De Novo Genes

L Zhao, N Svetec, DJ Begun - Annual Review of Genetics, 2024 - annualreviews.org
Although the majority of annotated new genes in a given genome appear to have arisen
from duplication-related mechanisms, recent studies have shown that genes can also …

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 …

[HTML][HTML] Computational tools to predict context-specific protein complexes

A Csikász-Nagy, E Fichó, S Noto, I Reguly - Current Opinion in Structural …, 2024 - Elsevier
Interactions between thousands of proteins define cells' protein–protein interaction (PPI)
network. Some of these interactions lead to the formation of protein complexes. It is …

[HTML][HTML] A genome-wide screen identifies silencers with distinct chromatin properties and mechanisms of repression

L Hofbauer, LM Pleyer, F Reiter, A Schleiffer, A Vlasova… - Molecular Cell, 2024 - cell.com
Differential gene transcription enables development and homeostasis in all animals and is
regulated by two major classes of distal cis-regulatory DNA elements (CREs): enhancers …

Redesigning the Drosophila histone gene cluster: an improved genetic platform for spatiotemporal manipulation of histone function

AT Crain, M Nevil, MP Leatham-Jensen, KB Reeves… - Genetics, 2024 - academic.oup.com
Mutating replication-dependent (RD) histone genes is an important tool for understanding
chromatin-based epigenetic regulation. Deploying this tool in metazoans is particularly …

Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes

S Balu, S Huget, JJ Medina Reyes… - Nucleic Acids …, 2025 - academic.oup.com
Abstract The Complex Portal (www. ebi. ac. uk/complexportal) is a manually curated
reference database for molecular complexes. It is a unifying web resource linking …

Tubulin sequence divergence is associated with the use of distinct microtubule regulators

AS Kennard, KB Velle, R Ranjan, D Schulz… - Current Biology, 2025 - cell.com
Diverse eukaryotic cells assemble microtubule networks that vary in structure and
composition. While we understand how cells build microtubule networks with specialized …

Comparative genomics uncovers the evolutionary dynamics of detoxification and insecticide target genes across 11 phlebotomine sand flies

J Charamis, S Balaska, P Ioannidis… - Genome Biology and …, 2024 - academic.oup.com
Sand flies infect more than 1 million people annually with Leishmania parasites and other
bacterial and viral pathogens. Progress in understanding sand fly adaptations to xenobiotics …

Linear poly-ubiquitin remodels the proteome and influences hundreds of regulators in Drosophila

O Nuga, K Richardson, NC Patel… - G3: Genes …, 2024 - academic.oup.com
Ubiquitin controls many cellular processes via its posttranslational conjugation onto
substrates. Its use is highly variable due to its ability to form poly-ubiquitin chains with …

Astrocyte-to-neuron H2O2 signalling supports long-term memory formation in Drosophila and is impaired in an Alzheimer's disease model

Y Rabah, JP Berwick, N Sagar, L Pasquer… - Nature …, 2025 - nature.com
Astrocytes help protect neurons from potential damage caused by reactive oxygen species
(ROS). While ROS can also exert beneficial effects, it remains unknown how neuronal ROS …