Experimental Design and Statistical Data Analysis: Multi-OMICS, biology, biomedical and population epidemiology, artificial intelligence, machine learning.
Computational Systems Biology and Bioinformatics: We can help you make sense of your results by placing them in biological context through annotation and integration with data sources.
Biomarker Discovery: Gene function prediction and annotation (PICRUSt2) to identify biofilm signatures like quorum sensing.
Custom Analyses: Tailored solutions for evolutionary, epidemiological, and microbial research needs.
High-throughput Sequencing Analysis: We analyze all types of high-throughput sequencing data from RNA-seq and single-cell RNA-seq to variant sequencing (exome or whole genome), to ChIP-seq, or bisulfite sequencing. With spatial profiling methods becoming more accessible, we have developed new workflows for spatial transcriptomic analysis and multimodal integration.
Metagenomic Data Preparation: Quality control (FastQC, MultiQC) and trimming (Trimmomatic) for robust sequence datasets.
Microbial Community Profiling: Taxonomic binning and diversity analysis (QIIME2) from 16S rRNA data, covering microbiome composition and functional traits.
Whole-Genome and Protein Analysis: Sequence comparison and evolutionary profiling (BLAST+) for microbial and genomic insights.
Phylogenetic Analysis: Sequence data collection (NCBI, UniProt), alignment (MAFFT), tree reconstruction (IQ-TREE, FastTree, USHER, Nextclade), and visualization (iTOL, Auspice) for evolutionary studies and pathogen tracking (e.g., SARS-CoV-2).
Biomedical Data Management: Data management plan, data storage, sharing, and publication.
Software Development: We develop software, primarily web applications and machine learning models, for use cases in cell, microbes, material, and agriculture science & engineering.
Training: We offer a dedicated bioinformatics training program for researchers interested in learning basic data skills and the analysis of high-throughput sequencing data. Our workshops focus on utilizing best practices in the field and research reproducibility.
Grant and Manuscript Support Services: Grant proposal development, manuscript preparation and editing, data analysis for publications, collaborative writing and review.