Research at the Wu Lab

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At the Wu Lab, we develop novel data science approaches to advance Open Science and FAIR (Findable, Accessible, Interoperable, and Reusable) data sharing. By integrating large-scale, heterogeneous biomedical data and knowledge, we build open infrastructure and intelligent tools that drive novel biomedical discoveries.

Open Science and FAIR Data Sharing

We build open tools and infrastructure to ensure biomedical datasets are easily discoverable, accessible, and reusable by the broader scientific community.

  • BioGPS (biogps.org)
    A community-driven gene portal for aggregating and exploring gene-centric annotations alongside genomic datasets.

    • For Data Providers: Accelerates dataset dissemination to the broader research community.
    • For Data Consumers: Helps researchers quickly find and explore relevant datasets alongside integrated biological knowledge.
    • For Wet-Lab Researchers: Simplifies the exploration of gene-centric annotations and their associated gene-level genomic patterns.

  • Data Discovery Engine (DDE) (discovery.biothings.io)
    Originally developed as part of the NIH Data to Health (CD2H) initiative (https://cd2h.org)—where Dr. Wu serves as PI and co-chair of the Resource Discovery Core—DDE enables research institutes and CTSA hubs to share datasets, software, and expertise in an open, standardized way.

    • Discoverability: Enhances dataset metadata so research outputs are indexable by both general search engines (Google, Bing) and domain-specific portals (such as CTSASearch, a search engine for CTSA program).
    • Schema development: Empowers researchers to define custom, FAIR-aligned metadata schemas extending existing standards and register them publicly.
    • Custom Portals: Provides metadata and schema utilities that simplify building and powering domain-specific data discovery portals.

  • NIAID Data Ecosystem (data.niaid.nih.gov)
    A centralized discovery portal with the focus on infectious and immune-mediated diseases (IIDs). Using the Data Discovery Engine as its underlying backbone, the portal harvests, standardizes, augments and indexes metadata across diverse repositories and resources into a single searchable catalog.

Knowledgebase Integration

Translating massive, fragmented biomedical data into actionable insights requires unified knowledge graphs and high-performance querying infrastructure.

  • BioThings APIs (MyGene.info | MyVariant.info | MyChem.info | MyDisease.info | MyTaxon.info | MyGeneset.info)
    A suite of high-performance, entity-centric Web APIs designed for rapid access to integrated, entity-centric biomedical knowledge (genes, variants, chemicals & drugs, diseases & phenotypes, taxonomy and functional genesets). While BioGPS serves web-based exploratory users, the BioThings APIs target bioinformaticians and computational biologists. Collectively, BioThings APIs are handling over 30 million requests per month from tens of thousands of users.

  • BioThings SDK
    An open-source Software Development Kit (SDK) underlying all BioThings APIs. It allows developers to quickly build and maintain high-performance, self-updating biomedical APIs. Dozens of Translator Knowledge Provider APIs (biothings.transltr.io) have been created using the BioThings SDK.

  • SmartAPI & BioThings Explorer (smart-api.info | explorer.biothings.io)
    Together, SmartAPI (a registry for biomedical RESTful APIs) and BioThings Explorer enable federated querying across distributed biomedical knowledge graphs. These tools serve as core infrastructure for the NCATS Biomedical Data Translator program, powering applications in precision medicine and drug repurposing.

Collaborations Enabling Biomedical Discovery

The data standards and computational tools developed in our lab foster close collaborations between data scientists and wet-lab researchers, directly contributing to novel biomedical discoveries.

Selected Collaborative Publications:

  • Outbreak. info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations K Gangavarapu, AA Latif, JL Mullen, M Alkuzweny, ... Nature Methods 20, 512–522
  • Functional annotation of the transcriptome of the pig, sus scrofa, based upon network analysis of an RNAseq transcriptional atlas KM Summers, SJ Bush, C Wu, AI Su, C Muriuki, EL Clark, HA Finlayson, ... Frontiers in genetics 10, 1355
  • exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids OD Murillo, W Thistlethwaite, J Rozowsky, SL Subramanian, R Lucero, ... Cell 177 (2), 463-477. e15
  • Diverse reprogramming codes for neuronal identity R Tsunemoto, S Lee, A Szucs, P Chubukov, I Sokolova, JW Blanchard, ... Nature 557 (7705), 375-380
  • Stress-independent activation of XBP1s and/or ATF6 reveals three functionally diverse ER proteostasis environments MD Shoulders, LM Ryno, JC Genereux, JJ Moresco, PG Tu, C Wu, ... Cell reports 3 (4), 1279-1292
  • Identification of serum-derived sphingosine-1-phosphate as a small molecule regulator of YAP E Miller, J Yang, M DeRan, C Wu, AI Su, GMC Bonamy, J Liu, EC Peters, ... Chemistry & biology 19 (8), 955-962
  • A small molecule accelerates neuronal differentiation in the adult rat H Wurdak, S Zhu, KH Min, L Aimone, LL Lairson, J Watson, G Chopiuk, ... Proceedings of the National Academy of Sciences 107 (38), 16542-16547

Research Programs and Funding

We are proud to lead and contribute to major national and international research initiatives:

Funding Support:
We gratefully acknowledge funding support from the National Institutes of Health (NCATS, NIAID, NLM, NIGMS, and NHGRI).