Hyun-Seok Park

UNLABELLED: FX is an RNA-Seq analysis tool, which runs in parallel on cloud computing infrastructure, for the estimation of gene expression levels and genomic variant calling. In the mapping of short RNA-Seq reads, FX uses a transcriptome-based reference primarily, generated from ~160 000 mRNA sequences from RefSeq, UCSC and Ensembl databases. This approach reduces the misalignment of reads originating from splicing junctions. Unmapped reads not aligned on known transcripts are then mapped on th

Skin cancer, particularly melanoma, is a severe health threat that necessitates early detection for effective treatment. This research introduces a skin lesion classification system that harnesses the capabilities of three advanced deep learning models: VGG16, Inception-V3, and ResNet-50. By integrating these models into an ensemble, the system leverages their individual strengths to improve classification accuracy and robustness. Every model in the ensemble brings its distinctive contribution,

Globally, breast cancer (BC) is considered a major cause of death among women. Therefore, researchers have used various machine and deep learning-based methods for its early and accurate detection using X-ray, MRI, and mammography image modalities. However, the machine learning model requires domain experts to select an optimal feature, obtains a limited accuracy, and has a high false positive rate due to handcrafting features extraction. The deep learning model overcomes these limitations, but

The early and accurate detection of skin cancer can reduce mortality rates and improve patient outcomes, but requires advanced diagnostics. The integration of artificial intelligence (AI) into healthcare enables the precise and timely detection of skin cancer. However, significant challenges remain including the difficulty in differentiating visually similar skin conditions and the limitations of diverse, representative datasets. In this study, we proposed DCAN-Net, a novel deep-learning framewo

This study addresses challenges in skin cancer detection, particularly issues like class imbalance and the varied appearance of lesions, which complicate segmentation and classification tasks. The research employs deep learning ensemble models for both segmentation (using U-Net, SegNet, and DeepLabV3) and classification (using VGG16, ResNet-50, and Inception-V3). The ISIC dataset is balanced through oversampling in classification, and preprocessing techniques such as data augmentation and post-p

Recent technical advances, such as chromatin immunoprecipitation combined with DNA microarrays (ChIp-chip) and chromatin immunoprecipitation-sequencing (ChIP-seq), have generated large quantities of high-throughput data. Considering that epigenomic datasets are arranged over chromosomes, their analysis must account for spatial or temporal characteristics. In that sense, simple clustering or classification methodologies are inadequate for the analysis of multi-track ChIP-chip or ChIP-seq data. Ap

Treating genomes just as languages raises the possibility of producing concise generalizations about information in biological sequences. Grammars used in this way would constitute a model of underlying biological processes or structures, and that grammars may, in fact, serve as an appropriate tool for theory formation. The increasing number of biological sequences that have been yielded further highlights a growing need for developing grammatical systems in bioinformatics. The intent of this re

Genomics & Informatics (NLM title abbreviation: Genomics Inform) is the official journal of the Korea Genome Organization. Text corpus for this journal annotated with various levels of linguistic information would be a valuable resource as the process of information extraction requires syntactic, semantic, and higher levels of natural language processing. In this study, we publish our new corpus called GNI Corpus version 1.0, extracted and annotated from full texts of Genomics & Informat

Epigenetic computational analyses based on Markov chains can integrate dependencies between regions in the genome that are directly adjacent. In this paper, the BED files of fifteen chromatin states of the Broad Histone Track of the ENCODE project are parsed, and comparative nucleotide frequencies of regional chromatin blocks are thoroughly analyzed to detect the Markov property in them. We perform various tests to examine the Markov property embedded in a frequency domain by checking for the pr

Treating genomes just as languages raises the possibility of producing concise generalizations about information in biological sequences. Grammars used in this way would constitute a model of underlying biological processes or structures, and that grammars may,in fact, serve as an appropriate tool for theory formation. The increasing number of biological sequences that have been yielded further highlights a growing need for developing grammatical systems in bioinformatics. The intent of this rev

The static approach of representing metabolic pathway diagrams offers no flexibility. Thus, many systems adopt automatic graph layout techniques to visualize the topological architecture of pathways. There are weaknesses, however, because automatically drawn figures are generally difficult to understand. The problem becomes even more serious when we attempt to visualize all of the information in a single, big picture, which usually results in a confusing diagram. To provide a partial solution to

Integrating various pathway data collections to create new biological knowledge is a challenge, for which novel computational tools play a key role. For this purpose, we developed the Java-based conversion modules KGML2SBML and KGML2BioPAX to translate KGML (KEGG Markup Language) into a couple of common data exchange formats: SBML (Systems Biology Markup Language) and BioPAX (Biological Pathway Exchange). We hope that our work will be beneficial for other Java developers when they extend their b

The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository. The full-text publications of volumes 10 through 17 are also directly downloadable from PubMed Central (PMC) as XML files. During the Biomedical Linked Annotation Hackathon 6 (BLAH6), we experimented with converting, annotating, and updating 301 PMC full-text articles of Genomics & Informatics using PubAnnotation, a system that provides a convenient way to add PMC publicatio

The basic graph layout technique, one of many visualization techniques, deals with the problem of positioning vertices in a way to maximize some measure of desirability in a graph. The technique is becoming critically important for further development of the field of systems biology. However, applying the appropriate automatic graph layout techniques to the genomic scale flow of metabolism requires an understanding of the characteristics and patterns of duplicate and shared vertices, which is cr

Recently, the necessity of using low-dose CT imaging with reduced noise has come to the forefront due to the risks involved in radiation. In order to acquire a high-resolution image from a low-resolution image which produces a relatively small amount of radiation, various algorithms including deep learning-based methods have been proposed. However, the current techniques have shown limited performance, especially with regard to losing fine details and blurring high-frequency edges. To enhance th