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Original article

March 31, 2023


Comprehensive investigation of the expression profiles of common long noncoding RNAs during microglial activation
Janghyun Kim, Bora Lee, Young Kim, Byeong C. Kim, Joon-Tae Kim, Hyong-Ho Cho
Genomics Inform. 2023;21(1):e2.

Microglia, similar to peripheral macrophages, are the primary immune cells of the central nervous system (CNS). Microglia exist in the resting state in the healthy CNS, but can be activated...

Original article

March 31, 2023


A bioinformatics approach to characterize a hypothetical protein Q6S8D9_SARS of SARS-CoV
Md. Foyzur Rahman, Rubait Hasan, Mohammad Shahangir Biswas, Jamiatul Husna Shathi, Md. Faruk Hossain, Aoulia Yeasmin, Mohammad Zakerin Abedin, Md. Tofazzal Hossain
Genomics Inform. 2023;21(1):e3.

Characterization as well as prediction of the secondary and tertiary structure of hypothetical proteins from their amino acid sequences uploaded in databases by in silico approach are the critical issues...

Original article

March 31, 2023


A network pharmacology and molecular docking approach in the exploratory investigation of the biological mechanisms of lagundi (Vitex negundo L.) compounds against COVID-19
Robertson G. Rivera, Patrick Junard S. Regidor, Edwin C. Ruamero Jr, Eric John V. Allanigue, Melanie V. Salinas
Genomics Inform. 2023;21(1):e4.

Coronavirus disease 2019 (COVID-19) is an inflammatory and infectious disease caused by severe acute respiratory syndrome coronavirus 2 virus with a complex pathophysiology. While COVID-19 vaccines and boosters are available,...

Original aricle

March 31, 2023


Antibiotic resistance in Neisseria gonorrhoeae: broad-spectrum drug target identification using subtractive genomics
Umairah Natasya Mohd Omeershffudin, Suresh Kumar
Genomics Inform. 2023;21(1):e5.

Neisseria gonorrhoeae is a Gram-negative aerobic diplococcus bacterium that primarily causes sexually transmitted infections through direct human sexual contact. It is a major public health threat due to its impact...

Original article

March 31, 2023


Novel potential drugs for the treatment of primary open-angle glaucoma using protein-protein interaction network analysis
Parisima Ghaffarian Zavarzadeh, Zahra Abedi
Genomics Inform. 2023;21(1):e6.

Glaucoma is the second leading cause of irreversible blindness, and primary open-angle glaucoma (POAG) is the most common type. Due to inadequate diagnosis, treatment is often not administered until symptoms...

Original article

March 31, 2023


In silico annotation of a hypothetical protein from Listeria monocytogenes EGD-e unfolds a toxin protein of the type II secretion system
Maisha Tasneem, Shipan Das Gupta, Monira Binte Momin, Kazi Modasser Hossain, Tasnim Binta Osman, Md. Fazley Rabbi
Genomics Inform. 2023;21(1):e7.

The gram-positive bacterium Listeria monocytogenes is an important foodborne intracellular pathogen that is widespread in the environment. The functions of hypothetical proteins (HP) from various pathogenic bacteria have been successfully...

Original article

March 31, 2023


Prognostic biomarkers and molecular pathways mediating Helicobacter pylori–induced gastric cancer: a network-biology approach
Farideh Kamarehei, Massoud Saidijam, Amir Taherkhani
Genomics Inform. 2023;21(1):e8.

Cancer of the stomach is the second most frequent cancer-related death worldwide. The survival rate of patients with gastric cancer (GC) remains fragile. There is a requirement to discover biomarkers...

Original article

March 31, 2023


Cinnamic acid derivatives as potential matrix metalloproteinase-9 inhibitors: molecular docking and dynamics simulations
Mohammad Hossein Malekipour, Farzaneh Shirani, Shadi Moradi, Amir Taherkhani
Genomics Inform. 2023;21(1):e9.

Matrix metalloproteinase-9 (MMP-9) is a zinc and calcium-dependent proteolytic enzyme involved in extracellular matrix degradation. Overexpression of MMP-9 has been confirmed in several disorders, including cancers, Alzheimer′s disease, autoimmune diseases,...

Genomic archive

March 31, 2023


Characterization of six new complete mitochondrial genomes of Chiasmodontidae (Scombriformes, Percomorpha) and considerations about the phylogenetic relationships of the family
Igor Henrique Rodrigues-Oliveira, Rubens Pasa, Fabiano Bezerra Menegidio, Karine Frehner Kavalco
Genomics Inform. 2023;21(1):e10.

The fishes of the Chiasmodontidae family, known as swallower fishes, are species adapted to live in deep seas. Several studies have shown the proximity of this family to Tetragonuridae and...

Clinical genomics

March 31, 2023


Generation and analysis of whole-genome sequencing data in human mammary epithelial cells
Jong-Lyul Park, Jae-Yoon Kim, Seon-Young Kim, Yong Sun Lee
Genomics Inform. 2023;21(1):e11.

Breast cancer is the most common cancer worldwide, and advanced breast cancer with metastases is incurable mainly with currently available therapies. Therefore, it is essential to understand molecular characteristics during...

Application note

March 31, 2023


Introduction of the Korea BioData Station (K-BDS) for sharing biological data
Byungwook Lee, Seungwoo Hwang, Pan-Gyu Kim, Gunwhan Ko, Kiwon Jang, Sangok Kim, Jong-Hwan Kim, Jongbum Jeon, Hyerin Kim, Jaeeun Jung, et al.
Genomics Inform. 2023;21(1):e12.

A wave of new technologies has created opportunities for the cost-effective generation of high-throughput profiles of biological systems, foreshadowing a "data-driven science" era. The large variety of data available from...

Application note

March 31, 2023


Effective microbial molecular diagnosis of periodontitis-related pathogen Porphyromonas gingivalis from salivary samples using rgpA gene
Jinuk Jeong, Yunseok Oh, Junhyeon Jeon, Dong-Heon Baek, Dong Hee Kim, Kornsorn Srikulnath, Kyudong Han
Genomics Inform. 2022;21(1):e13.

Importance of accurate molecular diagnosis and quantification of particular disease-related pathogenic microorganisms is highlighted as an introductory step to prevent and care for diseases. In this study, we designed a...

Application note

March 31, 2023


PyOncoPrint: a python package for plotting OncoPrints
Jeongbin Park, Nagarajan Paramasivam
Genomics Inform. 2023;21(1):e14.

OncoPrint, the plot to visualize an overview of genetic variants in sequencing data, has been widely used in the field of cancer genomics. However, still, there have been no Python...

Application note

March 31, 2023


A Python-based educational software tool for visualizing bioinformatics alignment algorithms
Elis Khatizah, Hee-Jo Nam, Hyun-Seok Park
Genomics Inform. 2023;21(1):e15.

Bioinformatics education can be defined as the teaching and learning of how to use software tools, along with mathematical and statistical analysis, to solve biological problems. Although many resources are...
Current Issue
Volume 21(1); Mar 2023
Korea BioData Station (K-BDS)
Taesung Park
Genomics Inform. 2023;21(1):e1.

Editorial

March 31, 2023
Comprehensive investigation of the expression profiles of common long noncoding RNAs during microglial activation
Janghyun Kim, Bora Lee, Young Kim, Byeong C. Kim, Joon-Tae Kim, Hyong-Ho Cho
Genomics Inform. 2023;21(1):e2.

Original article

March 31, 2023
A bioinformatics approach to characterize a hypothetical protein Q6S8D9_SARS of SARS-CoV
Md. Foyzur Rahman, Rubait Hasan, Mohammad Shahangir Biswas, Jamiatul Husna Shathi, Md. Faruk Hossain, Aoulia Yeasmin, Mohammad Zakerin Abedin, Md. Tofazzal Hossain
Genomics Inform. 2023;21(1):e3.

Original article

March 31, 2023
A network pharmacology and molecular docking approach in the exploratory investigation of the biological mechanisms of lagundi (Vitex negundo L.) compounds against COVID-19
Robertson G. Rivera, Patrick Junard S. Regidor, Edwin C. Ruamero Jr, Eric John V. Allanigue, Melanie V. Salinas
Genomics Inform. 2023;21(1):e4.

Original article

March 31, 2023
Antibiotic resistance in Neisseria gonorrhoeae: broad-spectrum drug target identification using subtractive genomics
Umairah Natasya Mohd Omeershffudin, Suresh Kumar
Genomics Inform. 2023;21(1):e5.

Original aricle

March 31, 2023
Novel potential drugs for the treatment of primary open-angle glaucoma using protein-protein interaction network analysis
Parisima Ghaffarian Zavarzadeh, Zahra Abedi
Genomics Inform. 2023;21(1):e6.

Original article

March 31, 2023
In silico annotation of a hypothetical protein from Listeria monocytogenes EGD-e unfolds a toxin protein of the type II secretion system
Maisha Tasneem, Shipan Das Gupta, Monira Binte Momin, Kazi Modasser Hossain, Tasnim Binta Osman, Md. Fazley Rabbi
Genomics Inform. 2023;21(1):e7.

Original article

March 31, 2023
Prognostic biomarkers and molecular pathways mediating Helicobacter pylori–induced gastric cancer: a network-biology approach
Farideh Kamarehei, Massoud Saidijam, Amir Taherkhani
Genomics Inform. 2023;21(1):e8.

Original article

March 31, 2023
Cinnamic acid derivatives as potential matrix metalloproteinase-9 inhibitors: molecular docking and dynamics simulations
Mohammad Hossein Malekipour, Farzaneh Shirani, Shadi Moradi, Amir Taherkhani
Genomics Inform. 2023;21(1):e9.

Original article

March 31, 2023
Characterization of six new complete mitochondrial genomes of Chiasmodontidae (Scombriformes, Percomorpha) and considerations about the phylogenetic relationships of the family
Igor Henrique Rodrigues-Oliveira, Rubens Pasa, Fabiano Bezerra Menegidio, Karine Frehner Kavalco
Genomics Inform. 2023;21(1):e10.

Genomic archive

March 31, 2023
Generation and analysis of whole-genome sequencing data in human mammary epithelial cells
Jong-Lyul Park, Jae-Yoon Kim, Seon-Young Kim, Yong Sun Lee
Genomics Inform. 2023;21(1):e11.

Clinical genomics

March 31, 2023
Introduction of the Korea BioData Station (K-BDS) for sharing biological data
Byungwook Lee, Seungwoo Hwang, Pan-Gyu Kim, Gunwhan Ko, Kiwon Jang, Sangok Kim, Jong-Hwan Kim, Jongbum Jeon, Hyerin Kim, Jaeeun Jung, et al.
Genomics Inform. 2023;21(1):e12.

Application note

March 31, 2023
Effective microbial molecular diagnosis of periodontitis-related pathogen Porphyromonas gingivalis from salivary samples using rgpA gene
Jinuk Jeong, Yunseok Oh, Junhyeon Jeon, Dong-Heon Baek, Dong Hee Kim, Kornsorn Srikulnath, Kyudong Han
Genomics Inform. 2022;21(1):e13.

Application note

March 31, 2023
PyOncoPrint: a python package for plotting OncoPrints
Jeongbin Park, Nagarajan Paramasivam
Genomics Inform. 2023;21(1):e14.

Application note

March 31, 2023
A Python-based educational software tool for visualizing bioinformatics alignment algorithms
Elis Khatizah, Hee-Jo Nam, Hyun-Seok Park
Genomics Inform. 2023;21(1):e15.

Application note

March 31, 2023

View More

Most View Most Cited
In silico annotation of a hypothetical protein from Listeria monocytogenes EGD-e unfolds a toxin protein of the type II secretion system Maisha Tasneem, Shipan Das Gupta, Monira Binte Momin, Kazi Modasser Hossain, Tasnim Binta Osman, Md. Fazley Rabbi Genomics Inform. 2023;21(1):e7. Sk Injamamul Islam, Moslema Jahan Mou, Saloa Sanjida, Muhammad Tariq, Saad Nasir, Sarower Mahfuj Genomics Inform. 2022;20(1):e11. Cited By 5
A bioinformatics approach to characterize a hypothetical protein Q6S8D9_SARS of SARS-CoV Md. Foyzur Rahman, Rubait Hasan, Mohammad Shahangir Biswas, Jamiatul Husna Shathi, Md. Faruk Hossain, Aoulia Yeasmin, Mohammad Zakerin Abedin, Md. Tofazzal Hossain Genomics Inform. 2023;21(1):e3. Sarmilah Mathavan, Chin Siang Kue, Suresh Kumar Genomics Inform. 2021;19(1):e4. Cited By 3
Comprehensive investigation of the expression profiles of common long noncoding RNAs during microglial activation Janghyun Kim, Bora Lee, Young Kim, Byeong C. Kim, Joon-Tae Kim, Hyong-Ho Cho Genomics Inform. 2023;21(1):e2. Md. Mehadi Hasan Sohag, Saleh Muhammed Raqib, Syaefudin Ali Akhmad Genomics Inform. 2021;19(2):e13. Cited By 3
Korea BioData Station (K-BDS) Taesung Park Genomics Inform. 2023;21(1):e1. A. M. U. B. Mahfuz, A. M. Zubair-Bin-Mahfuj, Dibya Joti Podder Genomics Inform. 2021;19(2):e16. Cited By 3
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