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A computational method for predicting regulation of human microRNAs on the influenza virus genome

Hao Zhang, Zhi Li, Yanpu Li, Yuanning Liu, Junxin Liu, Xin Li, Tingjie Shen, Yunna Duan, Minggang Hu, Dong Xu
2013 BMC Systems Biology  
Although many computational tools have been designed for miRNA target prediction, there is a need for cross-species prediction, especially for predicting viral targets of human miRNAs.  ...  While it has been suggested that host microRNAs (miRNAs) may downregulate viral gene expression as an antiviral defense mechanism, such a mechanism has not been explored in the influenza virus for human  ...  Acknowledgements "Human encoded miRNAs that regulate the influenza virus genome" A preliminary version of this paper was published in the proceedings of Proceedings of 2012 IEEE 6th International Conference  ... 
doi:10.1186/1752-0509-7-s2-s3 pmid:24565017 pmcid:PMC3851852 fatcat:n5w2grc5m5as3mixbg77eostay

sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression

2019 Nucleic Acids Research  
New microRNA reference databases were developed with different foci, either prioritizing accuracy (low number of false positives) or completeness (low number of false negatives).  ...  Finally, the number of microRNA sequencing studies deposited in GEO nearly triplicated from 2014 (280) to 2018 (764).  ...  ACKNOWLEDGEMENTS The authors acknowledge the usage of the computational infrastructure of the Computational Epigenomics Lab of the University of Granada.  ... 
doi:10.1093/nar/gkz415 pmid:31114926 pmcid:PMC6602500 fatcat:pzqld3qrmjfkxbe3tgfnmzcixy

Non-coding yet non-trivial: a review on the computational genomics of lincRNAs

Travers Ching, Jayson Masaki, Jason Weirather, Lana X. Garmire
2015 BioData Mining  
Long intergenic non-coding RNAs (lincRNAs) represent one of the most mysterious RNA species encoded by the human genome.  ...  Thanks to next generation sequencing (NGS) technology and its applications, we have recently witnessed a surge in non-coding RNA research, including lincRNA research.  ...  They hypothesized that many lncRNAs are simply unprocessed pre-cursors to small non-coding RNAs, such as microRNA, shRNA and siRNA [33] .  ... 
doi:10.1186/s13040-015-0075-z pmid:26697116 pmcid:PMC4687140 fatcat:6adlfaqsuzblri4w66mqrdl6rq

LeukmiR: a database for miRNAs and their targets in acute lymphoblastic leukemia

2019 Database: The Journal of Biological Databases and Curation  
For the user query, different search modules exist where either quick search can be carried out using any fuzzy term or by providing exact terms in specific modules.  ...  Recent studies suggest the involvement of multiple microRNAs in the tumorigenesis of various leukemias.  ...  Conflict of interest. Authors declare no competing interest.  ... 
doi:10.1093/database/baz151 pmid:32128558 pmcid:PMC7054207 fatcat:5w4kaqym5jcgvfjx5ewvyy3ifa

plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants

Deblina Patra, Mario Fasold, David Langenberger, Gerhard Steger, Ivo Grosse, Peter F. Stadler
2014 Frontiers in Plant Science  
The easy-to-use platform of plantDARIO quantifies RNA expression of annotated sncRNAs from different sncRNA databases together with new sncRNAs, annotated by our group.  ...  The moderate size of small RNA-seq datasets makes it feasible to provide free web services to the research community that provide many basic features of a small RNA-seq analysis, including quality control  ...  For miRNAs, plant miRNA pre-cursors were downloaded from miRBase and mapped against the genome using blast, employing a minimum alignment length of 60 nt and a sequence similarity of 80% as filter criteria  ... 
doi:10.3389/fpls.2014.00708 pmid:25566282 pmcid:PMC4274896 fatcat:s5fbyi7dcbatjme3hpeneohja4

The Emerging Role of Long Non-Coding RNAs and MicroRNAs in Neurodegenerative Diseases: A Perspective of Machine Learning

Ángela García-Fonseca, Cynthia Martin-Jimenez, George E. Barreto, Andres Felipe Aristizábal Pachón, Janneth González
2021 Biomolecules  
Therefore, we deepen in this branch of computer science, its different methods, and its meaningful application in the diagnosis of NDs from the dysregulated non-coding RNAs.  ...  In addition, we demonstrate the relevance of machine learning in NDs from the description of different investigations that showed an accuracy between 85% to 95% in the detection of the disease with this  ...  Conflicts of Interest: The authors declare no conflict of interest, financial or otherwise.  ... 
doi:10.3390/biom11081132 pmid:34439798 pmcid:PMC8391852 fatcat:h6d5sinfgfg23o5xrbngijjmpq

Computational analysis of regulatory mechanism and interactions of microRNAs

Takaya Saito, Pål Sætrom
2011 Zenodo  
This discovery led to identification of many classes of functional ncRNAs. MicroRNA (miRNA) is a class of such ncRNAs with ∼22 nucleotides that are quite abundant and found in most eukaryotic cells.  ...  RNAi is a regulatory process that uses small non-coding RNAs (ncRNAs) to suppress gene expression at the post-transcriptional level.  ...  RNAs PPV Positive predictive value; TP / (TP + FP) in a binary classification model PRC Precision; equivalent to PPV or Pos- itive predictive value pre-miRNA precursor miRNA; miRNA pre- cursor  ... 
doi:10.5281/zenodo.4902326 fatcat:2z2um4cglfaydanvwtvzu3ufn4

Circular RNA participates in the carcinogenesis and the malignant behavior of cancer

Zhen-Jun Zhao, Jun Shen
2015 RNA Biology  
Circular RNAs (circRNAs) are long, non-coding RNAs that result from the non-canonical splicing of linear pre-mRNAs.  ...  In this review, we illustrate the specific role of circRNAs in a wide variety of cancers and in regulating the biological behavior of cancers via miR-7 or miR-138 regulation.  ...  Considering the titanic number of microRNA and circRNA species, we are confident in finding other circRNAs that functions to regulate corresponding microRNA and participate in different aspect of cancer  ... 
doi:10.1080/15476286.2015.1122162 pmid:26649774 pmcid:PMC5449088 fatcat:rvy4pjp73nbs5edi26ypifoezm

Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries

Shuai Zeng, Zhen Lyu, Siva Ratna Kumari Narisetti, Dong Xu, Trupti Joshi
2019 BMC Genomics  
Using KBCommons' intuitive web interface, users can easily retrieve genomic data, multi-omics data and analysis results from workflow according to their requirements and interests.  ...  It provides a comprehensive framework for new plant-specific, animal-specific, virus-specific, bacteria-specific or human disease-specific knowledge base (KB) creation, for adding new genome versions and  ...  We also like to acknowledge new member on the team Yen On Chan for his involvement with the project.  ... 
doi:10.1186/s12864-019-6287-8 pmid:31856718 pmcid:PMC6923931 fatcat:ocilb6lk5rfmflcgnclljgl5py

IMIA LaMB WG related event: Proceedings of 3rd International Conference on Biomedical Ontology, 2012, Graz

Ronald Cornet, Robert Stevens, Melanie Courtot, Trish Whetzel, Janna Hastings, Stefan Schulz, Ludger Jansen
2019 Zenodo  
This conference carried on the tradition of discussing medical ontologies, increasingly used in biology and medicine, and their use in annotation of both clinical and experimental data is now a common  ...  It brings together representatives of all major communities involved in the development and application of ontologies in biomedical research ...  ...  ACKNOWLEDGEMENTS We acknowledge and appreciate funding from the US Food and Drug Administration's Center for Veterinary Medicine (FDA CVM) and the US Department of Agriculture -Animal and Plant Health  ... 
doi:10.5281/zenodo.3381830 fatcat:pnndilxgzzbujnoqz7pytggtdi

MicroRNAs in inflammatory lung disease - master regulators or target practice?

Irene K Oglesby, Noel G McElvaney, Catherine M Greene
2010 Respiratory Research  
MicroRNAs (miRNAs) have emerged as a class of regulatory RNAs with immense significance in numerous biological processes.  ...  Evaluation of the global expression of miRNAs provides a unique opportunity to identify important target gene sets regulating susceptibility and response to infection and treatment, and control of inflammation  ...  Acknowledgements Funding for work in this laboratory is gratefully acknowledged from Science Foundation Ireland, the Health Research Board of Ireland and Medical Research Charities Group, U.S.  ... 
doi:10.1186/1465-9921-11-148 pmid:21029443 pmcid:PMC2984500 fatcat:guzjjp2sofaptj6at444jkhbke

Insulin/IGF signaling in Drosophila and other insects: factors that regulate production, release and post-release action of the insulin-like peptides

Dick R. Nässel, Jozef Vanden Broeck
2015 Cellular and Molecular Life Sciences (CMLS)  
Thus, a set of median [32].  ...  different insect species.  ... 
doi:10.1007/s00018-015-2063-3 pmid:26472340 fatcat:izvbeuhw3fcbfhnj5bzs7ekg4q

Tecnologias, Técnicas e Tendências em Engenharia Biomédica [article]

Adriano de Oliveira Andrade, Alcimar Barbosa Soares, Alexandre Cardoso, Edgard Afonso Lamounier
2022 Zenodo  
Os editores agradecem a todos os revisores que doaram tempo e experiência, e também às agências de fomento (CAPES, CNPq, FAPEMIG) que financiaram a publicação da obra. Editores  ...  Devido à grande abrangência da EB muitas vezes pode ser difícil delimitar suas fronteiras.  ...  Dawn Walker from Computer Science Department, University of Sheffield, for the permission to publish figure 8 .  ... 
doi:10.5281/zenodo.6472648 fatcat:dmya6w645feg7oe54l5swdveuy

Full Issue PDF

2018 JACC: Basic to Translational Science  
All authors attest they are in compliance with human studies committees and animal welfare regulations of the authors' institutions and Food and Drug Administration guidelines, including patient consent  ...  All other data were nonparametric and not matched; thus, a Wilcoxon rank sum test was used to determine differences between groups with a significance level set a priori at p < 0.05.  ...  ; or 2) as a new IND submission that is separate and distinct from any existing IND, and is intended only for the purpose of making a drug available for treatment use (15).  ... 
doi:10.1016/s2452-302x(18)30124-4 pmid:32289098 pmcid:PMC7119135 fatcat:zv34cy4nxje45muwa3w7qt22va

Pancreatic cancer chemo-resistance is driven by tumor phenotype rather than tumor genotype

Mirna Swayden, Juan Iovanna, Philippe Soubeyran
2018 Heliyon  
Hence, the pre-existing or rapidly acquired resistance of pancreatic cancer cells to therapeutic drugs rely on other parameters and features developed by the cells and/or the micro-environment, that are  ...  Like any transformation process, initiation and development of PDCA are driven by a well known panel of genetic alterations, few of them are shared with most cancers, but many mutations are specific to  ...  These pre- cursor lesions are classified in to low-grade or high-grade [8].  ... 
doi:10.1016/j.heliyon.2018.e01055 pmid:30582059 pmcid:PMC6299038 fatcat:fw6ordzbj5aunhr7n45eqmq3km
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