A5023771318- Algorithms and Data Compression
- Hepatitis C virus research
- Hepatitis B Virus Studies
- DNA and Biological Computing
- Liver Disease Diagnosis and Treatment
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- SARS-CoV-2 and COVID-19 Research
- CRISPR and Genetic Engineering
- Cytokine Signaling Pathways and Interactions
- Chromosomal and Genetic Variations
- Microbial Natural Products and Biosynthesis
- Pancreatic and Hepatic Oncology Research
- Mobile Ad Hoc Networks
- Cellular Automata and Applications
- interferon and immune responses
- Energy Efficient Wireless Sensor Networks
- Antibiotic Resistance in Bacteria
- Mathematical Dynamics and Fractals
- Bladder and Urothelial Cancer Treatments
- Machine Learning in Bioinformatics
- Plant Molecular Biology Research
- Glaucoma and retinal disorders
- semigroups and automata theory
- Viral Infections and Vectors
Translational Genomics Research Institute
2020-2024
Korea National Institute of Health
2020-2024
City Of Hope National Medical Center
2022-2023
City of Hope
2022-2023
J. Craig Venter Institute
2011-2021
Global Viral
2020
Yonsei University
2015
Pohang University of Science and Technology
2007-2014
Purdue University West Lafayette
2006-2010
Seoul National University
2004
As next-generation sequencing projects generate massive genome-wide sequence variation data, bioinformatics tools are being developed to provide computational predictions on the functional effects of variations and narrow down search casual variants for disease phenotypes. Different classes at nucleotide level involved in human diseases, including substitutions, insertions, deletions, frameshifts, non-sense mutations. Frameshifts mutations likely cause a negative effect protein function....
Abstract Summary: We present a web server to predict the functional effect of single or multiple amino acid substitutions, insertions and deletions using prediction tool PROVEAN. The provides rapid analysis protein variants from any organisms, also supports high-throughput for human mouse at both genomic levels. Availability implementation: is freely available open all users with no login requirements http://provean.jcvi.org. Contact: achan@jcvi.org Supplementary information: data are...
Humans are a diploid species that inherit one set of chromosomes paternally and homologous maternally. Unfortunately, most human sequencing initiatives ignore this fact in they do not directly delineate the nucleotide content maternal paternal copies 23 individuals possess (i.e., 'phase' genome) often because costs complexities doing so. We compared 11 different widely-used approaches to phasing genomes using publicly available 'Genome-In-A-Bottle' (GIAB) phased version NA12878 genome as...
Recently we have developed a new algorithm, PROVEAN (<u>Pro</u>tein <u>V</u>ariation <u>E</u>ffect <u>An</u>alyzer), for predicting the functional effect of protein sequence variations, including single amino acid substitutions and small insertions deletions [2]. The prediction is based on change, caused by given variation, in similarity query to set its related sequences. For this prediction, algorithm required compute semi-global pairwise alignment score between each Using dynamic...
Abstract Background Infections by pan-drug resistant Acinetobacter baumannii plague military and civilian healthcare systems. Previous A. pan-genomic studies used modest sample sizes of low diversity comparisons to a single reference genome, limiting our understanding gene order content. A consensus representation multiple genomes will provide better framework for comparison. large-scale comparative study identify genomic determinants associated with their adaptation as successful pathogen....
Information theory traditionally deals with "conventional data," be it textual data, image, or video data. However, databases of various sorts have come into existence in recent years for storing "unconventional data" including biological social web topographical maps, and medical In compressing such one must consider two types information: the information conveyed by structure itself, data labels implanted structure. this paper, we attempt to address former problem studying graphical...
Antimicrobial resistance (AMR) is an ever-growing public health problem worldwide. The low rate of antibiotic discovery coupled with the rapid spread drug-resistant bacterial pathogens causing a global crisis. To facilitate drug processes, we present large-scale study reference challenge transcriptome profiles, which included 37 antibiotics across 6 mechanisms actions (MOAs) and provide economical approach to aid in antimicrobial dereplication process. We demonstrate that classical MOAs can...
The CoV disease 2019 (COVID-19) infectious 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, infected 40 million people, responsible for more than 1 deaths.
Chronic inflammation is one of the main causes cancer, yet molecular mechanism underlying this effect not fully understood. In study, we identified FAT10 as a potential target gene STAT3, expression which synergistically induced by NFκB co‐stimulation. STAT3 binding stabilizes on promoter and leads to maximum induction expression. Increased represses transcriptional activity tumor suppressor p53, protein that accelerates degradation FAT10. This FAT10‐p53 double‐negative regulation critical...
In clinical practice, point-of-care diagnostic testing has progressed rapidly in the last decade. For field of wound care, there is a compelling need to develop rapid alternatives for bacterial identification setting, where it generally takes over 24 hours receive positive identification. Even new molecular and biochemical methods require an initial incubation period several obtain sufficient number cells prior performing analysis. Here we report use inexpensive, disposable electrochemical...
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 biomedical science. However, rediscovery known antibiotics demonstrates need for approaches that accurately identify potential novelty higher throughput and reduced labor. Here we describe an explainable artificial intelligence classification methodology emphasizes prediction performance human interpretability by...
The heritability of gene expression is critical in understanding heterosis and dependent on allele-specific regulation by local remote factors the genome. We used RNA-Seq to test whether variation among F1 F2 intraspecific Salix purpurea progeny attributable cis- trans-regulatory divergence. assessed mode inheritance based levels for two distinct tissue types: shoot tip stem internode. In addition, we explored sexually dimorphic patterns regulatory divergence individuals. show that S....
Maize is a global crop and powerful system among grain crops for genetic genomic studies. However, the development of novel biological tools resources to aid in functional identification gene sequences greatly needed. Towards this goal, we have developed collection maize marker lines studying native expression specific cell types subcellular compartments using fluorescent proteins (FPs). To catalog FP expression, public repository, Cell Genomics (MCG) Database,...
PAF, which is composed of Paf1, Cdc73, Ctr9, Leo1, and Rtf1, a novel complex with multiple functions in transcription-related activities. The PAF interacts histone-modifying enzymes RNA polymerase II to regulate transcription. With general transcription regulatory potential yeast, Hyrax/Cdc73 has been reported associate beta-catenin control Wnt/Wg signal-specific Drosophila. Here, we present the first evidence IL-6 transcriptional regulation by SH2BP1/CTR9 mammals. Upon LPS injection mice,...
The comprehensive identification of functional transcription factor binding sites (TFBSs) is an important step in understanding complex transcriptional regulatory networks. This study presents a motif-based comparative approach, STAT-Finder, for identifying DNA STAT3 factor. STAT-Finder combines STAT-Scanner, which was designed to predict STAT TFBSs with improved sensitivity, and alignment minimize false positive prediction rates. Using two reference sets containing promoter sequences known...
In light of the ongoing antimicrobial resistance crisis, there is a need to understand role co-pathogens, commensals, and local microbiome in modulating virulence antibiotic resistance. To identify possible interactions that influence expression or survival mechanisms both multidrug-resistant organisms (MDROs) human host cells, unique cohorts clinical isolates were selected for whole genome sequencing with enhanced assembly full annotation, pairwise co-culturing, transcriptome profiling. The...
To investigate the genomic context of a novel resistance island (RI) in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates and global isolates.Using combination long short reads generated from Oxford Nanopore Illumina platforms, contiguous chromosomes plasmid sequences were determined. BLAST-based analysis was used to identify RI insertion target.Genomes four A. strains, US hospital system, belonging prevalent MLST ST2 (Pasteur scheme) ST281 (Oxford clade F sequenced...
Traditionally, the performance of distributed algorithms has been measured in terms time and message complexity.Message complexity concerns number messages transmitted over all edges during course algorithm. However, energy-constrained ad hoc wireless networks (e.g., sensor networks), energy is a critical factor measuring efficiency Transmitting between two nodes an associated cost (energy) moreover this can depend on distance them among other things). Thus addition to complexity, it...
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 public health economy. Testing strategies deployed on a population scale at day zero, i.e., time first reported case, would be significant value. Next-generation sequencing (NGS) such capabilities; however, it limited detection sensitivity low-copy-number pathogens. Here, we leverage CRISPR-Cas9 system effectively remove...