Explanipedia

D-cycloserine, a potential candidate for reducing Hepatitis B virus cccDNA in vitro Open

Yongwook Choi, Yong Kwang Park, Wonhee Hur, Gahee Kim, Songmee Bae · 2025

Hepatitis B virus (HBV) is a 3.2 kb hepatotropic DNA that possesses a unique episomal DNA form known as covalently closed circular DNA (cccDNA). cccDNA is the major risk factor for persistent HBV infection and consequently causes chronic l…

Borrelia PeptideAtlas: A proteome resource of common Borrelia burgdorferi isolates for Lyme research Open

Panga Jaipal Reddy, Zhi Sun, Helisa H. Wippel, David Baxter, Kristian E. Swearingen , et al. · 2024

Analysis of host factor networks during hepatitis B virus infection in primary human hepatocytes Open

Suhyun Hwangbo, Gahee Kim, Yongwook Choi, Yong Kwang Park, Songmee Bae , et al. · 2024

Analysis of Host Factor Networks during Hepatitis B Virus Infection in Primary Human Hepatocytes Open

Suhyun Hwangbo, Gahee Kim, Yongwook Choi, Yong Kwang Park, Songmee Bae , et al. · 2024

Background: Hepatitis B virus (HBV) affects around 250 million people worldwide, causing approximately 887,000 deaths annually, primarily owing to cirrhosis and hepatocellular carcinoma (HCC). The current approved treatments for chronic HB…

Borrelia PeptideAtlas: A proteome resource of commonBorrelia burgdorferiisolates for Lyme research Open

Panga Jaipal Reddy, Zhi Sun, Helisa H. Wippel, David Baxter, Kristian E. Swearingen , et al. · 2023

Lyme disease, caused by an infection with the spirochete Borrelia burgdorferi , is the most common vector-borne disease in North America. B. burgdorferi strains harbor extensive genomic and proteomic variability and further comparison is k…

A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness Open

Agnes P. Chan, Azeem Siddique, Yvain Desplat, Yongwook Choi, Sridhar Ranganathan , et al. · 2023

The lack of preparedness for detecting and responding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen (i.e., COVID-19) has caused enormous harm to public health and the economy. Testing strategies deployed on a…

Comparative transcriptomics reveals circadian and pluripotency networks as two pillars of longevity regulation Open

J. Yuyang Lu, Matthew Simon, Yang Zhao, Julia Ablaeva, Nancy Corson , et al. · 2022

A Universal Day Zero Infectious Disease Testing Strategy Leveraging CRISPR-based Sample Depletion and Metagenomic Sequencing Open

Agnes P. Chan, Azeem Siddique, Yvain Desplat, Yongwook Choi, Sridhar Ranganathan , et al. · 2022

The lack of preparedness for detecting the highly infectious SARS-CoV-2 pathogen, the pathogen responsible for the COVID-19 disease, has caused enormous harm to public health and the economy. It took ∼60 days for the first reverse transcri…

Hepatocyte Growth Factor-Dependent Antiviral Activity of Activated cdc42-Associated Kinase 1 Against Hepatitis B Virus Open

Hye Won Lee, Yongwook Choi, Ah Ram Lee, Cheol‐Hee Yoon, Kyun‐Hwan Kim , et al. · 2021

Activated cdc42-associated kinase 1 (ACK1) is a well-known non-receptor tyrosine kinase that regulates cell proliferation and growth through activation of cellular signaling pathways, including mitogen-activated protein kinase (MAPK). Howe…

Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.) Open

Craig H. Carlson, Yongwook Choi, Agnes P. Chan, Christopher D. Town, Lawrence B. Smart · 2021

Many studies have highlighted the complex and diverse basis for heterosis in inbred crops. Despite the lack of a consensus model, it is vital that we turn our attention to understanding heterosis in undomesticated, heterozygous, and polypl…

Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach Open

Josh L. Espinoza, Christopher L. Dupont, Aubrie O’Rourke, Sinem Beyhan, Pavel Morales , et al. · 2021

To better combat the expansion of antibiotic resistance in pathogens, new compounds, particularly those with novel mechanisms-of-action [MOA], represent a major research priority in biomedical science. However, rediscovery of known antibio…

Conserved Genomic Terminals of SARS-CoV-2 as Coevolving Functional Elements and Potential Therapeutic Targets Open

Agnes P. Chan, Yongwook Choi, Nicholas J. Schork · 2020

The CoV disease 2019 (COVID-19) infectious disease outbreak is having a dramatic global effect on public health and the economy. As of October 2020, SARS-CoV-2 has been detected in over 189 countries, has infected over 40 million people, a…

Recent Research and Knowledge on Treatment for Hepatitis B Open

Hye Won Lee, Yongwook Choi, Yong Kwang Park · 2020

Hepatitis B virus (HBV) infection is a major public health problem, with some 250 million people currently at high risk of developing chronic liver diseases. The current antiviral treatment for chronic hepatitis B (CHB) is effective in con…

Overview of anti-Hepatitis B virus agents Open

Hye Won Lee, Yong-kwang Park, Yongwook Choi · 2020

Since the first FDA approval of Lamivudine in 1998, many nucleo(t)side analogs such as Lamivudine, Adefovir, and Entecavir have been used. However, they only inhibit DNA synthesis, and if their administration is stopped a viral breakthroug…

Conserved Genomic Terminals of SARS-CoV-2 as Co-evolving Functional Elements and Potential Therapeutic Targets Open

Agnes P. Chan, Yongwook Choi, Nicholas J. Schork · 2020

To identify features in the genome of the SARS-CoV-2 pathogen responsible for the COVID-19 pandemic that may contribute to its viral replication, host pathogenicity, and vulnerabilities, we investigated how and to what extent the SARS-CoV-…

AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates Open

Agnes P. Chan, Yongwook Choi, Thomas H. Clarke, Lauren Brinkac, Richard C. White , et al. · 2020

Objectives To investigate the genomic context of a novel resistance island (RI) in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates and global isolates. Methods Using a combination of long and short reads generated f…

Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling Open

Aubrie O’Rourke, Sinem Beyhan, Yongwook Choi, Pavel Morales, Agnes P. Chan , et al. · 2020

Antimicrobial resistance (AMR) is an ever-growing public health problem worldwide. The low rate of antibiotic discovery coupled with the rapid spread of drug-resistant bacterial pathogens is causing a global health crisis. To facilitate th…

Identification of microRNAs and their targets in four Gossypium species using RNA sequencing Open

Venkateswara R. Sripathi, Yongwook Choi, Zachary B. Gossett, David M. Stelly, Elica M. Moss , et al. · 2018

MicroRNAs (miRNAs) are small non-coding endogenous riboregulators that play significant roles in plant growth, development, metabolism, defense, and stress responses. Upland cotton is best known for its economic value as natural fiber and …

Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells Open

Agnes P. Chan, Yongwook Choi, Lauren Brinkac, R. Krishnakumar, Jessica DePew , et al. · 2018

In light of the ongoing antimicrobial resistance crisis, there is a need to understand the role of co-pathogens, commensals, and the local microbiome in modulating virulence and antibiotic resistance. To identify possible interactions that…

Comparison of phasing strategies for whole human genomes Open

Yongwook Choi, Agnes P. Chan, Ewen F. Kirkness, Amalio Telenti, Nicholas J. Schork · 2018

Humans are a diploid species that inherit one set of chromosomes paternally and one homologous set of chromosomes maternally. Unfortunately, most human sequencing initiatives ignore this fact in that they do not directly delineate the nucl…

Dominance and Sexual Dimorphism Pervade the Salix purpurea L. Transcriptome Open

Craig H. Carlson, Yongwook Choi, Agnes P. Chan, Michelle J. Serapiglia, Christopher D. Town , et al. · 2017

The heritability of gene expression is critical in understanding heterosis and is dependent on allele-specific regulation by local and remote factors in the genome. We used RNA-Seq to test whether variation in gene expression among F1 and …

Electrochemical detection of Pseudomonas in wound exudate samples from patients with chronic wounds Open

Hunter J. Sismaet, Anirban Banerjee, Sean McNish, Yongwook Choi, Manolito Torralba , et al. · 2016

In clinical practice, point‐of‐care diagnostic testing has progressed rapidly in the last decade. For the field of wound care, there is a compelling need to develop rapid alternatives for bacterial identification in the clinical setting, w…

Application of mutant JAK2V617F for in vitro generation of red blood cells Open

Sun Ah Lee, Ji Yeon Kim, Yongwook Choi, Yonggoo Kim, Hyun Ok Kim · 2015

BACKGROUND In vitro generation of red blood cells (RBCs) from hematopoietic stem cells (HSCs) has been reported, but the collection of 1 × 10 5 to 1 × 10 6 CD34+ cells present in cord and peripheral blood is too small for expansion to 1 × …

A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii Open

Agnes P. Chan, Granger Sutton, Jessica DePew, R. Krishnakumar, Yongwook Choi , et al. · 2015

Background Infections by pan-drug resistant Acinetobacter baumannii plague military and civilian healthcare systems. Previous A. baumannii pan-genomic studies used modest sample sizes of low diversity and comparisons to a single reference …

Comparison of Serum-Free Media in RBC Differentiation from Human Hematopoietic Stem Cells Open

Kim J, Sinyoung Kim, You La Jeon, Yongwook Choi, Hyun Ok Kim · 2015

Background: Research on RBC production from hematopoietic stem cells has been conducted competitively in many countries. However those were in vitro successes and many hurdles still remain for large scale transfusable RBC production from s…

PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels Open

Yongwook Choi, Agnes P. Chan · 2015

Summary: We present a web server to predict the functional effect of single or multiple amino acid substitutions, insertions and deletions using the prediction tool PROVEAN. The server provides rapid analysis of protein variants from any o…

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