Article
Plant Sciences
Haiying Geng, Meng Wang, Jiazhen Gong, Yupu Xu, Shisong Ma
Summary: The study presents a computational approach named EXPLICIT to predict gene expression in Arabidopsis using transcription factors, demonstrating better accuracy in predicting transcriptomes compared to existing tools and offering new insights into transcriptional regulation in diverse plant pathways.
Article
Medicine, Research & Experimental
Kai Zhang, Xianyu Qin, Pengju Wen, Yueheng Wu, Jian Zhuang
Summary: This study identified 18 relatively independent and closely linked modules in the gene co-expression network associated with heart failure (HF). Pivot analysis revealed the involvement of four transcription factors and five noncoding RNAs in regulating HF. The upregulated hub genes ASPN, FMOD, NT5E, LUM, and OGN showed relatively high areas under the curve (AUC) in gene set variation analysis (GSVA) for HF. These results provide new insights into potential regulatory mechanisms in HF and may help in identifying effective therapeutic targets.
Article
Biochemical Research Methods
Sachin Bhatt, Prithvi Singh, Archana Sharma, Arpita Rai, Ravins Dohare, Shweta Sankhwar, Akash Sharma, Mansoor Ali Syed
Summary: This study investigates the molecular mechanism of HCC progression and identifies key genes, miRNAs, and transcription factors associated with HCC development.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Kazumasa Kanemaru, James Cranley, Daniele Muraro, Antonio M. A. Miranda, Siew Yen Ho, Anna Wilbrey-Clark, Jan Patrick Pett, Krzysztof Polanski, Laura Richardson, Monika Litvinukova, Natsuhiko Kumasaka, Yue Qin, Zuzanna Jablonska, Claudia I. Semprich, Lukas Mach, Monika Dabrowska, Nathan Richoz, Liam Bolt, Lira Mamanova, Rakeshlal Kapuge, Sam N. Barnett, Shani Perera, Carlos Talavera-Lopez, Ilaria Mulas, Krishnaa T. Mahbubani, Liz Tuck, Lu Wang, Margaret M. Huang, Martin Prete, Sophie Pritchard, John Dark, Kourosh Saeb-Parsy, Minal Patel, Menna R. Clatworthy, Norbert Hubner, Rasheda A. Chowdhury, Michela Noseda, Sarah A. Teichmann
Summary: In this study, single-cell and spatial transcriptomics data were used to explore cellular niches in eight regions of the human heart. Specific ion channels, G-protein-coupled receptors, and regulatory networks were identified in different cell types, highlighting the importance of FOXP2 in pacemaker cells. The sinoatrial node was found to be compartmentalized, with glial cells and fibroblasts supporting glutamatergic signaling. The study also introduced a drug target prediction tool, drug2cell, and revealed the presence of immune niches in the epicardium.
Review
Cardiac & Cardiovascular Systems
Abhishek Joshi, Marieke Rienks, Konstantinos Theofilatos, Manuel Mayr
Summary: Omics techniques generate large, multidimensional data that can be analyzed using informatics approaches and traditional statistical methods. Systems biology, utilizing network analysis and machine learning, addresses the complexity of biological processes. Novel approaches combining gene regulatory networks, proteomics, metabolomics, lipidomics, and phenomics with informatics techniques provide new insights into cardiovascular disease.
NATURE REVIEWS CARDIOLOGY
(2021)
Article
Immunology
Sreemol Gokuladhas, William Schierding, Evgeniia Golovina, Tayaza Fadason, Justin O'Sullivan
Summary: Integrating various data resources, the study identified genes regulated by both pleiotropic and non-pleiotropic SNPs, revealing complex interactions between shared and disease-specific genes, which co-occur within the same biological pathways.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemical Research Methods
Davide Chicco, Luca Oneto
Summary: Machine learning analysis of gene expression data from myocardial infarction patients revealed genes strongly associated with heart failure. Using a Random Forests classifier and feature elimination, accurate prediction of heart failure and identification of important genes were achieved.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Biotechnology & Applied Microbiology
Xiaojun Liu, Chengying Hong, Yichun Jiang, Wei Li, Youlian Chen, Yonghui Ma, Pengfei Zhao, Tiyuan Li, Huaisheng Chen, Xueyan Liu, Lixin Cheng
Summary: Sepsis is a life-threatening condition with high mortality rates, but little research has been done on its system biology aspect. This study conducted a comprehensive exploration of genome-wide expression alterations in sepsis and identified consistent modules across datasets, including potential regulators of sepsis. The study reveals the co-expression patterns of mRNAs and lncRNAs in sepsis and provides insight into the sepsis transcriptome, which may aid in the identification of therapeutic targets and biomarkers.
Article
Cardiac & Cardiovascular Systems
Weikang Bian, Zhicheng Wang, Xiaobo Li, Xiao-Xin Jiang, Hongsong Zhang, Zhizhong Liu, Dai-Min Zhang
Summary: In this study, weighted gene coexpression network analysis (WGCNA) was used to identify the key module and hub genes for heart failure (HF). Differential gene expression analysis, coexpression network construction, functional enrichment analysis, and protein-protein interaction network construction were conducted to identify potential hub genes. The results may provide potential biomarkers for the diagnosis of HF and enhance our understanding of the molecular mechanisms underlying HF.
Article
Cardiac & Cardiovascular Systems
Jiahui Fan, Huaping Li, Rong Xie, Xudong Zhang, Xiang Nie, Xiaolu Shi, Jiabing Zhan, Zhongwei Yin, Yanru Zhao, Beibei Dai, Shuai Yuan, Zheng Wen, Chen Chen, Dao Wen Wang
Summary: This study aimed to elucidate the role of lncRNA in dilated cardiomyopathy (DCM) and heart failure, with a focus on the ZNF593-AS molecule. Through a series of experiments and observations, the research demonstrated the critical function of ZNF593-AS in improving cardiac function in DCM, potentially offering a new avenue for therapeutic interventions in the future.
CIRCULATION RESEARCH
(2021)
Article
Biology
Tong Zhang, Yixuan Lin, Weimin He, FengXin Yuan, Yu Zeng, Shihua Zhang
Summary: Coronary heart disease is a common heart disease associated with lifestyle and dietary habits. Although some genes related to coronary heart disease have been identified, there are still many potential genes that have not been discovered. Therefore, it is urgent to use computational methods to identify these genes and conduct biological experiments for validation. This paper proposes a deep learning method based on biological networks, which is more accurate than other methods and is a reliable approach for predicting coronary heart disease-related genes.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Neurosciences
Kai Huang, Xinying Zhang, Jiahao Duan, Ruting Wang, Zifeng Wu, Chun Yang, Ling Yang
Summary: This study used bioinformatics network analysis to identify diagnostic biomarkers and therapeutic targets for heart failure comorbid with depression. Five hub genes, including STAT4 and COL1A2, were found to be involved in the comorbidity mechanisms of these two disorders. Shared pathways related to platelet activation, chemokine signaling, and focal adhesion were also identified. These findings provide new insights for understanding the pathogenesis and treatment of heart failure and depression.
BRAIN RESEARCH BULLETIN
(2022)
Article
Genetics & Heredity
Wangxiao Xia, Hui Jiang, Huifang Guo, Yaowen Liu, Xingchun Gou
Summary: In this study, we systematically analyzed the gene co-expression network of the moon jellyfish (Aurelia aurita) during its life cycle, and identified 35 relevant modules and hub genes for each stage. These hub genes are believed to play important roles in the developmental processes of the jellyfish, enhancing our understanding of its life cycle.
Article
Biochemistry & Molecular Biology
Alba Vilella-Figuerola, Alex Gallinat, Rafael Escate, Sonia Mirabet, Teresa Padro, Lina Badimon
Summary: This study analyzed the miRNA patterns in patients with chronic heart failure (HF) and identified pathways involved in the pathophysiology of HF. Several miRNAs were found to be up-regulated in HF patients and their combinations could discriminate between different types of HF. The study also proposed novel cellular mechanisms involved in the pathogenesis of chronic HF.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Xiuli Shao, Xiaolin Zhang, Lei Yang, Ruijia Zhang, Rongli Zhu, Rui Feng
Summary: Cardiac remodelling is a common characteristic of heart diseases, especially heart failure. MicroRNA and mRNA are potential diagnostic markers and therapeutic targets for heart failure. MicroRNA-mRNA interaction network analysis identified miR-542-3p-CILP as a potential new mechanism in ischaemic cardiomyopathy-induced heart failure.
Article
Chemistry, Organic
Yang Zhang, Zheng Zhang, Dong Wang, Jianzhen Xu, Yanhui Li, Hong Wang, Jin Li, Shaowen Mo, Yuncong Zhang, Yunqing Lin, Xiuzhao Fan, Enmin Li, Jian Huang, Huihui Fan, Ying Yi
LETTERS IN ORGANIC CHEMISTRY
(2019)
Article
Oncology
Lin Pang, Jing Hu, Feng Li, Huating Yuan, Min Yan, Gaoming Liao, Liwen Xu, Bo Pang, Yanyan Ping, Yun Xiao, Xia Li
Article
Biotechnology & Applied Microbiology
Yanyan Ping, Chaohan Xu, Liwen Xu, Gaoming Liao, Yao Zhou, Chunyu Deng, Yujia Lan, Fulong Yu, Jian Shi, Li Wang, Yun Xiao, Xia Li
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2020)
Article
Medicine, Research & Experimental
Jason R. Brown, Daniel K. Chan, Jessica J. Shank, Kent A. Griffith, Huihui Fan, Robert Szulawski, Kun Yang, R. Kevin Reynolds, Carolyn Johnston, Karen McLean, Shitanshu Uppal, J. Rebecca Liu, Lourdes Cabrera, Sarah E. Taylor, Brian C. Orr, Francesmary Modugno, Pooja Mehta, Michael Bregenzer, Geeta Mehta, Hui Shen, Lan G. Coffman, Ronald J. Buckanovich
Article
Oncology
Gaoming Liao, Xin Liang, Yanyan Ping, Yong Zhang, Jianlong Liao, Yihan Wang, Xiaobo Hou, Zedong Jiang, Xiaoqiu Dong, Chaohan Xu, Yun Xiao
Article
Medicine, Research & Experimental
Yanyan Ping, Yao Zhou, Jing Hu, Lin Pang, Chaohan Xu, Yun Xiao
MOLECULAR THERAPY-NUCLEIC ACIDS
(2020)
Article
Cell Biology
Huihui Fan, Huda Atiya, Yeh Wang, Thomas R. Pisanic, Tza-Huei Wang, Ie-Ming Shih, Kelly K. Foy, Leonard Frisbie, Ronald J. Buckanovich, Alison A. Chomiak, Rochelle L. Tiedemann, Scott B. Rothbart, Chelsea Chandler, Hui Shen, Lan G. Coffman
Article
Genetics & Heredity
Bo Pang, Fei Quan, Yanyan Ping, Jing Hu, Yujia Lan, Lin Pang
Summary: This study identified key lncRNAs involved in the development and progression of GBM through single-cell RNA-seq data analysis, revealing significant correlations with GBM invasion and poor survival of patients. The findings provide new insights into the molecular mechanisms underlying GBM invasion and potential therapeutic targets.
FRONTIERS IN GENETICS
(2021)
Article
Oncology
Hongzhong Li, Yi Xiao, Qin Li, Jun Yao, Xiangliang Yuan, Yuan Zhang, Xuedong Yin, Yohei Saito, Huihui Fan, Ping Li, Wen-Ling Kuo, Angela Halpin, Don L. Gibbons, Hideo Yagita, Zhongming Zhao, Da Pang, Guosheng Ren, Cassian Yee, J. Jack Lee, Dihua Yu
Summary: Antihistamines can improve survival in cancer patients by reversing T cell dysfunction through modulation of histamine receptor H1 (HRH1), thereby enhancing immunotherapy responses.
Article
Genetics & Heredity
Brittany L. Jewell, An Xu, Dandan Zhu, Mo-Fan A. Huang, Linchao Lu, Mo Liu, Erica Underwood, Jun Hyoung Park, Huihui Fan, Julian Gingold, Ruoji Zhou, Jian Tu, Zijun Huo, Ying K. Liu, Weidong A. Jin, Yi-Hung Chen, Yitian Xu, Shu-Hsia K. Chen, Nino Rainusso, Nathaniel Berg, Danielle Bazer, Christopher L. Vellano, Philip Jones, Holger Eltzschig, Zhongming Zhao, Benny Abraham Kaipparettu, Ruiying Zhao, Lisa Wang, Dung-Fang Lee
Summary: Rothmund-Thomson syndrome (RTS) is a genetic disorder with various clinical manifestations, including osteosarcoma. Researchers established a Type 2 RTS disease model and found that inhibiting mitochondrial respiratory complex I could be a potential therapeutic target for RTS-associated osteosarcoma.
Article
Oncology
Huihui Fan, Peilin Jia, Zhongming Zhao
Summary: Fibrosis plays a significant role in the tumor microenvironment and is closely linked to a range of human diseases, such as liver diseases and cancer. Single-cell level measurement of early fibrotic changes can aid in identifying new mechanisms and potential drug targets.
Article
Biology
Ashley K. Wiseman, Rochelle L. Tiedemann, Huihui Fan, Hui Shen, Zachary Madaj, Michael T. McCabe, Melissa B. Pappalardi, Peter A. Jones
Summary: The DNA methylation status of the X-chromosome in cancer cells is often overlooked, but it plays an important role in the epigenetic silencing of cancer-related genes.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jiajinlong Kang, Yulin Dai, Jinze Li, Huihui Fan, Zhongming Zhao
Summary: This article reports the first single-cell level analysis of eccDNA in glioblastoma (GBM) samples. The study revealed the presence of potential mobile enhancers acting in a trans-regulation manner in GBM. This research provides insights into the novel features of eccDNA in the cellular context of brain tumors, highlighting the importance of investigating eccDNA at the single-cell level.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Medicine, Research & Experimental
Huihui Fan, Jinze Li, Astrid M. Manuel, Zhongming Zhao
Summary: Prostate cancer is heterogeneous at both morphological and molecular levels, presenting challenges in early diagnosis and treatment. This study integrated single-cell sequencing to decode the epigenetic plasticity in prostate cancer cell lines upon enzalutamide treatment. Seven signature gene sets were identified, showing consistent trends of chromatin regulation and gene expression during early response and drug resistance. The findings provide potential biomarkers for predicting prognosis and suggest combinatory drug strategies to enhance treatment response or overcome resistance.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Meeting Abstract
Obstetrics & Gynecology
Jacqueline G. Parchem, Huihui Fan, Lovepreet K. Mann, Wencai Ma, Jing Wang, Qiuying Chen, Steven S. Gross, Zhongming Zhao, Ramesha Papanna, Raghu Kalluri
REPRODUCTIVE SCIENCES
(2022)
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.