Biomedical Informatics

The mission of the Bioinformatics Division of the BISR is to support HICCC investigators by giving them access to key expertise in the use of advanced data analysis tools and methodologies for research publications and grant proposals, reflecting established best practices, access to state of the art software, databases, and models for basic research, and access to high-performance computing infrastructure for data analysis and data sharing.


Services

The Bioinformatics Division of the BISR offers the following services:

Data analysis and database access services

These help HICCC investigators create preliminary data for research grant proposals and final data for publications and presentations. For instance, an often requested service includes normalizing and analyzing high-throughput sequencing data (RNASeq, ChIPSeq, ATACSeq), microarray data (expression profiles, ChIP on chip, genotyping, etc.), or proteomic data and then uploading it in standard repositories, such as GEO (Gene Expression Omnibus). Use of appropriate statistical tests and data mining tools, reflecting accepted best practices, is a key element of success in proposal and publication submissions. Other services include gene identification and molecular modeling.

Access to a variety of public and commercial bioinformatics web-tools

Which tools (or tool sub-functionality) to use to address a specific problem is a complex question, with answers that are in constant evolution. The BISR personnel help investigators select from a vast array of available tools the ones that best fit their requirements and reflect accepted best practices or specific publication requirements.

geWorkbench Integrated Genomics Web Site

Bioinformatics Web Sites

Custom bioinformatics workflow development

Although the typical experimental lab may have the ability to use bioinformatics software, given appropriate access and training, the ability to program customized data analysis workflows, to integrate multiple tools, is extremely rare. A typical example is the intersection of ChIP-on-chip and gene expression profile data, followed by sequence analysis to identify functionally active DNA binding sites for a given transcription factor. The BISR addresses this need by providing custom programming expertise. Over 80 papers have resulted from these collaborations.

Custom biological database development

An increasing number of HICCC investigators are producing high-throughput biological data, which often require stratification according to phenotypic information in clinical databases. The BISR helps investigators to develop and to host their custom databases and to integrate them with those containing clinical data.

Custom web site development for data sharing and dissemination

Based on the data sharing plan and on increasingly strict requirements from journals, HICCC investigators must share and disseminate their results to the research community. This is usually done using either an access controlled or an unrestricted access web portal. BISR personnel help design, develop, deploy, and host these portals in a more efficient and cost effective way than if they had to be developed and maintained by the individual HICCC investigator.

Access to high performance computing equipment for computationally intensive analyses

New generation bioinformatics tools, especially in the area of systems biology or when large genomic data scans are required, may require substantial computational power and storage requirements. Traditionally, research labs would either purchase and maintain their own hardware or seek collaboration with bioinformatics collaborators who can run these computationally intensive programs. The BISR has access to one of the largest academic computational clusters dedicated to research in molecular and systems biology.


Locations and Contacts

Aris Floratos, PhD, Director 
Tel: (212) 851-5139
Email:  af2202@cumc.columbia.edu
Irving Cancer Research Building, Room 801,
1130 St. Nicholas Avenue, New York, NY 10032

Richard A. Friedman, PhD
Specializing in gene expression analysis, functional, sequential, and structural genomics, and proteomics, biostatistics, and microbiomics.
Tel: (212)851-4765
Email: raf4@cumc.columbia.edu
Irving Cancer Research Building, Room 825,
1130 St. Nicholas Avenue, New York, NY 10032

Hyunjin Kim, PhD
Specializing in gene expression analysis, functional and sequential genomics, and outcome prediction. Database configuration and computer programming.
Email: hk2990@cumc.columbia.edu
Irving Cancer Research Building, Room 808D,
1130 St. Nicholas Avenue, New York, NY 10032


User Fees and Policies

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

  • Cancer Center Members: First 3 hours free; $90/hour thereafter
  • Non-Cancer Center Members: First 3 hours free; $120/hour thereafter
  • External users: $192/hour

Access to High Performance Computing Equipment

Access to cluster computing resources are available to users of the biomedical informatics shared resource through the department of Systems Biology.

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

Visit the Department of Systems Biology


Online Reservations

The Biomedical Informatics Shared Resource uses the iLab Core Management System for service requests and billing. Before you can request services, you must log into iLab and be approved as a lab member.


Affiliate Organizations