Lawrence Berkeley National Laboratory

1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

    

18. 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

19. 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

20. 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