Wenming Zhao

Parental Genome Assemblies of Suyunuo1 Reveal Structural Variation Underlying Edible Waxy Maize Evolution, Superior Hybrid Performance and Yield - Flavor Balance

The paper assembles high-quality genomes of two waxy maize inbreds, identifies structural variations contributing to yield and flavor traits, and highlights their role in hybrid performance.

An Artificial Intelligence Model for Longitudinal Assessment of TCR Repertoires in SARS-CoV-2 Vaccine Recipients

The paper develops a large language model to predict SARS-CoV-2-specific TCRs and shows their correlation with antibody levels post-vaccination.

OmniExtract: An automatic data extraction tool based on Large Language Model and Prompt Engineering

OmniExtract is a data extraction tool using LLM and prompt engineering that achieves high accuracy in extracting structured information from text and tables.

IFI207 promotes antiviral responses by modulating STING ubiquitination and degradation

This study shows IFI207 modulates STING ubiquitination and degradation, enhancing antiviral responses against MLV and herpesvirus simplex 1.

Dingent: An Easily Deployable Database Retrieval and Integration Agent framework

Dingent is a configurable agent framework that enables data retrieval from various sources using natural language and provides a web interface, demonstrated across three application scenarios.

A novel allele of Sh1 underlines the conversion of waxy corn to wx-sweet corn

The paper identifies a novel Sh1 allele in corn that synergizes with waxy1 to alter carbohydrate metabolism, resulting in a waxy-sweet texture in maize kernels.

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.

DHX15 inhibits mouse APOBEC3 deamination

This study identifies DHX15 as an inhibitor of mouse APOBEC3 deamination, showing it suppresses MLV replication and prevents DNA damage.

Lineage-associated Human Divergently-Paired Genes (DPGs) Exhibit Regulatory Characteristics and Evolutionary Trends

The paper identifies human divergently-paired genes (DPGs) and analyzes their conservation, regulatory features, and evolutionary patterns across vertebrate lineages.

Classification of dog breeds using convolutional neural network models and support vector machine

This study improves dog breed classification accuracy using a combination of CNN features, PCA, GWO, and SVM, achieving 95.24% and 99.34% accuracy for 120 and 76 breeds respectively.

IFI207, a young and fast-evolving protein, controls retroviral replication via the STING pathway

The paper identifies IFI207 as a rapidly evolving protein that controls retroviral replication through the STING pathway, highlighting its role in host-pathogen co-evolution.

OBIA: An Open Biomedical Imaging Archive

OBIA is a biomedical imaging archive that stores and provides access to imaging and clinical data from 937 individuals across multiple modalities and anatomical sites.

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.

Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2

The paper introduces Coronavirus GenBrowser (CGB), a tool for analyzing and visualizing SARS-CoV-2 genomic sequences to study transmission and evolution.

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.

Delta integrates 3D physical structure with topology and genomic data of chromosomes

Delta integrates 3D chromosomal structure with genomic data to visualize and analyze regulatory networks, revealing insights into gene regulation through a case study on the beta-globin region.