Article
Biochemical Research Methods
Nancy Y. A. Sey, Brandon M. Pratt, Hyejung Won
Summary: An important goal in modern genomics is to predict the functional consequences of noncoding variants associated with complex traits. To achieve this, researchers developed H-MAGMA, a tool that combines 3D chromatin information with gene-based analysis to identify key biological pathways related to brain disorders. They provide a protocol for generating H-MAGMA variant-gene annotation file using chromatin interaction data from the adult human brain, and demonstrate its use in studying Parkinson's disease. Additionally, they generated variant-gene annotation files for 28 tissues and cell types, serving as a valuable resource for researchers studying various genetic disorders.
Article
Biochemistry & Molecular Biology
Shiqi Lin, Song Wu, Wei Zhao, Zhanjie Fang, Hongen Kang, Xinxuan Liu, Siyu Pan, Fudong Yu, Yiming Bao, Peilin Jia
Summary: TargetGene is a comprehensive database that reports target genes for human genetic variants using multiple analytical tools and multi-omics data. This resource helps researchers study the regulatory mechanisms of genetic variants in complex human traits.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Vita Setrajcic Dragos, Ksenija Strojnik, Gasper Klancar, Petra Skerl, Vida Stegel, Ana Blatnik, Marta Banjac, Mateja Krajc, Srdjan Novakovic
Summary: In this study, we performed functional characterization of pathogenic/likely pathogenic variants in susceptibility genes that disrupt RNA splicing using RNAseq analysis. We successfully reclassified 50% of the investigated variants, leading to improved clinical management of the patient and the family members.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Infectious Diseases
Sunanda Paul, Momi Saikia, Supriyo Chakraborty
Summary: MicroRNAs are small, evolutionarily conserved regulatory RNA molecules that play a role in regulating various cellular activities and pathways. Viral miRNAs are smaller, less conserved, and less stable compared to miRNAs from other organisms. This study focuses on predicting potential miRNAs, secondary structures, and targets of Rous sarcoma virus miRNA for better understanding its regulatory network in sarcoma formation.
INFECTION GENETICS AND EVOLUTION
(2021)
Article
Plant Sciences
Yingting Zhang, Junjie Yang, Lijuan Zhu, Jinyu Xue, Hailiang Hu, Jiebing Cui, Jin Xu
Summary: This study identified a possible role of miRNA-regulated pathways in needle color in Cryptomeria fortunei, a conifer tree species. A miRNA-target pigment biosynthesis regulatory network was constructed, with miRNA-MYBs confirmed as key regulators of needle discoloration. These findings offer new insight into posttranscriptional regulatory mechanisms in gymnosperms and may contribute to genetic improvement of evergreen C. fortunei needles mediated by miRNAs.
Article
Biochemistry & Molecular Biology
Syed Muhammad Muntazir Mehdi, Sivakumar Krishnamoorthy, Michal Wojciech Szczesniak, Agnieszka Ludwikow
Summary: The study identified differentially expressed miRNAs in response to ABA treatment in wild-type Arabidopsis and mutant plants. Potential target genes of these miRNAs were identified and validated using psRNATarget and RT-PCR. The target genes of the identified miRNAs were found to be involved in diverse cellular processes, including development and stomatal movement.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Editorial Material
Oncology
Bibek Bhatta, Tomer Cooks
Summary: Indeglia and colleagues utilized the reduced tumor suppression activity of hypomorphic TP53 gene variants to establish PADI4 as a target of p53. This study significantly advances our understanding of the downstream implications of TP53-PDI4, including potential predictions of survival and the effectiveness of immunotherapy.
Article
Medicine, General & Internal
Li-Jun Wang, Bai-Quan Qiu, Ming-Ming Yuan, Hua-Xi Zou, Cheng-Wu Gong, Huang Huang, Song-Qing Lai, Ji-Chun Liu
Summary: In this study, we identified differentially expressed miRNAs and mRNAs related to dilated cardiomyopathy (DCM) through bioinformatics analysis. We identified hub genes and candidate drugs associated with DCM, providing new insights for the study of the pathogenesis and clinical treatment of DCM.
INTERNATIONAL JOURNAL OF GENERAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Rui Gong, Jonathan Greenbaum, Xu Lin, Yan Du, Kuan-Jui Su, Yun Gong, Jie Shen, Hong-Wen Deng
Summary: Using a statistical fine-mapping approach, this study successfully identified potential causal variants with biological effects on obesity-related traits (BMI and WHR) and partially validated corresponding genes. These results provide novel insight into our understanding of the genetics of obesity and demonstrate that fine mapping can improve upon the results identified by the original GWASs.
MOLECULAR GENETICS AND GENOMICS
(2023)
Article
Food Science & Technology
Lihua Wang, Wenjun Wang, Qingjun Wang, Tiantian Tang, Wenrui Liu, Zhidong Wang, Jie Zhang
Summary: This study suggests that nitrogen treatment can inhibit the browning process of fresh-cut potato. By using high-throughput sequencing, four differentially expressed miRNAs associated with browning were identified. These miRNAs and their target genes are closely related to the quality of fresh-cut potato.
INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tiziana Filardi, Giuseppina Catanzaro, Giuseppina Emanuela Grieco, Elena Splendiani, Sofia Trocchianesi, Carmela Santangelo, Roberto Brunelli, Elisa Guarino, Guido Sebastiani, Francesco Dotta, Susanna Morano, Elisabetta Ferretti
Summary: This study found that miR-222-3p and miR-409-3p are differentially expressed in gestational diabetes mellitus (GDM) and are correlated with fasting plasma glucose, birth weight, and gestational age. The deregulated miRNAs may be associated with the pathophysiology of type 2 diabetes and GDM.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Zahra Roudbari, Morteza Mokhtari, Abdolvahab Ebrahimpour Gorji, Tomasz Sadkowski, Ayeh Sadat Sadr, Masoud Shirali
Summary: This study employs a network-driven systems approach and clustering algorithm to uncover deeper insights into the genetic associations of dairy milk production. Results reveal significant involvement of influential genes and miRNAs, closely associated with key pathways essential for governing milk production.
Review
Biochemistry & Molecular Biology
Magdalena Machowska, Paulina Galka-Marciniak, Piotr Kozlowski
Summary: MicroRNAs (miRNAs) are small non-coding RNAs that posttranscriptionally regulate gene expression. Genetic variations in miRNA genes may affect their functioning and the development of human diseases.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
Yao Dai, Yumeng Cao, Jens Kohler, Aiping Lu, Shaohua Xu, Haiyun Wang
Summary: This study identified OAZ1 and hsa-miR-6835-3p as the most reliable individual reference genes for mRNA and miRNA quantification in cancer exosomes. A combination of reference genes - OAZ1/SERF2/MPP1 for mRNA and hsa-miR-6835-3p/hsa-miR-4468-3p for miRNA analyses is recommended for superior accuracy.
Article
Immunology
Lu Han, Shiyun Chen, Zhe Luan, Mengjiao Fan, Yanrong Wang, Gang Sun, Guanghai Dai
Summary: Colon cancer is a complex disease involving interactions between cancer cells and the immune microenvironment. Recent studies have shown that microRNAs (miRNAs) play a critical role in gene regulation in colon cancer, particularly in modulating the immune microenvironment. Identifying miRNAs associated with colon cancer and their regulation of immune function-related genes could provide insights into prognosis and guide personalized treatment strategies.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Infectious Diseases
Kanika Kanchan, Pankaj Jha, Sudhanshu S. Pati, Sanjib Mohanty, Saroj K. Mishra, Surya K. Sharma, Shally Awasthi, Vimala Venkatesh, Saman Habib
INFECTION GENETICS AND EVOLUTION
(2015)
Article
Biochemistry & Molecular Biology
Pankaj Jha, Dongsheng Lu, Yuan Yuan, Shuhua Xu
MOLECULAR GENETICS AND GENOMICS
(2015)
Article
Biotechnology & Applied Microbiology
Robert C. Williams, Robert C. Elston, Pankaj Kumar, William C. Knowler, Hanna E. Abboud, Sharon Adler, Donald W. Bowden, Jasmin Divers, Barry I. Freedman, Robert P. Igo, Eli Ipp, Sudha K. Iyengar, Paul L. Kimmel, Michael J. Klag, Orly Kohn, Carl D. Langefeld, David J. Leehey, Robert G. Nelson, Susanne B. Nicholas, Madeleine V. Pahl, Rulan S. Parekh, Jerome I. Rotter, Jeffrey R. Schelling, John R. Sedor, Vallabh O. Shah, Michael W. Smith, Kent D. Taylor, Farook Thameem, Denyse Thornley-Brown, Cheryl A. Winkler, Xiuqing Guo, Phillip Zager, Robert L. Hanson
Article
Genetics & Heredity
Shalini Datta, Abhijit Chowdhury, Malay Ghosh, Kaushik Das, Pankaj Jha, Roshan Colah, Mitali Mukerji, Partha P. Majumder
ANNALS OF HUMAN GENETICS
(2012)
Article
Evolutionary Biology
Ankita Narang, Pankaj Jha, Dhirendra Kumar, Rintu Kutum, Anupam Kumar Mondal, Debasis Dash, Mitali Mukerji
GENOME BIOLOGY AND EVOLUTION
(2014)
Article
Genetics & Heredity
Pramod Gautam, Pankaj Jha, Dhirendra Kumar, Shivani Tyagi, Binuja Varma, Debasis Dash, Arijit Mukhopadhyay, Mitali Mukerji
Article
Immunology
Abhimanyu, Pankaj Jha, Ashima Jain, Komal Arora, Mridula Bose
Article
Infectious Diseases
Abhimanyu, Irengbam Rocky Mangangcha, Pankaj Jha, Komal Arora, Mitali Mukerji, Jayant Nagesh Banavaliker, Vani Brahmachari, Mridula Bose
INFECTION GENETICS AND EVOLUTION
(2011)
Article
Infectious Diseases
Pankaj Jha, Swapnil Sinha, Kanika Kanchan, Tabish Qidwai, Ankita Narang, Prashant Kumar Singh, Sudhanshu S. Pati, Sanjib Mohanty, Saroj K. Mishra, Surya K. Sharma, Shally Awasthi, Vimala Venkatesh, Sanjeev Jain, Analabha Basu, Shuhua Xu, Mitali Mukerji, Saman Habib
INFECTION GENETICS AND EVOLUTION
(2012)
Article
Oncology
Shipra Agarwal, Mehar Chand Sharma, Prerana Jha, Pankaj Pathak, Vaishali Suri, Chitra Sarkar, Kunzang Chosdol, Ashish Suri, Shashank Sharad Kale, Ashok Kumar Mahapatra, Pankaj Jha
Article
Multidisciplinary Sciences
Pankaj Jha, Dongsheng Lu, Shuhua Xu
Article
Endocrinology & Metabolism
Paolo Piaggi, Cigdem Koroglu, Anup K. Nair, Jeff Sutherland, Yunhua L. Muller, Pankaj Kumar, Wen-Chi Hsueh, Sayuko Kobes, Alan R. Shuldiner, Hye In Kim, Nehal Gosalia, Cristopher V. Van Hout, Marcus Jones, William C. Knowler, Jonathan Krakoff, Robert L. Hanson, Clifton Bogardus, Leslie J. Baier
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2020)
Article
Ophthalmology
Lalit Kaurani, Mansi Vishal, Dhirendra Kumar, Anchal Sharma, Bharati Mehani, Charu Sharma, Subhadip Chakraborty, Pankaj Jha, Jharna Ray, Abhijit Sen, Debasis Dash, Kunal Ray, Arijit Mukhopadhyay
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2014)
Article
Immunology
Abhimanyu, Mridula Bose, Pankaj Jha
INDIAN JOURNAL OF MEDICAL RESEARCH
(2012)