Building pangenome graphs

E Garrison, A Guarracino, S Heumos, F Villani, Z Bao… - Nature …, 2024 - nature.com
Pangenome graphs can represent all variation between multiple reference genomes, but
current approaches to build them exclude complex sequences or are based upon a single …

From beer to breadboards: yeast as a force for biological innovation

HK Gaikani, M Stolar, D Kriti, C Nislow, G Giaever - Genome Biology, 2024 - Springer
The history of yeast Saccharomyces cerevisiae, aka brewer's or baker's yeast, is intertwined
with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors …

Loss of heterozygosity and its importance in evolution

C Smukowski Heil - Journal of Molecular Evolution, 2023 - Springer
Loss of heterozygosity (LOH) is a mitotic recombination event that converts heterozygous
loci to homozygous loci. This mutation event is widespread in organisms that have asexual …

GENA-LM: a family of open-source foundational DNA language models for long sequences

V Fishman, Y Kuratov, A Shmelev… - Nucleic Acids …, 2025 - academic.oup.com
Recent advancements in genomics, propelled by artificial intelligence, have unlocked
unprecedented capabilities in interpreting genomic sequences, mitigating the need for …

Telomere-to-telomere DNA replication timing profiling using single-molecule sequencing with Nanotiming

B Theulot, A Tourancheau… - Nature …, 2025 - nature.com
Current temporal studies of DNA replication are either low-resolution or require complex cell
synchronisation and/or sorting procedures. Here we introduce Nanotiming, a single …

Sister chromatid cohesion halts DNA loop expansion

N Bastié, C Chapard, A Cournac, S Nejmi, H Mboumba… - Molecular cell, 2024 - cell.com
Eukaryotic genomes are folded into DNA loops mediated by structural maintenance of
chromosomes (SMC) complexes such as cohesin, condensin, and Smc5/6. This …

Mathematical model linking telomeres to senescence in Saccharomyces cerevisiae reveals cell lineage versus population dynamics

A Rat, V Martinez Fernandez, M Doumic… - Nature …, 2025 - nature.com
Telomere shortening ultimately causes replicative senescence. However, identifying the
mechanisms driving replicative senescence in cell populations is challenging due to the …

Near-gapless genome and transcriptome analyses provide insights into fruiting body development in Lentinula edodes

N Shen, H **e, K Liu, X Li, L Wang, Y Deng… - International Journal of …, 2024 - Elsevier
Fruiting body development in macrofungi is an intensive research subject. In this study, high-
quality genomes were assembled for two sexually compatible monokaryons from a …

ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel

Z Miao, Y Ren, A Tarabini, L Yang, H Li… - Nucleic Acids …, 2025 - academic.oup.com
As a unicellular eukaryote, the budding yeast Saccharomyces cerevisiae strikes a unique
balance between biological complexity and experimental tractability, serving as a long …

Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast

EM Teyssonnière, P Trébulle, J Muenzner… - Proceedings of the …, 2024 - pnas.org
Gene expression varies between individuals and corresponds to a key step linking
genotypes to phenotypes. However, our knowledge regarding the species-wide genetic …