A5063552754- Geotechnical and construction materials studies
- Plant Physiology and Cultivation Studies
- Traffic Prediction and Management Techniques
- RNA and protein synthesis mechanisms
- Scientific Computing and Data Management
- Genomics and Chromatin Dynamics
- Cancer Immunotherapy and Biomarkers
- RNA modifications and cancer
- Cell Image Analysis Techniques
- Air Quality Monitoring and Forecasting
- Gene expression and cancer classification
- Research Data Management Practices
- Dental Implant Techniques and Outcomes
- Immune Cell Function and Interaction
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- T-cell and B-cell Immunology
- Cancer Genomics and Diagnostics
- Simulation Techniques and Applications
- Biochemical and Structural Characterization
- Bone fractures and treatments
- Vehicular Ad Hoc Networks (VANETs)
- Software System Performance and Reliability
- SARS-CoV-2 and COVID-19 Research
- Single-cell and spatial transcriptomics
University of Southern California
2022-2024
Tehran University of Medical Sciences
2022
Washington University in St. Louis
2022
University of Michigan
2020-2021
University of California, Los Angeles
2021
Chiba University Hospital
2019
Chiba University
2018-2019
The ability to identify and track T-cell receptor (TCR) sequences from patient samples is becoming central the field of cancer research immunotherapy. Tracking genetically engineered T cells expressing TCRs that target specific tumor antigens important determine persistence these quantify responses. available high-throughput method profile TCR repertoires generally referred as sequencing (TCR-Seq). However, TCR-Seq data are limited compared with RNA (RNA-Seq). In this paper, we have...
Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, lack practices sharing research outputs, such data, source code and methods, affects transparency reproducibility studies, which are critical advancement science. Many published studies not reproducible due insufficient documentation, code, shared. We conducted a comprehensive 453 manuscripts between 2016–2021 found that 50.1% them...
ABSTRACT The new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a zoonotic pathogen that has rapidly mutated and become transmissible to humans. There little existing data on the mutations in SARS-CoV-2 impact of these polymorphisms its transmission viral load. In this study, genomic sequence was analyzed identify variants within 3’UTR region cis-regulatory RNA elements. A 43-nucleotide genetic element with highly conserved stem-loop II-like motif (S2M), discovered. research...
It is extremely important to identify transcription factor binding sites (TFBSs). Some TFBSs are proposed be bipartite motifs known as two-block separated by gap sequences with variable lengths. While position weight matrix (PWM) commonly used for the representation and prediction of TFBSs, dinucleotide (DWM) enables expression interdependencies neighboring bases. By incorporating DWM into detection motifs, we have developed a novel tool ab initio motif detection, DIpartite (bipartite based...
As advancements in digital health lead to the generation of increasingly diverse and voluminous pharmaceutical data, it is critical that we teach trainee scientists how leverage this data future innovations healthcare research. To address need, University Southern California Alfred E. Mann School Pharmacy Pharmaceutical Sciences (USC Mann) incorporating science bioinformatics into graduate undergraduate curricula through introductory courses tailored for students without prior programming...
As the outbreak of novel coronavirus disease (COVID-19) continues to spread throughout world, steps are being taken limit impact on public health. In realm infectious diseases like COVID-19, social distancing is one effective measures avoid exposure virus and reduce its spread.Traveling transport can meaningfully facilitate propagation transmission diseases. Accordingly, responsive actions by transit agencies against risk factors effectively make systems safe. Among multitude that affect...
T cell receptor (TCR) studies have grown substantially with the advancement in sequencing techniques of repertoire (TCR-Seq). The analysis TCR-Seq data requires computational skills to run TCR tools. However biomedical researchers limited backgrounds face numerous obstacles properly and efficiently utilizing bioinformatics tools for analyzing data. Here we report pyTCR, a notebook-based solution comprehensive scalable analysis. Computational notebooks, which combine code, calculations,...
Motif discovery and characterization are important for gene regulation analysis. The lack of intuitive integrative web servers impedes the effective use motifs. Most motif tools either not designed non-expert users or lacking optimization steps when using default settings. Here we describe bipartite motifs learning (BML), a parameter-free server that provides user-friendly portal online analysis sequence motifs, high-throughput sequencing data as input. BML utilizes both position weight...
Abstract Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, lack practices sharing research outputs, such data, source code and methods, affects transparency reproducibility studies, which are critical advancement science. Many published studies not reproducible due insufficient documentation, code, shared. We conducted a comprehensive 453 manuscripts between 2016-2021 found that...
As advancements in digital health lead to the generation of increasingly diverse and voluminous pharmaceutical data, it is critical that we teach trainee scientists how leverage this data future innovations healthcare research. To address need, University Southern California Alfred E. Mann School Pharmacy Pharmaceutical Sciences (USC Mann) incorporating science bioinformatics into graduate undergraduate curricula through introductory courses tailored for students without prior programming...