Sean Davis

Selected publications

Full record: ORCID · Google Scholar
48,656 citations; h-index 66 (Google Scholar, Aug 2026)

Data infrastructure and Bioconductor

  1. Bioconductor's Computational Ecosystem for Genomic Data Science in Cancer

    Ramos M, Shepherd L, Sheffield NC, Mahmoud A, Pages H, Wokaty A, …, Davis S, et al.

    Methods in Molecular Biology, 2025

  2. BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures

    Geistlinger L, Mirzayi C, Zohra F, Azhar R, Elsafoury S, Grieve C, …, Davis S, et al.

    Nature Biotechnology, 2024

  3. GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases

    Oh S, Geistlinger L, Ramos M, Blankenberg D, van den Beek M, Taroni JN, …, Davis S, et al.

    Nature Communications, 2022

  4. MultiAssayExperiment: Software for the Integration of Multi-Omics Experiments in Bioconductor

    Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, …, Davis SR, et al.

    Cancer Research, 2017

  5. GenomicDataCommons: a Bioconductor Interface to the NCI Genomic Data Commons

    Morgan MT, Davis SR

    Bioinformatics, 2017

  6. Orchestrating high-throughput genomic analysis with Bioconductor

    Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, …, Davis S, et al.

    Nature Methods, 2015

  7. RCircos: an R package for Circos 2D track plots

    Zhang H, Meltzer P, Davis S

    BMC Bioinformatics, 2013

  8. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor

    Davis S, Meltzer PS

    Bioinformatics, 2007

Translational research: cancer genomics and oncology

  1. Meta-analysis of 22,710 human microbiome metagenomes defines an oral-to-gut microbial enrichment score and associations with host health and disease

    Manghi P, Antonello G, Schiffer L, Golzato D, Wokaty A, Beghini F, …, Davis S, et al.

    Nature Communications, 2025

  2. Integration of 168,000 samples reveals global patterns of the human gut microbiome

    Abdill RJ, Graham SP, Rubinetti V, Ahmadian M, Hicks P, Chetty A, …, Davis S, et al.

    Cell, 2025

  3. A pivotal role for Wnt antagonists in constraining Wnt activity to promote digit joint specification

    Huang BL, Davis S, Koyama E, Pacifici M, Mackem S

    bioRxiv (preprint), 2025

  4. Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours

    Ma X, Liu Y, Liu Y, Alexandrov LB, Edmonson MN, Gawad C, …, Davis S, et al.

    Nature, 2018

  5. ASXL3 Is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer

    Shukla V, Rao M, Zhang H, Beers J, Wangsa D, Wangsa D, …, Davis S, et al.

    Cancer Research, 2017

  6. Super-enhancers delineate disease-associated regulatory nodes in T cells

    Vahedi G, Kanno Y, Furumoto Y, Jiang K, Parker SCJ, Erdos MR, …, Davis SR, et al.

    Nature, 2015

  7. Lineage of origin in rhabdomyosarcoma informs pharmacological response

    Abraham J, Nunez-Alvarez Y, Hettmer S, Carrio E, Chen HIH, Nishijo K, …, Davis S, et al.

    Genes & Development, 2014

Policy, governance, and data ethics

  1. The Common Fund Data Ecosystem (CFDE)

    bioRxiv (preprint), 2026

  2. Lifecycle-aware evaluation of biomedical data ecosystems

    Zenodo (preprint; submitted to Cell Trends Open), 2026

  3. Ten simple rules for large-scale data processing

    Fungtammasan A, Lee A, Taroni J, Wheeler K, Chin CS, Davis S, et al.

    PLOS Computational Biology, 2022

  4. From Patient Engagement to Precision Oncology: Leveraging Informatics to Advance Cancer Care

    Griffin AC, Topaloglu U, Davis S, Chung AE

    Yearbook of Medical Informatics, 2020

  5. Resources for Interpreting Variants in Precision Genomic Oncology Applications

    Tsang H, Addepalli K, Davis SR

    Frontiers in Oncology, 2017

  6. Public data and open source tools for multi-assay genomic investigation of disease

    Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DMA, …, Davis S, et al.

    Briefings in Bioinformatics, 2016

Community building and training

  1. Exploring Cancer in Colorado using a novel data platform: the ECCO experience

    Lowery JT, Alquaddoomi F, Rubinetti V, Burus T, Jardine C, Warren AC, …, Davis S, et al.

    medRxiv, 2026

  2. Learning and teaching biological data science in the Bioconductor community

    Drnevich J, Tan FJ, Almeida-Silva F, Castelo R, Culhane AC, Davis S, et al.

    PLOS Computational Biology, 2025

  3. Orchestrating a community-developed computational workshop and accompanying training materials

    Davis S, Ramos M, Shepherd L, Turaga N, Geistlinger L, Morgan MT, et al.

    F1000Research, 2018

Current funding

Awards on which I currently hold a role, as listed in my CV.

  1. Comprehensive genetic ancestry annotation of existing human molecular data

    R01 Supplement · NIH · Co-Investigator · 2025–2030

  2. Big Data Training for Cancer Research

    R25 CA233429 · NIH · Co-Investigator · 2024–2029

  3. Exploiting Public Metagenomic Data to Uncover Cancer-Microbiome Relationships

    R01 CA230551 · NCI · Co-Investigator · 2024–2029

  4. Integration, Dissemination, and Evaluation (BRIDGE) Center for the NIH Bridge to Artificial Intelligence (BRIDGE2AI) Program

    U54 HG012513 · NIH · Co-Investigator · 2022–2026

  5. Cancer Genomics: Integrative and Scalable Solutions in R/Bioconductor

    U24 CA289073 · NIH · MPI · 2024–2029

  6. Oculomics as a Biomarker for Comprehensive and Non-Invasive Patient Health Assessment

    AWD-AAI2401 · Anschutz Acceleration Initiative, Anschutz Foundation · Co-Investigator · 2024–2029

  7. CONNECT: Collaborative Network for Nurturing Ecosystems of Common Fund Team Science

    U54 OD036472 · NIH · MPI · 2024–2029

  8. Leveraging whole-exome sequence data from diverse biobanks and cohorts to study rare coding variation in prostate cancer

    R01 CA276826 · NCI · Co-Investigator · 2023–2028

  9. University of Colorado Cancer Center Support Grant

    P30 CA046934 · NCI · Co-Investigator · 2023–2027

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