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Opinion: Strategy of Semi-Automatically Annotating a Full-Text Corpus of Genomics & Informatics

Park HS

There is a communal need for an annotated corpus consisting of the full texts of biomedical journal articles. In response to community needs, a prototype version of the full-text corpus...
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Integration of a Large-Scale Genetic Analysis Workbench Increases the Accessibility of a High-Performance Pathway-Based Analysis Method

Lee S, Park T

The rapid increase in genetic dataset volume has demanded extensive adoption of biological knowledge to reduce the computational complexity, and the biological pathway is one well-known source of such knowledge....
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HisCoM-GGI: Software for Hierarchical Structural Component Analysis of Gene-Gene Interactions

Choi S, Lee S, Park T

Gene-gene interaction (GGI) analysis is known to play an important role in explaining missing heritability. Many previous studies have already proposed software to analyze GGI, but most methods focus on...
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EFMDR-Fast: An Application of Empirical Fuzzy Multifactor Dimensionality Reduction for Fast Execution

Leem S, Park T

Gene-gene interaction is a key factor for explaining missing heritability. Many methods have been proposed to identify gene-gene interactions. Multifactor dimensionality reduction (MDR) is a well-known method for the detection...
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COEX-Seq: Convert a Variety of Measurements of Gene Expression in RNA-Seq

Kim SC, Yu D, Cho SB

Next generation sequencing (NGS), a high-throughput DNA sequencing technology, is widely used for molecular biological studies. In NGS, RNA-sequencing (RNA-Seq), which is a short-read massively parallel sequencing, is a major...
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Somatic Mutations from Whole Exome Sequencing Analysis of the Patients with Biliary Tract Cancer

Yoon KA, Woo SM, Kim YH, Kong SY, Han SS, Park SJ, Lee WJ

Biliary tract cancer (BTC) is a rare cancer and is associated with a poor prognosis. To understand the genetic characteristics of BTC, we analyzed whole-exome sequencing data and identified somatic...
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RNA-Seq De Novo Assembly and Differential Transcriptome Analysis of Korean Medicinal Herb Cirsium japonicum var. spinossimum

Roy NS, Kim JA, Choi AY, Ban YW, Park NI, Park KC, Yang HS, Choi IY, Kim S

Cirsium japonicum belongs to the Asteraceae or Compositae family and is a medicinal plant in Asia that has a variety of effects, including tumour inhibition, improved immunity with flavones, and...
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Multi-block Analysis of Genomic Data Using Generalized Canonical Correlation Analysis

Jun I, Choi W, Park M

Recently, there have been many studies in medicine related to genetic analysis. Many genetic studies have been performed to find genes associated with complex diseases. To find out how genes...
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Ovarian Cancer Prognostic Prediction Model Using RNA Sequencing Data

Jeong S, Mok L, Kim SI, Ahn T, Song YS, Park T

Ovarian cancer is one of the leading causes of cancer-related deaths in gynecological malignancies. Over 70% of ovarian cancer cases are high-grade serous ovarian cancers and have high death rates...
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Metabolic Syndrome Prediction Using Machine Learning Models with Genetic and Clinical Information from a Nonobese Healthy Population

Choe EK, Rhee H, Lee S, Shin E, Oh SW, Lee JE, Choi SH

The prevalence of metabolic syndrome (MS) in the nonobese population is not low. However, the identification and risk mitigation of MS are not easy in this population. We aimed to...
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Storing Digital Information in Long-Read DNA

Ahn T, Ban H, Park H

There is urgent need for effective and cost-efficient data storage, as the worldwide requirement for data storage is rapidly growing. DNA has introduced a new tool for storing digital information....
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A Universal Analysis Pipeline for Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes

Kim MJ, Kim SC, Kim YJ

Hybrid capture-based targeted sequencing is being used increasingly for genomic variant profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy...
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STADIUM: Species-Specific tRNA Adaptive Index Compendium

Yoon J, Chung YJ, Lee M

Due to the increasing interest in synonymous codons, several codon bias-related terms were introduced. As one measure of them, the tRNA adaptation index (tAI) was invented about a decade ago....
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A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of Roadmap Genomics ChromHMM Annotations: A Computational Perspective

Park HS

The non-coding DNA in eukaryotic genomes encodes a language that programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this study was to determine the effect...
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Functional Prediction of Hypothetical Proteins from Shigella flexneri and Validation of the Predicted Models by Using ROC Curve Analysis

Gazi MA, Mahmud S, Fahim SM, Kibria MG, Palit P, Islam MR, Rashid H, Das S, Mahfuz M, Ahmeed T

Shigella spp. constitutes some of the key pathogens responsible for the global burden of diarrhoeal disease. With over 164 million reported cases per annum, shigellosis accounts for 1.1 million deaths...
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Circulating HOTAIR LncRNA Is Potentially Up-regulated in Coronary Artery Disease

Avazpour N, Hajjari M, Yazdankhah S, Sahni A, Foroughmand AM

Coronary artery disease (CAD) is one of the leading causes of death and disability all around the world. Recent studies have revealed that aberrantly regulated long non-coding RNA (lncRNA) as...
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Evaluation of 16S rRNA Databases for Taxonomic Assignments Using a Mock Community

Park SC, Won S

Taxonomic identification is fundamental to all microbiology studies. Particularly in metagenomics, which identifies the composition of microorganisms using thousands of sequences, its importance is even greater. Identification is inevitably affected...
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Identification of Viral Taxon-Specific Genes (VTSG): Application to Caliciviridae

Kang S, Kim YC

Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence...
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Genome-Based Virus Taxonomy with the ICTV Database Extension

Kang S, Kim YC

In 1966, the International Classification of Viruses (ICNV) was established to standardize the naming of viruses. In 1975, the organization was renamed “International Committee on Taxonomy of Viruses (ICTV),” by...
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An Advanced Understanding of Uterine Microbial Ecology Associated with Metritis in Dairy Cows

Jeon SJ, Galvão KN

Metritis, the inflammation of the uterus caused by polymicrobial infections, is a prevalent and costly disease to the dairy industry as it decreases milk yield, survival, and the welfare of...
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