Article
Multidisciplinary Sciences
Krishan Gupta, Guangyu Wang, Shuo Zhang, Xinlei Gao, Rongbin Zheng, Yanchun Zhang, Qingshu Meng, Lili Zhang, Qi Cao, Kaifu Chen
Summary: Recent studies have found stripes as architectural features of three-dimensional chromatin and their connection to epigenetic regulation of transcription. While there are tools available to define stripes in a single sample, there is no reported method to quantitatively measure the dynamic change of each stripe between samples. In this study, a bioinformatics tool called StripeDiff was developed to detect differential stripes between samples. StripeDiff showed optimal performance in both simulation data analysis and real Hi-C data analysis. Applying StripeDiff to Hi-C data revealed new insights into the connection between change of chromatin stripe and change of chromatin modification, transcriptional regulation, and cell differentiation.
Article
Multidisciplinary Sciences
Dongmei Li, Martin S. Zand, Timothy D. Dye, Maciej L. Goniewicz, Irfan Rahman, Zidian Xie
Summary: RNA-seq is a widely used high-throughput sequencing technology for gene transcript discovery and quantification. This study compared the performance of eight popular RNA-seq differential analysis methods across different scenarios. The results showed that EBSeq performed better for small sample sizes with negative binomial distribution, while DESeq2 slightly outperformed other methods for larger sample sizes. Both DESeq and DESeq2 methods performed well for RNA-seq count data with log-normal distribution.
Article
Chemistry, Physical
Aimin Chen, Tianshou Zhou, Pamela Burrage, Tianhai Tian, Kevin Burrage
Summary: Stochastic differential equations (SDE) are a powerful tool for modeling biological regulatory processes, but numerical simulations of SDE models can be problematic when the noise terms are negative and large. To address this issue, the composite Patankar-Euler methods are proposed to obtain positive simulations of SDE models.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemical Research Methods
Jiajun Yang, Dongyang Wang, Yanbo Yang, Wenqian Yang, Weiwei Jin, Xiaohui Niu, Jing Gong
Summary: This study comprehensively evaluated the impact of eight commonly used normalization methods on eQTL identification using RNA-seq and genotype data from different cancer samples. Our results showed that different methods could cause 20-30% differences in the final results, with TMM identified as the optimal normalization method.
The combination of methods was found to not only identify more cis-eQTLs, but also improve the performance of the ROC curve, suggesting the potential benefits of considering pairwise combinations of normalization methods in eQTL analysis.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Hunyong Cho, Yixiang Qu, Chuwen Liu, Boyang Tang, Ruiqi Lyu, Bridget M. Lin, Jeffrey Roach, M. Andrea Azcarate-Peril, Apoena Aguiar Ribeiro, Michael Love, Kimon Divaris, Di Wu
Summary: Understanding the function of the human microbiome is important, but statistical methods for metatranscriptomics are still in their early stages. A comprehensive evaluation of 10 differential analysis methods was conducted to address this gap. The logistic-beta (LB) test showed the highest sensitivity and controlled type I error well, while the MAST test had inflated type I error. The LB and log-normal (LN) tests successfully identified genes associated with childhood dental disease in a study.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Lis Arend, Judith Bernett, Quirin Manz, Melissa Klug, Olga Lazareva, Jan Baumbach, Dario Bongiovanni, Markus List
Summary: Cytometry techniques are widely used for discovering cellular characteristics at single-cell resolution. This study systematically evaluated existing and novel approaches for differential expression analysis on real and simulated CyTOF data. A new method, CyEMD, was proposed to handle strong zero-inflation without being too sensitive. Additionally, a user-friendly R Shiny App tool called CYANUS was developed for cytometry data analysis.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Xue Bai, Tao Chen, Yuan Wu, Mingyong Tang, Zeng-Fu Xu
Summary: This study identified a series of reference genes in tiger nut that can serve as internal controls for gene expression studies, providing convenience for qRT-PCR analysis. Among the various tissues, UCE2, UBL5, and Rubisco showed more stable expression patterns, with TUB4 and UCE2 identified as optimal reference genes for tuber development stages.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Lionel Chiron, Matthias Le Bec, Celine Cordier, Sylvain Pouzet, Dimitrije Milunov, Alvaro Banderas, Jean-Marc Di Meglio, Benoit Sorre, Pascal Hersen
Summary: This paper introduces a method for advanced automated timelapse experiments using CyberSco.Py software. The software allows real-time image analysis and automatic adjustment of imaging acquisition parameters and device status based on the analysis. The authors demonstrate the significance of this method in cell biology through experiments related to yeast fermentation.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Takayuki Osabe, Kentaro Shimizu, Koji Kadota
Summary: The study demonstrated that a model-based clustering algorithm, MBCdeg, can be used for DE analysis. MBCdeg outperformed other methods when P-DEG was less than 50%, but showed less consistency in DEG identification. Using DEGES normalization with MBCdeg provided greater stability compared to the default normalization algorithm.
BMC BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Yiwei Meng, Yanhong Huang, Xiao Chang, Xiaoping Liu, Luonan Chen
Summary: Identifying differential genes can provide insights into biological processes and disease progression. The klDD method presented in this study quantifies changes in higher-order statistical information of genes and can effectively detect subtle differences in gene expression distributions. It has potential applications in cancer subtyping, single-cell clustering, and disease early-warning detection.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Yancong Zhang, Kelsey N. Thompson, Curtis Huttenhower, Eric A. Franzosa
Summary: Researcher designed and evaluated statistical models in metatranscriptomics that incorporate different combinations of DNA and RNA normalization, finding that models adjusting transcripts relative to their encoding gene copies are significantly more accurate in identifying differential expression. Additionally, normalization of MTX measurements within species and adjusting for total species RNA balance can improve sensitivity, specificity, and interpretability of DE detection.
Article
Biochemistry & Molecular Biology
Kathannan Sankar, Hyung Joo Yoon, Young Bo Lee, Kyeong Yong Lee
Summary: Bumble bees are important alternative pollinators and model insects. This study identified stable reference genes for the bumble bee species and their different lines and tissues using RT-qPCR procedures and four analysis programs. The results emphasized the need to evaluate the stability of candidate reference genes for any differently designed lines and tissue conditions in bumble bee species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Lulu Yan, Xiaoqiang Sun
Summary: This research comprehensively evaluates 14 deconvolution methods and proposes a new ensemble learning-based method, EnDecon, for more accurate deconvolution. The results show that cell2location, RCTD, and spatialDWLS are more accurate than other methods. Additionally, the study finds differences in the robustness of different methods to sequencing depth, spot size, and normalization choices, and most methods perform best when using the normalization method described in their original papers. This study provides valuable information and guidelines for the practical application of ST deconvolution tools and the development of new and more effective methods.
Article
Biochemistry & Molecular Biology
A. Stupnikov, C. E. McInerney, K. I. Savage, S. A. McIntosh, F. Emmert-Streib, R. Kennedy, M. Salto-Tellez, K. M. Prise, D. G. McArt
Summary: RNA-seq technology poses challenges in the analysis of differential gene expression, but five models have been found to demonstrate robustness to sequencing alterations. The study indicates that the robustness of these models is dataset-agnostic and reliable for drawing conclusions when sample sizes are sufficiently large.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Biochemical Research Methods
Mengyun Wu, Huangdi Yi, Shuangge Ma
Summary: This article presents selective review of vertical data integration methods for gene expression data, covering both marginal and joint analysis as well as supervised and unsupervised analysis, to provide a sketch of the vertical data integration paradigm and briefly discuss potential pitfalls and future directions.
BRIEFINGS IN BIOINFORMATICS
(2021)