Weiming He
A5103246312- Bioinformatics and Genomic Networks
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Computational Drug Discovery Methods
- Chromosomal and Genetic Variations
- Legume Nitrogen Fixing Symbiosis
- Genetic diversity and population structure
- Gene expression and cancer classification
- Genetic and Environmental Crop Studies
- Advances in Cucurbitaceae Research
- Agricultural pest management studies
- Cancer-related molecular mechanisms research
- Soybean genetics and cultivation
- Metabolomics and Mass Spectrometry Studies
- Machine Learning in Bioinformatics
- Rice Cultivation and Yield Improvement
- Wheat and Barley Genetics and Pathology
- RNA modifications and cancer
- Gene Regulatory Network Analysis
- Genetic and phenotypic traits in livestock
- Genetic Associations and Epidemiology
- RNA and protein synthesis mechanisms
- Microbial Metabolic Engineering and Bioproduction
- Plant and Fungal Interactions Research
- Plant Disease Resistance and Genetics
BGI Research
2024-2025
Botswana Geoscience Institute
2025
Harbin Institute of Technology
2013-2024
BGI Group (China)
2014-2023
Beijing Academy of Agricultural and Forestry Sciences
2022-2023
BGI Genomics
2017-2022
Ministry of Agriculture and Rural Affairs
2022
Heilongjiang Institute of Technology
2017-2021
Xi'an Jiaotong University
2018-2020
Yunnan University
2020
No Genetic Vertigo Peoples living in high altitudes have adapted to their situation (see the Perspective by Storz ). To identify gene regions that might contributed high-altitude adaptation Tibetans, Simonson et al. (p. 72 , published online 13 May) conducted a genome scan of nucleotide polymorphism comparing Han Chinese, and Japanese, while Yi 75 ) performed comparable analyses on coding all genes—their exomes. Both studies converged gene, endothelial Per-Arnt-Sim domain protein 1 (also...
Abstract Motivation Linkage disequilibrium (LD) decay is of great interest in population genetic studies. However, no tool available now to do LD analysis from variant call format (VCF) files directly. In addition, generation pair-wise measurements for whole genome SNPs usually resulting large storage wasting files. Results We developed PopLDdecay, an open source software, VCF It fast and able handle number variants sequencing data. also saving by avoiding exporting results measurements....
A draft sequence of the staple crop kabuli chickpea, together with resequencing and analysis 90 additional lines from 10 countries, provides a resource for breeders. Chickpea (Cicer arietinum) is second most widely grown legume after soybean, accounting substantial proportion human dietary nitrogen intake playing crucial role in food security developing countries. We report ∼738-Mb whole genome shotgun CDC Frontier, chickpea variety, which contains an estimated 28,269 genes. Resequencing...
Sequencing and analysing the diploid genome transcriptome of Aegilops tauschii provide new insights into role this in enabling adaptation bread wheat are a step towards understanding very large complicated hexaploid genomes species. The Triticum aestivum, designated AABBDD, evolved as result hybridization between three ancestral grasses. Two papers published issue Nature present sequences analysis two these progenitors. First, sequence wild T. urartu (ancestor A genome), which resembles...
The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component population-based genetic studies. However, current tools suffered from problem time memory consuming. Here, we developed LDBlockShow, an open source software, for visualizing LD blocks variant call format files. It saving. In a test dataset with 100 60 000 subjects, it was at least 10.60 times faster used only 0.03-13.33% physical as...
The Asian tiger mosquito, Aedes albopictus, is a highly successful invasive species that transmits number of human viral diseases, including dengue and Chikungunya fevers. This has large genome with significant population-based size variation. complete sequence was determined for the Foshan strain, an established laboratory colony derived from wild mosquitoes southeastern China, region within historical range origin species. comprises 1,967 Mb, largest mosquito sequenced to date, its results...
Seahorses have a specialized morphology that includes toothless tubular mouth, body covered with bony plates, male brood pouch, and the absence of caudal pelvic fins. Here we report sequencing de novo assembly genome tiger tail seahorse, Hippocampus comes. Comparative genomic analysis identifies higher protein nucleotide evolutionary rates in H. comes compared other teleost fish genomes. We identified an astacin metalloprotease gene family has undergone expansion is highly expressed pouch....
Tibetan barley (Hordeum vulgare L., qingke) is the principal cereal cultivated on Plateau for at least 3,500 years, but its origin and domestication remain unclear. Here, based deep-coverage whole-genome published exome-capture resequencing data a total of 437 accessions, we show that contemporary qingke derived from eastern domesticated it introduced to southern Tibet most likely via north Pakistan, India, Nepal between 4,500 years ago. The low genetic diversity suggests can be excluded as...
Abstract The silkworm Bombyx mori is an important economic insect for producing silk, the “queen of fabrics”. currently available genomes limit understanding its genetic diversity and discovery valuable alleles breeding. Here, we deeply re-sequence 1,078 silkworms assemble long-read 545 representatives. We construct a high-resolution pan-genome dataset representing almost entire genomic content in silkworm. find that population harbors high density variants identify 7308 new genes, 4260...
Abstract Summary Large-scale comparative genomic studies have provided important insights into species evolution and diversity, but also lead to a great challenge visualize. Quick catching or presenting key information hidden in the vast amount of data relationships among multiple genomes requires an efficient visualization tool. However, current tools for such remain inflexible layout and/or require advanced computation skills, especially genome-based synteny. Here, we developed easy-to-use...
Significance Hybrid rice developed in China has been contributing greatly to the world’s food production. The pioneer super hybrid by crossing 93–11 and Peiai 64s , Liang–You–Pei–Jiu widely grown other Asia-Pacific regions for its high yield. Here, quality genome sequences both parental lines were presented updated, a high-resolution map of genome-wide graphic genotypes was constructed deep resequencing core population 132 recombinant inbred lines. A series yield-associated loci fine-mapped,...
In order to understand the impact of breeding on genetic diversity and gain insights into temporal trends in chickpea, a set 100 chickpea varieties released 14 countries between 1948 2012 were re-sequenced. For analysis, re-sequencing data for 29 available from an earlier study was also included. Copy number variations presence absence identified present have potential drive phenotypic trait improvement. Re-sequencing large has provided opportunities inspect genomic changes reflecting...
Abstract Triploids are rare in nature because of difficulties meiotic and gametogenic processes, especially vertebrates. The Carassius complex cyprinid teleosts contains sexual tetraploid crucian carp/goldfish ( C. auratus ) unisexual hexaploid gibel carp/Prussian carp gibelio lineages, providing a valuable model for studying the evolution maintenance mechanism polyploids Here we sequence genomes two species assemble their haplotypes, which contain subgenomes (A B), to chromosome level....
BackgroundPenguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an life, some have successfully adapted hostile environments Antarctica. To study phylogenetic population history molecular basis their adaptations Antarctica, we sequenced genomes two Antarctic dwelling penguin species, Adélie [Pygoscelis adeliae] emperor [Aptenodytes forsteri].
Summary Reticulate speciation caused by interspecific hybridization is now recognized as an important mechanism in the creation of biological diversity. However, depicting patterns phylogenetic networks for lineages that have undergone gene flow challenging. Here we sequenced 25 taxa representing natural diversity genus Actinidia with average mapping depth 26× on reference genome to reconstruct their reticulate history. We found evidence, including significant tree discordance, cytonuclear...
Abstract Crop wild relatives are valuable resources for future genetic improvement. Here, we report the de novo genome assembly of Musa itinerans , a disease-resistant banana relative in subtropical China. The assembled size was 462.1 Mb, covering 75.2% (615.2Mb) and containing 32, 456 predicted protein-coding genes. Since approximate divergence around 5.8 million years ago, genomes acuminata have shown conserved collinearity. Gene family expansions contractions enrichment analysis revealed...
Abstract Bitter gourd ( Momordica charantia ) is a popular cultivated vegetable in Asian and African countries. To reveal the characteristics of genomic structure, evolutionary trajectory, genetic basis underlying domestication bitter gourd, we performed whole-genome sequencing cultivar Dali-11 wild small-fruited line TR resequencing 187 germplasms from 16 The major gene clusters Bi clusters) for biosynthesis cucurbitane triterpenoids, which confer taste, are highly conserved cucumber,...