Quality assessment of gene repertoire annotations with OMArk

Y Nevers, A Warwick Vesztrocy, V Rossier… - Nature …, 2025‏ - nature.com
In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding
gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure …

OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes

F Tegenfeldt, D Kuznetsov, M Manni… - Nucleic Acids …, 2025‏ - academic.oup.com
Abstract OrthoDB (https://www. orthodb. org) offers evolutionary and functional annotations
of orthologous genes in the widest sampling of eukaryotes, prokaryotes, and viruses …

DAVID Ortholog: an integrative tool to enhance functional analysis through orthologs

BT Sherman, G Panzade, T Imamichi, W Chang - Bioinformatics, 2024‏ - academic.oup.com
Abstract Motivation The Database for Annotation, Visualization, and Integrated Discovery
(DAVID) is a web-based bioinformatics system for the functional interpretation of large lists of …

[HTML][HTML] Fumarate reductase drives methane emissions in the genus Oryza through differential regulation of the rhizospheric ecosystem

J Hu, G Bedada, C Sun, CM Ryu, A Schnürer… - Environment …, 2024‏ - Elsevier
The emergence of waterlogged Oryza species∼ 15Mya (million years ago) supplied an
anoxic warm bed for methane-producing microorganisms, and methane emissions have …

Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data

S Park, M Kwak, SJ Park - Scientific Reports, 2024‏ - nature.com
Abies koreana EH Wilson is an endangered evergreen coniferous tree that is native to high
altitudes in South Korea and susceptible to the effects of climate change. Hybridization and …

Dog10K: an integrated Dog10K database summarizing canine multi-omics

T Zhou, SY Pu, SJ Zhang, QJ Zhou, M Zeng… - Nucleic Acids …, 2025‏ - academic.oup.com
The diversity observed in canine breed phenotypes, together with their risk for heritabily
disorders of relevance to dogs and humans, makes the species an ideal subject for studies …

Studying Target–Engagement of Anti-Infectives by Solvent-Induced Protein Precipitation and Quantitative Mass Spectrometry

L Bizzarri, D Steinbrunn, T Quennesson… - ACS Infectious …, 2024‏ - ACS Publications
Antimicrobial resistance (AMR) poses a serious threat to global health. The rapid
emergence of resistance contrasts with the slow pace of antimicrobial development …

[HTML][HTML] Unlocking biological insights from differentially expressed Genes: Concepts, methods, and future perspectives

H Yin, H Duo, S Li, D Qin, L **e, Y **ao, J Sun… - Journal of Advanced …, 2024‏ - Elsevier
Background Identifying differentially expressed genes (DEGs) is a core task of transcriptome
analysis, as DEGs can reveal the molecular mechanisms underlying biological processes …

Orthology inference at scale with FastOMA

S Majidian, Y Nevers, A Yazdizadeh Kharrazi… - Nature …, 2025‏ - nature.com
The surge in genome data, with ongoing efforts aiming to sequence 1.5 M eukaryotes in a
decade, could revolutionize genomics, revealing the origins, evolution and genetic …

Repeated shifts in sociality are associated with fine-tuning of highly conserved and lineage-specific enhancers in a socially flexible bee

BM Jones, AE Webb, SM Geib, S Sim… - Molecular biology …, 2024‏ - academic.oup.com
Comparative genomic studies of social insects suggest that changes in gene regulation are
associated with evolutionary transitions in social behavior, but the activity of predicted …