Article
Biochemistry & Molecular Biology
Sofiane Bendifallah, Yohann Dabi, Stephane Suisse, Ludmila Jornea, Delphine Bouteiller, Cyril Touboul, Anne Puchar, Emile Darai
Summary: A bioinformatics approach for saliva miRNA sequencing and analysis was developed and tested for diagnostic accuracy of endometriosis. Analysis of 200 saliva samples revealed differential expression of multiple miRNAs in patients with endometriosis, demonstrating potential for establishing a saliva signature for the condition.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medicine, General & Internal
Sofiane Bendifallah, Yohann Dabi, Stephane Suisse, Lea Delbos, Mathieu Poilblanc, Philippe Descamps, Francois Golfier, Ludmila Jornea, Delphine Bouteiller, Cyril Touboul, Anne Puchar, Emile Darai
Summary: The aim of this study was to use bioinformatics and Next Generation Sequencing (NGS) to analyze the miRNome in 200 plasma samples from patients with and without endometriosis. The results showed that out of 2633 miRNAs, 8.6% were found to be differentially expressed. A specific panel of miRNAs suitable for building a blood signature of endometriosis was detected using a combined bioinformatic and NGS approach.
Review
Biochemistry & Molecular Biology
Emanuela Chiarella, Annamaria Aloisio, Stefania Scicchitano, Heather Mandy Bond, Maria Mesuraca
Summary: Powerful bioinformatics tools have revealed the importance of miRNA-transcription factor networks in gene regulation, with ZNF521 identified as a key player in various cancers, making it a potential diagnostic and prognostic biomarker for cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Horticulture
Yuhan Zhou, Yushan Qiao, Zhiyou Ni, Jianke Du, Jinsong Xiong, Zongming Cheng, Fei Chen
Summary: In this study, a Genome Database for Strawberry (GDS) was developed to facilitate the reuse and exploration of strawberry genomic data and enable extensive analyses using various bioinformatics tools. The database integrates data from eight strawberry species and provides user-friendly tools for researchers in the field.
Article
Oncology
Zirong Huo, Xiaoguang Li, Jieyu Zhou, Yuqin Fan, Zhentao Wang, Zhihua Zhang
Summary: DNA methylation and miRNA-target genes are important in tumor development, and PLAU was found to be overexpressed in HNSCC, serving as an independent diagnostic and prognostic biomarker. The study also suggested that hypomethylation and downregulation of miR-23b-3p may contribute to the oncogenic role of PLAU in HNSCC.
CANCER CELL INTERNATIONAL
(2021)
Article
Biochemistry & Molecular Biology
Meile Mo, Bihu Liu, Yihuan Luo, Jennifer Hui Juan Tan, Xi Zeng, Xiaoyun Zeng, Dongping Huang, Changhua Li, Shun Liu, Xiaoqiang Qiu
Summary: This study identified three pivotal HCC-related circRNAs and provided novel insights into the underlying mechanisms of the circRNA-miRNA-mRNA regulatory network in HCC.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Medicine, General & Internal
Mengzhen Fan, Wenjie Song, Zheng Hao, Jing Zhang, Yang Li, Jinjie Fu
Summary: This study used bioinformatics to reveal the lncRNA-miRNA-mRNA regulatory network in bronchial epithelial cells (BECs) in severe asthma (SA), providing insights into the molecular mechanisms of SA. Four core differentially expressed genes (DEGs) were identified: CEACAM5, IL1R2, TFF3, and VEGFA. Enrichment analysis showed that the MAPK, Rap1, Ras, PI3K-Akt, and Calcium signaling pathways may play important roles in BECs in SA. A lncRNA-miRNA-mRNA regulatory network of severe asthmatic BECs was constructed.
Article
Medicine, Research & Experimental
Xiaomin Wei, Yiming Su, Qiyi Li, Zhiyong Zheng, Peiyong Hou
Summary: This study identified similarities in gene expression between VC and osteoblasts, with 43 shared genes. Functionally, CVSMCs were mainly enriched in cell cycle, extracellular matrix (ECM), inflammation, and chemotaxis-mediated signaling pathways. The protein-protein interaction network included 281 genes and 3650 edges, with 30 hub genes.
EXPERIMENTAL AND THERAPEUTIC MEDICINE
(2021)
Article
Veterinary Sciences
Olga Prasolova, Ekaterina Krylova, Alexandra Bogomazova, Irina Soltynskaya, Oleg Sklyarov, Veronika Gordeeva, Irina Timofeeva, Anton Motorygin, Alexander Panin
Summary: In Russia, immunization of cattle has been conducted using vaccines from Brucella abortus strains 82, 19, and 75/79 over the past decade. For the prevention of brucellosis in small ruminants, vaccines from Brucella melitensis strain REV-1 and B. abortus strain 19 have been employed, with greater use of the former. However, post-vaccination seropositivity has been observed to persist for an extended period, particularly in animals vaccinated with B. abortus strain 19 and B. melitensis strain REV-1. This study aimed to perform whole genome sequencing of Brucella vaccine strains from Russia and analyze their phylogenetic relationships and potential virulence determinants.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Review
Psychiatry
Anastasia Levchenko, Maria Plotnikova
Summary: This review summarizes recent discoveries of modified epigenetic control associated with genetic variants in bipolar disorder. It highlights the potential biological roles of specific genes in the pathogenesis of bipolar disorder and emphasizes the need for more research to understand the underlying molecular mechanisms and improve prognosis and treatment options. The findings confirm the complex nature of bipolar disorder and suggest directions for future research towards personalized approaches.
FRONTIERS IN PSYCHIATRY
(2023)
Article
Biochemistry & Molecular Biology
Daniel Perez-Cremades, Ana B. Paes, Xavier Vidal-Gomez, Ana Mompeon, Carlos Hermenegildo, Susana Novella
Summary: This study identified a comprehensive regulatory network controlling transcriptomic changes in endothelial cells exposed to estradiol, highlighting the important role of estrogen in regulating endothelial function. The analysis revealed interactions between miRNAs and transcription factors, as well as downstream target genes, involved in key signaling pathways such as hypoxia signaling and cell adhesion.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
George Lambrou, Myrto Poulou, Krinio Giannikou, Marios Themistocleous, Apostolos Zaravinos, Maria Braoudaki
Summary: Epigenetic mechanisms, particularly miRNA expression and DNA methylation, play a significant role in childhood central nervous system tumors. The study identified frequent methylation of genes like CASP8 and RASSF1 in tumor samples, which correlated with tumor staging and type. Simultaneous methylation of multiple genes' promoters showed significant results, indicating the importance of epigenetic regulation in tumor progression and pathophysiology.
Article
Biochemical Research Methods
Michael Roth, Pranjal Jain, Jinkyu Koo, Somali Chaterji
Summary: The study developed an effective method, named Theia, for predicting miRNA-gene interactions and regulatory comodules simultaneously. Applying this method to RNA sequencing data from breast invasive carcinoma samples demonstrated its effectiveness in discovering biologically significant regulatory comodules enriched in spatial miRNA clusters, biological pathways, and various cancers.
BMC BIOINFORMATICS
(2021)
Article
Biotechnology & Applied Microbiology
Xiaotong Peng, Yanqun Mo, Junliang Liu, Huining Liu, Shuo Wang
Summary: This study found that miRNAs play a crucial role in the development of uterine fibroids and identified the functions of candidate DEGs and DEMs in UF. By constructing PPI networks and miRNA-mRNA networks, key DEGs and DEMs were identified and clinically validated. These findings contribute to a better understanding of the pathogenesis of UF and provide novel targets for the diagnosis and treatment of UF.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Immunology
Ayorinde O. Afolayan, Johan Fabian Bernal, June M. Gayeta, Melissa L. Masim, Varun Shamanna, Monica Abrudan, Khalil Abudahab, Silvia Argimon, Celia C. Carlos, Sonia Sia, Kadahalli L. Ravikumar, Iruka N. Okeke, Pilar Donado-Godoy, David M. Aanensen, Anthony Underwood
Summary: Whole genome sequencing for antimicrobial resistance surveillance not only determines increasing resistance rates, but also reveals evolutionary mechanisms and transmission routes. Implementing WGS involves a series of processes and operations combining informatics and bioinformatics. Overcoming barriers to WGS implementation can lead to the discovery of novel resistance mechanisms and high-risk clones.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Ashwani Jha, Ganesh Panzade, Rajesh Pandey, Ravi Shankar
NUCLEIC ACIDS RESEARCH
(2015)
Article
Biotechnology & Applied Microbiology
Ashwani Jha, Ravi Shankar
Article
Biotechnology & Applied Microbiology
Anita Kumari, Heikham Russiachand Singh, Ashwani Jha, Mohit Kumar Swarnkar, Ravi Shankar, Sanjay Kumar
Article
Biology
Ashwani Jha, Mrigaya Mehra, Ravi Shankar
JOURNAL OF BIOSCIENCES
(2011)
Article
Multidisciplinary Sciences
Ashwani Jha, Rohit Chauhan, Mrigaya Mehra, Heikham Russiachand Singh, Ravi Shankar
Article
Multidisciplinary Sciences
Ashwani Jha, Ravi Shankar
Article
Multidisciplinary Sciences
Asosii Paul, Ashwani Jha, Shruti Bhardwaj, Sewa Singh, Ravi Shankar, Sanjay Kumar
SCIENTIFIC REPORTS
(2014)
