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Bioinformatics

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Penn State College of Medicine provides a variety of bioinformatics and biostatistics services, including analysis, prediction and software support.

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Instrumentation and Services

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  • DNA Next Generation Sequencing (NGS) analysis
  • Exome-Sequencing analysis
  • ChIP-Seq analysis (narrow peaks or wider domains)
  • RNA-Seq analysis
  • DNA Methylation Sequencing analysis
  • Ribo-Seq analysis
  • Differential expression (RNA-Seq and DNA methylation)
  • Variant discovery (DNA and RNA-Seq)
  • Junction-based analysis of splicing events
  • ENCODE correlations with NGS datasets
  • The Cancer Genome Atlas (TCGA) NGS datasets
  • Epigenetic signature discovery
  • Transcription Factor Motif discovery
  • Phosphorylation prediction
  • microRNA target prediction
  • Virus de novo Assembly
  • Microarray analysis
  • Biomarker panel design
  • Pathway analysis
  • Gene ontology analysis
  • Proteomics analysis
  • qPCR analysis
  • Machine learning
  • Custom scripts/software
Software Support Expand answer
  • Ingenuity Pathways
  • MATLAB
  • Bioinformatics public software (bowtie, bwa, MACS, RSEG, tophat, cufflinks, samtools, picard, IGV, GATK, GSEA, DAVID, hmmer, etc.)
  • R, Python, Perl, Java and other programming languages

Procedures, Protocols and Forms

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Investigators should cite Penn State College of Medicine Bioinformatics and list the names of the software and the personnel services utilized either in the Materials and Methods section or the Acknowledgements section of any article.

Work With Bioinformatics

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