Xin Liu

This paper introduces SpliceAI2, a deep learning model that improves identification and quantification of splice-altering variants and their effects on transcripts and disease.

STID provides a standardized framework for analyzing spatial transcriptomic data in infectious diseases, enabling pathogen background correction, niche identification, and multi-sample comparative analyses.

dbGIST is a multi-omics resource for GIST research that integrates diverse datasets and provides analytical tools for target exploration and cross-dataset validation.

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

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

This study identifies RipAV, an effector from Ralstonia solanacearum, as a protein that targets plant PUB proteins and CPK28 to suppress immunity by promoting BIK1 degradation.

This study shows that TaPGS1 overexpression increases flavonol accumulation, disrupts auxin transport, delays endosperm cellularization, and enlarges wheat grains.

The paper introduces TAC-C, a method combining ATAC-seq and Hi-C to study chromatin interactions in crops, revealing SPL-mediated photosynthesis regulation and chromatin loop structures.

StereoMM integrates spatial transcriptomic data and histological images to improve spatial domain recognition and tumor heterogeneity analysis in cancer tissues.

This study identifies exosomal hemoglobin transfer from non-neuronal cells to neurons under hypoxia as a mechanism to maintain mitochondrial homeostasis and protect against neurological injury.

SCIITensor constructs actionable TME modules by analyzing spatially resolved intercellular communications in ST data, identifying immunosuppressive patterns and sample-common immune-infiltration modules.

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

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.

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.

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.

This study evaluates 12 protein stability predictors for identifying pathogenic missense mutations and finds FoldX performs best, though structural predictors are less effective than variant effect predictors overall.

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

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 introduces TRAP-seq to quantify CRISPR editing efficiency and uses it to design improved gRNAs for Cas9, ABE, and CBE with high accuracy and efficiency.

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

This study presents a chromosome-level genome assembly of the African pike, Hepsetus odoe, using long-read and Hi-C sequencing technologies, providing a resource for evolutionary and functional studies.

This study analyzes genomes of wild and domestic ducks to reveal their evolutionary history and identify genetic factors underlying phenotypic variation.

This paper presents the first draft genome of the star-fruit plant, identifying genes and conducting phylogenomic analysis to provide resources for nutritional and medicinal studies.

This study presents three Osteoglossidae genomes to explore ancient teleost evolution, revealing divergence times and genomic changes linked to continental drift and dietary adaptations.

This study examines intratumor heterogeneity and evolution patterns in colorectal cancer, finding a Darwinian pattern with differences between right-sided and left-sided tumors.

The paper reports complete chloroplast genomes of 14 mangrove species and performs phylogenetic and genomic comparative analyses to understand their evolutionary relationships.

The paper presents high-quality draft genomes for jackfruit and breadfruit, revealing expanded gene families and insights into starch and sugar metabolism.

TGS-GapCloser closes gaps in genome assemblies using error-prone long reads, improving contig N50 and gene completeness while being faster than existing tools.