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Lawrence Berkeley National Laboratory's Articles

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Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics

Authors: Patrick T. West, Samantha L. Peters, Matthew R. Olm, Feiqiao B. Yu, Haley Gause, Yue Clare Lou, Brian A. Firek, Robyn Baker, Alexander D. Johnson, Michael J. Morowitz, Robert L. Hettich and Jillian F. Banfield

Citation: Microbiome 2021 9:142

Content type: Research

Published on: 21 June 2021
Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

Authors: Paula B. Matheus Carnevali, Adi Lavy, Alex D. Thomas, Alexander Crits-Christoph, Spencer Diamond, Raphaël Méheust, Matthew R. Olm, Allison Sharrar, Shufei Lei, Wenming Dong, Nicola Falco, Nicholas Bouskill, Michelle E. Newcomer, Peter Nico, Haruko Wainwright, Dipankar Dwivedi…

Citation: Microbiome 2021 9:121

Content type: Research

Published on: 22 May 2021
Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium

Authors: Le Thanh Mai Pham, Kai Deng, Trent R. Northen, Steven W. Singer, Paul D. Adams, Blake A. Simmons and Kenneth L. Sale

Citation: Biotechnology for Biofuels 2021 14:108

Content type: Research

Published on: 29 April 2021
Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

Authors: Javier A. Ceja-Navarro, Yuan Wang, Daliang Ning, Abelardo Arellano, Leila Ramanculova, Mengting Maggie Yuan, Alyssa Byer, Kelly D. Craven, Malay C. Saha, Eoin L. Brodie, Jennifer Pett-Ridge and Mary K. Firestone

Citation: Microbiome 2021 9:96

Content type: Research

Published on: 28 April 2021
Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice

Authors: Jessica L. Haigh, Anna Adhikari, Nycole A. Copping, Tyler Stradleigh, A. Ayanna Wade, Rinaldo Catta-Preta, Linda Su-Feher, Iva Zdilar, Sarah Morse, Timothy A. Fenton, Anh Nguyen, Diana Quintero, Samrawit Agezew, Michael Sramek, Ellie J. Kreun, Jasmine Carter…

Citation: Genome Medicine 2021 13:69

Content type: Research

Published on: 26 April 2021
Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass

Authors: James Kirby, Gina M. Geiselman, Junko Yaegashi, Joonhoon Kim, Xun Zhuang, Mary Bao Tran-Gyamfi, Jan-Philip Prahl, Eric R. Sundstrom, Yuqian Gao, Nathalie Munoz, Kristin E. Burnum-Johnson, Veronica T. Benites, Edward E. K. Baidoo, Anna Fuhrmann, Katharina Seibel, Bobbie-Jo M. Webb-Robertson…

Citation: Biotechnology for Biofuels 2021 14:101

Content type: Research

Published on: 21 April 2021
Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals

Authors: T. Keller-Costa, A. Lago-Lestón, J. P. Saraiva, R. Toscan, S. G. Silva, J. Gonçalves, C. J. Cox, N. Kyrpides, U. Nunes da Rocha and R. Costa

Citation: Microbiome 2021 9:72

Content type: Research

Published on: 25 March 2021
Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages

Authors: Davide Albanese, Claudia Coleine, Omar Rota-Stabelli, Silvano Onofri, Susannah G. Tringe, Jason E. Stajich, Laura Selbmann and Claudio Donati

Citation: Microbiome 2021 9:63

Content type: Research

Published on: 19 March 2021
Prebiotic properties of Bacillus coagulans MA-13: production of galactoside hydrolyzing enzymes and characterization of the transglycosylation properties of a GH42 β-galactosidase

Authors: Martina Aulitto, Andrea Strazzulli, Ferdinando Sansone, Flora Cozzolino, Maria Monti, Marco Moracci, Gabriella Fiorentino, Danila Limauro, Simonetta Bartolucci and Patrizia Contursi

Citation: Microbial Cell Factories 2021 20:71

Content type: Research

Published on: 18 March 2021
Iron incorporation both intra- and extra-cellularly improves the yield and saccharification of switchgrass (Panicum virgatum L.) biomass

Authors: Chien-Yuan Lin, Bryon S. Donohoe, Yannick J. Bomble, Haibing Yang, Manal Yunes, Nicholas S. Sarai, Todd Shollenberger, Stephen R. Decker, Xiaowen Chen, Maureen C. McCann, Melvin P. Tucker, Hui Wei and Michael E. Himmel

Citation: Biotechnology for Biofuels 2021 14:55

Content type: Research

Published on: 4 March 2021
Synthesis, antibiotic structure–activity relationships, and cellulose dissolution studies of new room-temperature ionic liquids derived from lignin

Authors: Shihong Liu, Michael Gonzalez, Celine Kong, Scott Weir and Aaron M. Socha

Citation: Biotechnology for Biofuels 2021 14:47

Content type: Research

Published on: 23 February 2021
Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes

Authors: I. Raimundo, R. Silva, L. Meunier, S. M. Valente, A. Lago-Lestón, T. Keller-Costa and R. Costa

Citation: Microbiome 2021 9:43

Content type: Research

Published on: 14 February 2021
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

Authors: Jiarong Guo, Ben Bolduc, Ahmed A. Zayed, Arvind Varsani, Guillermo Dominguez-Huerta, Tom O. Delmont, Akbar Adjie Pratama, M. Consuelo Gazitúa, Dean Vik, Matthew B. Sullivan and Simon Roux

Citation: Microbiome 2021 9:37

Content type: Software article

Published on: 1 February 2021
Expression of a bacterial 3-dehydroshikimate dehydratase (QsuB) reduces lignin and improves biomass saccharification efficiency in switchgrass (Panicum virgatum L.)

Authors: Zhangying Hao, Sasha Yogiswara, Tong Wei, Veronica Teixeira Benites, Anagh Sinha, George Wang, Edward E. K. Baidoo, Pamela C. Ronald, Henrik V. Scheller, Dominique Loqué and Aymerick Eudes

Citation: BMC Plant Biology 2021 21:56

Content type: Research article

Published on: 21 January 2021
Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species

Authors: Antonio Suppa, Jouni Kvist, Xiaojing Li, Vignesh Dhandapani, Hanan Almulla, Antoine Y. Tian, Stephen Kissane, Jiarui Zhou, Alessio Perotti, Hayley Mangelson, Kyle Langford, Valeria Rossi, James B. Brown and Luisa Orsini

Citation: Microbiome 2020 8:170

Content type: Research

Published on: 15 December 2020
Conversion of poplar biomass into high-energy density tricyclic sesquiterpene jet fuel blendstocks

Authors: Gina M. Geiselman, James Kirby, Alexander Landera, Peter Otoupal, Gabriella Papa, Carolina Barcelos, Eric R. Sundstrom, Lalitendu Das, Harsha D. Magurudeniya, Maren Wehrs, Alberto Rodriguez, Blake A. Simmons, Jon K. Magnuson, Aindrila Mukhopadhyay, Taek Soon Lee, Anthe George…

Citation: Microbial Cell Factories 2020 19:208

Content type: Research

Published on: 12 November 2020
An automated workflow to screen alkene reductases using high-throughput thin layer chromatography

Authors: Brett M. Garabedian, Corey W. Meadows, Florence Mingardon, Joel M. Guenther, Tristan de Rond, Raya Abourjeily and Taek Soon Lee

Citation: Biotechnology for Biofuels 2020 13:184

Content type: Methodology

Published on: 9 November 2020
Enhanced production of taxadiene in Saccharomyces cerevisiae

Authors: Behnaz Nowrouzi, Rachel A. Li, Laura E. Walls, Leo d’Espaux, Koray Malcı, Lungang Liang, Nestor Jonguitud-Borrego, Albert I. Lerma-Escalera, Jose R. Morones-Ramirez, Jay D. Keasling and Leonardo Rios-Solis

Citation: Microbial Cell Factories 2020 19:200

Content type: Research

Published on: 2 November 2020
Development of genetic tools for the thermophilic filamentous fungus Thermoascus aurantiacus

Authors: Raphael Gabriel, Julia Prinz, Marina Jecmenica, Carlos Romero-Vazquez, Pallas Chou, Simon Harth, Lena Floerl, Laure Curran, Anne Oostlander, Linda Matz, Susanne Fritsche, Jennifer Gorman, Timo Schuerg, André Fleißner and Steven W. Singer

Citation: Biotechnology for Biofuels 2020 13:167

Content type: Research

Published on: 10 October 2020
ADEPT: a domain independent sequence alignment strategy for gpu architectures

Authors: Muaaz G. Awan, Jack Deslippe, Aydin Buluc, Oguz Selvitopi, Steven Hofmeyr, Leonid Oliker and Katherine Yelick

Citation: BMC Bioinformatics 2020 21:406

Content type: Software

Published on: 15 September 2020

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Lawrence Berkeley National Laboratory

Lawrence Berkeley National Laboratory's Articles

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium

Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice

Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals

Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages

Prebiotic properties of Bacillus coagulans MA-13: production of galactoside hydrolyzing enzymes and characterization of the transglycosylation properties of a GH42 β-galactosidase

Iron incorporation both intra- and extra-cellularly improves the yield and saccharification of switchgrass (Panicum virgatum L.) biomass

Synthesis, antibiotic structure–activity relationships, and cellulose dissolution studies of new room-temperature ionic liquids derived from lignin

Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

Expression of a bacterial 3-dehydroshikimate dehydratase (QsuB) reduces lignin and improves biomass saccharification efficiency in switchgrass (Panicum virgatum L.)

Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species

Conversion of poplar biomass into high-energy density tricyclic sesquiterpene jet fuel blendstocks

An automated workflow to screen alkene reductases using high-throughput thin layer chromatography

Enhanced production of taxadiene in Saccharomyces cerevisiae

Development of genetic tools for the thermophilic filamentous fungus Thermoascus aurantiacus

ADEPT: a domain independent sequence alignment strategy for gpu architectures