Bioinformatics Support

Bioinformatics resources and tools, consultation, training, and services offered by the Medical Library are free for any Yale affiliate including faculty, students, postdocs, and staff.


Consultation Services

Consultation is available (free of charge) to individuals, groups or team to address bioinformatics-related research questions and needs. Consultation is mainly provided in-person but less complex questions may be addressed over email or by phone. Contact Rolando Milian to schedule a consultation service: 203-785-6194 or

Examples of consultation topics are:

  • Analysis of microarray and next-generation sequencing (NGS) data using library-licensed bioinformatics tools
  • Enrichment (pathway and network) analysis of differentially regulated molecules.  
  • Finding, retrieving, and using public datasets for cross-referencing research results or hypothesis testing  
  • Complex literature searches. 
  • Identification of appropriate bioinformatics software or databases to answer specific research questions
  • Development or narrowing hypothesis in silico by using existing public omics data and literature
  • Hands-on tutorials on bioinformatics software licensed by the Medical Library

The Yale Cushing/Whitney Medical Library Bioinformatics End User Support Program provides letters of support for grant applications. In addition, it offers collaborative data analysis services (co-authorship) for complex high-throughput data analysis projects.

Databases and Software

The CWML End User Bioinformatics Support license a variety of commercial bioinformatics software in support of the biomedical research data lifecycle. These tools are free of charge to Yale biomedical researchers (including students, postdocs, and staff). Click on each link below to request/register for an account. Contact Rolando Milian (203-785-6194 - or Lindsay Barnett (203-785-2883 for questions or comment on these programs.   

  • REGISTER TO ACCESS Ingenuity Pathway Analysis (IPA). This is a manually-curated knowledge base obtained from the peer-reviewed biomedical literature, public and private databases. With IPA, you can identify relevant biomarkers, contextualize metabolomics, proteomics, toxicogenomics, and transcriptomics data, and perform pathway network analysis among others. Login to IPA (once you are registered)
  • REGISTER TO ACCESS MetaCore (Thomson Reuters) MetaCore is an online software based on manually-curated knowledgebase of transcription factors, receptor/ligands, kinase, drugs from the biomedical literature. MetaCore can be used for the functional analysis of the NextGen sequence data, CNV, microarray, proteomics, metabolic, SAGE, proteomics, siRNA, microRNA, and screening data. Login to MetaCore (once you are registered)
  • REGISTER TO ACCESS Partek Flow. This software is used for the analysis of next generation sequencing data including RNA, small RNA, and DNA sequencing. It has a user-friendly graphical interface that allows to build your own custom analysis pipelines for Alignment, Quantification, Quality control, Statistics, and Visualization. Login to Partek Flow (once registered)
  • BIOBASE Knowledge Library ( TRANSFAC) The BIOBASE Knowledge Library™ (BKL) is a collection of gene-regulation and protein oriented scientific databases created from the peer-reviewed scientific literature. The TRANSFAC®, and PROTEOME™ products are included in BIOBASE.
  • REGISTER TO ACCESS Ingenuity Variant Analysis. You can identify variants and verify them. Find disease-causing variants faster by using 16+ years of expert manual curation of the scientific literature. By indexing all known disease-causing biological processes, it can deliver new insights and increased likelihood of homing in on the causal variant you’re seeking. Login to IVA once registered
  • BioCyc is a genome and metabolic pathway web portal covering more than 5,500 organisms. It enables visualization of metabolomics data on individual pathway diagrams and on the organism-specific metabolic map diagrams that are available for every BioCyc organism. In addition, it has online tools for browsing metabolic/regulatory networks, gene, metabolites within the networks, examine the connectivity of the network, and other functionalities. 
  • REGISTER TO ACCESS Qlucore Omics Explorer facilitates a dynamic, visualization-guided analysis of OMICs data, applicable to various phases of a discovery cycle. With Qlucore, you can visualize, perform quality control, apply statistics, perform 3D principal component analysis, and create publication-ready graphics, heat maps, and various 2D plots. GSEA and GO are available for biological exploration. Use valuable public data (TCGA, GEO) to test your ideas, or generate/narrow new hypotheses, with an easy download and integration into your data analysis.

Training and Presentations

The Bioinformatics Support Program offers wide variety of bioinformatics training, presentations and demos for any Yale affiliate including students, postdocs, and staff. Training is free but registration is required due to limited seating. 

Check the Calendar for upcoming bioinformatics events.

Please register at to receive announcements of upcoming training, new licensed software, and services.