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Lawrence Berkeley National Laboratory's Articles

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Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces

Authors: Katharina O. Barros, Megan Mader, David J. Krause, Jasmyn Pangilinan, Bill Andreopoulos, Anna Lipzen, Stephen J. Mondo, Igor V. Grigoriev, Carlos A. Rosa, Trey K. Sato and Chris Todd Hittinger

Citation: Biotechnology for Biofuels and Bioproducts 2024 17:20

Content type: Research Published on: 7 February 2024
An evaluation of GPT models for phenotype concept recognition

Authors: Tudor Groza, Harry Caufield, Dylan Gration, Gareth Baynam, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall and Justin T. Reese

Citation: BMC Medical Informatics and Decision Making 2024 24:30

Content type: Research Published on: 31 January 2024
Proteome profiling of enriched membrane-associated proteins unraveled a novel sophorose and cello-oligosaccharide transporter in Trichoderma reesei

Authors: Karoline Maria Vieira Nogueira, Vanessa Mendes, Karthik Shantharam Kamath, Anusha Cheruku, Letícia Harumi Oshiquiri, Renato Graciano de Paula, Claudia Carraro, Wellington Ramos Pedersoli, Lucas Matheus Soares Pereira, Luiz Carlos Vieira, Andrei Stecca Steindorff, Ardeshir Amirkhani, Matthew J. McKay, Helena Nevalainen, Mark P. Molloy and Roberto N. Silva

Citation: Microbial Cell Factories 2024 23:22

Content type: Research Published on: 16 January 2024
Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Authors: Clement Coclet, Patrick O. Sorensen, Ulas Karaoz, Shi Wang, Eoin L. Brodie, Emiley A. Eloe-Fadrosh and Simon Roux

Citation: Microbiome 2023 11:237

Content type: Research Published on: 27 October 2023
IMA genome-F18

Authors: Cobus M. Visagie, Donato Magistà, Massimo Ferrara, Felipe Balocchi, Tuan A. Duong, Ales Eichmeier, David Gramaje, Janneke Aylward, Scott E. Baker, Irene Barnes, Sara Calhoun, Maria De Angelis, Jens C. Frisvad, Eliska Hakalova, Richard D. Hayes, Jos Houbraken…

Citation: IMA Fungus 2023 14:21

Content type: Fungal Genomes Published on: 6 October 2023
A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)

Authors: Jose Diesel, Gary Molano, Gabriel J. Montecinos, Kelly DeWeese, Sara Calhoun, Alan Kuo, Anna Lipzen, Asaf Salamov, Igor V. Grigoriev, Daniel C. Reed, Robert J. Miller, Sergey V. Nuzhdin and Filipe Alberto

Citation: BMC Genomics 2023 24:543

Content type: Research Published on: 13 September 2023
Galba: genome annotation with miniprot and AUGUSTUS

Authors: Tomáš Brůna, Heng Li, Joseph Guhlin, Daniel Honsel, Steffen Herbold, Mario Stanke, Natalia Nenasheva, Matthis Ebel, Lars Gabriel and Katharina J. Hoff

Citation: BMC Bioinformatics 2023 24:327

Content type: Research Published on: 31 August 2023
rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating

Authors: Richard Border and Osman Asif Malik

Citation: BMC Bioinformatics 2023 24:314

Content type: Software Published on: 18 August 2023
Non-canonical d-xylose and l-arabinose metabolism via d-arabitol in the oleaginous yeast Rhodosporidium toruloides

Authors: Paul A. Adamczyk, Samuel T. Coradetti and John M. Gladden

Citation: Microbial Cell Factories 2023 22:145

Content type: Research Published on: 3 August 2023
Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts

Authors: Samuel T. Coradetti, Paul A. Adamczyk, Di Liu, Yuqian Gao, Peter B. Otoupal, Gina M. Geiselman, Bobbie-Jo M. Webb-Robertson, Meagan C. Burnet, Young-Mo Kim, Kristin E. Burnum-Johnson, Jon Magnuson and John M. Gladden

Citation: Microbial Cell Factories 2023 22:144

Content type: Research Published on: 3 August 2023
Engineered Escherichia coli platforms for tyrosine-derivative production from phenylalanine using phenylalanine hydroxylase and tetrahydrobiopterin-regeneration system

Authors: Yasuharu Satoh, Keita Fukui, Daisuke Koma, Ning Shen and Taek Soon Lee

Citation: Biotechnology for Biofuels and Bioproducts 2023 16:115

Content type: Research Published on: 18 July 2023
Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

Authors: Mária Džunková, James J. La Clair, Tomáš Tyml, Devin Doud, Frederik Schulz, Samuel Piquer-Esteban, Dafne Porcel Sanchis, Andrew Osborn, David Robinson, Katherine B. Louie, Ben P. Bowen, Robert M. Bowers, Janey Lee, Vicente Arnau, Wladimiro Díaz-Villanueva, Ramunas Stepanauskas…

Citation: Microbiome 2023 11:130

Content type: Research Published on: 13 June 2023
Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability

Authors: Cassandra L. Ettinger, Morgan Saunders, Laura Selbmann, Manuel Delgado-Baquerizo, Claudio Donati, Davide Albanese, Simon Roux, Susannah Tringe, Christa Pennacchio, Tijana G. del Rio, Jason E. Stajich and Claudia Coleine

Citation: Microbiome 2023 11:103

Content type: Brief Report Published on: 8 May 2023
NREM sleep as a novel protective cognitive reserve factor in the face of Alzheimer's disease pathology

Authors: Zsófia Zavecz, Vyoma D. Shah, Olivia G. Murillo, Raphael Vallat, Bryce A. Mander, Joseph R. Winer, William J. Jagust and Matthew P. Walker

Citation: BMC Medicine 2023 21:156

Content type: Research article Published on: 3 May 2023
Engineering osmolysis susceptibility in Cupriavidus necator and Escherichia coli for recovery of intracellular products

Authors: Jeremy David Adams, Kyle B. Sander, Craig S. Criddle, Adam P. Arkin and Douglas S. Clark

Citation: Microbial Cell Factories 2023 22:69

Content type: Research Published on: 12 April 2023
Microbial production of high octane and high sensitivity olefinic ester biofuels

Authors: David N. Carruthers, Jinho Kim, Daniel Mendez-Perez, Eric Monroe, Nick Myllenbeck, Yuzhong Liu, Ryan W. Davis, Eric Sundstrom and Taek Soon Lee

Citation: Biotechnology for Biofuels and Bioproducts 2023 16:60

Content type: Research Published on: 4 April 2023
The effect of ambient ozone exposure on three types of diabetes: a meta-analysis

Authors: Sirui Yu, Mingzhi Zhang, Jiamin Zhu, Xu Yang, Francis Manyori Bigambo, Antoine M. Snijders, Xu Wang, Weiyue Hu, Wei Lv and Yankai Xia

Citation: Environmental Health 2023 22:32

Content type: Research Published on: 30 March 2023
The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond

Authors: Lauren E. Chan, Anne E. Thessen, William D. Duncan, Nicolas Matentzoglu, Charles Schmitt, Cynthia J. Grondin, Nicole Vasilevsky, Julie A. McMurry, Peter N. Robinson, Christopher J. Mungall and Melissa A. Haendel

Citation: Journal of Biomedical Semantics 2023 14:3

Content type: Database Published on: 24 February 2023
Effects of forest degradation classification on the uncertainty of aboveground carbon estimates in the Amazon

Authors: Ekena Rangel Pinagé, Michael Keller, Christopher P. Peck, Marcos Longo, Paul Duffy and Ovidiu Csillik

Citation: Carbon Balance and Management 2023 18:2

Content type: Research Published on: 14 February 2023
Evaluation of engineered low-lignin poplar for conversion into advanced bioproducts

Authors: Chien-Yuan Lin, Gina M. Geiselman, Di Liu, Harsha D. Magurudeniya, Alberto Rodriguez, Yi-Chun Chen, Venkataramana Pidatala, Faride Unda, Bashar Amer, Edward E. K. Baidoo, Shawn D. Mansfield, Blake A. Simmons, Seema Singh, Henrik V. Scheller, John M. Gladden and Aymerick Eudes

Citation: Biotechnology for Biofuels and Bioproducts 2022 15:145

Content type: Research Published on: 25 December 2022

Lawrence Berkeley National Laboratory

Lawrence Berkeley National Laboratory's Articles

Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces

An evaluation of GPT models for phenotype concept recognition

Proteome profiling of enriched membrane-associated proteins unraveled a novel sophorose and cello-oligosaccharide transporter in Trichoderma reesei

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

IMA genome-F18

A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)

Galba: genome annotation with miniprot and AUGUSTUS

rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating

Non-canonical d-xylose and l-arabinose metabolism via d-arabitol in the oleaginous yeast Rhodosporidium toruloides

Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts

Engineered Escherichia coli platforms for tyrosine-derivative production from phenylalanine using phenylalanine hydroxylase and tetrahydrobiopterin-regeneration system

Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability

NREM sleep as a novel protective cognitive reserve factor in the face of Alzheimer's disease pathology

Engineering osmolysis susceptibility in Cupriavidus necator and Escherichia coli for recovery of intracellular products

Microbial production of high octane and high sensitivity olefinic ester biofuels

The effect of ambient ozone exposure on three types of diabetes: a meta-analysis

The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond

Effects of forest degradation classification on the uncertainty of aboveground carbon estimates in the Amazon

Evaluation of engineered low-lignin poplar for conversion into advanced bioproducts