Wen Harold Chen

Wen Harold Chen

Doctor of Philosophy

About

13
Publications
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Introduction
My research focuses on using computational approaches to decipher the function of long non-coding RNAs. In my previous work, by analyzing public RNA-Seq data, I did a comprehensive analysis and function annotation of zebrafish lncRNAs (https://www.biochen.org/zflnc). My most recent work is "GCEN: an easy-to-use toolkit for Gene Co-Expression Network analysis and lncRNAs annotation" (https://www.biochen.org/gcen).

Publications

Publications (13)
Article
Full-text available
Background: Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to...
Article
Full-text available
The CRISPR/Cas9 system, as a revolutionary genome editing tool for all areas of molecular biology, provides new opportunities for research on lncRNA’s function. However, designing a CRISPR/Cas9 sgRNA for lncRNA is not easy with an unwarrantable effectiveness. Thus, it is worthy of collecting validated sgRNAs, to assist in efficiently choosing sgRNA...
Article
Full-text available
There is emerging evidence showing that lncRNAs can be involved in various critical biological processes. Zebrafish is a fully developed model system being used in a variety of basic research and biomedical studies. Hence, it is an ideal model organism to study the functions and mechanisms of lncRNAs. Here, we constructed ZFLNC-a comprehensive data...
Article
Full-text available
Gene co-expression network analysis has been widely used in gene function annotation, especially for long noncoding RNAs (lncRNAs). However, there is a lack of effective cross-platform analysis tools. For biologists to easily build a gene co-expression network and to predict gene function, we developed GCEN, a cross-platform command-line toolkit de...
Article
Full-text available
Background Long non-coding RNAs (lncRNAs) play vital roles in many important biological processes in plants. Currently, a large fraction of plant lncRNA studies center at lncRNA identification and functional analysis. Only a few plant lncRNA studies focus on understanding their evolutionary history, which is crucial for an in-depth understanding of...
Article
Full-text available
Background Jatropha curcas L. is an important non-edible oilseed crop with a promising future in biodiesel production. However, little is known about the molecular biology of oil biosynthesis in this plant when compared with other established oilseed crops, resulting in the absence of agronomically improved varieties of Jatropha . To extensively di...
Article
Cancer cells acquire numerous biological properties (designated 'cancer hallmarks'), such as cell survival and energy metabolism, that facilitate tumor growth and metastatic dissemination during development. To date, eight hallmarks of cancer have been identified that provide a logical framework for understanding the remarkable diversity of neoplas...
Article
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Background: Tumor necrosis factor α-induced protein 1 (TNFAIP1) is frequently downregulated in cancer cell lines and promotes cancer cell apoptosis. However, its role, clinical significance and molecular mechanisms in hepatocellular carcinoma (HCC) are unknown. Methods: The expression of TNFAIP1 in HCC tumor tissues and cell lines was measured b...
Article
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Background: Jatropha curcas is an oil-bearing plant, and has seeds with high oil content (~ 40%). Several advantages, such as easy genetic transformation and short generation duration, have led to the emergence of J. curcas as a model for woody energy plants. With the development of high-throughput sequencing, the genome of Jatropha curcas has bee...
Article
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Background Recent studies demonstrated that long non-coding RNAs (lncRNAs) could be intricately implicated in cancer-related molecular networks, and related to cancer occurrence, development and prognosis. However, clinicopathological and molecular features for these cancer-related lncRNAs, which are very important in bridging lncRNA basic research...
Article
Full-text available
Background Long noncoding RNAs (lncRNAs) are widely involved in the initiation and development of cancer. Although some computational methods have been proposed to identify cancer-related lncRNAs, there is still a demanding to improve the prediction accuracy and efficiency. In addition, the quick-update data of cancer, as well as the discovery of n...
Article
Full-text available
Long fragment cloning is a challenge for its difficulty in accurate amplifying and tendency to get unwanted mutation. Here we discuss Restriction-based Multiple-fragment Assembly Strategy's advantages and limitations. In this strategy, rather than PCR amplifying the entire coding sequence (CDS) at one time, we amplified and sequenced smaller fragme...

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Project
My research focuses on using computational approaches to decipher the function of long non-coding RNAs.