sequence data

Adapted laboratory evolution of Thermotoga sp. strain RQ7 under carbon starvation

Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates

Overexpression of the rice BAHD acyltransferase AT10 increases xylan-bound p-coumarate and reduces lignin in Sorghum bicolor

A synthetic promoter system for well-controlled protein expression with different carbon sources in Saccharomyces cerevisiae

Age, vascular disease, and Alzheimer’s disease pathologies in amyloid negative elderly adults

Evaluation of bacterial hosts for conversion of lignin-derived p-coumaric acid to 4-vinylphenol

Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage

CAZymes from the thermophilic fungus Thermoascus aurantiacus are induced by C5 and C6 sugars

Glacier ice archives nearly 15,000-year-old microbes and phages