Detection of minimal residual disease (MRD) in cancer patients after surgery can provide an early marker for disease recurrence and guide subsequent treatment decisions. Accurate and sensitive estimat...
Electronic health record (EHR)-linked biobank data facilitate large-scale scientific discoveries such as genome-wide association study (GWAS) on a multitude of phenotypic traits and biomarkers routine...
In the era of precision medicine, genome-wide epigenetic modifications offer rich data that could inform risk prediction. However, these data are high-dimensional and exhibit complex dependence struct...
Sequence-to-function models predict molecular phenotypes from complete sequence windows. At genome-wide association study loci, however, the prevailing design perturbs only the lead variant on the ref...
Genome-scale metabolic models (GEMs) are essential tools for systems biology and rational chassis design, but conventional top-down reconstruction depends heavily on sequence homology and often leaves...
The ability to estimate and predict pathogen variant dynamics can inform public health responses, including planning for increased transmission or severity, shifts in population immunity, or changes t...
Gene regulatory networks (GRNs) link transcription factor (TF) proteins to their target genes, yet reconstructing these networks from genome-wide data remains challenging under practical and methodolo...
Metatranscriptomic sequencing has expanded our knowledge of the RNA virosphere far more rapidly than novel viruses can be taxonomically classified. Taxonomic assignment above the family level is parti...
Large Language Models (LLMs) and Vision-Language Models (VLMs) increasingly generate indoor scenes through intermediate structures such as layouts and scene graphs, yet evaluation still relies on LLM ...
In genome wide association studies (GWASs) based on a case-control design, single nucleotide polymorphisms (SNPs) are typically evaluated for an association test and a Hardy-Weinberg equilibrium (HWE)...
The reductive citric acid (rTCA) and reverse oxidative TCA (roTCA) cycles are used by autotrophic Bacteria to fix dissolved inorganic carbon (DIC) at deep-sea and terrestrial hot springs, water treatm...
The deep-sea shrimp, Aristeus alcocki Ramadan, 1938, is an economically valuable species belonging to the family Aristeidae under the superfamily Penaeoidea. In this study, we report the complete mito...
The Greenland shark (Somniosus microcephalus) is a deep-sea vertebrate inhabiting the cold waters of the North Atlantic and Arctic Ocean and is renowned for its exceptional longevity, with individuals...
A marine hydrocarbonoclastic actinobacterium Kocuria flava IOS11 was isolated from 3500 m deep-sea water of the Indian Ocean. The isolate efficiently degraded phenanthrene (250 mg/L) achieving 82 and ...
Microbial genomes and metagenomes contain millions of proteins whose enzymatic functions remain unknown, the enzyme dark matter. While deep learning has improved protein function prediction, most meth...
Anaerobic methanotrophic (ANME) archaea have been primarily documented by metagenomic analysis of environmental samples. The mechanisms that drive their diversification and speciation are poorly under...
The origin and maintenance of marine biodiversity remain poorly understood, particularly in highly connected oceanic environments where extensive dispersal is expected to limit population differentiat...
Iron is one of the most important elements of the Earth, yet its bioavailability is limited in oceanic environments. In this context, deep-sea hydrothermal ecosystems represent one of the major source...
In this study, we report the complete mitochondrial genome of the deep-sea hydrothermal vent shrimp Mirocaris fortunata (Alvinocarididae) from shotgun sequencing data on an individual tail tissue. The...
Xylophaga dorsalis is a common Atlantic-Mediterranean mollusc that plays a crucial role in deep-sea habitats, where it digests wood that reaches the seabed through a unique symbiosis with specialised ...
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