Applied Bioinformatics Core

The Applied Bioinformatics Core (ABC) is a central service group that specializes in providing data management and analysis support to large genomic centers and research groups. The objective of the core is to provide analytical capabilities to support and advance biomedical research.

We have ample expertise analyzing biological data from diverse types of experiments including, but not limited to, high-throughput genomic assays.

We have extensive experience in building standardized workflows as well as customized, in-depth analyses with emphasis on thorough quality control and statistical rigor.

We perform detailed computational analyses that are driven by specific biological questions defined by the investigators.

We provide extensive reports with publication-ready images as well as the analysis source code.

The example projects should give you an impression of the most commonly performed analyses - we are by no means limited to them and are happy to tackle new challenges. Please contact us at for inquiries.



Single-cell RNA-seq | Spatial transcriptomics | CITE-seq | Differential gene expression analysis with bulk RNA-seq | General RNA biology assays such as CLIP-seq or PRO-seq

Example Projects:

  • Single-cell RNA-seq of in vitro differentiated embryonic stem cells
  • Transcriptome changes induced by deletion of a GTPase
  • Combined CITE-seq and TCR-seq for understanding T cell populations driving autoimmunity


ChIP-seq | ATAC-seq | Reduced representation bisulfite sequencing (RRBS) or targeted methylation | Whole Genome Bisulfite sequencing

Example Projects:

  • Effects of cancer drugs on chromatin accessibility
  • Whole-genome bisulfite sequencing of neuronal cells
  • Identifying key genes of neuronal differentiation using CUT&TAG


Variant calling and annotation | Evolution of viral sequences | Classifications of pathogens

Example Projects:

  • Identification & annotation of genomic variants in different mutants of a rodent parasite
  • Functional annotation of sequence variants in a gene possibly related to a bleeding phenotype

Functional Analyses

GO term enrichments | Gene set enrichments | Pathway Analyses | DNA motifs | Integration of diverse data sets

Example Projects:

  • Understanding cancer-induced transcriptome changes in blood cells
  • Characterizing the effects of inhibitors of chromatin-associated molecules for immune cell functions

Computational Pipelines

Large-scale automation of analysis pipeline | Distribution and management of large datasets | Shiny apps

Example Projects:

  • HIPAA-certified pipeline for the identification of genomic variants in tumor patient samples (for the Institute for Precision Medicine)
  • PubShare data portal for downloading and sharing genomic data
  • Interactive application for storing, visualizing, and analyzing proteomics data

Training and Consulting

Walk-in clinic

Consulting and hands-on help with questions relating to performing bioinformatics tasks
Currently held online. Please email for details.

Hands-on workshops

Regularly held, intensive 12-hours-long courses open to members of the Tri-Institutional network

  • Introduction to R
  • Introduction to UNIX
  • Differential gene expression analysis using RNA-seq



Dr. Doron Betel

Dr. Doron Betel

Core Director

Dr. Maider Astorkia Amiama

Dr. Maider Astorkia Amiama

Computational Genomic Scientist

Paul Zumbo

Paul Zumbo

Senior Staff Associate of Computational Genomics

Selected Publications

Get in touch