About

Bioinformatics (HICCC)

Overview of Services

The core performs bioinformatics analyses with emphasis on a wide range of whole 'omic data.

Transcriptomics: 

  • Bulk RNASeq:
    • Bulk differential gene and differential transcript expression.
    • Deconvolution for differential cell-type abundance and cell-type specific differential expression.
  • Single Cell RNASeq:
    • Cell-type specific differential abundance and gene expression.
  • Microarray (several platforms) Differential gene and transcript expression.
  • MicroRNA differential expression: RNASeq and microarrays.
  • Spatial transcriptomics.


Proteomics: Mass Spectrometric, microarray,and aptamer based differential protein abundance.

Epigenomics: CHIPSeq and CUT&RUN differential transcription factor and histone tag binding. Microarrays for differential methylation. ATACSeq for differential DNA Opening.

Metabolomics: Dfferential metabolite concentration.

Microbiomics: Community diversity

Mechanistic and integrative analysis: Signaling Pathway Enrichment Analysis; Overrepresentation analysis for pathways and genesets; Gene set enrichment analysis (several methods). Multiomic data integration with the MOFA suite.

Sequence Analysis: Homology identification; Sequence alignment; The MEME suite for protein-DNA binding site analysis. 

Structural Bioinformatics: Homology identification and modeling. Protein-protein and small-molecule protein interactions. Biomolecular structure graphics.

Classification: 

  • Unsupervised learning: Heirarchical clustirng and and heatmaps; UMAP.
  • Supervised learning: Various machine learning methods for classification and outcome prediction.    

Clinical and Population methods:

  • Clinical trials and population studies.
  • Survival analysis.
  • Drug binding curves. 

Deposit of data in public databases.

Other kinds of analyses available on request.

Publications with core memebders as co-authors
https://pubmed.ncbi.nlm.nih.gov/collections/61254450/?sort=pubdate

 

User Fees and Policies

All data analysis, support, consulting, and web site development services:

    Cancer Center Members: First 3 hours free; $110/hour thereafter
    Non-Cancer Center Members: First 3 hours free; $140/hour thereafter
    External users: $220/hour

Access to High Performance Computing Equipment

Access to cluster computing resources are available to clients of the Bioinformatics Core through the Department of Systems Biology Information Technlogy service.

Details about infrastructure and usage fees can be found at the Department of Systems Biology Information Technlogy website.

 

Affiliate Organizations

Department of Systems Biology

Department of Biomedical Informatics

 

Location and hours of operation

Hours:

Monday - Thursday 9:00 AM - 6:00 PM

Fridays: 9:00 AM - 3:00 PM

Sundays: 3:00 PM - 6:00 PM
Location: Irving Cancer Research Building
Room 825
1130 St. Nicholas Avenue
New York, NY 10032

Bioinformatics Core

Dr. Richard Friedman, Manager
Tel: (212) 851-4765
Email: raf4@cumc.columbia.edu
Irving Cancer Research Building, Room 825,
1130 St. Nicholas Avenue, New York, NY 10032

 

 

 

 

 

Links and Resources

For Details of Our Services, please visit our homepage: Biomedical Informatics

Contacts

Name Role Phone Email Location
Dr. Richard Friedman

 

 
raf4@cumc.columbia.edu