Genomes OnLine Database (GOLD) v. 8: overview and updates

S Mukherjee, D Stamatis, J Bertsch… - Nucleic acids …, 2021 - academic.oup.com
Abstract The Genomes OnLine Database (GOLD)(https://gold. jgi. doe. gov/) is a manually
curated, daily updated collection of genome projects and their metadata accumulated from …

Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

AP Fuentes‐Pardo, DE Ruzzante - Molecular ecology, 2017 - Wiley Online Library
Whole‐genome resequencing (WGR) is a powerful method for addressing fundamental
evolutionary biology questions that have not been fully resolved using traditional methods …

IMG/M v. 5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes

IMA Chen, K Chu, K Palaniappan, M Pillay… - Nucleic acids …, 2019 - academic.oup.com
Abstract The Integrated Microbial Genomes & Microbiomes system v. 5.0 (IMG/M: https://img.
jgi. doe. gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya …

Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v. 9

S Mukherjee, D Stamatis, CT Li… - Nucleic acids …, 2023 - academic.oup.com
Abstract The Genomes OnLine Database (GOLD)(https://gold. jgi. doe. gov/) at the
Department of Energy Joint Genome Institute (DOE-JGI) continues to maintain its role as one …

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

R Seshadri, SC Leahy, GT Attwood, KH Teh… - Nature …, 2018 - nature.com
Productivity of ruminant livestock depends on the rumen microbiota, which ferment
indigestible plant polysaccharides into nutrients used for growth. Understanding the …

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes

S Roux, M Krupovic, RA Daly, AL Borges… - Nature …, 2019 - nature.com
Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique
morphology, genome content and infection cycle. One of the most striking features of …

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

DW Waite, I Vanwonterghem, C Rinke… - Frontiers in …, 2017 - frontiersin.org
The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria,
known primarily for clinical relevance and for chemolithotrophy in various terrestrial and …

Genomes OnLine database (GOLD) v. 7: updates and new features

S Mukherjee, D Stamatis, J Bertsch… - Nucleic acids …, 2019 - academic.oup.com
Abstract The Genomes Online Database (GOLD)(https://gold. jgi. doe. gov) is an open online
resource, which maintains an up-to-date catalog of genome and metagenome projects in the …

Recent advances in machine learning applications in metabolic engineering

P Patra, BR Disha, P Kundu, M Das, A Ghosh - Biotechnology Advances, 2023 - Elsevier
Metabolic engineering encompasses several widely-used strategies, which currently hold a
high seat in the field of biotechnology when its potential is manifesting through a plethora of …

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

S Mukherjee, R Seshadri, NJ Varghese… - Nature …, 2017 - nature.com
We present 1,003 reference genomes that were sequenced as part of the Genomic
Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence …