What we do

The Bioinformatics Core has been enhancing large-scale data analytics for Wilmer/JHU vision researchers since 2003. We use/develop computational biology approaches to extract useful information from a wide range of large datasets generated by rapidly evolving ‘omics technologies including RNA-seq, ATAC-seq, ChIP-seq, genomic sequencing, proteomics, and integrative data analysis. An emphasis of recent work has been on single-cell sequencing data technologies. In addition, we will aid vision researchers prepare new grant applications by processing preliminary and/or published ‘omics datasets, helping to design bioinformatics projects, writing/editing bioinformatics sections, and providing letters of support/collaboration.

Who we support

The Core prioritizes support for NEI R01-funded investigators. However, we are equally committed to help early-stage researchers who have not yet secured NIH funding, those who are weathering a gap in funding support, and investigator new to vision science.

Accessing our services

We often need to deeply involved in the projects we provide assistance on. The process typically starts with a discussion with the PI(s) who request our assistance with project design. As projects mature, our role expands into computational data analysis, data presentation, data interpretation, and manuscript writing. The users can also fill the online form to request the service and we will be in touch to discuss your needs.

Wilmer Bioinformatics Team

Director, Dr. Jiang Qian, Ph.D., Karl H Hagen Professor of Ophthalmology, has overseen the Bioinformatics Core since its inception, and his arrival to Wilmer, in 2003. He has broad experience in computational biology and bioinformatics. His lab is funded by grants from the National Institutes of Health and other funding sources. Dr. Qian has been/is involved in a variety of bioinformatics projects and established exciting and fruitful collaborations with a number of vision science investigators at Wilmer and across JHU.

Dr. Mohammed Amanullah (Aman), Ph.D., is a bioinformatics specialist who spends ~60% of his effort on the Core service. His expertise is in single-cell RNA-seq, ATAC-seq, differentially expressed genes, and pathway analysis.

Dr. Pin Lyu, Ph. D., has been working on single-cell RNA-seq, ATAC-seq, and constructing regulatory networks relevant to retinal biology. He is often assigned projects related to regulatory gene network construction, which requires the integration of RNA-seq and ATAC-seq data.

Dr. Yin Xing, Ph. D., has been working on cell-cell interactions using single-cell sequencing datasets. She has been helping other investigators on predicting ligand-receptor interactions between retinal cells during different biological processes.

Dr. Yang Jin, Ph. D., has expertise in single-cell sequencing data analysis and pathway analysis. He helps other investigators to analyze cell-cell communication networks mediated by neurotransmitters and also helps to analyze spatial transcriptomics data.

Dr. Yvonne Zhai has been working on single-cell databases. She is building a single-cell expression database specific to retinal cells so that the investigators can query the genes of interest and obtain the cell-specificity of the query genes.

Contact Information

Wilmer Bioinformatics Center
M03017 Smith Building
Phone: 443-287-3882
Email: jiang.qian@jhmi.edu