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Revealing neural circuit topography in multi-color.

Published in Journal of visualized experiments : JoVE

Neural circuits are organized into functional topographic maps. In order to visualize complex circuit architecture we developed an approach to reliably label the global patterning of multiple topographic projections. The cerebellum is an ideal model to study the orderly arrangement of neural circuits. For example, the compartmental organization of ...

Leveraging big data bioinformatics approaches to extract knowledge from Staphylococcus aureus public omics data.

Published in Critical reviews in microbiology

Staphylococcus aureus is a notorious pathogen posing challenges in the medical industry due to drug resistance and biofilm formation. The horizon of knowledge on S. aureus pathogenesis has expanded with the advancement of data-driven bioinformatics techniques. Mining information from sequenced genomes and their expression data is an economic approa...

Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins

Published in Journal of Proteome Research

Using data from 183 public human data sets from PRIDE, a machine learning model was trained to identify tissue and cell-type specific protein patterns. PRIDE projects were searched with ionbot and tissue/cell type annotation was manually added. Data from physiological samples were used to train a Random Forest model on protein abundances to classif...

Epidemiological Analysis of Coronavirus Disease 2019 (COVID-19) in 2 Cities in China Based on Public Data.

Published in Disaster medicine and public health preparedness

Based on the public data from the health departments of Tianjin and Shenzhen, we conducted a comparative analysis of the coronavirus disease 2019 (COVID-19) epidemic situation between these 2 cities. The aim of this study was to evaluate the role of public data in epidemic prevention and control of COVID-19, providing a scientific advice for the su...

What can be learned from Repository-Scale Public Mass Spectrometry Data?

High-throughput tandem mass spectrometry has enabled the detection and identification of over 75\% of all human proteins predicted to result in translated gene products from an available tens of terabytes of public data in thousands of datasets. This thesis explores what we can learn from this, as well as the challenges that arise when considering ...

Multidrug Resistance Dynamics in Salmonella in Food Animals in the United States: An Analysis of Genomes from Public Dat...

Published in Microbiology spectrum

The number of bacterial genomes deposited each year in public databases is growing exponentially. However, efforts to use these genomes to track trends in antimicrobial resistance (AMR) have been limited thus far. We used 22,102 genomes from public databases to track AMR trends in nontyphoidal Salmonella in food animals in the United States. In 201...

Machine Learning–Based Prediction of COVID-19 Mortality With Limited Attributes to Expedite Patient Prognosis and Triage...

Published in Jmirx Med

Background The onset and development of the COVID-19 pandemic have placed pressure on hospital resources and staff worldwide. The integration of more streamlined predictive modeling in prognosis and triage–related decision-making can partly ease this pressure. Objective The objective of this study is to assess the performance impact of dimensionali...