Browsing by Author "Liu, Yu-Chen"

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A Fast Route Towards Freestanding Single-Crystalline Oxide Thin Films by Using YBa(2)Cu(3)O(7-x)as a Sacrificial Layer
(2020-08-28)
Chang, Yao-Wen
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Wu, Ping-Chun
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Yi, Jhih-Bang
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Liu, Yu-Chen
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Chou, Yi
Researchers have long been seeking multifunctional materials that can be adopted for next-generation nanoelectronics, and which, hopefully, are compatible with current semiconductor processing for further integration. Along this vein, complex oxides have gained numerous attention due to their versatile functionalities. Despite the fact that unbounded potential of complex oxides has been examined over the past years, one of the major challenges lies in the direct integration of these functional oxides onto existing devices or targeted substrates that are inherently incompatible in terms of oxide growth. To fulfill this goal, freestanding processes have been proposed, in which wet etching of inserted sacrificial layers is regarded as one of the most efficient ways to obtain epitaxial high-quality thin films. In this study, we propose using an alternative oxide, YBa2Cu3O7(YCBO), as a sacrificial layer, which can be easily dissolved in light hydrochloric acid in a more efficient way, while protecting selected complex oxides intact. The high epitaxial quality of the selected complex oxide before and after freestanding process using YBCO as a sacrificial layer is comprehensively studied via a combination of atomic force microscopy, X-ray diffraction, transmission electron microscopy, and electrical transports. This approach enables direct integration of complex oxides with arbitrary substrates and devices and is expected to offer a faster route towards the development of low-dimensional quantum materials.
Biclustering of transcriptome sequencing data reveals human tissue-specific circular RNAs
(2018-01-19)
Liu, Yu-Chen
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Chiu, Yu-Jung
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Li, Jian-Rong
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Sun, Chuan-Hu
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Liu, Chun-Chi
Background: Emerging evidence has been experimentally confirmed the tissue-specific expression of circRNAs (circRNAs). Global identification of human tissue-specific circRNAs is crucial for the functionality study, which facilitates the discovery of circRNAs for potential diagnostic biomarkers. Results: In this study, circRNA back-splicing junctions were identified from 465 publicly available transcriptome sequencing samples. The number of reads aligned to these identified junctions was normalized with the read length and sequence depth for each sample. We generated 66 models representing enriched circRNAs among human tissue transcriptome through biclustering algorithm. The result provides thousands of newly identified human tissue-specific circRNAs. Conclusions: This result suggests that expression of circRNAs is not prompted by random splicing error but serving molecular functional roles. We also identified circRNAs enriched within circulating system, which, along with identified tissue-specific circRNAs, can serve as potential diagnostic biomarkers.
Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model
(2019-12-01)
Liu, Chengyu
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Liu, Yu-Chen
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Huang, Hsien-Da
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Wang, Wei
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生物資訊及系統生物研究所
Motivation: In recent years, multiple circular RNAs (circRNA) biogenesis mechanisms have been discovered. Although each reported mechanism has been experimentally verified in different circRNAs, no single biogenesis mechanism has been proposed that can universally explain the biogenesis of all tens of thousands of discovered circRNAs. Under the hypothesis that human circRNAs can be categorized according to different biogenesis mechanisms, we designed a contextual regression model trained to predict the formation of circular RNA from a random genomic locus on human genome, with potential biogenesis factors of circular RNA as the features of the training data. Results: After achieving high prediction accuracy, we found through the feature extraction technique that the examined human circRNAs can be categorized into seven subgroups, according to the presence of the following sequence features: RNA editing sites, simple repeat sequences, self-chains, RNA binding protein binding sites and CpG islands within the flanking regions of the circular RNA back-spliced junction sites. These results support all of the previously reported biogenesis mechanisms of circRNA and solidify the idea that multiple biogenesis mechanisms co-exist for different subset of human circRNAs. Furthermore, we uncover a potential new links between circRNA biogenesis and flanking CpG island. We have also identified RNA binding proteins putatively correlated with circRNA biogenesis.
CircNet: a database of circular RNAs derived from transcriptome sequencing data
(2016-01-04)
Liu, Yu-Chen
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Li, Jian-Rong
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Sun, Chuan-Hu
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Andrews, Erik
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Chao, Rou-Fang
Circular RNAs (circRNAs) represent a new type of regulatory noncoding RNA that only recently has been identified and cataloged. Emerging evidence indicates that circRNAs exert a new layer of post-transcriptional regulation of gene expression. In this study, we utilized transcriptome sequencing datasets to systematically identify the expression of circRNAs (including known and newly identified ones by our pipeline) in 464 RNA-seq samples, and then constructed the CircNet database (http://circnet.mbc.nctu.edu.tw/) that provides the following resources: (i) novel circRNAs, (ii) integrated miRNAtarget networks, (iii) expression profiles of circRNA isoforms, (iv) genomic annotations of circRNA isoforms (e. g. 282 948 exon positions), and (v) sequences of circRNA isoforms. The CircNet database is to our knowledge the first public database that provides tissue-specific circRNA expression profiles and circRNA-miRNA-gene regulatory networks. It not only extends themost up to date catalog of circRNAs but also provides a thorough expression analysis of both previously reported and novel circRNAs. Furthermore, it generates an integrated regulatory network that illustrates the regulation between circRNAs, miRNAs and genes.
Gene expression profiling of tumor-associated macrophages after exposure to single-dose irradiation
(2017-08-01)
Kung, Wei-Hsiang
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Yu, Ching-Fang
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Lee, Andy Chi-Lung
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Yang, Chi-Dung
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Liu, Yu-Chen
Radiotherapy (RT) is a common cancer treatment approach that accounts for nearly 50% of patient treatment; however, tumor relapse after radiotherapy is still a major issue. To study the crucial role of tumor-associated macrophages (TAMs) in the regulation of tumor progression post-RT, microarray experiments comparing TAM gene expression profiles between unirradiated and irradiated tumors were conducted to discover possible roles of TAMs in initiation or contribution to tumor recurrence following RT, taking into account the relationships among gene expression, tumor microenvironment, and immunology. A single dose of 25 Gy was given to TRAMP C-1 prostate tumors established in C57/B6 mice. CD11b-positive macrophages were extracted from the tumors at one, two and three weeks post-RT. Gene ontology (GO) term analysis using the DAVID database revealed that genes that were differentially expressed at one and two weeks after irradiation were associated with biological processes such as morphogenesis of a branching structure, tube development, and cell proliferation. Analysis using Short Time-Series Expression Miner (STEM) revealed the temporal gene expression profiles and identified 13 significant patterns in four main groups of profiles. The genes in the upregulated temporal profile have diverse functions involved in the intracellular signaling cascade, cell proliferation, and cytokinemediated signaling pathway. We show that tumor irradiation with a single 25-Gy dose can initiate a time series of differentially expressed genes in TAMs, which are associated with the immune response, DNA repair, cell cycle arrest, and apoptosis. Our study helps to improve our understanding of the function of the group of genes whose expression changes temporally in an irradiated tumor microenvironment. (C) 2017 Elsevier Ltd. All rights reserved.
Mechanical stretch induces hair regeneration through the alternative activation of macrophages
(2019-04-03)
Chu, Szu-Ying
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Chu, Chih-Hung
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Hsien-DaHuang
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Yen, Meng-Hua
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Hong, Hsiao-Chin
Tissues and cells in organism are continuously exposed to complex mechanical cues from the environment. Mechanical stimulations affect cell proliferation, differentiation, and migration, as well as determining tissue homeostasis and repair. By using a specially designed skinstretching device, we discover that hair stem cells proliferate in response to stretch and hair regeneration occurs only when applying proper strain for an appropriate duration. A counterbalance between WNT and BMP-2 and the subsequent two-step mechanism are identified through molecular and genetic analyses. Macrophages are first recruited by chemokines produced by stretch and polarized to M2 phenotype. Growth factors such as HGF and IGF-1, released by M2 macrophages, then activate stem cells and facilitate hair regeneration. A hierarchical control system is revealed, from mechanical and chemical signals to cell behaviors and tissue responses, elucidating avenues of regenerative medicine and disease control by demonstrating the potential to manipulate cellular processes through simple mechanical stimulation.
Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis
(2018-05-09)
Liu, Yu-Chen
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Hong, Hsiao-Chin
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Yang, Chi-Dung
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Lee, Wei-Hsiang
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Huang, Hsin-Tzu
Background: Emerging evidence indicates that Circular RNAs (circRNAs) exert post-transcriptional regulation of gene expression. A subclass of circRNA was found enriched with miRNA target sites. This evidence suggests that this kind of circRNA functions as natural miRNA sponge. Noticing the potential impacts of circular RNA research, we were motivated to identify novel circRNAs as well as putative circRNA-miRNA interactions through retroactive sourced transcriptome sequencing samples. Results: Through the analysis in 465 RNA-seq runs and 22 reports published in recent years, putatively circRNA sponged miRNA that had been experimentally verified targeting circRNA host gene were found. From this observation, supporting evidence of the competitive endogenous relationship of circRNAs and miRNAs targeting circRNA host genes can be observed. Given the self-regulation and self-induction nature of these circRNAs, this kind of hypothetical phenomenon was hereby called Ouroboros Resembling Competitive Endogenous Loop (ORCEL) in circular RNAs. Conclusions: The fact that miRNA sponge circRNA originated from region miRNA target sites enriched regions, while genes encoded from these regions are conserved to be miRNA targets rationalize the existence of ORCEL.
Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi
(2017-01-01)
Liu, Yu-Chen
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Chen, Wen Liang
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Kung, Wei-Hsiang
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Huang, Hsien-Da
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生物科技學系
Background: Emerging evidence indicates that plant miRNAs can present within human circulating system through dietary intake and regulate human gene expression. Hence we deduced that comestible plants miRNAs can be identified in the public available small RNA sequencing data sets. Results: In this study, we identified abundant plant miRNAs sequences from 410 human plasma small RNA sequencing data sets. One particular plant miRNA miR2910, conserved in fruits and vegetables, was found to present in high relative amount in the plasma samples. This miRNA, with same 6mer and 7mer-A1 target seed sequences as hsa-miR-4259 and hsa-miR-4715-5p, was predicted to target human JAK-STAT signaling pathway gene SPRY4 and transcription regulation genes. Conclusions: Through analysis of public available plasma small RNA sequencing data, we found the supporting evidence for the plant miRNAs cross kingdom RNAi within human circulating system.
Room temperature continuous wave operation and characterization of photonic crystal nanolaser on a sapphire substrate
(2009-05-21)
Shih, M. H.
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Yang, Yi-Chun
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Liu, Yu-Chen
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Chang, Zi-Chang
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Hsu, Kung-Shu
A compact photonic crystal defect nanocavity was fabricated on a sapphire substrate. Continuous wave lasing at room temperature was achieved with a low threshold power. We characterized the operated mode, quality factor and radiative efficiency for the compact laser. The thermal properties of the nanolaser were also investigated.
Scalable van der Waals Heterojunctions for High-Performance Photodetectors
(2017-10-18)
Yeh, Chao-Hui
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Liang, Zheng-Yong
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Lin, Yung-Chang
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Wu, Tien-Lin
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Fan, Ta
Atomically thin two-dimensional (2D) materials have attracted increasing attention for optoelectronic applications in view of their compact, ultrathin, flexible, and superior photosensing characteristics. Yet, scalable growth of 2D heterostructures and the fabrication of integrable optoelectronic devices remain unaddressed. Here, we show a scalable formation of 2D stacks and the fabrication of phototransistor arrays, with each photosensing element made of a graphene-WS2 vertical heterojunction and individually addressable by a local top gate. The constituent layers in the heterojunction are grown using chemical vapor deposition in combination with sulfurization, providing a clean junction interface and processing scalability. The aluminum top gate possesses a self-limiting oxide around the gate structure, allowing for a self-aligned deposition of drain/source contacts to reduce the access (litigated) channel regions and to boost the device performance. The generated photo current, inherently restricted by the limited optical absorption cross section of 2D materials, can be enhanced by 2 orders of magnitude by top gating. The resulting photoresponsivity can reach 4.0 A/W under an illumination power density of 0.5 mW/cm(2), and the dark current can be minimized to few picoamperes, yielding a low noise-equivalent power of 2.5 x 10(-16) W/Hz(1/2). Tailoring 2D heterostacks as well as the device architecture moves the applications of 2D-based optoelectronic devices one big step forward.
The aquatic animals' transcriptome resource for comparative functional analysis
(2018-05-09)
Chou, Chih-Hung
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Huang, Hsi-Yuan
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Huang, Wei-Chih
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Hsu, Sheng-Da
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Hsiao, Chung-Der
Background: Aquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in next-generation sequencing techniques, large amounts of RNA-seq data for aquatic animals are publicly available. However, currently there is no comprehensive resource exist for the analysis, unification, and integration of these datasets. This study utilizes computational approaches to build a new resource of transcriptomic maps for aquatic animals. This aquatic animal transcriptome map database dbATM provides de novo assembly of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome. Results: To improve the assembly quality, three computational tools (Trinity, Oases and SOAPdenovo-Trans) were employed to enhance individual transcriptome assembly, and CAP3 and CD-HIT-EST software were then used to merge these three assembled transcriptomes. In addition, functional annotation analysis provides valuable clues to gene characteristics, including full-length transcript coding regions, conserved domains, gene ontology and KEGG pathways. Furthermore, all aquatic animal genes are essential for comparative genomics tasks such as constructing homologous gene groups and blast databases and phylogenetic analysis. Conclusion: In conclusion, we establish a resource for non model organism aquatic animals, which is great economic and ecological importance and provide transcriptomic information including functional annotation and comparative transcriptome analysis.
Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome
(2016-01-01)
Liu, Yu-Chen
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Hsu, Sheng-Da
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Chou, Chih-Hung
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Huang, Wei-Yun
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Chen, Yu-Hung
Background: Anguilla japonica (Japanese eel) is currently one of the most important research subjects in eastern Asia aquaculture. Enigmatic life cycle of the organism makes study of artificial reproduction extremely limited. Henceforth genomic and transcriptomic resources of eels are urgently needed to help solving the problems surrounding this organism across multiple fields. We hereby provide a reconstructed transcriptome from deep sequencing of juvenile (glass eels) whole body samples. The provided expressed sequence tags were used to annotate the currently available draft genome sequence. Homologous information derived from the annotation result was applied to improve the group of scaffolds into available linkage groups. Results: With the transcriptome sequence data combined with publicly available expressed sequence tags evidences, 18,121 genes were structurally and functionally annotated on the draft genome. Among them, 3,921 genes were located in the 19 linkage groups. 137 scaffolds covering 13 million bases were grouped into the linkage groups in additional to the original partial linkage groups, increasing the linkage group coverage from 13 to 14 %. Conclusions: This annotation provide information of the coding regions of the genes supported by transcriptome based evidence. The derived homologous evidences pave the way for phylogenetic analysis of important genetic traits and the improvement of the genome assembly.