Molecular Biology Techniques and Applications

gQuant improves normalizer gene identification in qRT-PCR data by using ensemble voting classifiers, showing better consistency and accuracy than existing tools.

The paper re-analyzes RNA sequencing data comparing gene expression in living and postmortem human brain tissue, finding that living samples had lower quality, and questions the validity of previous conclusions about postmortem studies.

The paper introduces a mathematical framework for improving qPCR gene expression normalization by optimizing weighted aggregation of reference genes using scale-invariant functions.

This study compares DNA fidelity between in vitro enzymatic synthesis and E. coli-produced DNA, finding that E. coli yields significantly fewer mutations.

This paper introduces three new statistical methods for variance estimation in digital PCR experiments, showing they provide more accurate results than classical binomial methods.

The paper introduces a low-cost system for high-throughput RNA isolation from tissues, combining CryoGrid for storage/sampling with PIXUL-based methods using a PK buffer to enable efficient transcript analysis.

This paper introduces a novel hydrogel capsule-based digital PCR method that improves stability, sensitivity, and cost-effectiveness compared to traditional ddPCR.

This paper introduces a method to increase digital PCR multiplexing to 15-plex using color combination and validates its statistical framework and sensitivity.

The paper identifies stable reference genes for qRT-PCR in insect endosymbiotic models using transcriptomic data from Sitophilus oryzae.

The paper introduces an in-house RNA isolation method using magnetic silica beads that produces high-quality RNA comparable to commercial kits, without DNA digestion or separate small RNA kits.

The paper describes a plasmid, pHAPE, that allows the generation of DNA size markers through restriction enzyme digestions, reducing costs associated with commercial DNA ladders.

This paper develops an optimized RNA extraction method for rat intrinsic laryngeal muscles, achieving high-quality RNA suitable for RNA-seq.

The paper introduces and compares two Direct PCR methods for Arabidopsis and rice, finding Line-PCR to be faster, cheaper, and more accurate than existing methods.

This paper introduces Ultra-dPCR, a next generation digital PCR system that enables single-molecule DNA counting with a 6-log dynamic range, demonstrating its potential for non-invasive prenatal testing.

The paper shows that gene expression profiles from partially degraded RNA can still be valid, using PCR-based analysis and normalization to housekeeping genes.

The paper describes an optimized LCM protocol for extracting high-quality RNA from specific mouse brain regions.

This paper develops a method to estimate time since deposition of bloodstains using RNA quality metrics from degrading blood samples without amplification.

This study shows that delayed processing of blood samples affects mRNA-based biomarkers by altering transcript abundance in peripheral white blood cells.

This paper introduces an adaptive filtering framework to improve classification accuracy in multiplex digital PCR by removing non-specific and low-efficient reactions using sigmoidal trends and outlier detection.

This study shows that using a robust statistical method to select reference genes from randomly chosen candidates is as effective as selecting stable genes from RNA-Seq data for qPCR normalization.

This paper introduces VPdPCR, a method that enhances digital PCR's ability to detect multiple targets per sample, improving accuracy and reducing variance in chromosomal counting.

The paper develops a statistical model to estimate population allele frequency from qPCR ΔΔCq measures of bulk samples, showing improved precision over simple averaging.

This paper evaluates sex bias in housekeeping gene expression in adipose tissue using transcriptomics data and identifies sex-unbiased housekeeping genes suitable for use as internal controls.

The paper describes a cost-effective method for preparing cDNA synthesis and real-time PCR mastermixes that match commercial kits' efficiency, addressing financial barriers in low-resource settings.

This study evaluates miRNA reference genes in zebrafish across strains, developmental stages, and kidney disease models, identifying dre-miR-92b-3p as the most stable reference gene.

The paper evaluates the reliability of RT-qPCR for quantifying maternal transcripts in sea urchin egg cortices using normalization with reference genes.

Auto-qPCR automates qPCR data analysis, reducing errors and time by providing a web-based tool for DNA quantification and gene expression analysis.

The paper identifies an incorrect qPCR primer for zebrafish 18s rRNA and recommends corrected primer sets to avoid erroneous results in future studies.

The paper investigates how RNA integrity numbers (RINs) affect mRNA expression in control autopsy brain tissue, finding pathway-specific and non-linear degradation patterns.