Shijie Zheng
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View article: Variations in Innate Immune Cell Subtypes Correlate with Epigenetic Clocks, Inflammaging and Health Outcomes
Variations in Innate Immune Cell Subtypes Correlate with Epigenetic Clocks, Inflammaging and Health Outcomes Open
Epigenetic clocks in blood have shown promise as tools to quantify biological age, displaying robust associations with morbidity and all‐cause mortality. Whilst the effect of cell‐type heterogeneity on epigenetic clock estimates has been e…
View article: Atomistic visualization of photoinduced electron transfer process in a nonpolar solvent
Atomistic visualization of photoinduced electron transfer process in a nonpolar solvent Open
Electron transfer, the process of one electron relocating from one chemical entity to another, is one of the most ubiquitous elementary reactions and plays a critical role in almost all fields of chemistry. While seminal theories such as M…
View article: Unified high-resolution immune cell fraction estimation in blood tissue from birth to old age
Unified high-resolution immune cell fraction estimation in blood tissue from birth to old age Open
Background Blood is composed of many different immune cell-types, whose proportions vary throughout life. If not accounted for, these variations can seriously cause confounding or hamper interpretation of DNAm-based biomarkers. Although ce…
View article: A Fine-Grained Image Classification Method Based on ConvNeXt Heatmap Localization and Contrastive Learning
A Fine-Grained Image Classification Method Based on ConvNeXt Heatmap Localization and Contrastive Learning Open
Aiming at the challenges of high intra-class disparity and low inter-class disparity in fine-grained image classification, a multi-branch fine-grained image classification method based on ConvNeXt network as the backbone and using GradCAM …
View article: Genetic dissection of Meloidogyne incognita resistance genes based on VIGS functional analysis in Cucumis metuliferus
Genetic dissection of Meloidogyne incognita resistance genes based on VIGS functional analysis in Cucumis metuliferus Open
The southern root-knot nematode, Meloidogyne incognita, is a highly serious plant parasitic nematode species that causes significant economic losses in various crops, including cucumber (Cucumis sativus L.). Currently, there are no commerc…
View article: Identification and Analysis of WRKY Transcription Factors in Response to Cowpea Fusarium Wilt in Cowpea
Identification and Analysis of WRKY Transcription Factors in Response to Cowpea Fusarium Wilt in Cowpea Open
In plants, WRKY transcription factors play a crucial role in plant growth, development, and response to abiotic and biotic stress. Cowpea (Vigna unguiculata) is an important legume crop. However, cowpea Fusarium wilt (CFW), caused by Fusar…
View article: HotCFuzz: Enhancing Vulnerability Detection through Fuzzing and Hotspot Code Coverage Analysis
HotCFuzz: Enhancing Vulnerability Detection through Fuzzing and Hotspot Code Coverage Analysis Open
Software vulnerabilities present a significant cybersecurity threat, particularly as software code grows in size and complexity. Traditional vulnerability-mining techniques face challenges in keeping pace with this complexity. Fuzzing, a k…
View article: Genome-wide transcriptome profiling reveals molecular response pathways of Trichoderma harzianum in response to salt stress
Genome-wide transcriptome profiling reveals molecular response pathways of Trichoderma harzianum in response to salt stress Open
Trichoderma harzianum exhibits a strong biological control effect on many important plant pathogens, such as Fusarium oxysporum , Botrytis cinerea , and Meloidogyne . However, its biocontrol effectiveness is weakened or reduced under salt …
View article: Pumping the brakes on RNA velocity by understanding and interpreting RNA velocity estimates
Pumping the brakes on RNA velocity by understanding and interpreting RNA velocity estimates Open
Background RNA velocity analysis of single cells offers the potential to predict temporal dynamics from gene expression. In many systems, RNA velocity has been observed to produce a vector field that qualitatively reflects known features o…
View article: A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes
A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes Open
Background Changes in cell-type composition of tissues are associated with a wide range of diseases and environmental risk factors and may be causally implicated in disease development and progression. However, these shifts in cell-type fr…
View article: A meta-analysis of immune cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes
A meta-analysis of immune cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes Open
Background: Changes in cell-type composition of complex tissues are associated with a wide range of diseases, environmental risk factors and may be causally implicated in disease development and progression. However, these shifts in cell-t…
View article: Limb development genes underlie variation in human fingerprint patterns
Limb development genes underlie variation in human fingerprint patterns Open
Fingerprints are of long-standing practical and cultural interest, but little is known about the mechanisms that underlie their variation. Using genome-wide scans in Han Chinese cohorts, we identified 18 loci associated with fingerprint ty…
View article: The First GECAM Observation Results on Terrestrial Gamma-ray Flashes and Terrestrial Electron Beams
The First GECAM Observation Results on Terrestrial Gamma-ray Flashes and Terrestrial Electron Beams Open
Gravitational wave high-energy Electromagnetic Counterpart All-sky Monitor (GECAM) is a space-borne instrument dedicated to monitoring high-energy transients, thereinto Terrestrial Gamma-ray Flashes (TGFs) and Terrestrial Electron Beams (T…
View article: Pumping the brakes on RNA velocity – understanding and interpreting RNA velocity estimates
Pumping the brakes on RNA velocity – understanding and interpreting RNA velocity estimates Open
RNA velocity analysis of single cells promises to predict temporal dynamics from gene expression. Indeed, in many systems, it has been observed that RNA velocity produces a vector field that qualitatively reflects known features of the sys…
View article: Universal prediction of cell-cycle position using transfer learning
Universal prediction of cell-cycle position using transfer learning Open
Background The cell cycle is a highly conserved, continuous process which controls faithful replication and division of cells. Single-cell technologies have enabled increasingly precise measurements of the cell cycle both as a biological p…
View article: Data for Universal prediction of cell cycle position using transfer learning
Data for Universal prediction of cell cycle position using transfer learning Open
The repo contains the data for Universal prediction of cell cycle position using transfer learning (https://www.biorxiv.org/content/10.1101/2021.04.06.438463v2). The scripts to analyze and generate all figures could be found at https://git…
View article: Data for Universal prediction of cell cycle position using transfer learning
Data for Universal prediction of cell cycle position using transfer learning Open
The repo contains the data for Universal prediction of cell cycle position using transfer learning (https://www.biorxiv.org/content/10.1101/2021.04.06.438463v2). The scripts to analyze and generate all figures could be found at https://git…
View article: Data for Universal prediction of cell cycle position using transfer learning
Data for Universal prediction of cell cycle position using transfer learning Open
The repo contains the data for Universal prediction of cell cycle position using transfer learning (https://www.biorxiv.org/content/10.1101/2021.04.06.438463v2). The scripts to analyze and generate all figures could be found at https://git…
View article: recount3: summaries and queries for large-scale RNA-seq expression and splicing
recount3: summaries and queries for large-scale RNA-seq expression and splicing Open
We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to the data, we provide the reco…
View article: Universal prediction of cell cycle position using transfer learning
Universal prediction of cell cycle position using transfer learning Open
Background The cell cycle is a highly conserved, continuous process which controls faithful replication and division of cells. Single-cell technologies have enabled increasingly precise measurements of the cell cycle both as a biological p…
View article: Calling differential DNA methylation at cell-type resolution: avoiding misconceptions and promoting best practices
Calling differential DNA methylation at cell-type resolution: avoiding misconceptions and promoting best practices Open
The accurate detection of cell-type specific DNA methylation alterations in the context of general epigenome studies is an important task to improve our understanding of epigenomics in disease development. Although a number of statistical …
View article: EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUI
EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUI Open
Summary It is well recognized that cell-type heterogeneity hampers the interpretation of Epigenome-Wide Association Studies (EWAS). Many tools have emerged to address this issue, including several R/Bioconductor packages that infer cell-ty…
View article: Calling differential DNA methylation at cell-type resolution: an objective status-quo
Calling differential DNA methylation at cell-type resolution: an objective status-quo Open
Due to cost and logistical reasons, Epigenome-Wide-Association Studies (EWAS) are normally performed in complex tissues, resulting in average DNA methylation profiles over potentially many different cell-types, which can obscure important …
View article: ebGSEA: an improved Gene Set Enrichment Analysis method for Epigenome-Wide-Association Studies
ebGSEA: an improved Gene Set Enrichment Analysis method for Epigenome-Wide-Association Studies Open
Motivation The biological interpretation of differentially methylated sites derived from Epigenome-Wide-Association Studies (EWAS) remains a significant challenge. Gene Set Enrichment Analysis (GSEA) is a general tool to aid biological int…
View article: Cell and tissue type independent age-associated DNA methylation changes are not rare but common
Cell and tissue type independent age-associated DNA methylation changes are not rare but common Open
Age-associated DNA methylation changes have been widely reported across many different tissue and cell types. Epigenetic 'clocks' that can predict chronological age with a surprisingly high degree of accuracy appear to do so independently …
View article: ebayGSEA: An improved Gene Set Enrichment Analysis method for Epigenome-Wide-Association Studies
ebayGSEA: An improved Gene Set Enrichment Analysis method for Epigenome-Wide-Association Studies Open
Motivation The biological interpretation of differentially methylated sites derived from Epigenome-Wide-Association Studies remains a significant challenge. Gene Set Enrichment Analysis (GSEA) is a general tool to help aid biological inter…
View article: Cell and tissue type independent age-associated DNA methylation changes are not rare but common
Cell and tissue type independent age-associated DNA methylation changes are not rare but common Open
Age-associated DNA methylation changes have been widely reported across many different tissue and cell types. Epigenetic ‘clocks’ that can predict chronological age with a surprisingly high degree of accuracy appear to do so independently …