-
Article
Open AccessPowerful and accurate detection of temporal gene expression patterns from multi-sample multi-stage single-cell transcriptomics data with TDEseq
We present a non-parametric statistical method called TDEseq that takes full advantage of smoothing splines basis functions to account for the dependence of multiple time points in scRNA-seq studies, and uses ...
-
Article
Effect of Nitrate Concentration on Anaerobic Methane Oxidation Coupled to Denitrification in Membrane Biofilm Reactor After Prolonged Storage
The effects of the influent nitrate (NO3−-N) concentration on reactor performance and microbial communities of anaerobic methane oxidation coupled to denitrification in a membrane biofilm reactor were emphaticall...
-
Article
Open AccessAspartate beta-hydroxylase domain containing 1 as a prognostic marker associated with immune infiltration in skin cutaneous melanoma
Skin cutaneous melanoma (SKCM) is an extremely malignant tumor and accounts for the majority of skin cancer deaths. Aspartate beta-hydroxylase domain containing 1 (ASPHD1) may participate in cancer progression...
-
Article
Open AccessDelineating the dynamic evolution from preneoplasia to invasive lung adenocarcinoma by integrating single-cell RNA sequencing and spatial transcriptomics
The cell ecology and spatial niche implicated in the dynamic and sequential process of lung adenocarcinoma (LUAD) from adenocarcinoma in situ (AIS) to minimally invasive adenocarcinoma (MIA) and subsequent inv...
-
Article
Exploring the photocatalytic inactivation mechanism of Microcystis aeruginosa under visible light using Ag3PO4/g-C3N4
In this work, a series of Ag3PO4/g-C3N4 (AG) photocatalysts were synthesized. After characterizing the properties, the effects of mass ratio, light intensity, and material dosages on photodegradation were investi...
-
Article
Open AccessThe pyroptosis-related gene signature predicts prognosis and indicates immune activity in hepatocellular carcinoma
Hepatocellular carcinoma (HCC) remains one of the most common malignant tumors with poor survival. Pyroptosis is a kind of programmed cell death that can regulate the proliferation, invasion, and metastasis of...
-
Article
Open AccessGenome-wide analysis of circular RNAs and validation of hsa_circ_0086354 as a promising biomarker for early diagnosis of cerebral palsy
Cerebral palsy (CP) is a spectrum of non-progressive motor disorders caused by brain injury during fetal or postnatal periods. Current diagnosis of CP mainly relies on neuroimaging and motor assessment. Here, ...
-
Article
Open AccessA novel nonparametric computational strategy for identifying differential methylation regions
DNA methylation has long been known as an epigenetic gene silencing mechanism. For a motivating example, the methylomes of cancer and non-cancer cells show a number of methylation differences, indicating that ...
-
Article
Open AccessIdentifying discriminative features for diagnosis of Kashin-Beck disease among adolescents
Diagnosing Kashin-Beck disease (KBD) involves damages to multiple joints and carries variable clinical symptoms, posing great challenge to the diagnosis of KBD for clinical practitioners. However, it is still ...
-
Article
Open AccessSPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies
Spatial transcriptomic studies are becoming increasingly common and large, posing important statistical and computational challenges for many analytic tasks. Here, we present SPARK-X, a non-parametric method f...
-
Article
Open AccessTesting and controlling for horizontal pleiotropy with probabilistic Mendelian randomization in transcriptome-wide association studies
Integrating results from genome-wide association studies (GWASs) and gene expression studies through transcriptome-wide association study (TWAS) has the potential to shed light on the causal molecular mechanis...
-
Article
Magnetic-activated carbon composites derived from iron sludge and biological sludge for sulfonamide antibiotic removal
Novel magnetic-activated carbon composites (MACs) were synthesized via coupling of a glucose-assisted hydrothermal pretreatment and subsequent thermal treatment using iron sludge and biological sludge. The ads...
-
Article
Open AccessIntegrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies
Differential expression (DE) analysis and gene set enrichment (GSE) analysis are commonly applied in single cell RNA sequencing (scRNA-seq) studies. Here, we develop an integrative and scalable computational m...
-
Article
Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies
Identifying genes that display spatial expression patterns in spatially resolved transcriptomic studies is an important first step toward characterizing the spatial transcriptomic landscape of complex tissues....
-
Article
Open AccessAccuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis
Dimensionality reduction is an indispensable analytic component for many areas of single-cell RNA sequencing (scRNA-seq) data analysis. Proper dimensionality reduction can allow for effective noise removal and...
-
Article
Open AccessIMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL map** and allele-specific analysis
Identifying genetic variants that are associated with methylation variation—an analysis commonly referred to as methylation quantitative trait locus (mQTL) map**—is important for understanding the epigenetic...
-
Article
Open AccessA fast and efficient count-based matrix factorization method for detecting cell types from single-cell RNAseq data
Single-cell RNA sequencing (scRNAseq) data always involves various unwanted variables, which would be able to mask the true signal to identify cell-types. More efficient way of dealing with this issue is to ex...
-
Article
Open AccessHigher-order partial least squares for predicting gene expression levels from chromatin states
Extensive studies have shown that gene expression levels are strongly affected by chromatin mark combinations via at least two mechanisms, i.e., activation or repression. But their combinatorial patterns are s...
-
Article
The combined genotypes effect of ESR and FSHβ genes on litter size traits in five different pig breeds
Estrogen receptor (ESR) and Follicular-stimulating hormone beta subunit (FSHβ) genes were chosen as candidates to determine whether they control litter size and some other reproductive traits in swine. 269 sow...
-
Article
FSHB subunit gene is associated with major gene controlling litter size in commercial pig breeds
An insertion fragment in porcine FSHβ subunit gene was cloned by PCR. Sequencing data show that the insertion is a retroposon of 292 bp siting in intron I at the site between + 809 and +810 base. Based on thes...
