The Southern Ocean (SO) plays a key role in regulating global biogeochemical cycles and climate, yet microbial genes sustaining its biological activity remain poorly characterized. We introduce a micr...
Genomic foundation models trained on DNA sequences have demonstrated remarkable capabilities across diverse biological tasks, from variant effect prediction to genome design. These models are typicall...
Short tandem repeats (STRs) are low-entropy regions in the genome, consisting of a short (1-6 bp) unit that is consecutively repeated multiple times. They are known for high mutational instability, du...
Haplotype phasing, the process of resolving parental allele inheritance patterns in diploid genomes, is critical for precision medicine and population genetics, yet the underlying optimization is NP-h...
Lindaspio polybranchiata is a deep-sea spionid annelid and an early colonizer of cold seep ecosystems, but genomic resources for this genus remain limited. Here, we present haplotype-resolved chromoso...
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to d...
Nanopore sequencing can read substantially longer sequences of nucleic acid molecules than other sequencing methods, which has led to advances in genomic analysis such as the gapless human genome asse...
The exploration of early evolutionary processes, particularly focusing on archaea, provides valuable insights into the beginnings of life on Earth. Archaea, one of the three domains of life, have sign...
Bacterial phase variation enables reversible, locus-specific phenotypic switching, often driven by DNA inversion (invertons). To identify these events, researchers commonly rely on sequencing reads th...
The Gulf of Mexico/Gulf of America provides ecosystem services derived from marine biodiversity and oil and gas resources. Threats posed by unintended releases of oil and gas can be attenuated by micr...
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