Enhui Shen
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View article: A transcriptomic profiling across tissues, developmental stages, and types of Nicotiana tabacum
A transcriptomic profiling across tissues, developmental stages, and types of Nicotiana tabacum Open
Nicotiana tabacum is one of the most important globally economic crops and also a model plant for studying secondary metabolism. N. tabacum is further classified into different types such as flue-cured, cigar, and sun-cured and so on, whic…
View article: Multiomic analysis of the synthetic pathways of secondary metabolites in tobacco leaves at different developmental stages
Multiomic analysis of the synthetic pathways of secondary metabolites in tobacco leaves at different developmental stages Open
Introduction Nicotiana tabacum , widely cultivated for its economic and scientific value, produces a broad range of secondary metabolites that play critical roles in determining leaf quality and flavor. Despite substantial progress, the co…
View article: Single‐microbe RNA sequencing uncovers unexplored specialized metabolic functions of keystone species in the human gut
Single‐microbe RNA sequencing uncovers unexplored specialized metabolic functions of keystone species in the human gut Open
The human body is inhabited by trillions of microorganisms that play a crucial role in health and diseases. Our understanding of the species and functional composition of the human gut microbiome is rapidly expanding, but it is still mainl…
View article: Robust Diagnosis of Acute Bacterial and Viral Infections via Host Gene Expression Rank-Based Ensemble Machine Learning Algorithm: A Multi-Cohort Model Development and Validation Study
Robust Diagnosis of Acute Bacterial and Viral Infections via Host Gene Expression Rank-Based Ensemble Machine Learning Algorithm: A Multi-Cohort Model Development and Validation Study Open
Background The accurate and prompt diagnosis of infections is essential for improving patient outcomes and preventing bacterial drug resistance. Host gene expression profiling as an approach to infection diagnosis holds great potential in …
View article: Identification of cell‐type specificity, <i>trans</i>‐ and <i>cis</i>‐acting functions of plant <scp>lincRNAs</scp> from single‐cell transcriptomes
Identification of cell‐type specificity, <i>trans</i>‐ and <i>cis</i>‐acting functions of plant <span>lincRNAs</span> from single‐cell transcriptomes Open
Summary Long noncoding RNAs, including intergenic lncRNAs (lincRNAs), play a key role in various biological processes throughout the plant life cycle, and the advent of single‐cell RNA sequencing (scRNA‐seq) technology has opened up a valu…
View article: The dynamic transcriptome reveals response patterns to black shank disease in tobacco (Nicotiana tabacum L.)
The dynamic transcriptome reveals response patterns to black shank disease in tobacco (Nicotiana tabacum L.) Open
Black shank disease, caused by Phytophthora nicotianae, is one of the major causes of yield loss in tobacco production. The present study aimed to explore the dynamic transcriptome in tobacco genotypes resistant or susceptible to black sha…
View article: Retrospect and prospect of Nicotiana tabacum genome sequencing
Retrospect and prospect of Nicotiana tabacum genome sequencing Open
Investigating plant genomes offers crucial foundational resources for exploring various aspects of plant biology and applications, such as functional genomics and breeding practices. With the development in sequencing and assembly technolo…
View article: Are mi<scp>RNA</scp>s applicable for balancing crop growth and defense trade‐off?
Are mi<span>RNA</span>s applicable for balancing crop growth and defense trade‐off? Open
Summary Securing agricultural supplies for the increasing population without negative impacts on environment demands new crop varieties with higher yields, better quality, and stronger stress resilience. But breeding such super crop variet…
View article: High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in human gut microbiome
High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in human gut microbiome Open
Microbial communities such as those residing in the human gut are highly diverse and complex, and many with important implications for health and diseases. The effects and functions of these microbial communities are determined not only by…
View article: MicroRNAs constitute an additional layer in plant response to simultaneous bio‐ and abiotic stresses as exemplified by UV‐B radiation and flg22‐treatment on <i>Arabidopsis thaliana</i>
MicroRNAs constitute an additional layer in plant response to simultaneous bio‐ and abiotic stresses as exemplified by UV‐B radiation and flg22‐treatment on <i>Arabidopsis thaliana</i> Open
Plants are confronted with various environmental stresses and develop sophisticated adaptive mechanisms. Our previous work demonstrated that the crosstalk of flg22 and ultraviolet (UV)‐B‐induced signalling cascades reprograms the expressio…
View article: GSCtool: A Novel Descriptor that Characterizes the Genome for Applying Machine Learning in Genomics
GSCtool: A Novel Descriptor that Characterizes the Genome for Applying Machine Learning in Genomics Open
Machine learning (ML) is one of the core driving forces for the next breeding stage, and Breeding 4.0. Genotype matrix based on single‐nucleotide polymorphisms (SNPs) is often used in ML for genome‐to‐phenotype prediction. Genotype matrix …
View article: A syntelog-based pan-genome provides insights into rice domestication and de-domestication
A syntelog-based pan-genome provides insights into rice domestication and de-domestication Open
Background Asian rice is one of the world’s most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is …
View article: Dynamic associations between the respiratory tract and gut antibiotic resistome of patients with COVID-19 and its prediction power for disease severity
Dynamic associations between the respiratory tract and gut antibiotic resistome of patients with COVID-19 and its prediction power for disease severity Open
The antibiotic resistome is the collection of all antibiotic resistance genes (ARGs) present in an individual. Whether an individual's susceptibility to infection and the eventual severity of coronavirus disease 2019 (COVID-19) is influenc…
View article: A syntelog-based pan-genome provides insights into rice domestication and de-domestication
A syntelog-based pan-genome provides insights into rice domestication and de-domestication Open
Asian rice is one of the world’s most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under…
View article: Dynamic changes in the respiratory tract and gut antibiotic resistome of patients with COVID-19 and its association with disease severity
Dynamic changes in the respiratory tract and gut antibiotic resistome of patients with COVID-19 and its association with disease severity Open
Background The antibiotic resistome is the collection of all the antibiotic resistance genes (ARGs) present in an individual. Whether an individual’s susceptibility to infection and the eventual severity of coronavirus disease 2019 (COVID-…
View article: Editorial: The roles of ncRNAs in the genome evolution and cross-kingdom regulation
Editorial: The roles of ncRNAs in the genome evolution and cross-kingdom regulation Open
EDITORIAL article Front. Plant Sci., 03 February 2023Sec. Plant Bioinformatics Volume 14 - 2023 | https://doi.org/10.3389/fpls.2023.1133096
View article: The Conservation of Long Intergenic Non-Coding RNAs and Their Response to Verticillium dahliae Infection in Cotton
The Conservation of Long Intergenic Non-Coding RNAs and Their Response to Verticillium dahliae Infection in Cotton Open
Long intergenic non-coding RNAs (lincRNAs) have been demonstrated to be vital regulators of diverse biological processes in both animals and plants. While many lincRNAs have been identified in cotton, we still know little about the reposit…
View article: The complete chloroplast genome of weedy rye <i>Secale cereale</i> subsp. <i>segetale</i>
The complete chloroplast genome of weedy rye <i>Secale cereale</i> subsp. <i>segetale</i> Open
Weedy rye (Secale cereale subsp. segetale Zhukov 1928) is a problematic weed species in wheat field. However, it can potentially provide valuable genetics resources to increase the genetic variations and introduce desirable genes for rye a…
View article: Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome
Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome Open
Background Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 m below sea level. Howe…
View article: The complete chloroplast genome of <i>Nicotiana plumbaginifolia</i>
The complete chloroplast genome of <i>Nicotiana plumbaginifolia</i> Open
Nicotiana plumbaginifolia Vivianiis 1802 is an annual herb, native to Mexico and South America. It is one of the most widely distributed tobacco species. As a wild tobacco, N. plumbaginifolia has provided several economically important dis…
View article: Additional file 2 of Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome
Additional file 2 of Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome Open
Additional file 2. Datasets S1: metagenomic data information. Dataset S2: key words which were used to extract the hmm models to construct the ARGfams from Pfam (v 30.0) and TIGRFAMs. Dataset S3: ARG types and subtypes' information of doma…
View article: Expansion of <i>MIR482/2118</i> by a class‐II transposable element in cotton
Expansion of <i>MIR482/2118</i> by a class‐II transposable element in cotton Open
SUMMARY Some plant microRNA (miRNA) families contain multiple members generating identical or highly similar mature miRNA variants. Mechanisms underlying the expansion of miRNA families remain elusive, although tandem and/or segmental dupl…
View article: miR159 Represses a Constitutive Pathogen Defense Response in Tobacco
miR159 Represses a Constitutive Pathogen Defense Response in Tobacco Open
MicroR159 (miR159) regulation of GAMYB expression is highly conserved in terrestrial plants; however, its functional role remains poorly understood. In Arabidopsis (Arabidopsis thaliana), although GAMYB-like genes are constitutively transc…
View article: A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum)
A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum) Open
Background N on-coding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), accomplish remarkable variety of biological functions. However, the composition of ncRNAs and their interactions with c…
View article: Genome‐wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed
Genome‐wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed Open
Summary Brassica napus ( AACC , 2 n = 38) is an important oilseed crop grown worldwide. However, little is known about the population evolution of this species, the genomic difference between its major genetic groups, such as European and …