Customized Reference Genomes/Transcriptomes

Generate customized reference genomes/transcriptomes using pre-defined mutations or gene fusions
Enhance sensitivity of detecting genomic alterations in next-generation sequencing data
Improve results from downstream bioinformatics analyses
Identifying Your Mechanism of Action – UGenome AI

Utilize bioinformatics pipelines to identify how a target of interest affects a specific disease on a molecular level
Narrow down potential therapeutic strategies
Provide direction for the experimental design process
Single cell RNA-seq analysis

Profile transcriptomes of cells in biological research
Analyze data to identify rare cell subtypes
Utilize expertise and in-house pipelines for QC, clustering, and differential expression analysis
RNA-Sequencing Analysis

End-to-end processing of bulk-RNA seq data
Align to a standard reference genome, quantify aligned reads, and perform data quality checks
Normalize and batch correct data as necessary
Differential Expression Analysis

Perform differential expression analysis using statistical methods (t-tests, ANOVA, edgeR, DESeq2)
Identify differentially expressed genes
Hone in on top differentially expressed genes using significance thresholds
Treatment response prediction

Discover molecular biomarkers that predict response to therapy
Use machine learning approaches and validation strategies
Provide biomarkers with the most predictive power and robustness across external datasets
Diagnostic/prognostic Biomarker discovery

Perform multicohort analysis integrating multiple datasets
Identify gene signatures with diagnostic/prognostic utility
Validate gene signatures using machine learning framework and external datasets
Pre-Clinical Patient Selection Strategies

Develop a molecular strategy to determine which subset of patients would most likely respond to a therapy regimen
Combine internal, external, and literature data
Create a customized score to guide patient selection
Classifier development (ML/AI)

Build and optimize classifiers using cross-validation strategies
Deploy classifiers on medical devices or online health systems
Evaluate multiple classifiers (logistic regression, tree-based classifiers, XGBoost, Neural Nets, Genomic ensembling algorithms)
Experiment/Project design consulting

Help clients design experiments or projects where data needs to be generated to address specific questions
Understand the types of analyses that are possible
Generate data for maximum analytical insight
Genetics (GWAS, Exome-Seq)

Analyze genetic data (GWAS, Exome-Seq)
Identify genetic variations associated with diseases or traits
Develop personalized medicine strategies
Epigenetics (microarray, NGS)

Analyze epigenetic data (microarray, NGS)
Identify epigenetic modifications associated with diseases or traits
Develop precision medicine strategies
Transcriptomics (RNA-Seq, microarray)

Analyze transcriptome data (RNA-Seq, microarray)
Identify differentially expressed genes
Understand gene regulation and disease mechanisms
Single cell genomics (10X)

Analyze single cell genomic data (10X)
Identify cell types and their molecular profiles
Discover cell-cell interactions and disease mechanisms
Proteomics (somalogic, olink, Luminex)

Analyze proteomic data (somalogic, olink, Luminex)
Identify proteins and their modifications
Understand protein-protein interactions and disease mechanisms
Metabolites (untargeted)

Analyze untargeted metabolomics data
Identify metabolites and their concentrations
Understand metabolic pathways and disease mechanisms
Flow cytometry

Analyze flow cytometry data
Identify cell populations and their characteristics
Understand immune cell function and disease mechanisms
Public data found in GEO

Analyze public data from GEO repository
Identify datasets relevant to research questions
Integrate public data with experimental data
Biostatistics services

Design experiments, perform statistical analyses, and interpret results
Provide statistical support for research projects
Ensure the validity and reliability of research findings
Data interpretation service

Interpret complex data across multiple therapeutic areas
Identify meaningful patterns and trends
Draw conclusions and make recommendations based on data analysis

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UGenome Bioinformatics Services

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