Shiheng Tao
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View article: Tumor organoids in immunotherapy: from disease modeling to translational research
Tumor organoids in immunotherapy: from disease modeling to translational research Open
Tumor organoids have emerged as transformative tools in cancer research, enabling the study of tumor biology and immunology in a physiologically relevant, three-dimensional in vitro environment. Derived from patient tumor samples, these se…
View article: La/Fe-Bimetallic-Modified Red Brick Powder for Phosphate Removal from Wastewater: Characterization, Adsorption, and Mechanism
La/Fe-Bimetallic-Modified Red Brick Powder for Phosphate Removal from Wastewater: Characterization, Adsorption, and Mechanism Open
The use of construction waste red brick powder (RBP) to prepare adsorbents for phosphate removal from wastewater represents a promising technology with substantial research potential. This study investigates the preparation of La-based mag…
View article: Comparative analysis of complete mitochondrial genomes of Panorpidae (Insecta: Mecoptera) and new perspectives on the phylogenetic position of Furcatopanorpa
Comparative analysis of complete mitochondrial genomes of Panorpidae (Insecta: Mecoptera) and new perspectives on the phylogenetic position of Furcatopanorpa Open
The scorpionfly genus Furcatopanorpa Ma & Hua, 2011 is a monotypic taxon of Panorpidae with a series of unique characters. However, the phylogenetic position of Furcatopanorpa in Panorpidae has not been satisfactorily resolved yet. Based o…
View article: Correction for Sun et al., “Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder”
Correction for Sun et al., “Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder” Open
View article: Reply to Červenák et al., “Primary Scientific Literature Represents an Essential Source of Telomeric Repeat Sequences”
Reply to Červenák et al., “Primary Scientific Literature Represents an Essential Source of Telomeric Repeat Sequences” Open
View article: Metagenomics insights into responses of rhizobacteria and their alleviation role in licorice allelopathy
Metagenomics insights into responses of rhizobacteria and their alleviation role in licorice allelopathy Open
Background Allelopathy is closely associated with rhizosphere biological processes, and rhizosphere microbial communities are essential for plant development. However, our understanding of rhizobacterial communities under influence of alle…
View article: Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder
Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder Open
Telomeres are reported to be highly correlated with the cell cycle and aging. As a result, research on telomere composition and evolution has become more and more urgent.
View article: Additional file 1 of Metagenomics insights into responses of rhizobacteria and their alleviation role in licorice allelopathy
Additional file 1 of Metagenomics insights into responses of rhizobacteria and their alleviation role in licorice allelopathy Open
Additional file 1: Table S1. PCR primers used in this study. HMGR, 3-hydroxy-3-methylglutary coenzyme A reductase gene; β-AS, bamyrin synthetase gene; CYP88D6 and CYP72A154, cytochrome P450 monooxygenases gene; LUS, lupeol synthase gene; C…
View article: Natural selection pressure exerted on “Silent” mutations during the evolution of SARS-CoV-2: Evidence from codon usage and RNA structure
Natural selection pressure exerted on “Silent” mutations during the evolution of SARS-CoV-2: Evidence from codon usage and RNA structure Open
From the first emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) till now, multiple mutations that caused synonymous and nonsynonymous substitutions have accumulated. Among them, synonymous substitutions were regard…
View article: Edging on Mutational Bias, Induced Natural Selection From Host and Natural Reservoirs Predominates Codon Usage Evolution in Hantaan Virus
Edging on Mutational Bias, Induced Natural Selection From Host and Natural Reservoirs Predominates Codon Usage Evolution in Hantaan Virus Open
The molecular evolutionary dynamics that shape hantaviruses’ evolution are poorly understood even now, besides the contribution of virus-host interaction to their evolution remains an open question. Our study aimed to investigate these two…
View article: Additional file 12 of Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis
Additional file 12 of Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis Open
Additional file 12 Supplementary Datasets (S1-S6) provide the identified F-box protein sequences for C. brenneri, C. briggsae, C. elegans, C. japonica, C. remanei, and P. pacificus, respectively.
View article: Additional file 13 of Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis
Additional file 13 of Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis Open
Additional file 13: Supplementary File 1. shows the analysis results of gene structural and functional diversification and selection pressure of closely related paralogs from C.elegans and C.briggsae, respectively.
View article: Genome-Wide Characterization, Evolution, Structure, and Expression Analysis of the F-box Genes in Caenorhabditis
Genome-Wide Characterization, Evolution, Structure, and Expression Analysis of the F-box Genes in Caenorhabditis Open
Background: F-box proteins represent a diverse class of adaptor proteins of ubiquition proteasome system (UPS) that play critical roles in cell signaling pathway and immune response. Among closely related organisms of Caenorhabditis, treme…
View article: CRISPR-CBEI: a Designing and Analyzing Tool Kit for Cytosine Base Editor-Mediated Gene Inactivation
CRISPR-CBEI: a Designing and Analyzing Tool Kit for Cytosine Base Editor-Mediated Gene Inactivation Open
Life science has been in pursuit of precise and efficient genome editing in living cells since the very beginning of the first restriction cloning attempt. The introduction of RNA-guided CRISPR-associated (Cas) nucleases contributed to thi…
View article: Origin and Evolution of Fusidane-Type Antibiotics Biosynthetic Pathway through Multiple Horizontal Gene Transfers
Origin and Evolution of Fusidane-Type Antibiotics Biosynthetic Pathway through Multiple Horizontal Gene Transfers Open
Fusidane-type antibiotics represented by fusidic acid, helvolic acid, and cephalosporin P1 have very similar core structures, but they are produced by fungi belonging to different taxonomic groups. The origin and evolution of fusidane-type…
View article: Codon Usage Bias Analysis of Bluetongue Virus Causing Livestock Infection
Codon Usage Bias Analysis of Bluetongue Virus Causing Livestock Infection Open
Bluetongue virus (BTV) is a double-stranded RNA virus with multiple segments and belongs to the genus Orbivirus within the family Reoviridae. BTV is spread to livestock through its dominant vector, biting midges of genus C…
View article: The mitochondrial genomes of Panorpidae: sequence, structure and phylogenetic analysis
The mitochondrial genomes of Panorpidae: sequence, structure and phylogenetic analysis Open
Background: Mitochondrial genomes play a significant role in reconstructing phylogenetic relationships and revealing molecular evolution in insects. However, only two species of Panorpidae have been documented for mitochondrial genomes in …
View article: Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts
Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts Open
View article: Additional file 2 of Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts
Additional file 2 of Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts Open
Additional file 2: Figure S1. Neighbor-joining species tree based on the 2110 single-copy core genes shared by 50 rhizobial genomes used in this study. The name of each strain is preceded by the cluster number indicated in Additional file …
View article: Additional file 1 of Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts
Additional file 1 of Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts Open
Additional file 1: Table S1. Genomes used in this study. Table S2. Core genes for which phylogenies are strictly consistent with the species tree. Table S3. Recent horizontal gene transfer (HGT) predictions among 50 Rhizobium strains. Tabl…
View article: RSVdb: A comprehensive database of transcriptome RNA structure
RSVdb: A comprehensive database of transcriptome RNA structure Open
RNA fulfills a crucial regulatory role in cells by folding into a complex RNA structure. To date, a chemical compound, dimethyl sulfate (DMS), has been developed to effectively probe the RNA structure at the transcriptome level. We propose…
View article: Deciphering the rules of mRNA structure differentiation in <i>Saccharomyces cerevisiae in vivo</i> and <i>in vitro</i> with deep neural networks
Deciphering the rules of mRNA structure differentiation in <i>Saccharomyces cerevisiae in vivo</i> and <i>in vitro</i> with deep neural networks Open
The structure of mRNA in vivo is unwound to some extent in response to multiple factors involved in the translation process, resulting in significant differences from the structure of the same mRNA in vitro. In this study, we…
View article: CellSim: a novel software to calculate cell similarity and identify their co-regulation networks
CellSim: a novel software to calculate cell similarity and identify their co-regulation networks Open
View article: Deciphering the rules of mRNA structure differentiation in <i>Saccharomyces cerevisiae in vivo</i> and <i>in vitro</i> with deep neural networks
Deciphering the rules of mRNA structure differentiation in <i>Saccharomyces cerevisiae in vivo</i> and <i>in vitro</i> with deep neural networks Open
The structure of mRNA in vivo is unwound to some extent in response to multiple factors involved in the translation process, resulting in significant differences from the structure of the same mRNA in vitro. In this study, we…
View article: Rapid Identification of Major QTLS Associated With Near- Freezing Temperature Tolerance in Saccharomyces cerevisiae
Rapid Identification of Major QTLS Associated With Near- Freezing Temperature Tolerance in Saccharomyces cerevisiae Open
Temperatures had a strong effect on many life history traits, including growth, development and reproduction. At near-freezing temperatures (0-4°C), yeast cells could trigger series of biochemical reactions to respond and adapt to the stre…
View article: An enigmatic new species of Panorpa Linneaus from the Bashan Mountains (Mecoptera, Panorpidae)
An enigmatic new species of Panorpa Linneaus from the Bashan Mountains (Mecoptera, Panorpidae) Open
A new species of Panorpidae, Panorpabashanicola sp. n. , is described and illustrated from the Bashan Mountains in central China. The new species is characterized by the following characters: vertex black, with two pale longitudinal stripe…
View article: Deciphering the rules of mRNA structure differentiation in vivo and in vitro with deep neural networks in Saccharomyces cerevisiae
Deciphering the rules of mRNA structure differentiation in vivo and in vitro with deep neural networks in Saccharomyces cerevisiae Open
The structure of mRNA in vivo is influenced by various factors involved in the translation process, resulting in significant differentiation of mRNA structure from that in vitro . Because multiple factors cause the differentiation of in vi…
View article: A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Rhizobium Strains
A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Rhizobium Strains Open
Recent horizontal gene transfer (HGT) is crucial for enabling microbes to rapidly adapt to their novel environments without relying upon rare beneficial mutations that arise spontaneously. For several years now, computational approaches ha…
View article: An enigmatic new species of Panorpa Linneaus from the Bashan Mountains (Mecoptera, Panorpidae)
An enigmatic new species of Panorpa Linneaus from the Bashan Mountains (Mecoptera, Panorpidae) Open
This dataset contains the digitized treatments in Plazi based on the original journal article Hua, Yuan, Tao, Shi-Heng, Hua, Bao-Zhen (2018): An enigmatic new species of Panorpa Linneaus from the Bashan Mountains (Mecoptera, Panorpidae). Z…
View article: Codon Usage in Signal Sequences Affects Protein Expression and Secretion Using Baculovirus/Insect Cell Expression System
Codon Usage in Signal Sequences Affects Protein Expression and Secretion Using Baculovirus/Insect Cell Expression System Open
By introducing synonymous mutations into the coding sequences of GP64sp and FibHsp signal peptides, the influences of mRNA secondary structure and codon usage of signal sequences on protein expression and secretion were investigated using …