The Bioinformatics Core offers a collaborative service to help vision scientists take advantage of rapidly evolving data-driven technologies in genomics, proteomics, and data analytics.
Our team is available to assist at all stages of a project including planning, optimization, implementation, analysis, and interpretation. We routinely work with labs looking to perform new experiments or re-analyze previously published data.
We have expertise in generation and analysis of data from the following techniques among others:
- scRNA-seq
- bulk RNA-seq
- ATAC-seq
- Massively Parallel Reporter Assays (MPRA/CRE-seq)
- CRISPR screening
- Metagenomic profiling
Examples of projects to which we have recently contributed
Shen N, Fitzpatrick MJ, Harding EG, Rebba S, Ruzycki PA, Kerschensteiner D. A genome-wide in vivo CRISPR screen identifies neuroprotective strategies in the mouse and human retina. bioRxiv [Preprint]. 2025 Mar 24:2025.03.22.644712. doi: 10.1101/2025.03.22.644712. PMID: 40492201; PMCID: PMC12148056.
Soto F, Lin CI, Jo A, Chou SY, Harding EG, Ruzycki PA, Seabold GK, Petralia RS, Kerschensteiner D. Molecular mechanism establishing the OFF pathway in vision. Nat Commun. 2025 Apr 18;16(1):3708. doi: 10.1038/s41467-025-59046-0. PMID: 40251167; PMCID: PMC12008213.
Concepcion C, Xia Y, Korshunova Y, Bligard GW, Taylor A, Paley MA, Ruzycki PA, Hassman LM. Compositional variation in eye-infiltrating immune cells distinguishes human uveitis subtypes. iScience. 2025 Jan 30;28(3):111928. doi: 10.1016/j.isci.2025.111928. PMID: 40060903; PMCID: PMC11889669.
Hernández-Núñez I, Urman A, Zhang X, Jacobs W, Hoffman C, Rebba S, Harding EG, Li Q, Mao F, Cani AK, Chen S, Dawlaty MM, Rao RC, Ruzycki PA, Edwards JR, Clark BS. Active DNA demethylation is upstream of rod-photoreceptor fate determination and required for retinal development. bioRxiv [Preprint]. 2025 Feb 3:2025.02.03.636318. doi: 10.1101/2025.02.03.636318. PMID: 39975078; PMCID: PMC11838574.
Paley MA, Yang X, Hassman LM, Penkava F, Garner LI, Paley GL, Linskey N, Agnew R, Arantes de Faria PH, Feng A, Li SY, Simone D, Roberson ED, Ruzycki PA, Esaulova E, Laurent J, Feigl-Lenzen L, Springer LE, Liu C, Gillespie GM, Bowness P, Garcia KC, Yokoyama WM. Mucosal signatures of pathogenic T cells in HLA-B*27+ anterior uveitis and axial spondyloarthritis. JCI Insight. 2024 Jul 18;9(16):e174776. doi: 10.1172/jci.insight.174776. PMID: 39024572; PMCID: PMC11343591.
Bergmans S, Noel NCL, Masin L, Harding EG, Krzywańska AM, De Schutter JD, Ayana R, Hu CK, Arckens L, Ruzycki PA, MacDonald RB, Clark BS, Moons L. Age-related dysregulation of the retinal transcriptome in African turquoise killifish. Aging Cell. 2024 Aug;23(8):e14192. doi: 10.1111/acel.14192. Epub 2024 May 14. PMID: 38742929; PMCID: PMC11320354.
Zhou Y, Bennett TM, Ruzycki PA, Guo Z, Cao YQ, Shahidullah M, Delamere NA, Shiels A. A Cataract-Causing Mutation in the TRPM3 Cation Channel Disrupts Calcium Dynamics in the Lens. Cells. 2024 Jan 30;13(3):257. doi: 10.3390/cells13030257. PMID: 38334649; PMCID: PMC10854584.
Lin JB, Santeford A, Colasanti JJ, Lee Y, Shah AV, Wang TJ, Ruzycki PA, Apte RS. Targeting cell-type-specific, choroid-peripheral immune signaling to treat age-related macular degeneration. Cell Rep Med. 2024 Jan 16;5(1):101353. doi: 10.1016/j.xcrm.2023.101353. PMID: 38232696; PMCID: PMC10829736.
Lee TJ, Sasaki Y, Ruzycki PA, Ban N, Lin JB, Wu HT, Santeford A, Apte RS. Catalytic isoforms of AMP-activated protein kinase differentially regulate IMPDH activity and photoreceptor neuron function. JCI Insight. 2024 Jan 16;9(4):e173707. doi: 10.1172/jci.insight.173707. PMID: 38227383; PMCID: PMC11143937.
Meet the Bioinformatics Core Team
Philip Ruzycki, PhD
Assistant Professor, Ophthalmology and Visual Sciences
- Email: p.ruzycki@nospam.wustl.edu
