Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction

K Chen, Y Zhou, M Ding, Y Wang, Z Ren… - Briefings in …, 2024‏ - academic.oup.com
Abstract Language models pretrained by self-supervised learning (SSL) have been widely
utilized to study protein sequences, while few models were developed for genomic …

Wildlife forensic genetics—Biological evidence, DNA markers, analytical approaches, and challenges

S Kanthaswamy - Animal Genetics, 2024‏ - Wiley Online Library
Wildlife‐related crimes are the second most prevalent lawbreaking offense globally. This
illicit trade encompasses hunting, breeding and trafficking. Besides diminishing many …

Comparative Genomics and Epigenomics of Transcriptional Regulation

H Zhou, E Clark, D Guan, S Lagarrigue… - Annual review of …, 2024‏ - annualreviews.org
Transcriptional regulation in response to diverse physiological cues involves complicated
biological processes. Recent initiatives that leverage whole genome sequencing and …

Inferring the Demographic History of Aye-Ayes (Daubentonia madagascariensis) from High-Quality, Whole-Genome, Population-Level Data

JW Terbot, V Soni, CJ Versoza… - Genome biology and …, 2025‏ - academic.oup.com
The nocturnal aye-aye, Daubentonia madagascariensis, is one of the most elusive lemurs
on the island of Madagascar. The timing of its activity and arboreal lifestyle has generally …

Automated high-throughput biological sex identification from archeological human dental enamel using targeted proteomics

C Koenig, P Bortel, RS Paterson, B Rendl… - Journal of Proteome …, 2024‏ - ACS Publications
Biological sex is key information for archeological and forensic studies, which can be
determined by proteomics. However, the lack of a standardized approach for fast and …

junctionCounts: comprehensive alternative splicing analysis and prediction of isoform-level impacts to the coding sequence

AJ Ritter, A Wallace, N Ronaghi… - NAR Genomics and …, 2024‏ - academic.oup.com
Alternative splicing (AS) is emerging as an important regulatory process for complex
biological processes. Transcriptomic studies therefore commonly involve the identification …

Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation

AG Duncan, JA Mitchell, AM Moses - Bioinformatics, 2024‏ - academic.oup.com
Motivation Supervised deep learning is used to model the complex relationship between
genomic sequence and regulatory function. Understanding how these models make …

The utility of animal models to inform the next generation of human space exploration

I Duporge, T Pereira, SC de Obeso, JGB Ross… - npj …, 2025‏ - nature.com
Animals have played a vital role in every stage of space exploration, from early sub-orbital
flights to contemporary missions. New physiological and psychological challenges arise with …

Unprecedented female mutation bias in the aye-aye, a highly unusual lemur from Madagascar

RJ Wang, Y Peña-García, M Raveendran… - PLoS …, 2025‏ - journals.plos.org
Every mammal studied to date has been found to have a male mutation bias: male parents
transmit more de novo mutations to offspring than female parents, contributing increasingly …

Advancing evolutionary medicine with complete primate genomes and advanced biotechnologies

K Ma, X Yang, Y Mao - Trends in Genetics, 2024‏ - cell.com
Evolutionary medicine, which integrates evolutionary biology and medicine, significantly
enhances our understanding of human traits and disease susceptibility. However, previous …