Guangyi Fan

The paper structures and engineers deep-sea halophilic PET hydrolases to improve their salt tolerance and catalytic efficiency for industrial applications.

This study isolates a deep ocean diatom and shows it maintains metabolic activity through latent photosynthesis and carbon utilization in the twilight zone.

This study reconstructs the evolutionary assembly of a conserved cortical axis across vertebrates using spatial transcriptomics and single-nucleus RNA-seq, revealing conserved molecular programs and convergent evolution in brain circuitry.

This study analyzes the genetic diversity of the deep sea, linking protein structures to genetic variants and identifying biotechnologically relevant features.

The paper presents 11 deep-sea coral genome assemblies, revealing evolutionary dynamics, environmental adaptation, and genetic differences between deep-sea and shallow-sea corals.

ExMODE is a multi-omics database for extremophiles that integrates and standardizes data to enable comparative analysis and bioprospecting.

This study reconstructs 3D spatial transcriptomic models of planarians to map cell type distribution and positional gene regulation, identifying candidate genes involved in regeneration.

NanoporeDB is a structural database of multimeric protein nanopores, providing 3D models and quantitative metrics to support nanopore-based sensing and synthetic biology.

This study constructs a 4D spatiotemporal transcriptomic map of planarian regeneration using Stereo-seq, identifying dynamic gradients and an injury-induced regenerative zone.

The paper develops ACCESS, a multimodal graph neural network to annotate functional dark matter proteins from extreme environments beyond homology-based methods.

Stereopy provides a framework for analyzing multi-sample spatial transcriptomics data to model comparative and spatiotemporal cellular heterogeneity through three key algorithms.

SpaGRN predicts spatially informed gene regulatory networks from spatial transcriptomics data, revealing spatiotemporal regulatory patterns in Drosophila development.

This paper introduces a DNA data storage scheme using 5-methylcytosine to increase information density, achieving high data recovery rates in experimental validation.

This study maps gene expression and developmental trajectories in zebrafish embryos using Stereo-seq and scRNA-seq, identifying spatial gene modules and signaling interactions.

This study uses metatranscriptomics to analyze carbon fixation potentials across plankton lineages in the South China Sea, revealing lineage-specific contributions and the role of proteorhodopsin in non-Calvin carbon fixation.

This paper presents the first chromosome-level genome of the Bicolor Angelfish, providing insights into coral reef fish evolution and conservation.

The paper compiles and analyzes 190 marine invertebrate genomes to explore their diversity, function, and evolutionary relationships.

The paper compiles and analyzes 191 algae genomes to study genome features and evolutionary relationships, revealing the phylogenetic path from Glaucophyte to terrestrial plants.

The paper analyzes 630 aquatic vertebrate genomes to create a compendium, revealing TE diversity and gene family evolution related to the water-to-land transition.

The paper uses Stereo-seq to map single-cell transcriptomes of axolotl telencephalon during development and regeneration, identifying a key radial glial cell subtype involved in early wound healing.

The paper presents draft genomes of male and female Australian jacky dragons, providing insights into lizard evolution and sex determination.

MetaTrass improves metagenome assembly by binning first and assembling later, producing more high-quality draft genomes from human gut microbiome samples.

The paper introduces a de novo scaffolding tool for synthetic long reads that improves assembly quality significantly, especially for assemblies from next-generation sequencing reads.

The paper establishes high-confidence structural variant calls in an Asian individual using long-read sequencing technologies and validates them through PCR and Sanger sequencing.

This study evaluates CNV detection performance of DNBSEQ and Illumina platforms using WGS data from NA12878, showing DNBSEQ detects more CNVs with similar sensitivity and precision.

Symbiont-Screener separates host sequences from contaminants in long reads or co-barcoded reads using unsupervised clustering without reference alignment, achieving high accuracy in simulated and real data.

The paper announces the Fish10K project to sequence 10,000 fish genomes and describes a workflow for biospecimen procurement, sequencing, and assembly.

The paper constructs a high-confidence Asian variant benchmark using multiple sequencing methods and identifies novel variants in challenging regions.

The paper introduces HAST, a tool for haplotype-resolved assembly using trio binning, achieving high accuracy and completeness in haplotype reconstruction from synthetic long reads.

The paper reports the first whole genome sequence of Mekong tiger perch, resolving phylogenetic relationships and providing insights into its demographic history and conservation.