19 papers · ranked by Valyu relevance
Dominik Robak, Guillem Ylla
In recent years, Piwi-interacting RNAs (piRNAs) have been found to be involved in different biological roles beyond their initially identified role of protecting the germline genome. However, there is a lack of robust computational tools that facilitate their accurate annotation, analysis, and visualization, which…
Pooneh Mokarram, Maryam Niknam, Mohammadamin Sadeghdoust, Farnaz Aligolighasemabadi + 4 more
'Farnaz Aligolighasemabadi' 'Morvarid Siri' 'Sanaz Dastghaib' 'Hassan Brim' 'Hassan Ashktorab'] Title: ABSTRACT As a currently identified small non-coding RNAs (ncRNAs) category, the PIWI-interacting RNAs (piRNAs) are crucial mediators of cell biology. The human genome comprises over 30.000 piRNA genes. Although…
Kai Zheng, Zhu-Hong You, Lei Wang, Leon Wong + 2 more
PIWI proteins and Piwi-Interacting RNAs (piRNAs) are commonly detected in human cancers, especially in germline and somatic tissues, and correlates with poorer clinical outcomes, suggesting that they play a functional role in cancer. As the problem of combinatorial explosions between ncRNA and disease exposes out…
Kai Zheng, Zhu-Hong You, Lei Wang, Leon Wong + 1 more
Emerging evidence suggests that PIWI-interacting RNAs (piRNAs) are one of the most influential small non-coding RNAs (ncRNAs) that regulate RNA silencing. piRNA and PIWI proteins have been confirmed for disease diagnosis and treatment as novel biomarkers due to its abnormal expression in various cancers. However, the…
Alisson Hayasi da Costa, Renato Augusto C. dos Santos, Ricardo Cerri
PIWI-Interacting RNAs (piRNAs) form an important class of non-coding RNAs that play a key role in the genome integrity through the silencing of transposable elements. However, despite their importance and the large application of deep learning in computational biology for classification tasks, there are few studies of…
Songqian Huang, Kazutoshi Yoshitake, Shuichi Asakawa, Fabio Martelli
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs (sncRNAs) that perform crucial biological functions in metazoans and defend against transposable elements (TEs) in germ lines. Recently, ubiquitously expressed piRNAs were discovered in soma and germ lines using small RNA sequencing (sRNA-seq) in…
Ye Cheng, Qian Wang, Wei Jiang, Yonghua Bian + 5 more
'Anxing Gou' 'Wenling Zhang' 'Kai Fu' 'Weihong Shi'] PiRNAs are a small class of non-coding small RNAs newly discovered in recent years. Millions of piRNAs have been discovered to date, and more than 20,000 piRNA genes have been found in the human genome. Due to the relatively small number of studies related to piRNA…
Ismael Riquelme, Pablo Pérez-Moreno, Pablo Letelier, Priscilla Brebi + 2 more
'Juan Carlos Roa' 'Lyndsay Rhodes'] Simple Summary Gastrointestinal (GI) cancers are high mortality malignancies due to late diagnosis, the presence of metastasis and drug resistance development. Novel and more reliable biomarkers and therapeutic targets are still needed for these diseases. PIWI-interacting RNAs…
Jie Yao, Mei Xie, Xidong Ma, Jialin Song + 2 more
PIWI-interacting RNAs (piRNAs) are a less-studied class of small non-coding RNAs approximately 24-31 nucleotides in length. They express in germline and somatic cells and form complexes with PIWI proteins to exert regulatory effects. New studies show that piRNAs are aberrantly expressed in various cancers. In this…
Jingcheng Zhang, Wentao Zhang, Yuchao Liu, Man Pi + 10 more
'Ailiyaer Ainiwaer' 'Shiyu Mao' 'Haotian Chen' 'Yuefei Ran' 'Shuwen Sun' 'Wei Li' 'Xudong Yao' 'Zhengyan Chang' 'Yang Yan'] The piRNA (PIWI-interacting RNA) is P-Element induced wimpy testis (PIWI)-interacting RNA which is a small molecule, non-coding RNA with a length of 24-32nt. It was originally found in germ cells…
Ali Ebrahimpour-Boroojeny, Sanjay Rajopadhye, Hamidreza Chitsaz
A few elite classes of RNA-RNA interaction (RRI), with complex roles in cellular functions such as miRNA-target and lncRNAs in human health, have already been studied. Accordingly, RRI bioinformatics tools tailored for those elite classes have been proposed in the last decade. Interestingly, there are somewhat…
Daniel A Chaves, Hui Dai, Lichao Li, James J Moresco + 5 more
Eukaryotic cells regulate 5’ triphosphorylated (ppp-) RNAs to promote cellular functions and prevent recognition by antiviral RNA sensors. For example, RNA capping enzymes possess triphosphatase domains that remove the γ phosphates of ppp-RNAs during RNA capping. Members of the closely related PIR1 family of RNA…
Janet Sasso, Barbara Ambrose, Rumiana Tenchov, Ruchira Datta + 3 more
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA…
Tianye Yang, Peng Guo, Wenyu Liu, Xuefeng Liu + 1 more
—Device-free localization (DFL) based on pyroelectric infrared (PIR) sensors has attracted much attention due to its advantages of low cost, low power consumption, and privacy protection. However, most existing PIR-based DFL methods require high deployment density to achieve high localization accuracy. Recently, a few…
Seunghyun Park, Seonwoo Min, Hyun-Soo Choi, Sungroh Yoon
Since microRNAs (miRNAs) play a crucial role in post-transcriptional gene regulation, miRNA identification is one of the most essential problems in computational biology. miRNAs are usually short in length ranging between 20 and 23 base pairs. It is thus often difficult to distinguish miRNA-encoding sequences from…
Danyu Li, Rubing Huang, Chenhui Cui, Dave Towey + 3 more
Comprehensive Survey Authors: ['Danyu Li' 'Rubing Huang' 'Chenhui Cui' 'Dave Towey' 'Ling Zhou' 'Jinyu Tian' 'Bin Zou'] The interaction between Ribonucleic Acids (RNAs) and proteins, also called RNA Protein Interaction (RPI), plays an important role in the life activities of organisms, including in various regulatory…
Hirotake Udono, Minzhi Fan, Yoko Saito, Hirohisa Ohno + 4 more
Programmable droplets, artificial liquid-like condensates of nucleic acids, are intelligent out-of-equilibrium systems that allow the critical aspects of their biological counterparts to be harnessed programmably, such as molecular sensing and phase-state change. While DNA has been central to the previous efforts, less…
Muhammad Nabeel Asima, Muhammad Imran Malik, Andreas Dengela, Sheraz Ahmed
'Sheraz Ahmed'] Functional or non-coding RNAs are attracting more attention as they are now potentially considered valuable resources in the development of new drugs intended to cure several human diseases. The identification of drugs targeting the regulatory circuits of functional RNAs depends on knowing its family, a…
Nilay Chheda, Manish K. Gupta
—RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a single class or type. Many different types of techniques exist to classify RNA…