As Head of Bioinformatics of the Genome Sciences and Bioinformatics Core at the Penn State College of Medicine, I would be happy to discuss your bioinformatics needs (Contact). Following are examples of bioinformatics analyses we have provided in the past (Publications). Our clients are investigators from Penn State and external institutions including Yale and research institutes in Europe and Japan, as well as private companies such as Aptagen, LLC.
- DNA Next Generation Sequencing (NGS) analysis
- ChIP-Seq analysis (narrow peaks or wider domains)
- RNA-Seq analysis
- DNA Methylation Sequencing analysis
- Ribo-Seq analysis
- Differential Expression (RNA-Seq & DNA methylation)
- Variant Discovery (DNA & RNA-Seq)
- Junction-based analysis of splicing events
- Microbial community structure analysis based on 16S rDNA NGS
- Identification of transgenes genomic insertion sites by NGS
- ENCODE correlations with NGS datasets
- The Cancer Genome Atlas (TCGA) NGS datasets
- Epigenetic Signature discovery
- Transcription Factor Motif discovery
- Phosphorylation prediction
- Immune Epitope prediction
- microRNA Target prediction
- Virus de novo Assembly
- Virus Host Integration Sites discovery
- Microarray analysis
- Time-series Microarray analysis
- Biomarker Panel design
- Pathway analysis
- Gene Ontology analysis
- Proteomics analysis
- qPCR analysis
- Machine Learning
- Custom scripts/software
