Article
Multidisciplinary Sciences
Jennie Louise, Andrea R. Deussen, Jodie M. Dodd
Summary: This study systematically compared various methods for processing and analyzing DNA methylation data. The results showed that different choices in data processing led to different results, and some choices may generate false significant findings. The study suggests a need for more focus on replication and greater use of sensitivity analyses.
Article
Oncology
H. Welsh, C. M. P. F. Batalha, W. Li, K. L. Mpye, N. C. Souza-Pinto, M. S. Naslavsky, E. J. Parra
Summary: This study evaluated the performance of different normalization methods on the Infinium EPIC array and found that the SeSAMe 2 method was the best performing method, while quantile-based methods were the worst performing. Normalizing the data with SeSAMe 2 improved the reproducibility of CpG sites, suggesting that the reliability of the data is primarily due to limited biological variation rather than technical measurement variation.
CLINICAL EPIGENETICS
(2023)
Article
Biochemical Research Methods
Zihan Cui, Yuhang Liu, Jinfeng Zhang, Xing Qiu
Summary: Super-delta2 is a differential gene expression analysis pipeline for RNA-seq data, which achieves tight control of type I error through trimming and bias-correction in the normalization step. In comparisons, super-delta2 not only demonstrates excellent statistical power, but also is the only method that effectively controls type I error at the nominal level. When applied to breast cancer data, super-delta2 selects more biologically relevant pathways than other methods.
Article
Biotechnology & Applied Microbiology
Hasindu Gamaarachchi, Hiruna Samarakoon, Sasha P. Jenner, James M. Ferguson, Timothy G. Amos, Jillian M. Hammond, Hassaan Saadat, Martin A. Smith, Sri Parameswaran, Ira W. Deveson
Summary: SLOW5 is an alternative file format designed for efficient parallelization and acceleration of nanopore data analysis, significantly reducing runtime and file size in DNA methylation profiling of a human genome.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Hongxu Ding, Ioannis Anastopoulos, Andrew D. Bailey, Joshua Stuart, Benedict Paten
Summary: This study introduces a deep learning framework that can predict the characteristic ionic currents of nucleotides to enable novel detection of nucleotide modifications, particularly methylated cytosine and guanine, without the need for controls.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Anders Berglund, Ryan M. Putney, Imene Hamaidi, Sungjune Kim
Summary: Bioinformatics tools help identify the evasion of the immune system by cancer, with abnormal genomic chemical modifications playing a crucial role. Immunotherapy is a powerful weapon against cancer, but tumors often evade it by subduing the immune response through epigenetic dysregulation. Tools and resources are available to help decipher the cancer epigenome and potentially lead to better therapies.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2021)
Article
Genetics & Heredity
Chunmei Zhu, Shuyuan Zhang, Di Liu, Qingqing Wang, Ningning Yang, Zhewen Zheng, Qiuji Wu, Yunfeng Zhou
Summary: This study identified the DNA methylation landscape in breast cancer and established promising methylation and methylation-based gene prognostic signatures, which could serve as potential prognostic biomarkers and therapeutic targets for breast cancer.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Bo Yan, Duan Wang, Romualdas Vaisvila, Zhiyi Sun, Laurence Ettwiller
Summary: Covalent modifications of genomic DNA are essential for the survival of organisms. Methyl-SNP-seq is a novel technology that can extract methylation and original sequence information using the complementarity of the double helix. It allows detection of the methylation status of any DNA, even without a reference genome.
Article
Biochemical Research Methods
Sapir Margalit, Yotam Abramson, Hila Sharim, Zohar Manber, Surajit Bhattacharya, Yi-Wen Chen, Eric Vilain, Hayk Barseghyan, Ran Elkon, Roded Sharan, Yuval Ebenstein
Summary: This study explored the methylation status of enhancer-promoter pairs using long-read optical methylome data, and developed various analysis approaches for deconvolving cell-type mixtures. Results showed that these pairs can be used for detecting rare cancerous transformations in a given cell population, with accurate estimates obtained through promoter methylation and enhancer-promoter pairwise methylation analysis. Additionally, the analysis can be applied to resolve different cell populations of the same cell type in subtle scenarios.
Article
Genetics & Heredity
Huei-Chung Huang, Yilin Wu, Qihang Yang, Li-Xuan Qin
Summary: This is a new R package for evaluating the performance of data normalization and sample classification methods. It provides two microRNA microarray datasets and corresponding tools for simulating and evaluating data normalization and classification methods under different sample-to-array assignments and signal-to-noise ratios. Additionally, it allows users to customize their own methods and implements various normalization and classification methods. This is the first available tool of its kind.
FRONTIERS IN GENETICS
(2022)
Article
Cell Biology
Xubin Zheng, Qiong Wu, Haonan Wu, Kwong-Sak Leung, Man-Hon Wong, Xueyan Liu, Lixin Cheng
Summary: This study introduced the most prevalent methods for processing bisulfite sequencing data and evaluated the consistency of the data acquired from different measurements in liver cancer. Differential methylated genes measured by various bisulfite sequencing assays and 450 k beadchip were consistently hypo-methylated in liver cancer with high functional similarity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Clinical Neurology
Coleman Breen, Ligia A. Papale, Lindsay R. Clark, Phillip E. Bergmann, Andy Madrid, Sanjay Asthana, Sterling C. Johnson, Sunduz Keles, Reid S. Alisch, Kirk J. Hogan
Summary: In this study, whole genome methylation sequencing (WGMS) was used to analyze blood samples and identified differentially methylated positions and genes between individuals with Alzheimer's disease (AD) and cognitively unimpaired individuals. These differentially methylated positions and genes are related to the mechanisms of AD.
ALZHEIMERS & DEMENTIA
(2023)
Article
Multidisciplinary Sciences
Taotao Li, Duo Du, Dandan Zhang, Yicheng Lin, Jiakang Ma, Mengyu Zhou, Weida Meng, Zelin Jin, Ziqiang Chen, Haozhe Yuan, Jue Wang, Shulong Dong, Shaoyang Sun, Wenjing Ye, Bosen Li, Houbao Liu, Zhao Zhang, Yuchen Jiao, Zhi Xie, Wenqing Qiu, Yun Liu
Summary: Constructing high-quality haplotype-resolved genome assemblies has improved the ability to detect genetic variants. The authors demonstrated a targeted approach using CRISPR-based enrichment to assemble MHC haplotypes, enabling population genetic studies and disease mechanism elucidation.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Jianxiong Tang, Jianxiao Zou, Mei Fan, Qi Tian, Jiyang Zhang, Shicai Fan
Summary: CaMelia, a CatBoost gradient boosting method, predicts missing methylation states based on locally paired intercellular methylation similarity. It significantly improves imputation performance on real single-cell methylation datasets, helping to discover intercellular differentially methylated loci masked by sparsity in raw data. The results demonstrate that CaMelia preserves cell-cell relationships, enhances cell type identification, and improves subpopulation detection.
Article
Biology
Luca Visentin, Giorgia Scarpellino, Giorgia Chinigo, Luca Munaron, Federico Alessandro Ruffinatti
Summary: BioTEA is a software tool for analyzing gene expression differences, which allows easy, quick, and reproducible analysis of gene expression data. It combines multiple functions, including gene filtering, batch effect handling, and sample pairing, to adapt to the structure of different datasets. Additionally, BioTEA has a detailed log file that provides accurate information about each step of the analysis.
Editorial Material
Clinical Neurology
Mingyue Wang, Lingjuan Li
ACTA NEUROLOGICA BELGICA
(2023)
Article
Chemistry, Physical
Anlian Zhu, Jingyi Wang, Mingyue Wang, Dongshuang Fan, Lingjun Li
Summary: A series of ionic liquids were synthesized and their synergetic effects on the Cu catalyzed one-pot A(3) coupling reactions were investigated for the synthesis of propargylamines. The combined catalytic system based on ionic liquid [MEA] [H2PO4 ] and CuI showed excellent catalytic activity and selectivity for propargylamine synthesis, achieving good to excellent yields for various aromatic and heteroaromatic aldehydes.
Article
Chemistry, Analytical
Lianming Zhang, Dan Li, Shuhuai Li, Jianping Li, Xionghui Ma, Mingyue Wang
Summary: A dual recognition strategy based on a protein and an ion-imprinted polymer (IIP) was proposed to develop highly sensitive sensors for copper(II) ions (Cu2+). The sensor showed high sensitivity due to the amplification effect of GO/Au NPs. The sensor exhibited a recovery rate of 93.2-105.6% for Cu2+ detection in actual samples.
MICROCHEMICAL JOURNAL
(2023)
Article
Computer Science, Information Systems
Ming-Yue Wang, Anjan Biswas, Yakup Yildirim, Luminita Moraru, Simona Moldovanu, Abdulah A. Alghamdi
Summary: This paper addresses the study of optical solitons in magneto-optic waveguides using Kudryashov's law of nonlinear refractive index in the presence of chromatic dispersion and Hamiltonian-type perturbation terms. The trial solution approach yielded a variety of soliton solutions, which are listed in this paper.
Article
Computer Science, Information Systems
Ming-Yue Wang, Anjan Biswas, Yakup Yildirim, Luminita Moraru, Simona Moldovanu, Hashim M. M. Alshehri
Summary: This paper uses the trial equation approach to address the newly proposed concatenation model. The concatenation model is a chain model that combines the nonlinear Schrodinger's equation, Lakshmanan-Porsezian-Daniel model, and Sasa-Satsuma equation. The recovered solutions are displayed in various forms such as dark solitons, singular solitons, cnoidal waves, and singular periodic waves. The trial equation approach allows for a wide range of solutions to be recovered. Numerical schemes provide a visual perspective to the analytically derived solutions.
Article
Telecommunications
Xiayun Hu, Mingyue Wang, Jiajia Yan, Jiajun Deng, Hai Dong
Summary: This paper proposes a wireless positioning algorithm called NRAP, which utilizes the nearest reliable anchors to address the issue of topology irregularities in multi-hop networks, leading to improved positioning performance.
WIRELESS PERSONAL COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Mingyue Wang, Qiulin Zhang, Meilin Zou, Jingge Wang, Danrui Zhu, Jiaying Liu, Junwei Wang, Yang Zuo, Jianjun Chen, Ping Ning
Summary: The development of superior low-temperature catalytic performance and inexpensive catalysts for the removal of volatile organic compounds (VOCs) is crucial for their industrial application. CuO/Ce0.6Zr0.4O2 catalysts calcinated at different temperatures (Cu/CZ-X) were prepared and used to eliminate toluene. Cu/CZ-550 showed the highest low-temperature catalytic activity, with the lowest temperature for 50% conversion of toluene, highest normalized reaction rate, and lowest apparent activation energy. The strong interaction between Cu and support in Cu/CZ-550 facilitated the adsorption and activation of toluene, resulting in its superior catalytic performance.
Article
Chemistry, Multidisciplinary
Meilin Zou, Mingyue Wang, Jingge Wang, Danrui Zhu, Jiaying Liu, Junwei Wang, Qingchao Xiao, Jianjun Chen
Summary: Regulating the metal-support interaction is crucial for efficient catalytic oxidation of VOCs. CuO/TiO2(imp) exhibited higher catalytic activity at lower temperatures compared to CuO-TiO2(coll). The optimized catalyst (CuO/TiO2(imp)) had abundant Cu2+ active species and small CuO particles, leading to enhanced concentration of reducible oxygen species and superior redox property.
Article
Computer Science, Information Systems
Weiwei Li, Zijing Zhang, Mingyue Wang, Hang Chen
Summary: A fabric defect detection method based on saliency region and similarity location is proposed in this paper to solve the problem of defect detection and accurate segmentation of periodic texture fabric images. The image to be detected is processed through color space conversion, Gaussian filtering, and contrast enhancement, and a frequency-tuned salient region detection algorithm is used to estimate a saliency map. The fabric image is divided into image blocks of the same size with overlapping areas, and the statistical parameters of each block are calculated. Outliers in the statistical parameters are filtered out using inter-quartile range (IQR). Through positioning and processing of image defects, abnormal elimination is carried out, and the defect outline is obtained. Experimental results show that the proposed method performs better in terms of qualitative characterization.
Review
Biochemical Research Methods
Jun Wang, Marc Horlacher, Lixin Cheng, Ole Winther
Summary: RNA localization is important for spatial translation regulation, and this review discusses its molecular mechanisms, experimental techniques, and machine learning-based prediction tools. The three main molecular mechanisms controlling RNA localization to distinct cellular compartments, including directed transport, mRNA degradation protection, and diffusion/local entrapment, are reviewed. Advances in experimental methods provide ample data resources for the design of powerful machine learning models in RNA localization prediction. The review also covers publicly available predictive tools, serving as a guide for users and encouraging the development of more effective prediction models. Lastly, an overview of multimodal learning is presented as a potential new avenue for RNA localization prediction.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Engineering, Environmental
Liuzhi Hao, Shuwen Huang, Tongling Huang, Dan Yi, Chenmin Wang, Lixin Cheng, Min Guan, Jun Wu, Di Chen, Haobo Pan, William W. Lu, Xiaoli Zhao
Summary: This study provides a feasible and effective strategy for modifying engineered exosomes to enhance bone regeneration.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Chemistry, Physical
Li Ning, Ming-Yue Wang, Jiao Yue, Su Yi
Summary: A submicron sheet-like silicon-based titanium dioxide photocatalyst was synthesized using titanium-containing furnace slag from Panzhihua, Sichuan as the raw material. Under UV and visible light irradiation, the photocatalyst showed stable performance and excellent crystallinity, demonstrating effective degradation of organic dyes.
REACTION KINETICS MECHANISMS AND CATALYSIS
(2023)
Article
Biochemical Research Methods
Lixin Cheng, Haonan Wu, Xubin Zheng, Ning Zhang, Pengfei Zhao, Ran Wang, Qiong Wu, Tao Liu, Xiaojun Yang, Qingshan Geng
Summary: This study developed an ensemble gene pair signature based on the IDH and 1p/19q status, which can serve as an independent predictor for risk stratification and survival prediction in glioma. The results showed that this ensemble signature had higher predictive accuracy compared to other prognostic signatures.
Article
Biochemical Research Methods
Qizhi Li, Xubin Zheng, Jize Xie, Ran Wang, Mengyao Li, Man-Hon Wong, Kwong-Sak Leung, Shuai Li, Qingshan Geng, Lixin Cheng
Summary: A diagnostic model based on host gene expression was used to diagnose acute infections. However, its clinical usage was limited due to small sample sizes. In this study, a large-scale dataset was constructed and analyzed using a sophisticated strategy to build gene pair signatures for bacterial, viral, and noninfected patients. These signatures were further combined into an antibiotic decision model with strong performance in distinguishing bacterial and viral infections.
Article
Environmental Studies
Mingyue Wang
Summary: This article constructs an evaluation index system for urban green transportation, proposes an evaluation model based on BP neural network, and tests it. The results show that the model has a high accuracy and suggests strategic measures for the development of urban ecological transportation.
INTERNATIONAL JOURNAL OF GLOBAL ENERGY ISSUES
(2023)
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.
