The Applied Bioinformatics Laboratories, part of NYU Langone’s Institute for Computational Medicine, provides computational analysis and support services for biomedical data including next-generation sequencing and imaging data. Our mission is to accelerate scientific discoveries by guiding experimental design, performing robust data quality assessment, carrying out comprehensive computational analyses, and integrating multi-modal biomedical datasets to provide insights into biological function and mechanisms of disease. We contribute to all aspects of the research cycle, including generating ideas and preliminary results for grant applications; performing data management, analysis, and interpretation; and preparing manuscripts for publication.

Our overarching goal is to provide robust and reproducible analysis of biomedical data, including multi-omics, imaging, and clinical data. We accomplish this by using a variety of established and novel computational workflows, methods, and tools that can process data generated in all other cores at NYU Langone, including genomics, proteomics, and metabolomics, as well as imaging and molecular pathology data.

The results of the bioinformatics analyses we conduct are shared with investigators via a customized interface and are also accessible via the High-Performance Computing Core.

Services

Our services are broadly divided into five categories.

Basic/Standardized Analyses

Examples include quality assessment and processing of the most common types of genomics data (for example, DNA-seq, RNA-seq, ATAC-seq, and ChIP-seq) using established computational pipelines.

Advanced/Customized Analyses

Such analyses typically involve integration of multiple types of genomics data, development of new computational workflows, and mining of publicly available data.

Innovation and Development of Novel Computational Tools and Workflows

Bioinformaticians at the Applied Bioinformatics Laboratories not only improve computational workflows and pipelines, but also develop new methods for data analysis. Examples include sns, a platform for basic genomics analysis; iCellR, a comprehensive tool for the analysis of single-cell RNA-seq and CITE-seq data; HiC-bench, a platform for analysis and integration of three-dimensional conformation capture data; and DeepPATH, a workflow for the analysis of whole-slide histopathology images using deep learning.

Education and Training

We offer a variety of training options for biologists and junior bioinformaticians at NYU Langone. We are actively involved in teaching courses to MS and PhD students, and offer training to our broader scientific community through workshops, bioinformatics internships, and tutoring. In collaboration with Institute for Computational Medicine, we have launched the Single-Cell Analysis Club, which holds a monthly event that focuses on how to best analyze data generated from single-cell experiments.

Clinical Genomics Services

Our clinical bioinformatics staff provides support for the validation, deployment, and operation of clinical molecular testing. As an example, together with the Molecular Pathology Lab, we have designed, tested, and deployed a new cancer gene panel comprising approximately 600 genes.

Learn more about the Applied Bioinformatics Laboratories.