A5025474727- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Algorithms and Data Compression
- RNA Research and Splicing
- MicroRNA in disease regulation
- VLSI and FPGA Design Techniques
- Cancer-related molecular mechanisms research
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- VLSI and Analog Circuit Testing
- Epigenetics and DNA Methylation
- RNA Interference and Gene Delivery
- Machine Learning in Bioinformatics
- Low-power high-performance VLSI design
- Gene Regulatory Network Analysis
- Integrated Circuits and Semiconductor Failure Analysis
- CRISPR and Genetic Engineering
- Computational Drug Discovery Methods
- Cancer-related gene regulation
- Mass Spectrometry Techniques and Applications
- Single-cell and spatial transcriptomics
- Genetic Syndromes and Imprinting
- Genetics and Neurodevelopmental Disorders
National Yang Ming Chiao Tung University
2016-2025
National Tsing Hua University
2006-2025
China Medical University
2022
National Sun Yat-sen University
2022
China Medical University Hospital
2022
Chung Yuan Christian University
2010-2021
ORCID
2020
Institute of Bioinformatics and Systems Biology
2016-2018
National Yunlin University of Science and Technology
2016-2017
Institute of Bioinformatics
2016
In Drosophila, microRNAs (miRNAs) typically guide Argonaute1 to repress messenger RNA (mRNA), whereas small interfering RNAs (siRNAs) Argonaute2 destroy viral and transposon RNA. Unlike siRNAs, miRNAs rarely form extensive numbers of base pairs the mRNAs they regulate. We find that complementarity between a target an Argonaute1-bound miRNA triggers tailing 3'-to-5' trimming. flies, Argonaute2-bound RNAs--but not those bound Argonaute1--bear 2'-O-methyl group at their 3' ends. This...
The Encyclopedia of DNA Elements (ENCODE) consortium aims to identify all functional elements in the human genome including transcripts, transcriptional regulatory regions, along with their chromatin states and methylation patterns. ENCODE project generates data utilizing a variety techniques that can enrich for such as immunoprecipitation (ChIP), micrococcal nuclease (MNase) digestion DNase I digestion, followed by deeply sequencing resulting DNA. As part project, we have developed...
Since the initial annotation of miRNAs from cloned short RNAs by Ambros, Tuschl, and Bartel groups in 2001, more than a hundred studies have sought to identify additional various species. We report here meta-analysis RNA data Drosophila melanogaster , aggregating published libraries with 76 sets that we generated for modENCODE project. In total, began 1 billion raw reads 187 comprising diverse developmental stages, specific tissue- cell-types, mutant conditions, and/or Argonaute...
Despite its wide usage in biological databases and applications, the role of gene ontology (GO) network analysis is usually limited to functional annotation genes or sets with auxiliary information on correlations ignored. Here, we report new capabilities VisANT—an integrative software platform for visualization, mining, modeling networks—which extend application GO inference. The VisANT functions can be classified into three categories. (i) Visualization: a tree-based browser allows...
Recombinant adeno-associated viruses (rAAVs) that can cross the blood-brain-barrier and achieve efficient stable transvascular gene transfer to central nervous system (CNS) hold significant promise for treating CNS disorders. However, following intravascular delivery, these vectors also target liver, heart, skeletal muscle, other tissues, which may cause untoward effects. To circumvent this, we used tissue-specific, endogenous microRNAs (miRNAs) repress rAAV expression outside CNS, by...
Abstract Background MicroRNAs (miRNAs) play a critical role in down-regulating gene expression. By coupling with Argonaute family proteins, miRNAs bind to target sites on mRNAs and employ translational repression. A large amount of miRNA-target interactions (MTIs) have been identified by the crosslinking immunoprecipitation (CLIP) photoactivatable-ribonucleoside-enhanced CLIP (PAR-CLIP) along next-generation sequencing (NGS). PAR-CLIP shows high efficiency RNA co-immunoprecipitation, but it...
This protocol illustrates the steps of searching a sequence database with BLAST, which in essence performs pairwise alignment between query and each target database. Steps for performing multiple alignments ClustalW are then described. Argonaute 2 (Ago2) is an essential component small interfering RNA (siRNA)-directed interference (RNAi) fruit flies. uses Ago2 to demonstrate how search all paralogs fly proteome using BLAST obtain these sequences ClustalW.
Uridylation of RNA species represents an emerging theme in post-transcriptional gene regulation. In the microRNA pathway, such modifications regulate small biogenesis and stability plants, worms, mammals. Here, we report Tailor, uridylyltransferase that is required for majority 3′ end microRNAs Drosophila predominantly targets precursor hairpins. modulates characteristic two-nucleotide overhang hairpins, which regulates processing by Dicer-1 destabilizes Tailor preferentially uridylates...
Abstract We report the performance of ZDOCK and ZRANK algorithms in CAPRI rounds 13–19 introduce a novel measure atom contact frequency (ACF). To compute ACF, we identify residues that most often make with binding partner complete set predictions for each target. used ACF to predict interface proteins, which, combination biological data available literature, is valuable addition our docking pipeline. Furthermore, incorporated straightforward efficient clustering algorithm two purposes: (1)...
Abstract One of the important challenges to post-genomic biology is relating observed phenotypic alterations underlying collective in genes. Current inferential methods, however, invariably omit large bodies information on relationships between We present a method that takes account such - expressed terms topology correlation network and we apply context current procedures for gene set enrichment analysis.
In modern paired-end sequencing protocols short DNA fragments lead to adapter-appended reads. Current adapter removal approaches trim by scanning the fragment of on 3' end reads, which are not competent in some applications. Here, we propose a fast and highly accurate adapter-trimming algorithm, PEAT, designed specifically for sequencing. PEAT requires no priori adaptor sequence, is convenient large-scale meta-analyses. We assessed performance with many trimmers both simulated real life...
In embryonic stem cells (ESCs), the Tip60 histone acetyltransferase activates genes required for proliferation and silences that promote differentiation. Here we show class II deacetylase Hdac6 co-purifies with Tip60-p400 complex from ESCs. is necessary regulation of most target genes, particularly those repressed by complex. Unlike differentiated cells, where mainly cytoplasmic, largely nuclear in ESCs, neural (NSCs), some cancer cell lines, interacts each. localizes to promoters bound...
The cost and time to develop a drug continues be major barrier widespread distribution of medication. Although the genomic revolution appears have had little impact on this problem, might even exacerbated it because flood additional usually ineffective leads, emergence high throughput resources promises possibility rapid, reliable systematic identification approved drugs for originally unintended uses. In paper we apply method identifying such repositioned candidates against breast cancer,...
The mammalian imprinted Dlk1-Dio3 locus produces multiple long non-coding RNAs (lncRNAs) from the maternally inherited allele, including Meg3 (i.e., Gtl2) in genome. Although this has well-characterized functions stem cell and tumor contexts, its role during neural development is unknown. By profiling types at each stage of embryonic cell-derived motor neurons (ESC~MNs) that recapitulate spinal cord development, we uncovered lncRNAs expressed are predominantly gradually enriched rostral...
Gene expression profiling refers to the simultaneous measurement of levels a large number genes (often all in genome), typically multiple experiments spanning variety cell types, treatments, or environmental conditions. Expression is accomplished by assaying mRNA with microarrays next-generation sequencing technologies (RNA-seq). This introduction describes normalization and analysis data generated from microarray RNA-seq experiments.
In flies, 22-23-nucleotide (nt) microRNA duplexes typically contain mismatches and begin with uridine, so they bind Argonaute1 (Ago1), whereas 21-nt siRNA are perfectly paired cytidine, promoting their loading into Ago2. A subset of Drosophila endogenous siRNAs-the hairpin-derived hp-esiRNAs-are born as mismatched that often uridine. These would be predicted to load Ago1, yet accumulate at steady-state bound vitro, such hp-esiRNA assemble Ago1. vivo, encounter complementary target mRNAs...
Spinal muscular atrophy (SMA) is a neurodegenerative disease characterized by the selective loss of spinal motor neurons (MNs) and concomitant muscle weakness. Mutation SMN1 known to cause SMA, restoring SMN protein levels via antisense oligonucleotide treatment effective for ameliorating symptoms. However, this approach hindered exorbitant costs, invasive procedures, poor responses some patients. Here, we seek circumvent these hurdles identifying reliable biomarkers that could predict...
This paper presents the first end-to-end next-generation sequencing (NGS) data analysis accelerator for short-read mapping, haplotype calling, variant and genotyping. It supports both single-end paired-end short-reads (or reads) uses FM-index, a compact index structure, exact-match in mapping. For inexact match part of dynamic programming array is proposed to determine mapping results. To reduce workload rapid similarity calculation designed. A rescue technique also adopted increase overall...