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HisCoM-PCA: software for hierarchical structural component analysis for pathway analysis based using principal component analysis

Jiang N, Lee S, Park T

In genome-wide association studies, pathway-based analysis has been widely performed to enhance interpretation of single-nucleotide polymorphism association results. We proposed a novel method of hierarchical structural component model (HisCoM) for...
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Accelerating next generation sequencing data analysis: an evaluation of optimized best practices for Genome Analysis Toolkit algorithms

Franke KR, Crowgey EL

Advancements in next generation sequencing (NGS) technologies have significantly increased the translational use of genomics data in the medical field as well as the demand for computational infrastructure capable processing...
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Associations between an MDM2 gene polymorphism and ulcerative colitis by ARMS-PCR

Doulabi MS, Moghaddam , Salehzadeh A

Ulcerative colitis is a form of inflammatory bowel disease characterized by chronic inflammation of the colon and rectum. The abnormal lesions in the digestive system caused by ulcerative colitis...
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Bioinformatics services for analyzing massive genomic datasets

Ko G, Kim PG, Cho Y, Jeong S, Kim JY, Kim KH, Lee HY, Han J, Yu N, Ham S, Jang I, Kang B, Shin S, Kim L, Lee SW, Nam D, Kim JF, Kim N, Kim SY, Lee S, Roh TY, Lee B

The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent...
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A note on the distance distribution paradigm for Mosaab-metric to process segmented genomes of influenza virus

Daoud M

In this paper, we present few technical notes about the distance distribution paradigm for Mosaab-metric using 1, 2, and 3 grams feature extraction techniques to analyze composite data points in...
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Strong concordance between RNA structural and single nucleotide variants identified via next generation sequencing techniques in primary pediatric leukemia and patient-derived xenograft samples

Barwe SP, Gopalakrisnapillai A, Mahajan N, Druley TE, Kolb EA, Crowgey EL

Acute leukemia represents the most common pediatric malignancy comprising diverse subtypes with varying prognosis and treatment outcomes. New and targeted treatment options are warranted for this disease. Patient-derived xenograft (PDX)...
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PAIVS: prediction of avian influenza virus subtype

Park HC, Shin J, Cho SM, Kang S, Chung YJ, Jung SH

Highly pathogenic avian influenza (HPAI) viruses have caused severe respiratory disease and death in poultry and human beings. Although most of the avian influenza viruses (AIVs) are of low pathogenicity...
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Quantitative evaluation of the molecular marker using droplet digital PCR

Shin W, Kim H, Oh DY, Kim DH, Han K

Transposable elements (TEs) constitute approximately half of Bovine genome. They can be a powerful species-specific marker without regression mutations by the structure variation (SV) at the time of genomic evolution....
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Validity of patient-derived xenograft mouse models for lung cancer based on exome sequencing data

Kim J, Rhee H, Kim J, Lee S

Patient-derived xenograft (PDX) mouse models are frequently used to test the drug efficacy in diverse types of cancer. They are known to recapitulate the patient characteristics faithfully, but a systematic...
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Detecting outliers in segmented genomes of flu virus using an alignment-free approach

Daoud M

In this paper, we propose a new approach to detecting outliers in a set of segmented genomes of the flu virus, a data set with a heterogeneous set of sequences....
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Editor’s introduction to this issue (G&I 18:1, 2020)

Park T

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