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| http://dx.doi.org/10.1186/s12863-021-00990-3 | DOI Listing |
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Highly effective batch effect correction method for RNA-seq count data.
Comput Struct Biotechnol J
December 2024
Department of Computer Science and Information Science, California State University San Marcos, 333 S. Twin Oaks Valley Rd, San Marcos, CA 92096, USA.
RNA sequencing (RNA-seq) has become a cornerstone of transcriptomics, providing detailed insights into gene expression across diverse biological conditions and sample types. However, RNA-seq data are often confounded by batch effects, systematic non-biological variations that compromise data reliability and obscure true biological differences. To address these challenges, we introduce ComBat-ref, a refined batch effect correction method designed to enhance the statistical power and reliability of differential expression analysis in RNA-seq data.
View Article and Find Full Text PDFmicroRNA as an Important Mediator in the Regulation of Male Reproduction: Current State of the Problem.
Int J Mol Sci
December 2024
Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, Saint-Petersburg 196625, Russia.
During all periods of male ontogenesis, physiological processes responsible for the correct functioning of reproductive organs and spermatogenesis are under the influence of various factors (neuro-humoral, genetic, and paratypical). Recently, the attention of researchers has increasingly turned to the study of epigenetic factors. In scientific publications, one can increasingly find references to the direct role of microRNAs, small non-coding RNAs involved in post-transcriptional regulation of gene expression, in the processes of development and functioning of reproductive organs.
View Article and Find Full Text PDFBiomiX, a user-friendly bioinformatic tool for democratized analysis and integration of multiomics data.
BMC Bioinformatics
January 2025
LBAI, UMR1227, Univ Brest, Inserm, Laboratory of Immunology, CHU Brest, Brest, France.
Background: Interpreting biological system changes requires interpreting vast amounts of multi-omics data. While user-friendly tools exist for single-omics analysis, integrating multiple omics still requires bioinformatics expertise, limiting accessibility for the broader scientific community.
Results: BiomiX tackles the bottleneck in high-throughput omics data analysis, enabling efficient and integrated analysis of multiomics data obtained from two cohorts.
Transcriptome-wide association study identifies genes associated with bladder cancer risk.
Sci Rep
January 2025
Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
Genome-wide association studies (GWAS) have detected several susceptibility variants for urinary bladder cancer, but how gene regulation affects disease development remains unclear. To extend GWAS findings, we conducted a transcriptome-wide association study (TWAS) using PrediXcan to predict gene expression levels in whole blood using genome-wide genotype data for 6180 bladder cancer cases and 5699 controls included in the database of Genotypes and Phenotypes (dbGaP). Logistic regression was used to estimate adjusted gene-level odds ratios (OR) per 1-standard deviation higher expression with 95% confidence intervals (CI) for bladder cancer risk.
View Article and Find Full Text PDFUnveiling the molecular mechanisms of recurrent miscarriage through endoplasmic reticulum stress related gene expression.
Sci Rep
January 2025
Department of TCM, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, 100026, China.
Recurrent miscarriage (RM) is a reproductive disorder affecting couples worldwide. The underlying molecular mechanisms remain elusive, even though emerging evidence has implicated endoplasmic reticulum stress (ERS). We investigated RM- and ERS-related genes to develop a diagnostic model that can enhance predictive ability.
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