Yīmíng Bào

First community challenge for automated virus taxonomy

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

NeoAtlas and NeoBert: A Database and A Predictive Model for Canonical and Noncanonical Tumor Neoantigens

The paper curates noncanonical neoantigen-HLA pairs and develops predictive models, providing a public resource for neoantigen research and vaccine development.

New Evidence of Altered Gut Microbiota in Autism Spectrum Disorders through Metagenomic Analysis

This study identifies altered gut microbiota in ASD children through metagenomic analysis, highlighting fungal dysbiosis and metabolic pathway changes linked to ASD pathogenesis.

The GSA Family in 2025: A Broadened Sharing Platform for Multi-Omics and Multimodal Data

The paper introduces the GSA Family, a platform for sharing multi-omics and multimodal data, with expanded databases and improved features.

EryDB: a transcriptomic profile database for erythropoiesis and erythroid-related diseases

EryDB is a database that collects and integrates transcriptomic data for erythropoiesis and erythroid-related diseases, enabling analysis and visualization of gene expression across species and tissues.

RCoV19: A One-stop Hub for SARS-CoV-2 Genome Data Integration, Variants Monitoring, and Risk Pre-warning

RCoV19 integrates SARS-CoV-2 genome data, monitors variants, and provides risk pre-warning tools for COVID-19 response.

Machine learning detection of SARS-CoV-2 high-risk variants

This paper develops a machine learning model using LightGBM to predict high-risk SARS-CoV-2 variants based on haplotype network features, achieving high accuracy in identifying variants of concern and interest.

McAN: an ultrafast haplotype network construction algorithm

McAN constructs haplotype networks using a minimum-cost arborescence approach, achieving speeds two orders of magnitude faster than existing methods.

Genomic perspectives on the emerging SARS-CoV-2 Omicron variant

This study analyzes the genomic features of the SARS-CoV-2 Omicron variant, identifying its high mutation rate, spike protein alterations, and distinct evolutionary patterns.

GMQN: A reference-based method for correcting batch effects as well as probes bias in HumanMethylation BeadChip

The Genome Sequence Archive Family: Towards Explosive Data Growth and Diverse Data Types

The paper introduces the GSA family of repositories to manage explosive growth and diverse data types in genomic data archiving.

Genome Warehouse: A Public Repository Housing Genome-scale Data

The Genome Warehouse (GWH) is a public repository for genome-scale data that provides storage, submission, and visualization tools for genome assemblies across species.

The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR

The paper describes the 2019nCoVR resource, which curates and analyzes SARS-CoV-2 genomes, variants, and haplotypes globally, providing daily updates and integration with literature and databases.

Characterization and identification of long non-coding RNAs based on feature relationship

This study characterizes long non-coding RNAs (lncRNAs) by analyzing feature relationships and introduces LGC, an algorithm that accurately identifies lncRNAs across species without prior knowledge.