Hongkun Zheng
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View article: Prompt-Based Bioinformatic Pipeline Generation for a Multi-Step Metaviral Workflow
Prompt-Based Bioinformatic Pipeline Generation for a Multi-Step Metaviral Workflow Open
Motivation The rapid evolution of bioinformatics tools and multi-step analytic procedure presents a challenge for building effective pipelines, particularly for researchers without extensive programming expertise. This study demonstrates t…
View article: Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions
Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions Open
Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and …
View article: Expression of kinetochore component NDC80 promotes esophageal squamous cell carcinoma cells proliferation and migration
Expression of kinetochore component NDC80 promotes esophageal squamous cell carcinoma cells proliferation and migration Open
CNVs were identified as the predominant genetic variation of NDC80 gene in ESCC patients. In vitro assays suggested that NDC80 was not only involved into proliferation and apoptosis but also migration and invasion of ESCC cells.
View article: A reference genome assembly of the alpine forage grass <i>Elymus nutans</i>
A reference genome assembly of the alpine forage grass <i>Elymus nutans</i> Open
Elymus nutans Griseb. (Poaceae: Triticeae, 2n=6x=42) is a dominant perennial plant species in the Qinghai-Tibetan Plateau in China, which is an important forage resource in high-altitude and cold regions and is the most popular species use…
View article: TAGLN-RhoA/ROCK2-SLC2A3-mediated Mechano-metabolic Axis Promotes Skin Fibrosis
TAGLN-RhoA/ROCK2-SLC2A3-mediated Mechano-metabolic Axis Promotes Skin Fibrosis Open
Skin fibrotic diseases are characterized by abnormal fibroblast function and excessive deposition of extracellular matrix. Our previous single-cell sequencing results identified an enriched fibroblast subcluster in skin fibrotic tissues th…
View article: OrchidBase 6.0: Increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis
OrchidBase 6.0: Increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis Open
Background: Containing the largest number of species, the orchid family provides not only material for studying plant evolution and environmental adaptation, but also economically and culturally important ornamental plants for the human so…
View article: MolluscDB 2.0: a comprehensive functional and evolutionary genomics database for over 1400 molluscan species
MolluscDB 2.0: a comprehensive functional and evolutionary genomics database for over 1400 molluscan species Open
Mollusca represents the second-largest animal phylum but remains less explored genomically. The increase in high-quality genomes and diverse functional genomic data holds great promise for advancing our understanding of molluscan biology a…
View article: Chemotherapy affects the development of pathological scarring after general thoracic surgery in children
Chemotherapy affects the development of pathological scarring after general thoracic surgery in children Open
Globally, a great number of children have been suffering from physical dysfunction and psychological stress due to uncontrollable scar growth and a lack of effective modalities. Despite chemotherapy's established role as a primary treatmen…
View article: Recent advances in strategies to target the behavior of macrophages in wound healing
Recent advances in strategies to target the behavior of macrophages in wound healing Open
Chronic wounds and scar formation are widespread due to limited suitable remedies. The macrophage is a crucial regulator in wound healing, controlling the onset and termination of inflammation and regulating other processes related to woun…
View article: Chinese fir genome and the evolution of gymnosperms
Chinese fir genome and the evolution of gymnosperms Open
Seed plants comprise angiosperms and gymnosperms. The latter includes gnetophytes, cycads, Ginkgo, and conifers. Conifers are distributed worldwide, with 630 species distributed across eight families and 70 genera. Their distinctiveness ha…
View article: Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-Right Shell Asymmetry in Bivalves
Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-Right Shell Asymmetry in Bivalves Open
Bivalves are species-rich mollusks with prominent protective roles in coastal ecosystems. Across these ancient lineages, colony-founding larvae anchor themselves either by byssus production or by cemented attachment. The latter mode of ses…
View article: The<i>Chrysanthemum lavandulifolium</i>genome and the molecular mechanism underlying diverse capitulum types
The<i>Chrysanthemum lavandulifolium</i>genome and the molecular mechanism underlying diverse capitulum types Open
Cultivated chrysanthemum (Chrysanthemum × morifolium Ramat.) is a beloved ornamental crop due to the diverse capitula types among varieties, but the molecular mechanism of capitulum development remains unclear. Here, we report a 2.60 Gb ch…
View article: Seadragon genome analysis provides insights into its phenotype and sex determination locus
Seadragon genome analysis provides insights into its phenotype and sex determination locus Open
The genome of the seadragon permits lifting the veil on its mysterious looks and sex-determining locus.
View article: Golden pompano genome resource enables discovery of valuable gene determining growth traits
Golden pompano genome resource enables discovery of valuable gene determining growth traits Open
One important goal of fish genetic breeding is to identify valuable loci and genes that can facilitate growth and thereby productivity. Few such loci or genes have been identified in golden pompano ( Trachinotus ovatus ), a species of sign…
View article: Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity
Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity Open
Understanding the roles of genetic divergence and phenotypic plasticity in adaptation is central to evolutionary biology and important for assessing adaptive potential of species under climate change. Analysis of a chromosome-level assembl…
View article: A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes
A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes Open
Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an …
View article: Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation
Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation Open
Over the last several hundred years, donkeys have adapted to high-altitude conditions on the Tibetan Plateau. Interestingly, the kiang, a closely related equid species, also inhabits this region. Previous reports have demonstrated the impo…
View article: Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity
Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity Open
We provide the details for genome annotation of estuarine oyster, including gene locations (.gff3), protein models (.pep), CDS (.cds) and exon (.exon) sequences.
View article: A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]
A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis] Open
Non-heading Chinese cabbage (NHCC) is an important leafy vegetable cultivated worldwide. Here, we report the first high-quality, chromosome-level genome of NHCC001 based on PacBio, Hi-C, and Illumina sequencing data. The assembled NHCC001 …
View article: Identification of Loci and Candidate Genes Analyses for Tocopherol Concentration of Soybean Seed
Identification of Loci and Candidate Genes Analyses for Tocopherol Concentration of Soybean Seed Open
Tocopherol (Toc) occurs in soybean seeds and is extracted together with the soybean oil. Toc is utilized as an antioxidant in food and an additive in animal feed. A total of 180 representative accessions and 144 recombinant inbred lines (R…