Author

D. Spakowicz

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Immunology· 2 Cancer Biology· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Organism:human· 4 Approach:statistical model· 4 Assay:bulk RNA-seq· 3 Research Focus:differential expression· 3 Research Focus:gene regulatory network inference· 3 Research Focus:host-pathogen & immune response· 2 Approach:benchmark study· 1 Research Focus:cell-cell communication· 1

Frequent Co-Authors

N. Denko· 3 shared R. Hoyd· 3 shared A. A. Tarhini· 2 shared A. C. Tan· 2 shared A. E. G. Osman· 2 shared A. P. Ikeguchi· 2 shared C. E. Wheeler· 2 shared C. M. Ulrich· 2 shared

Activity by Year

2022-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersImmunology

N. Denko

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Author profile →

4 papers

Recent·Most cited

Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease

X. Zhou, X. Shen, J. Johnson, D. Spakowicz, M. Agnello, W. Zhou, M. Avina, A. Honkala, F. Chleilat, S. J. Chen, K. Cha, S. Leopold, C. Zhu, L. Chen, L. Lyu, , M. P. Snyder

This study tracks microbiome changes across four body sites in 86 participants over six years, revealing site-specific stability, individualized dynamics, and altered patterns in insulin-resistant individuals.

bioRxiv · Feb 1, 2024Microbiology

The tumor microbiome reacts to hypoxia and can influence response to radiation treatment in colorectal cancer

M. Benej, R. Hoyd, M. Kreamer, C. E. Wheeler, D. J. Grencewicz, F. Choueiry, C. H. Chan, Y. Zakharia, Q. Ma, R. D. Dodd, C. M. Ulrich, S. Hardikar, M. L. Churchman, A. A. Tarhini, L. A. Robinson, , D. Spakowicz

The paper examines how hypoxia affects the tumor microbiome and its interaction with radiation response in colorectal cancer using RNA-seq data and experimental models.

bioRxiv · Sep 1, 2023Immunology

The tumor microbiome as a predictor of outcomes in patients with metastatic melanoma treated with immune checkpoint inhibitors

C. E. Wheeler, , S. S. Coleman, R. Hoyd, L. Denko, C. H. F. Chan, M. L. Churchman, N. Denko, R. D. Dodd, I. Eljilany, S. Hardikar, M. Husain, A. P. Ikeguchi, N. Jin, Q. Ma, M. D. McCarter, , A. C. Tan

This study identifies microbes associated with immunotherapy response in metastatic melanoma and shows that combining microbe abundances with gene expression improves survival prediction.

bioRxiv · May 24, 2023 · PreprintImmunology

Exogenous sequences in tumors and immune cells (exotic): a tool for estimating the microbe abundances in tumor RNAseq data

R. Hoyd, C. Wheeler, Y. Liu, M. S. J. Singh, M. Muniak, N. Denko, D. P. Carbone, M. Xiaokui, D. Spakowicz

The paper introduces a tool to estimate microbe abundances in tumor RNAseq data and identifies associations between microbes and clinical outcomes.

bioRxiv · Aug 16, 2022Cancer Biology