About Us
The Florida Research & Innovation Center Bioinformatics & Protein Engineering Core provides expert support and consulting across two broad areas: advanced bioinformatics analysis and state-of-the-art protein engineering.
On the bioinformatics side, we support the analyses of Bulk RNA sequencing (Bulk RNA-seq) data to identify which genes change under different conditions and what is the impact of these changes in a given biological context, such as a pathogen infection or in a disease state. This includes mapping of the differentially regulated genes on biological pathways, functional categories, and interaction networks to uncover meaningful patterns.
We also support Multiomics data analysis and visualization with a special focus on transcriptomics, proteomics and metabolomics data. In the follow-up analysis, we support conducting various types of in-depth functional analyses which include identification of protein complexes, cellular regulation of the targets of high interest and deciphering cellular crosstalk pathways.
In addition, our core also specializes in extracting insights from Intrinsically Disordered Regions (IDRs) as well as performing Short Linear Motif (SLiM) discovery to unravel the mechanism of interactions in the proteins of interest, for instance, we can help in deciphering the kinase substrate relationships from a list of candidate phosphosites. Given SLiMs are known to be mutated in diseases and can be mimicked by several pathogens, our pipelines can provide novel druggable insights for diseases such as cancer as well as in the context of infectious diseases.
Our protein engineering services enable the rational design of therapeutic proteins, antibodies, and enzymes thus helping drive innovation in diagnostics, biologics, personalized medicine and other synthetic biology applications. Specifically, we help researchers in improving proteins by integrating computational analyses of protein sequences, 3D structures, protein interaction interfaces and post-translational modifications among other contextually relevant features. We support modeling, design, miniaturization and optimization of proteins by deploying AI-driven methods alongside classical computational approaches. We work closely with scientists to plan mutagenesis strategies, identify disease variants, repurpose drugs, and support therapeutic and synthetic biology projects.
We are happy to discuss and offer custom solutions for specialized projects too, ensuring flexible support for evolving research needs. Through close collaboration with investigators, our core aims to accelerate discoveries from bench to bedside, improving patient care and advancing the future of medicine.
Contacts
Manjeet Kumar, PhD
Assistant Staff
Director of the Bioinformatics Core and Protein Engineering
[email protected]
Services
Instructions for accessing example reports for standard analyses can be found on the FRIC Bioinformatics Connect Today page (Cleveland Clinic employees only).
- Bulk RNA-seq data analysis, including:
- Differential gene expression analysis
- Differential exon usage and splice variant analysis
- Functional interrogation of gene sets using enrichment (GSEA, GO, KEGG, REACTOME, WikiPathways etc.)
- Pathway integration and interpretation
- Multi-omics integration and visualization, including:
- transcriptome
- proteome
- metabolome
- heatmaps, volcano plots, PCA, t-SNE, UMAP, circos and UpSet plots, networks, graphs etc.
- Protein bioinformatics: sequence analysis, structure prediction (AI-driven approaches and classical computational methods), network analysis, phylogenetics
- Prediction and analysis of protein-protein interactions (PPIs) in health and disease contexts
- Analysis and prediction of intrinsically disordered proteins (IDPs) and Short Linear Motifs (SLiMs)
- Molecular modeling, Docking (protein-protein, protein-ligand, protein-RNA, protein-DNA, protein-small molecule) and Simulations
- Engineering of therapeutic enzymes and antibodies
- Rational design of proteins for enhanced stability, activity, solubility, binding affinity, or novel functions
- De novo protein design for synthetic biology and therapeutic innovation