Daniel Spakowicz — Curriculum Vitae

584 BRT, 460 W 12th Ave, Columbus, OH 43210
(614) 293-1797 · Daniel.Spakowicz@osumc.edu · ORCID 0000-0003-2314-6435

Last updated: October 2, 2026

Current Position

Assistant Professor, Division of Medical Oncology, The Ohio State University Wexner Medical Center, Columbus, Ohio (2022–present)

Education

• 2017–2018 — MS, Biomedical Informatics, Yale University, New Haven, CT

• 2007–2013 — Ph.D., Biophysics, Yale University, New Haven, CT

• 2000–2004 — B.S., Biochemistry and Ecology, University of Minnesota, Minneapolis, MN

Academic Appointments

• 2022–present — Assistant Professor, Division of Medical Oncology

  The Ohio State University Wexner Medical Center

  Columbus, Ohio

• 2018-2022 — Research Assistant Professor, Division of Medical Oncology

  The Ohio State University Wexner Medical Center

  Columbus, Ohio

Professional Positions and Experience

• 2015-2018 — National Library of Medicine Postdoctoral Fellow in Biomedical Informatics, Yale University, New Haven, CT

• 2014-2015 — Postdoctoral Research Associate, Jackson Laboratory, Farmington, CT, and Yale University, New Haven, CT

• 2013-2014 — Instructor, Molecular Biophysics and Biochemistry 230: Rainforest Expedition and Laboratory, Farmington, CT and Yale University, New Haven, CT

• 2007-2013 — Graduate Student, Mol. Biophysics and Biochem, Yale University, New Haven, CT

• 2004-2007 — Junior Researcher, Dept. of Biophysics, University of Minnesota, Minneapolis, MN

Honors and Awards

• 2026 — Midwest Microbiome Symposium Excellence in Mentoring Award

• 2026 — Voices of Pelotonia Cohort

• 2026 — Leadership Education through Advanced Practice 2026 Cohort

• 2025 — Mentoring Honorarium, Center for Cancer Mentoring, Education, Leadership and Oncology-Related Training

• 2024 — American Cancer Society Research Scholar

• 2023 — Mentor of the Year, The Ohio State University Comprehensive Cancer Center (shared)

• 2023 — American Lung Association Innovator Award

• 2023 — Invited Speaker Travel Award, Oncology Research Information Exchange Network Annual Meeting

• 2022 — Mentor of the Year, The Ohio State University Comprehensive Cancer Center

• 2022 — Aspen Cancer Fellow

• 2022 — First Place Presentation Award, Ohio SuperComputing Center Annual Meeting

• 2022 — Invited Speaker Travel Award, Oncology Research Information Exchange Network Annual Meeting

• 2021 — Career Development Award, National Institutes of Aging

• 2020 — Nye-Raden Cancer Research Scholar

• 2020 — Finalist, OSU Innovator of the Year

• 2019 — Young Investigator in Immuno-Oncology Research Award

• 2018 — Pelotonia New Investigator Award

• 2015 — National Library of Medicine Postdoctoral Fellowship

• 2012 — Poster Award - Yale Molecular Biophysics and Biochemistry, Yale University, New Haven, CT

• 2011 — Poster Award - Yale Climate and Energy Institute Conference, Yale University, New Haven, CT

• 2011 — Yale Excellence in Teaching Award, Yale University, New Haven, CT

Grants and Contract Awards

(Total number: 35, as PI: 21)

(Total Direct Costs: $28,137,714)

2026 (4, as PI = 2)

$1,800,000

• 10/01/2026 – 09/30/2028 · $75,000 — 2026 Spielman Fund Bridge-to-Impact Clinical Trial Award (AWD-122995; Non-OSP; Co-PI: Spakowicz)

  Ohio State University Internal Award

  The Vaginal Microbiome as a Biomarker of Vaginal Health in Women with Breast Cancer

• 01/01/2026 - 12/31/2027 · $275,000 — R21CA2973842 (PI: Spakowicz, Bradley, Zhu)

  National Cancer Institute

  Lachnospiraceae characterization to affect diet-mediated improvement of cancer treatment outcomes

  Goal: To determine how Lachnospiraceae alters cancer immunotherapy outcomes and to identify potential biotherapeutic targets. Specifically, the project aims to identify and isolate Lachno genes associated with tumor reduction and to test the causal relationship between these isolates, their metabolites, and ICB response using preclinical mouse models.

• 07/01/2026 – 06/30/2027 · $50,000 — Harold and Barbara Rosenbaum Family Foundation Cervical Cancer Diversity in Prevention & Clinical Research Grant (PI: O’Connor)

  Foundation for Women’s Cancer

  Probiotic and Dietary Fiber Supplementation to Potentiate Immunotherapy Response in Cervical Cancer

  Goal: To examine how specific beneficial gut bacteria and dietary fiber work together to improve the body’s response to immunotherapy in cervical cancer. This translational research will provide mechanistic insights to inform future clinical trials testing diet- and microbiome-based strategies to amplify the magnitude of immunotherapy benefit and to improve outcomes for patients fighting cervical cancer.

  Role: Mentor

• 07/01/2026 – 06/30/2030 · $1,400,000 — Ovarian Cancer Clinical Trial Academy – Early-Career Investigator Award (PI: Chambers)

  Department of War Ovarian Cancer Research Program

  Modulating the Microbiome to Transform Platinum-Based Care in Ovarian Cancer

  Goal: The objective of the PRO-PLATINUM trial is to determine whether probiotic supplementation during platinum-based chemotherapy can improve outcomes in patients with OC by altering the gut and vaginal microbiome

  Role: Mentor

2025 (3, as PI = 1)

$105,000

• 12/01/2025 – 11/30/2026 · $50,000 — Stephanie Spielman Research Funds (PI: Spakowicz, Jhawar, Myers)

  The Ohio State University Comprehensive Cancer Center

  Spatial association of tumor microbes and the tumor microenvironment in breast cancer subtypes

  Goal: To understand how the tumor microbiome affects treatment outcomes in breast cancer.

• 05/01/2025 - 04/30/2026 · $30,000 — Radiation Oncology Departmental Seed Grant (PIs: Quick and Pitter)

  Vaginal DHEA for Women with Gynecologic and Gastrointestinal Cancer After Radiation

  Goal: To evaluate the effect of vaginal dehydroepiandosterone (DHEA) alters the vaginal microbiome in a way that affects treatment outcomes and toxicity following pelvic radiation.

  Role: Co-Investigator

• 06/01/2025 – 05/31/2027 · $25,000 — Wendy Brewster, MD, PhD Accelerator (PI: Chambers)

  Foundation for Women’s Cancers

  “PROPLATINUM Study: Leveraging microbes to improve women’s cancer outcomes”

  Goal: To assess whether a probiotic supplement will improve treatment outcomes in the context of platinum-based therapies for gynecologic cancers

  Role: Co-Investigator

2024 (8, as PI = 5)

$1,703,316

• 12/13/2024 - 02/11/2025 · $196,000 — FastTrack Program Grant (PI: Presley)

  Bristol Myers Squibb

  “LiveWellLung: A Prehabilitation Education and Intervention Program Prior to Lung Cancer Surgery”

  Goal: To reduce the incidence of post-surgical complications through pre-treatment lifestyle-based modifications including those expected to operate via the microbiome.

  Role: Co-Investigator

• 11/01/2024 – 12/31/2025 · $15,000 — CCC Transitional Therapeutics FY25 seed award (PIs: Vershraegen, Spakowicz, Presley, and Burd)

  The Ohio State University Comprehensive Cancer Center

  Investigation of Age-Specific Effects of Indole Supplementation on Immune Function and irAE Development

  Goal: To establish a mouse model to study how microbes and microbial metabolites affect immune checkpoint-derived colitis and pneumonitis.

• 11/1/2024 – 10/31/2026 · $75,000 — CFAES-CCC-FFH Joint Seed Grant (PIs: Belury, Spakowicz, Pyter)

  The Ohio State University

  “Prevention of Cancer Cachexia by Dietary Naringenin: Impact on the Gut-Brain Axis”

  Goal: To understand how a naringenin dietary supplement affects cancer treatment outcomes in model systems.

• 10/1/2024 -02/2025 · $20,000 — 2024 Breast Cancer Translational Research Program Team Science Pilot Grant (PIs: Spakowicz, Jhawar)

  The Ohio State University Comprehensive Cancer Center

  “Spatial Association of Tumor Microbes and the Tumor Microenvironment in Breast Cancer Subtypes”

  Goal: To use spatial transcriptomics and in situ hybridization approaches to relate microbes to tumor microenvironment features in different breast cancer subtypes.

• 07/01/2024-06/30/2026 · $405,316 — R21CA294050 (PI: Tabung)

  National Cancer Institute

  Role of the inflammatory dietary pattern in gut and colon tissue microbiomes and impact on survival outcomes among colorectal cancer patients

  Goal: To determine the gut microbial profile of an inflammatory dietary pattern (EDIP) among CRC patients, characterize the EDIP-related microbiome and immune cell profiles in the CRC TME, and determine their impact on CRC survival outcomes for the first time.

  Role: Co-Investigator

• 03/01/2024 -2/28/2028 · $792,000 — Research Scholar (RSG-23-1023205) (PI: Spakowicz)

  American Cancer Society

  Lifestyle-based microbiome modification in older adults to promote response to immunotherapy

  Goal: To understand the causal mechanisms by which the exercise-modified microbiome affects the response to cancer treatment with immune checkpoint inhibitors.

• 01/01/2024 – 12/31/2024 · $50,000 — SIGMA Nursing Research Grant (PI: Han)

  Oncology Nursing Foundation

  Social determinants of health and race effects on the microbiome and gastro-intestinal toxicity in colorectal cancer

  Goal: Investigate the use of gut microbiome-immune interactions to prevent and manage GI symptom toxicity for 5-fluoro-uracil-based chemotherapy in colon cancer patients.

  Role: Co-Investigator

• 04/01/2024 – 03/31/2025 · $150,000 — Chief of Science Seedling (PIs: Spakowicz, Bradley, Zhu)

  Air Force Research Lab

  Next-Generation Culturomics: Cultivation of uncultured gut microbes to optimize warfighter health and performance

  Goal: To establish methods for cultivating microbes from complex communities for use in experiments to establish causality and as future therapeutics.

2023 (4, as PI = 1)

$20,762,481

• 09/14/2023 - 08/31/2028 · $19,962,481 — U54CA287392 (PI: Wagener)

  National Cancer Institute

  The Ohio State University tobacco center of regulatory science (OSU-TCORS)

  Goal: This project aims to support FDA regulation of new nicotine-containing products by contributing to the understanding of their health and behavioral effects. Dr. Spakowicz will support a project exploring the effect of new nicotine products on the oral microbiome and host markers of inflammation.

  Role: Co-Investigator

• 07/01/2023 – 06/30/2025 · $150,000 — Innovator Award (104661) (PI: Spakowicz)

  American Lung Association

  Adenosine as a mediator of tumor and tumor-microbe interactions in non-small cell lung cancer

  Goal: To understand how microbial purine excretion in the gut and tumor affects immunotherapy treatment outcomes.

• 02/01/2023-01/31/2027 · $450,000 — Early Career Investigator Grant

  Ovarian Cancer Research Alliance

  The Impact of Gut Microbiome and Probiotics on Chemotherapy Response in Ovarian Cancer Patients

  Goal: To use the prospective collection of gut microbiome samples in a patient cohort and pre-clinical models to assess the microbes associated with chemotherapy response and resistance in ovarian cancer and how outcomes may be altered with probiotics.

  Role: Co-Investigator

• 01/01/2023 – 12/31/2024 · $200,000 — National Comprehensive Cancer Center Network/AstraZeneca (PI: Alamadi)

  Improving the Quality of Care and Application of Best Practices in the Treatment of Patients with Small Cell Lung Cancer

  The Impact of Area Deprivation Index on Clinical Outcomes for Extensive Stage Small Cell Lung Cancer

  Goal: To use retrospective databases and molecular data to understand how socioeconomic and environmental factors influence outcomes in small-cell lung cancer.

  Role: Co-Investigator

2022 (4, as PI = 2)

$500,000

• 10/01/2022 – 09/30/2024 · $50,000 — Oncology Nursing Science Grant (PI: Arthur)

  The Oncology Nursing Foundation

  The Vaginal Microbiome as a Biomarker of Vaginal Health in Women with Breast Cancer

  Goal: To collect longitudinal vaginal microbiome samples in women receiving hormone therapy for breast cancer and evaluate the extent to which the microbiome can be used to predict treatment outcomes.

  Role: Co-Investigator

• 07/01/2022 – 6/30/2024 · $200,000 — Discovery Catalyst Award (PI: Bittoni)

  American Lung Association

  BEFIT: An exercise intervention study in a cohort at high risk for developing lung cancer

  Goal: To assess the feasibility of an exercise intervention in a high-risk cohort and estimate the effect on blood markers of inflammation and the microbiome.

  Role: Co-Investigator

• 07/01/2022 – 6/30/2023 · $50,000 — Sarcoma Foundation of America Research Award (PIs: Spakowicz, Tinoco)

  Sarcoma Foundation of America

  The sarcoma tumor microbiome as a therapeutic target

  Goal: to survey the tumor microbiome in sarcoma and explore its use as a clinical biomarker of treatment response for immunotherapy.

• 01/01/2022 – 12/31/2023 · $200,000 — Pelotonia Population Health Award (PIs: Spakowicz, Zhu)

  Pelotonia Non-profit Research Foundation

  Dietary interventions to modify the response to immunotherapy: a companion assessment within the NutriCare Study

  Goal: To identify changes to the gut microbiome associated with a three-month, three meals-per-day dietary intervention and to establish the causal effect of the changes to the microbiome on the response to immunotherapy in preclinical models.

2021 (4, as PI = 3)

$3,891,093

• 07/01/2021 – 06/30/2026 · $562,750 — K01AG070310 Mentored Career Development Award (PI: Spakowicz)

  NIH-National Institutes on Aging

  The microbiome in older adults with lung cancer association of treatment regimens and diet with protective microbial profiles

  Goal: To define the microbiomes of older adults with lung cancer, modify the microbiomes to promote response using dietary interventions, and study the causal mechanisms using pre-clinical models.

• 07/01/2021-06/30/2023 · $118,008 — OSU Department of Internal Medicine Seed Grant (PI: Malalur, Spakowicz)

  Circulating microbial DNA as a non-invasive biomarker for colorectal cancer

  Goal: To develop methods for non-invasive prediction of cancer, treatment or outcomes using blood-based analysis of microbial DNA.

• 02/01/2021-01/31/2026 · $3,023,907 — 1R01CA248741-01A1 (PI: Carbone, Dikov)

  NIH-NCI

  Targeting immunosuppressive adenosine in patients with metastatic non-small cell lung cancer

  Goal: To evaluate (1) the safety and tolerability of combination PBF-1129 with nivolumab, (2) the correlation between immunological parameters and adenosine generation, the microbiome and signaling, and (3) the efficacy of PBF-1129 in targeting adenosine-mediated immunosuppression.

  Role: Co-Investigator

• 01/01/2021-12/31/2023 · $186,428 — Pelotonia Clinical Trial Award (PI: Spakowicz, Arthur)

  Pelotonia Non-profit Research Foundation

  The vaginal microbiome as a biomarker of pelvic health and patient-reported outcomes in women receiving pelvic radiation.

  Goal: This award aims to correlate the microbiome with patient reported outcomes following pelvic radiation. All microbiome processing, data generation, analysis and integration will be performed in my lab.

2020 (6, as PI = 4)

$425,896

• 11/01/2020-05/31/2021 · $7,896 — 2020 Intramural Supportive Care Pilot Research Award (PI: Spakowicz, Arthur)

  OSU Comprehensive Cancer Center Intramural Research Program

  Preliminary studies of the vaginal microbiome as a biomarker of pelvic health and patient-reported outcomes in women receiving pelvic radiation.

  Goal: This award will fund the collection of microbiome samples as part of a study of patient reported outcomes aims to modify the microbiome with the eventual goal of tailoring gut flora to match desired outcomes in terms of response to treatment or to promote health All microbiome processing, data generation, analysis and integration will be performed in my lab.

• 08/01/2020-07/31/2021 · $20,000 — Pilot Grant Award (PI: Mo)

  OSU Department of Biomedical Informatics

  The Epigenetic Landscape and Correlation with Microbiome in the Early Onset Colorectal Cancer

  Goal: To explore associations between intra-tumor microbes and epigenetic modifications with early onset colorectal cancer using publicly available and the oncology research information exchange network data.

  Role: Co-Investigator

• 07/01/2020-06/30/2022 · $98,000 — Nye-Rayden Cancer Research Award (PI: Spakowicz)

  OSU Division of Medical Oncology

  Increasing response to immunotherapy through diet-based alterations of the microbiome: a mouse validation study

  Goal: This proposal will bridge the ongoing BE WELL trial to cancer ICI response in preclinical models. Specifically, we will determine whether the microbiome shifts elicited by BRB in the clinical study affect response ICIs in a mouse model of lung cancer. We will also use metagenomics and metabolomics to evaluate the mechanism by which the foods lead to microbial community changes.

• 07/01/2020-06/30/2022 · $100,000 — Research Award Seed Grant (PI: Jin, Spakowicz)

  OSU Division of Medical Oncology

  The Epigenetic Landscape and Correlation with Microbiome in the Early Onset Colorectal Cancer

  Goal: To observe the correlations between the tumor microbiome and methylation in colorectal cancer as a potential mechanism for the rise in early onset colorectal cancer.

• 01/01/2020-06/30/2022 · $200,000 — Young Investigator Research Award in Immuno-oncology (PI: Spakowicz)

  LCFA-BMS/ILC Foundation

  Evaluating modifiable biomarkers for the prediction of immunotherapy response and toxicity

  Goal: This award is to evaluate the predictive strength of the microbiome and physical activity for cancer treatment responses, relative and in addition to tumor biomarkers such as PD1/PDL1 and tumor mutational burden. The hope is that, because these biomarkers can be modified, we will estimate to what extent the response to treatment can be altered by controlling these two variables.

2019 (6, as PI = 5)

$425,928

• 12/14/2019-05/31/2020 · $15,000 — Secondary Analysis of Existing Datasets (PI: Spakowicz, Mo)

  2019 CCTS Pilot Translational & Clinical Studies Program

  Exogenous sequences in unmapped transcriptome data from the ORIEN consortium

  Goal: With this award, we will create a computational pipeline to process and analyze tumor biopsy RNAseq data collected at the OSU Comprehensive Cancer Center and members of the ORIEN consortium. We will link microbes with immune cell profiles and expression to predict treatment outcomes.

• 09/01/2019-08/31/2020 · $25,000 — Foods for Health (FFH) Discovery Theme Seed Grants (PI: Zhu, Spakowicz, Ma)

  Internal OSU

  Food Products for the Targeted Enrichment of Gut Microbes

  Goal: With this award we will set up a model gut system to rapidly assess the effects of food molecules on microbial communities in vitro. In addition, we will develop a model for predicting the response to inputs by combining two tools created by OSU faculty, Spakowicz and Ma.

• 07/02/2019-06/30/2020 — 2K12CA133250-06A1 (PI: Byrd, Awardee: Presley)

  NCI

  OSU K12 Training Grant For Clinical Faculty Investigators

  Goal: The goal of this proposal is to mentor and effectively train faculty-level investigators in basic science and/or clinically oriented approaches to translational research.

  Role: Co-Investigator

• 01/01/2019-12/31/2020 · $149,500 — Pelotonia New Investigator Award (PI: Spakowicz)

  Pelotonia Non-profit Research Foundation

  The Effect of the Microbiome on Immune Checkpoint Inhibitor Response and Corticosteroid Use in Melanoma

  Goal: This award will study the how the microbiome interacts with the immune system in the context of immunotherapy for melanoma with specific focus on toxicity and corticosteroid use. All microbiome processing, data generation, analysis and integration will be performed in my lab.

• 01/01/2019-12/31/2020 · $186,428 — Pelotonia Clinical Trial Award (PIs: Spakowicz, Carbone, Clinton)

  Pelotonia Non-profit Research Foundation

  Pilot study to define compliance and impact of a novel black raspberry food product on the microbiome and immune functions in a high-risk cohort for lung cancer.

  Goal: This award seeks to modify the microbiome with the eventual goal of tailoring gut flora to match desired outcomes in terms of response to treatment or to promote health. All microbiome processing, data generation, analysis, and integration will be performed in my lab.

• 01/01/2019-12/31/2020 · $50,000 — OSU Hematology Department Research Funds (PI: Choe, Spakowicz)

  Longitudinal analysis of the impact of Vitamin A on stool microbiota post-hematopoietic stem cell transplantation (HSCT).

  Goal: This award seeks to modify the microbiome by decreasing gut tight junction leakiness, thereby reducing bloodstream infections and graft versus host disease.

  Role: Co-PI

2018 (2, as PI = 0)

$300,000

• 07/01/2018-06/30/2020 · $100,000 — Davis Bremmer Award (PI: Presley)

  OSU Center for Clinical & Translational Science (CCTS)

  The Aging Immune System, Treatment Response, and Functional Decline among Older Adults with Lung Cancer

  Goal: This award will study how the microbiome interacts with the aging immune system in the context of lung cancer therapy. All microbiome processing, data generation, analysis, and integration will be performed in my lab.

  Role: Co-I

• 07/01/2018-06/30/2020 · $200,000 — Pelotonia New Investigator Award (PI: Presley)

  Pelotonia Non-profit Research Foundation

  The Aging Immune System, Treatment Response, and Functional Decline among Older Adults with Lung Cancer

  Goal: This award will study how the microbiome interacts with the aging immune system in the context of lung cancer therapy. All microbiome processing, data generation, analysis, and integration will be performed in my lab.

  Role: Co-I

Inventions

• T2026-085 — Systems and methods for predicting treatment-related toxicity in patients with metastatic melanoma. Released September 30, 2026.

Publications

(See the complete list)

Accompanying public software and analysis code are noted below the relevant publications. Links point to the latest verified release, which may postdate the publication; unversioned repositories are identified separately.

2026 (14)

1. Chambers LM, Spakowicz D, Chalif J, O’Connor R, Kistenfeger Q, Mehra Y, Mohssen M, Abdeen C, Haight P, Nagel C, Neff R, Cohn D, Copeland LJ, Backes F, Cosgrove C, Hays J, Dravillas C, McLaughlin E, O’Malley D. PRO-PLATINUM: A randomized, double-blind, placebo controlled study to investigate the efficacy of a probiotic intervention on the gut and vaginal microbiome of ovarian cancer patients undergoing treatment with platinum chemotherapy. Gynecol Oncol. 2026 Aug;211:74-78. doi: 10.1016/j.ygyno.2026.06.016. PMID: 42364424.

2. Zhou Q, Lu Y, Wang L, Zhou W, Oba H, Zhou Y, Shen M, Qu X, De Souza C, Rayner A, Chen Y, Cheng TY, Ling Z, Li L, Liu C, Voigt AY, Xiong R, Oh J, Spakowicz D, Dravillas C, Tian AW, Nicolls MR, Huynh AT, Chen X, Hu J, He M, He F, Snyder MP, Yang J, Zhou X. Power and sample-size estimation in human microbiome research. Med. 2026 Jul 10;7(7):101174. doi: 10.1016/j.medj.2026.101174. PMID: 42302785.

3. Li M, Spakowicz DJ, Zhao S, Kwon H, Chian K, Khorasanchi A, Guo Y, Wei L, Meng L, Yang Y, Alahmadi A, Memmott RM, Kaufman J, He K, Shields PG, Mace TA, Phelps MA, Coss CC, Li Z, Kendra KL, Carbone DP, Otterson GA, Presley CJ, Owen DH. Association between obesity, sex, medical comorbidities, and survival in cancer patients treated with immune checkpoint inhibitors. J Cancer. 2026;17(6):1117-1124. doi: 10.7150/jca.130032. PMID: 42327585; PMCID: PMC13280536.

4. Bukovac J, Husain M, Sapper T, O’Dell A, Bittoni M, Gastier H, Chebbi A, Hockenhull V, Dohar Z, Moon J, Tabung F, Verschraegen C, Wu R, Kendra K, Yang Y, Volek J, Spakowicz D. How the Ketogenic Diet Shapes the Microbiome to Influence Cancer Immunotherapy Outcomes: An Exploration of Clinical Trials and Their Results. Nutr Cancer. 2026;78(6):367-396. doi: 10.1080/01635581.2026.2658807. PMID: 42077003; PMCID: PMC13247657.

   Accompanying public software/code release: keto-rev v1.0.

5. Chalif J, Moruzzi C, Velasquez J, O’Connor R, Fulton J, Mehra Y, Cohn DE, Copeland LJ, Cosgrove CM, Nagel CI, O’Malley DM, Monovich L, Spakowicz DJ, Chambers LM. Implementing non-invasive biospecimen collection in gynecologic oncology: Insights from a prospective gut microbiome feasibility study. Gynecol Oncol. 2026 May;208:63-68. doi: 10.1016/j.ygyno.2026.03.008. PMID: 41905324.

6. Liu CC, Grencewicz D, Chakravarthy K, Li L, Liepold R, Wolf M, Marcho LM, Sangwan N, Tzeng A, Hoyd R, Jhawar SR, Grobmyer SR, Al-Hilli Z, Sciallis AP, Spakowicz D, Ni Y, Eng C. Breast tumor microbiome regulates anti-tumor immunity and T cell-associated metabolites. Sci Rep. 2026 Apr 16;16(1):17587. doi: 10.1038/s41598-026-48719-5. PMID: 41991647; PMCID: PMC13243561.

   Accompanying public software/code release: staph-brca v1.0.

7. Sekar N, Zhao S, Rudich A, Johns N, Hwang JD, Su PL, Hu J, Spakowicz D, Wei L, Yang Y, Cheng TD, Coss C, Phelps M, Parang B, Gheeya J, Roof L, Alahmadi A, Memmott R, Kaufman J, Presley C, He K, Burns T, Shields P, Rolfo C, Carbone D, Owen D, Li M. CLO26-084: Prognostic Value of Sarcopenia in Patients With Metastatic NSCLC Receiving First-Line Immune Checkpoint Inhibitors. J Natl Compr Canc Netw. 2026 Mar 31;24(3.5):CLO26-084. doi: 10.6004/jnccn.2025.7467. PMID: 42061416.

8. Hwang JD, Su PL, Zhao S, Hu J, Spakowicz D, Wei L, Baiu I, D’Souza D, Merritt R, Kneuertz P, Parang B, Gheeya J, Roof L, Alahmadi A, Memmott R, Kaufman J, Presley C, He K, Burns T, Shields P, Rolfo C, Carbone D, Owen D, Li M. CLO26-114: Association Between Neoadjuvant Chemoimmunotherapy-Induced Anemia and Survival in Patients With Resectable Non-Small Cell Lung Cancer. J Natl Compr Canc Netw. 2026 Mar 31;24(3.5):CLO26-114. doi: 10.6004/jnccn.2025.7321. PMID: 42061423.

9. Petouhoff A, Hicks R, Husain M, Hoyd R, Xu M, Dravillas C, Patel SH, Johns A, Grogan M, Li M, Lopez G, Miah A, Liu Y, Muniak M, Schmidt M, Das A, Lathrop H, Das P, Secor A, Haddad T, Tinoco G, Carbone D, Kendra K, Otterson GA, Presley CJ, Mace T, Spakowicz D, Owen DH. Impact of proton pump inhibitors on immunotherapy is modulated by prior chemotherapy and linked to gut microbiome-immune cell signatures. Cancer Immunol Immunother. 2026 Mar 9;75(4):98. doi: 10.1007/s00262-026-04346-7. PMID: 41801404; PMCID: PMC12972483.

   Accompanying public software/code release: ppiio v1.0.0.

10. Han C, Spakowicz D, Von Ah D, Noonan A, Pyter L. Gut Microbiota and Nutritional Profiles of Colon Cancer Patients Undergoing Chemotherapy: A Longitudinal Pilot Study. Nutrients. 2026 Jan 29;18(3):438. doi: 10.3390/nu18030438. PMID: 41683263; PMCID: PMC12899050.

11. Chow Z, Liu J, He D, Wang C, Gan T, Mansour A, Shaker N, Dravillas C, Hoyd R, Durbin E, Napier D, Gao T, Schaberg K, Huang L, Ulrich N, Siegel E, Edge S, Cook L, Salhia B, Churchman M, Kolesar J, Spakowicz D, Evers BM, Bocklage T. Colon cancer in Appalachian Kentucky: Unique genetic, microbiome and obesity findings in a cohort comparison. HGG Adv. 2026 Jan 15;7(1):100527. doi: 10.1016/j.xhgg.2025.100527. Epub 2025 Oct 9. PMID: 41063459; PMCID: PMC12554973.

12. Obermayer A, Davis J, Talada DP, Teng M, Eschrich S, Yin V, Spakowicz D, Chatterjee D, Rounbehler RJ, Churchman ML, Tarhini AA, Wang X, Gupta S, Markowitz J, Goecks J, Li R, Rodrigues Pessoa R, Manley BJ, Tan AC, Grass GD, Chen DT, Shaw TI. ShinyEvents: harmonizing longitudinal data for real-world survival estimation. NPJ Precis Oncol. 2026 Jan 13. doi: 10.1038/s41698-025-01212-0. Epub ahead of print. PMID: 41526666.

13. Marcho LM, Chakravarthy KB, Jhawar SR, Spakowicz DJ. Tumor-infiltrating microbes and therapy response: a new frontier in triple-negative breast cancer precision oncology. J Immunother Cancer. 2026 Jan 7;14(1):e013314. doi: 10.1136/jitc-2025-013314. PMID: 41500775; PMCID: PMC12781984.

14. Jhawar SR, Spakowicz D. Tumor bacterial burden dictates immunotherapy fate in head and neck cancer. Nat Cancer. 2026 Jan 2. doi: 10.1038/s43018-025-01074-2. Epub ahead of print. PMID: 41482525.

2025 (15)

1. Zarich S, Cole RM, Fairchild K, Spakowicz D, Sparagna G, Madison A, Ni A, Belury MA. Effects of Walnuts on Postprandial Cognitive Function in Adults With Subjective Cognitive Impairment: Protocol for a Randomized Crossover Trial. JMIR Res Protoc. 2025 Dec 19;14:e82032. doi: 10.2196/82032. PMID: 41418290; PMCID: PMC12759297.

2. Owen DH, Wu R, Wei L, Dikov M, Suman S, Su PL, Amann J, Guan S, Spakowicz D, Schweitzer C, Pilcher C, Smith MB, Ferguson S, Palomino JC, Pérez SF, Bertino EM, Shields PG, He K, Presley CJ, Otterson GA, Carson WE, Carbone DP. Phase 1 dose escalation trial of the selective adenosine A2B antagonist PBF-1129 in patients with metastatic non-small cell lung cancer. Invest New Drugs. 2025 Dec 3. doi: 10.1007/s10637-025-01591-y. Epub ahead of print. PMID: 41335275.

3. Parajuli B, Midya V, Kiddle R, De Jager N, Eggers S, Spakowicz D, Hoyd R, Salhia B, Chan CHF, Churchman ML, Rounbehler RJ, Yao S, Rutkowski MR, Tarhini AA, Mudaranthakam DP, Masood A, Bocklage TJ, Lentz RW, Hatoum H, Ilozumba MN, Hardikar S, Ulrich CM, Round JL, Riedlinger G, Shriver CD, Bosch DE. Primary tumor microbiomes predict distant metastasis of colorectal cancer. NPJ Precis Oncol. 2025 Nov 24. doi: 10.1038/s41698-025-01188-x. Epub ahead of print. PMID: 41286005.

4. Jin N, Hoyd R, Yilmaz AS, Zhu J, Liu Y, Jagjit Singh MS, Grencewicz DJ, Mo X, Kalady MF, Rosenberg DW, Dravillas CE, Singer EA, Carpten JD, Chan CHF, Churchman ML, Denko N, Di Clemente F, Dodd RD, Eljilany I, Fei N, Hardikar S, Ikeguchi AP, Ma A, Ma Q, McCarter MD, Osman AEG, Riedlinger G, Robinson LA, Schneider BP, Tarhini AA, Tinoco G, Figueiredo JC, Zakharia Y, Ulrich CM, Tan AC, Spakowicz D. Epigenetic Modulation, Intratumoral Microbiome, and Immunity in Early-Onset Colorectal Cancer. Cancer Res Commun. 2025 Nov 1;5(11):1985-1997. doi: 10.1158/2767-9764.CRC-25-0177. PMID: 41134679; PMCID: PMC12606411.

   Accompanying public software/code release: exorien-exogieo v1.0.

5. Patel SH, Zhao S, Li M, Wei L, Husain M, Spakowicz D, Grogan M, Johns A, Burkart J, Alahmadi A, Lopez G, He K, Bertino EM, Shields PG, Carbone DP, Verschraegen CF, Otterson GA, Kendra K, Presley CJ, Owen DH. Early Changes in Lymphocyte/Monocyte Ratio on Treatment as a Prognostic Marker to Predict Overall Survival in Patients with Advanced Cancer Treated with Immune Checkpoint Inhibitors. Cancer Invest. 2025 Oct;43(9):717-725. doi: 10.1080/07357907.2025.2557004. Epub 2025 Oct 10. PMID: 41070402.

6. Chalif J, Morton M, Haight P, Mehra Y, O’Malley D, Spakowicz D, Chambers L. Assessment of probiotic and prebiotic use in gynecologic cancer patients: a systematic review. Am J Obstet Gynecol. 2025 Oct 8:S0002-9378(25)00715-X. doi: 10.1016/j.ajog.2025.09.042. Epub ahead of print. PMID: 41072704.

7. Li Y, Ma A, Johnson E, Eng C, De S, Jiang S, Li Z, Spakowicz D*, Ma Q*. The new microbiome on the block: challenges and opportunities of using human tumor sequencing data to study microbes. Nat Methods. 2025 Sep;22(9):1788-1799. doi: 10.1038/s41592-025-02807-y. PMID: 40954302; PMCID: PMC12701766.

*Co-corresponding author

8. Li M, Su PL, Zhao S, Cheng G, Jones N, Chian K, Johns N, Khorasanchi A, Adeluola A, Petouhoff A, Spakowicz DJ, Wei L, Wang X, Coss C, Phelps MA, Meng L, Yang Y, Meara A, Elsaid MI, Gheeya J, Roof L, Alahmadi A, Memmott RM, Kaufman J, He K, Presley CJ, Shields PG, Carbone DP, Otterson GA, Prosek J, Owen DH. Early Acute Kidney Injury and Its Association With Survival in Patients With Metastatic Non-Small-Cell Lung Cancer Treated with Front-Line Immunotherapy-Based Therapies. Cancer Med. 2025 Aug;14(15):e71058. doi: 10.1002/cam4.71058. PMID: 40719750; PMCID: PMC12302575.

9. Chalif J, Morton M, McLaughlin E, Gonzalez A, Fulton J, Sciuva J, Marcu I, Bixel KL, Cohn DE, Cosgrove CM, Copeland LJ, Nagel CI, Backes F, O’Malley DM, Spakowicz DJ, Chambers LM. Exploratory evaluation of immunotherapy response and medication use in endometrial and cervical carcinoma. Gynecol Oncol Rep. 2025 Jun 21;60:101782. doi: 10.1016/j.gore.2025.101782. PMID: 40896728; PMCID: PMC12399256.

10. Kistenfeger Q, Haight PJ, Levine M, Wang H, Backes FJ, Bixel KL, Copeland LJ, Cohn DE, Cosgrove CM, O’Malley DM, Nagel CI, Spakowicz DJ, Chambers LM. The impact of antibiotics, proton pump inhibitors, H2-receptor antagonists, and steroids on survival in ovarian cancer patients receiving PARP inhibitor therapy. Gynecol Oncol. 2025 May 31;198:90-95. doi: 10.1016/j.ygyno.2025.05.012. Epub ahead of print. PMID: 40450912.

11. Nepal S, Shi N, Hoyd R, Spakowicz DJ, Orwoll E, Shikany JM, Napoli N, Tabung FK. Role of insulinemic and inflammatory dietary patterns on gut microbial composition and circulating biomarkers of metabolic health among older American men. Gut Microbes. 2025 Dec;17(1):2497400. doi: 10.1080/19490976.2025.2497400. Epub 2025 Apr 28. PMID: 40296253.

12. Chalif J, Goldstein N, Mehra Y, Spakowicz D, Chambers LM. The Role of the Microbiome in Cancer Therapies: Current Evidence and Future Directions. Hematol Oncol Clin North Am. 2025 Apr;39(2):269-294. doi: 10.1016/j.hoc.2024.12.005. PMID: 39856008; PMCID: PMC12150864.

13. McDonald HG, Reagan AM, Faisal ASM, Goettl R, Wang C, Hoyd R, Spakowicz D, Evers BM, Kim J, Bhakta AS. Survival Disparity and the Unique Genomic and Microbiome Profiles of Colon Cancer in Appalachian Kentucky. J Am Coll Surg. 2025 Apr 1;240(4):612-624. doi: 10.1097/XCS.0000000000001299. Epub 2025 Mar 17. PMID: 39868697.

14. Johns N, Rudich A, Zhao S, Chian K, Su PL, Khorasanchi A, Gheeya J, Spakowicz D, Wei L, Roof L, Alahmadi A, Memmott R, Kaufman J, Presley C, He K, Shields P, Rolfo C, Carbone D, Owen D, Li M. CLO25-053: Real-World Evidence of Survival in Patients With Metastatic NSCLC Treated With First-Line Immune Checkpoint Inhibitors Beyond Progression. J Natl Compr Canc Netw. 2025 Mar 28;23(3.5):CLO25-053. doi: 10.6004/jnccn.2024.7160. PMID: 40159135.

15. Rudich A, Johns N, Zhao S, Chian K, Su PL, Khorasanchi A, Gheeya J, Spakowicz D, Wei L, Roof L, Alahmadi A, Memmott R, Kaufman J, Presley C, He K, Shields P, Rolfo C, Carbone D, Li M, Owen D. CLO25-080: Outcomes of Extreme Low PD-L1 Expression in Advanced Non-Small Cell Lung Cancer: Implications for Treatment Approaches. J Natl Compr Canc Netw. 2025 Mar 28;23(3.5):CLO25-080. doi: 10.6004/jnccn.2024.7166. PMID: 40154411.

2024 (18)

1. Zhou X, Ganz AB, Rayner A, Cheng TY, Oba H, Rolnik B, Lancaster S, Lu X, Li Y, Johnson JS, Hoyd R, Spakowicz DJ, Slavich GM, Snyder MP. Dynamic human gut microbiome and immune shifts during an immersive psychosocial intervention program. Brain Behav Immun. 2024 Dec 17:S0889-1591(24)00756-6. doi: 10.1016/j.bbi.2024.12.027. Epub ahead of print. PMID: 39701328.

2. Shi N, Nepal S, Hoobler R, Menni C, Playdon MC, Spakowicz D, Wells PM, Steves CJ, Clinton SK, Tabung FK. Pro-inflammatory and hyperinsulinaemic dietary patterns are associated with specific gut microbiome profiles: a TwinsUK cohort study. Gut Microbiome (Camb). 2024 Dec 5;5:e12. doi: 10.1017/gmb.2024.14. PMID: 39703541; PMCID: PMC11658949.

3. Eljilany I, Coleman S, Tan AC, McCarter MD, Carpten J, Colman H, Naqash AR, Puzanov I, Arnold SM, Churchman ML, Spakowicz D, Salhia B, Marin J, Ganesan S, Ratan A, Shriver C, Hwu P, Dalton WS, Weiner GJ, Conejo-Garcia JR, Rodriguez P, Tarhini AA. Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy. Cells. 2024 Dec 3;13(23):1993. doi: 10.3390/cells13231993. PMID: 39682743; PMCID: PMC11640164.

4. Liu Z, Sun Y, Li Y, Ma A, Willaims NF, Jahanbahkshi S, Hoyd R, Wang X, Zhang S, Zhu J, Xu D, Spakowicz D, Ma Q, Liu B. An Explainable Graph Neural Framework to Identify Cancer-Associated Intratumoral Microbial Communities. Adv Sci (Weinh). 2024 Sep 3:e2403393. doi: 10.1002/advs.202403393. Epub ahead of print. PMID: 39225619.

5. Presley CJ, Grogan M, Compston A, Hock K, Knauss B, Redder E, Arrato NA, Lo SB, Janse S, Benedict J, Hoyd R, Williams N, Hayes S, Wells-Di Gregorio S, Gill TM, Allore H, Focht B, Quist M, Carbone DP, Spakowicz D, Paskett ED, Andersen BL. Resiliency among older adults receiving lung cancer treatment (ROAR-LCT): A novel supportive care intervention for older adults with advanced lung cancer. J Geriatr Oncol. 2024 Aug 21:101844. doi: 10.1016/j.jgo.2024.101844. Epub ahead of print. PMID: 39174449.

6. Chambers L, Grencewicz D, Spakowicz D. From poo to promise: Fecal microbiota transplants support immunotherapy re-sensitization in solid tumors. Cell Host Microbe. 2024 Aug 14;32(8):1217-1218. doi: 10.1016/j.chom.2024.07.015. PMID: 39146792.

7. Dravillas CE, Coleman SS 4th, Hoyd R, Caryotakis G, Denko L, Chan CHF, Churchman ML, Denko N, Dodd RD, Eljilany I, Hardikar S, Husain M, Ikeguchi AP, Jin N, Ma Q, McCarter MD, Osman AEG, Robinson LA, Singer EA, Tinoco G, Ulrich CM, Zakharia Y, Spakowicz D, Tarhini AA, Tan AC; exORIEN Consortium. The Tumor Microbiome as a Predictor of Outcomes in Patients With Metastatic Melanoma Treated with Immune Checkpoint Inhibitors. Cancer Res Commun. 2024 Aug 1;4(8):1978-1990. doi: 10.1158/2767-9764.CRC-23-0170. PMID: 39015091; PMCID: PMC11307144.

   Accompanying public software/code release: exorien-melio v0.1.

8. Han CJ, Ning X, Burd CE, Spakowicz DJ, Tounkara F, Kalady MF, Noonan AM, McCabe S, Von Ah D. Chemotoxicity and Associated Risk Factors in Colorectal Cancer: A Systematic Review and Meta-Analysis. Cancers (Basel). 2024 Jul 20;16(14):2597. doi: 10.3390/cancers16142597. PMID: 39061235; PMCID: PMC11274507.

9. Chambers L, Haight P, Chalif J, Mehra Y, Spakowicz D, Backes FJ, Cosgrove CM, O’Malley DM, Vargas R, Corr BR, Bae-Jump VL, Arend RC. Bridging the Gap from Bench to Bedside: A Call for In Vivo Preclinical Models to Advance Endometrial Cancer and Cervical Cancer Immuno-oncology Research. Clin Cancer Res. 2024 Jul 15;30(14):2905-2909. doi: 10.1158/1078-0432.CCR-23-2570. PMID: 38662438; PMCID: PMC11250463.

10. Benej M, Hoyd R, Kreamer M, Wheeler CE, Grencewicz DJ, Choueiry F, Chan CHF, Zakharia Y, Ma Q, Dodd RD, Ulrich CM, Hardikar S, Churchman ML, Tarhini AA, Robinson LA, Singer EA, Ikeguchi AP, McCarter MD, Tinoco G, Husain M, Jin N, Tan AC, Osman AEG, Eljilany I, Riedlinger G, Schneider BP, Benejova K, Kery M, Papandreou I, Zhu J, Denko N, Spakowicz D; exORIEN Consortium. The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer. Cancer Res Commun. 2024 Jul 1;4(7):1690-1701. doi: 10.1158/2767-9764.CRC-23-0367. PMID: 38904265; PMCID: PMC11234499.

Accompanying public software/code release: exorien-recrad v1.0.

11. Shantaram D, Hoyd R, Blaszczak AM, Antwi L, Jalilvand A, Wright VP, Liu J, Smith AJ, Bradley D, Lafuse W, Liu Y, Williams NF, Snyder O, Wheeler C, Needleman B, Brethauer S, Noria S, Renton D, Perry KA, Nagareddy P, Wozniak D, Mahajan S, Rana PSJB, Pietrzak M, Schlesinger LS, Spakowicz DJ, Hsueh WA. Obesity-associated microbiomes instigate visceral adipose tissue inflammation by recruitment of distinct neutrophils. Nat Commun. 2024 Jun 27;15(1):5434. doi: 10.1038/s41467-024-48935-5. PMID: 38937454; PMCID: PMC11211470.

Accompanying public software/code release: atbac v2.0.

12. Grogan M, Hoyd R, Benedict J, Janse S, Williams N, Naughton M, Burd CE, Paskett ED, Rosko A, Spakowicz DJ, Presley CJ. The FITNESS study: longitudinal geriatric assessment, treatment toxicity, and biospecimen collection to assess functional disability among older adults with lung cancer. Front Aging. 2024 Jun 7;5:1268232. doi: 10.3389/fragi.2024.1268232. PMID: 38911592; PMCID: PMC11190321.

Accompanying public software/code release: fitness v1.0.

13. Upadhyay R, Dhakal A, Wheeler C, Hoyd R, Jagjit Singh M, Karivedu V, Bhateja P, Bonomi M, Valentin S, Gamez ME, Konieczkowski DJ, Baliga S, Grecula JC, Blakaj DM, Gogineni E, Mitchell DL, Denko NC, Spakowicz D*, Jhawar SR. Comparative analysis of the tumor microbiome, molecular profiles, and immune cell abundances by HPV status in mucosal head and neck cancers and their impact on survival. Cancer Biol Ther. 2024 Dec 31;25(1):2350249. doi: 10.1080/15384047.2024.2350249. Epub 2024 May 9. PMID: 38722731; PMCID: PMC11086009.

14. Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMS, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host Microbe. 2024 Apr 10;32(4):506-526.e9. doi: 10.1016/j.chom.2024.02.012. Epub 2024 Mar 12. PMID: 38479397; PMCID: PMC11022754.

15. Han CJ, Rosko AE, Spakowicz DJ, Hammer MJ, Von Ah D. Associations of frailty with symptoms, and HRQOL in older cancer survivors after cancer treatments: a systematic review and meta-analyses. Qual Life Res. 2024 Mar;33(3):583-598. doi: 10.1007/s11136-023-03537-4. Epub 2023 Oct 28. PMID: 37897643.

16. Madison AA, Burd CE, Andridge R, Wilson SJ, Bailey MT, Belury MA, Spakowicz DJ, Malarkey WB, Kiecolt-Glaser JK. Gut Microbiota Richness and Diversity Track With T Cell Aging in Healthy Adults. J Gerontol A Biol Sci Med Sci. 2024 Mar 1;79(3):glad276. doi: 10.1093/gerona/glad276. PMID: 38123141; PMCID: PMC10878250.

17. Wang C, Ma A, Li Y, McNutt ME, Zhang S, Zhu J, Hoyd R, Wheeler CE, Robinson LA, Chan CHF, Zakharia Y, Dodd RD, Ulrich CM, Hardikar S, Churchman ML, Tarhini AA, Singer EA, Ikeguchi AP, McCarter MD, Denko N, Tinoco G, Husain M, Jin N, Osman AEG, Eljilany I, Tan AC, Coleman SS, Denko L, Riedlinger G, Schneider BP, Spakowicz D, Ma Q; exORIEN Consortium. A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset. Cancer Res Commun. 2024 Feb 5;4(2):293-302. doi: 10.1158/2767-9764.CRC-23-0213. PMID: 38259095; PMCID: PMC10840455.

Accompanying public software: MEGA (tag 0.0.5).

18. Chalif J, Wang H, Spakowicz D, Quick A, Arthur EK, O’Malley D, Chambers LM. The microbiome and gynecologic cancer: cellular mechanisms and clinical applications. Int J Gynecol Cancer. 2024 Feb 5;34(2):317-327. doi: 10.1136/ijgc-2023-004894. PMID: 38088183.

*Equal contributions

2023 (10)

1. Meng L, Collier KA, Wang P, Li Z, Monk P, Mortazavi A, Hu Z, Spakowicz D, Zheng L, Yang Y. Emerging Immunotherapy Approaches for Advanced Clear Cell Renal Cell Carcinoma. Cells. 2023 Dec 22;13(1):34. doi: 10.3390/cells13010034. PMID: 38201238; PMCID: PMC10777977.

2. Evans JV, Suman S, Goruganthu MUL, Tchekneva EE, Guan S, Arasada RR, Antonucci A, Piao L, Ilgisonis I, Bobko AA, Driesschaert B, Uzhachenko RV, Hoyd R, Samouilov A, Amann J, Wu R, Wei L, Pallerla A, Ryzhov SV, Feoktistov I, Park KP, Kikuchi T, Castro J, Ivanova AV, Kanagasabai T, Owen DH, Spakowicz DJ, Zweier JL, Carbone DP, Novitskiy SV, Khramtsov VV, Shanker A, Dikov MM. Improving combination therapies: targeting A2B-adenosine receptor to modulate metabolic tumor microenvironment and immunosuppression. J Natl Cancer Inst. 2023 Nov 8;115(11):1404-1419. doi: 10.1093/jnci/djad091. PMID: 37195421; PMCID: PMC10637048.

3. Hoyd R, Wheeler CE, Liu Y, Jagjit Singh MS, Muniak M, Jin N, Denko NC, Carbone DP, Mo X, Spakowicz DJ. Exogenous sequences in tumors and immune cells (exotic): a tool for estimating the microbe abundances in tumor RNAseq data. Cancer Res Commun. 2023 Oct 18. doi: 10.1158/2767-9764.CRC-22-0435. Epub ahead of print. PMID: 37850841.

   Accompanying public software/code release: exotic v2.0; exotic-manuscript 1.0.

4. Haight PJ, Kistenfeger Q, Riedinger CJ, Khadraoui W, Backes FJ, Bixel KL, Copeland LJ, Cohn DE, Cosgrove CM, O’Malley DM, Nagel CI, Spakowicz DJ, Chambers LM. The impact of antibiotic and proton pump inhibitor use at the time of adjuvant platinum-based chemotherapy on survival in patients with endometrial cancer. Gynecol Oncol. 2023 Sep 21;178:14-22. doi: 10.1016/j.ygyno.2023.09.005. Epub ahead of print. PMID: 37741201.

5. Hu M, Coleman S, Fadlullah MZH, Spakowicz D, Chung CH, Tan AC. Deciphering the Tumor-Immune-Microbe Interactions in HPV-Negative Head and Neck Cancer. Genes (Basel). 2023 Aug 8;14(8):1599. doi: 10.3390/genes14081599. PMID: 37628651; PMCID: PMC10454300.

6. Johns AC, Yang M, Wei L, Grogan M, Spakowicz D, Patel SH, Li M, Husain M, Kendra KL, Otterson GA, Rosko AE, Andersen BL, Carbone DP, Owen DH, Presley CJ. Risk Factors for Immune Checkpoint Inhibitor Immunotherapy Toxicity Among Older Adults with Cancer. Oncologist. 2023 Aug 3;28(8):e625-e632. doi: 10.1093/oncolo/oyad097. PMID: 37085156; PMCID: PMC10400153.

7. Rosario SR, Dong B, Zhang Y, Hsiao HH, Isenhart E, Wang J, Siegel EM, Monjazeb AM, Owen DH, Dey P, Tabung FK, Spakowicz DJ, Murphy WJ, Edge S, Yendamuri S, Ibrahimi S, Kolesar JM, McDonald PH, Vadehra D, Churchman M, Liu S, Kalinski P, Mukherjee S. Metabolic Dysregulation Explains the Diverse Impacts of Obesity in Males and Females with Gastrointestinal Cancers. Int J Mol Sci. 2023 Jun 29;24(13):10847. doi: 10.3390/ijms241310847. PMID: 37446025; PMCID: PMC10342094.

8. Spakowicz D, Hoyd R, Wheeler C. spakowiczlab/exotic: Exogenous sequences in tumors and immune cells. Zenodo; 2023. Available from: https://zenodo.org/record/7726041

9. Li M, Zhao S, Lopez G, Secor A, Das P, Surya N, Grogan M, Patel S, Chakravarthy K, Miah A, Spakowicz D, Tinoco G, Li Z, Wei L, He K, Bertino E, Alahmadi A, Memmott R, Kaufman J, Shields PG, Carbone DP, Presley CJ, Otterson GA, Owen DH. Mean platelet volume, thrombocytosis, and survival in non-small cell lung cancer patients treated with first-line pembrolizumab alone or with chemotherapy. Cancer Immunol Immunother. 2023 Feb 16. doi: 10.1007/s00262-023-03392-9. PMID: 36795122.

10. Johns AC, Yang M, Wei L, Grogan M, Patel SH, Li M, Husain M, Kendra KL, Otterson GA, Burkart JT, Spakowicz D, Hoyd R, Owen DH, Presley CJ. Association of medical comorbidities and cardiovascular disease with toxicity and survival among patients receiving checkpoint inhibitor immunotherapy. Cancer Immunol Immunother. 2023 Feb 4. doi: 10.1007/s00262-023-03371-0. Epub ahead of print. PMID: 36738310.

Accompanying public software/code release: co-mo-io v1.0.0.

2022 (7)

1. Presley CJ, Mohamed MR, Culakova E, Flannery M, Vibhakar PH, Hoyd R, Amini A, VanderWalde N, Wong ML, Tsubata Y, Spakowicz DJ, Mohile S. A Geriatric Assessment Intervention to Reduce Treatment Toxicity Among Older Adults With Advanced Lung Cancer: A Subgroup Analysis From a Cluster Randomized Controlled Trial. Front Oncol. 2022;12:835117. doi: 10.3389/fonc.2022.835117. PMID: 35433441.

2. Guo Y, Wei L, Patel SH, Lopez G, Grogan M, Li M, Haddad T, Johns A, Ganesan LP, Yang Y, Spakowicz DJ. Serum Albumin: Early Prognostic Marker of Benefit for Immune Checkpoint Inhibitor Monotherapy But Not Chemoimmunotherapy. Clin Lung Cancer. 2022 Jan 8. PMID: 35131184.

3. Dhakal A, Upadhyay R, Wheeler C, Hoyd R, Karivedu V, Gamez ME, Valentin S, Vanputten M, Bhateja P, Bonomi M, Konieczkowski DJ, Baliga S, Mitchell DL, Grecula JC, Blakaj DM, Denko NC, Jhawar SR, Spakowicz D. Association between Tumor Microbiome and Hypoxia across Anatomic Subsites of Head and Neck Cancers. Int J Mol Sci. 2022;23(24):15531. PMID: 36555172.

   Accompanying public software/code release: exohnsc v1.

4. Hoyd R, Liu Y, Wheeler C, Spakowicz D. spakowiczlab/mt.surv: Multi-threshold survival analysis, initial release. Zenodo; 2022. Available from: https://zenodo.org/record/6644267

5. Miah A, Tinoco G, Zhao S, Wei L, Johns A, Patel S, Li M, Grogan M, Lopez G, Husain M, Spakowicz D. Immune checkpoint inhibitor-induced hepatitis injury: risk factors, outcomes, and impact on survival. J Cancer Res Clin Oncol. 2022;1–8. PMID: 36070148.

6. Quick AM, Pardo DAD, Miller ED, Arnett ALH, Pitter KL, Kim J, Flora L, Williams N, Hoyd R, Wheeler C, Mo X, Chambers L, Spakowicz D, Arthur E. Vaginal Microbiome as a Biomarker of Vaginal Health and Patient-Reported Outcomes in Women Receiving Pelvic Radiation. Int J Radiat Oncol Biol Phys. 2022 Nov 1;114(3):e462–e463.

7. Zhou X, Wang B, Demkowicz PC, Johnson JS, Chen Y, Spakowicz DJ, Zhou Y, Dorsett Y, Chen L, Sodergren E, Kuchel GA, Weinstock GM. Exploratory studies of oral and fecal microbiome in healthy human aging. Front Aging. 2022;3:1002405. PMCID: PMC9631447. PMID: 36338834.

2021 (5)

1. Presley C, Mohamed M, Culakova E, Flannery M, Vibhakar P, Spakowicz D, Amini A, VanderWalde N, Wong M, Mohile S. A Geriatric Assessment (GA) intervention to reduce treatment toxicity among older adults with advanced lung cancer: A subgroup analysis from a cluster randomized controlled trial (CRCT). J Geriatr Oncol. 2021;12(8):S54.

2. Liu J*, Spakowicz DJ*, Ash GI, Hoyd R, Ahluwalia R, Zhang A, Lou S, Lee D, Zhang J, Presley C, others. Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions. PLoS Comput Biol. 2021;17(8):e1009303. PMID: 34424894.

   Accompanying public code: mhealthCI (no GitHub release currently listed).

*These authors contributed equally

3. Qin A, Zhao S, Miah A, Wei L, Patel S, Johns A, Grogan M, Bertino EM, He K, Shields PG, Kalemkerian GP, Gadgeel SM, Ramnath N, Schneider BJ, Hassan KA, Szerlip N, Chopra Z, Journey S, Waninger J, Spakowicz D, Carbone DP, Presley CJ, Otterson GA, Green MD, Owen DH. Bone Metastases, Skeletal-Related Events, and Survival in Patients With Metastatic Non-Small Cell Lung Cancer Treated With Immune Checkpoint Inhibitors. J Natl Compr Canc Netw. 2021 Apr 20:1-7. doi: 10.6004/jnccn.2020.7668. Epub ahead of print. PMID: 33878726.

4. Johns AC, Wei L, Grogan M, Hoyd R, Bridges JFP, Patel SH, Li M, Husain M, Kendra KL, Otterson GA, Burkart JT, Rosko AE, Andersen BL, Carbone DP, Owen DH, Spakowicz DJ, Presley CJ. Checkpoint inhibitor immunotherapy toxicity and overall survival among older adults with advanced cancer. J Geriatr Oncol. 2021 Feb 21:S1879-4068(21)00011-4. doi: 10.1016/j.jgo.2021.02.002. Epub ahead of print. PMID: 33627226.

5. Spakowicz D, Bibi A, Muniak M, Williams NF, Hoyd R, Presley CJ. The aging microbiome and response to immunotherapy: Considerations for the treatment of older adults with cancer. J Geriatr Oncol. 2021 Feb 18:S1879-4068(21)00010-2. doi: 10.1016/j.jgo.2021.02.001. Epub ahead of print. PMID: 33612452.

   Accompanying public software/code release: mageio v1.0.1.

2020 (8)

1. Zhou X, Johnson JS, Spakowicz D, Zhou W, Zhou Y, Sodergren E, Snyder M, Weinstock GM. Longitudinal Analysis of Serum Cytokine Levels and Gut Microbial Abundance Links IL-17/IL-22 With Clostridia and Insulin Sensitivity in Humans. Diabetes. 2020;69(8):1833–1842. doi: 10.2337/db19-0592. PMID: 32366680.

2. Li M, Spakowicz D, Zhao S, Patel SH, Johns A, Grogan M, Miah A, Husain M, He K, Bertino EM, Shields PG, Wei L, Carbone DP, Otterson GA, Presley CJ, Owen DH. Brief report: inhaled corticosteroid use and the risk of checkpoint inhibitor pneumonitis in patients with advanced cancer. Cancer Immunol Immunother. 2020 Nov;69(11):2403-2408. doi: 10.1007/s00262-020-02674-w. Epub 2020 Jul 29. PMID: 32728772; PMCID: PMC7572636.

3. Tabung FK, Noonan A, Lee DH, Song M, Clinton SK, Spakowicz D, Wu K, Cheng E, Meyerhardt JA, Fuchs CS, Giovannucci EL. Post-diagnosis dietary insulinemic potential and survival outcomes among colorectal cancer patients. BMC Cancer. 2020 Aug 27;20(1):817. doi: 10.1186/s12885-020-07288-0. PMID: 32854644; PMCID: PMC7450968.

4. Spakowicz D and Malalur P. The tumor microbiome and why it may unlock the next advancement in cancer treatment. Oncology Central, 12 August, 2020. https://www.oncology-central.com/the-tumor-microbiome-and-why-it-may-unlock-the-next-advancement-in-cancer-treatment/

5. Adaku N, Park HB, Spakowicz DJ, Tiwari MK, Strobel SA, Crawford JM, Rogers FA. A DNA Repair Inhibitor Isolated from an Ecuadorian Fungal Endophyte Exhibits Synthetic Lethality in PTEN-Deficient Glioblastoma. J Nat Prod. 2020 Jun 26;83(6):1899-1908. doi: 10.1021/acs.jnatprod.0c00012. Epub 2020 May 14. PMID: 32407116.

6. Spakowicz D, Lou S, Barron B, Gomez JL, Li T, Liu Q, Grant N, Yan X, Hoyd R, Weinstock G, Chupp GL, Gerstein M. Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients. Genome Biol. 2020 Jun 22;21(1):150. doi: 10.1186/s13059-020-02033-z. PMID: 32571363; PMCID: PMC7310008.

   Accompanying public software/code release: decoasthma v1.0.

7. Lou S, Li T, Spakowicz D, Yan X, Chupp GL, Gerstein M. Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients. BMC Bioinformatics. 2020;21:457. doi: 10.1186/s12859-020-03785-y. PMID: 33059594.

8. Spakowicz D, Hoyd R, Muniak M, Husain M, Bassett JS, Wang L, Tinoco G, Patel SH, Burkart J, Miah A, Li M, Johns A, Grogan M, Carbone DP, Verschraegen CF, Kendra KL, Otterson GA, Li L, Presley CJ, Owen DH. Inferring the role of the microbiome on survival in patients treated with immune checkpoint inhibitors: causal modeling, timing, and classes of concomitant medications. BMC Cancer. 2020 May 6;20(1):383. doi: 10.1186/s12885-020-06882-6. PMID: 32375706; PMCID: PMC7201618.

   Accompanying public software/code release: co-med-io v1.0.1.

2019 (4)

1. Li M, Spakowicz D, Burkhart J, Patel S, Husain M, He K, Bertino EM, Shields PG, Carbone DP, Verschraegen CF, Presley CJ, Otterson GA, Kendra K, Owen DH. Change in neutrophil to lymphocyte ratio during immunotherapy treatment is a non-linear predictor of patient outcomes in advanced cancers. J Cancer Res Clin Oncol. 2019 Oct;145(10):2541-2546. PMID: 31367835.

   Accompanying public code: nlr-io (no versioned release currently listed).

2. Proctor LM, Creasy HH, Fettweis JM, Lloyd-Price J, Mahurkar A, Zhou W, Buck GA, Snyder MP, Strauss JF, Weinstock GM, White O, Huttenhower C; The Integrative HMP (iHMP) Research Network Consortium. The Integrative Human Microbiome Project. Nature. 2019 May;569(7758):641–648.

3. Johnson J*, Spakowicz DJ*, Hong B, Petersen LM, Demkowicz P, Chen L, Leopold SR, Hanson BMM, Agresta HO, Gerstein M, Sodergren E, Weinstock GM. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun. 2019;10:5029. PMID: 31695033.

*These authors contributed equally

4. Zhou W, Sailani MR, Contrepois K, Zhou Y, Ahadi S, Leopold SR, Zhang MJ, Rao V, Avina M, Mishra T, Johnson J, Lee-McMullen B, Chen S, Metwally AA, Tran TDB, Nguyen H, Zhou X, Albright B, Hong B-Y, Petersen L, Bautista E, Hanson B, Chen L, Spakowicz D, Bahmani A, Salins D, Leopold B, Ashland M, Dagan-Rosenfeld O, Rego S, Limcaoco P, Colbert E, Allister C, Perelman D, Craig C, Wei E, Chaib H, Hornburg D, Dunn J, Liang L, Rose SMS-F, Kukurba K, Piening B, Rost H, Tse D, McLaughlin T, Sodergren E, Weinstock GM, Snyder M. Longitudinal multi-omics of host–microbe dynamics in prediabetes. Nature. 2019 May;569(7758):663. PMID: 31142858.

2018 (1)

1. Piening BD, Zhou W, Contrepois K, Röst H, Urban GJG, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz DJ, Kukurba K, Perelman D, Craig C, Colbert E, Salins D, Rego S, Lee S, Zhang C, Wheeler J, Sailani MR, Liang L, Abbott C, Gerstein M, Mardinoglu A, Smith U, Pitteri E, Sodergren E, McLaughlin TL, Weinstock GM, Snyder MP. Integrative Personal Omics Profiles During Periods of Weight Gain and Loss. Cell Syst. 2018;6:1–14. PMID: 29361466; PMCID: PMC6021558.

2017 (1)

1. de Sena Filho JG, Barreto IC, Soares Filho AO, Nogueira PCL, Teodoro AV, Cruz da Silva AV, Xavier HS, Rabbani ARC, Spakowicz DJ, Duringer JM. Volatile Metabolomic Composition of Vitex Species: Chemodiversity Insights and Acaricidal Activity. Front Plant Sci. 2017;8:1931. doi: 10.3389/fpls.2017.01931. PMID: 29184560; PMCID: PMC5694497.

2016 (1)

1. Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M. The Real Cost of Sequencing: Scaling Computation to Keep Pace with Data Generation. Genome Biol. 2016;17. PMCID: PMC4806511. PMID: 27009100.

2015 (7)

1. Shaw JJ*, Spakowicz DJ*, Dalal RS, Davis JH, Lehr NA, Dunican BF, Orellana EA, Narváez-Trujillo A, Strobel SA. Biosynthesis and genomic analysis of medium-chain hydrocarbon production by the endophytic fungal isolate Nigrograna mackinnonii E5202H. Appl Microbiol Biotechnol. 2015. PMCID: PMC4667366. PMID: 25672844.

*These authors contributed equally

2. Shaw JJ, Berbasova T, Sasaki T, Jefferson-George K, Spakowicz DJ, Dunican BF, Portero CE, Narvaez-Trujillo A, Strobel SA. Identification of a Fungal 1,8-cineole Synthase from Hypoxylon sp. with Common Specificity Determinants to the Plant Synthases. J Biol Chem. 2015. PMCID: PMC4375501. PMID: 25648891.

3. Sena Filho JG de, Quin MB, Spakowicz DJ, Shaw JJ, Kucera K, Dunican B, Strobel SA, Schmidt-Dannert C. Genome of Diaporthe Sp. Provides Insights into the Potential Inter-Phylum Transfer of a Fungal Sesquiterpenoid Biosynthetic Pathway. Fungal Biol. 2016. PMCID: PMC4987500. PMID: 27521636.

4. Patridge EV, Darnell A, Kucera K, Phillips GM, Bokesch HR, Gustafson KR, Spakowicz DJ, Zhou L, Hungerford WM, Plummer M, and others. Pyrrolocin A, a 3-Decalinoyltetramic Acid with Selective Biological Activity, Isolated from Amazonian Cultures of the Novel Endophyte Diaporthales sp. E6927E. Nat Prod Commun. 2015;10(10):1649–1654. PMID: 26669095.

5. Forcina GC, Castro A, Bokesch HR, Spakowicz DJ, Legaspi ME, Kucera K, Villota S, Narváez-Trujillo A, McMahon JB, Gustafson KR, and others. Stelliosphaerols A and B, Sesquiterpene–Polyol Conjugates from an Ecuadorian Fungal Endophyte. J Nat Prod. 2015. PMID: 26651879.

6. Rundell SM, Spakowicz DJ, Narváez-Trujillo A, Strobel SA. The Biological Diversity and Production of Volatile Organic Compounds by Stem-Inhabiting Endophytic Fungi of Ecuador. J Fungi. 2015;1(3):384–396. PMCID: PMC5753131. PMID: 29376917.

7. Spakowicz DJ, Strobel SA. Biosynthesis of Hydrocarbons and Volatile Organic Compounds by Fungi: Bioengineering Potential. Appl Microbiol Biotechnol. 2015;99(12):4943–4951. PMCID: PMC4677055. PMID: 25957494.

2012 (1)

1. Gianoulis TA*, Griffin MA*, Spakowicz DJ*, Dunican BF, Alpha CJ, Sboner A, Sismour AM, Kodira C, Egholm M, Church GM, Strobel SA. Genomic Analysis of the Hydrocarbon-Producing, Cellulolytic, Endophytic Fungus Ascocoryne sarcoides. PLoS Genet. 2012;8:e1002558. PMCID: PMC3291568. PMID: 22396667.

*These authors contributed equally

2010 (5)

1. Tomsheck AR, Strobel GA, Booth E, Geary B, Spakowicz DJ, Knighton B, Floerchinger C, Sears J, Liarzi O, Ezra D. Hypoxylon sp., an endophyte of Persea indica, producing 1,8-cineole and other bioactive volatiles with fuel potential. Microb Ecol. 2010;60:903–914. PMID: 20953951.

2. Strobel G, Tomsheck A, Geary B, Spakowicz D, Strobel S, Mattner S, Mann R. Endophyte strain NRRL 50072 producing volatile organics is a species of Ascocoryne. Mycology. 2010;1(3):187–194.

3. Strobel GA, Knighton WB, Kluck K, Ren Y, Livinghouse T, Griffin M, Spakowicz D, Sears J. The production of myco-diesel hydrocarbons and their derivatives by the endophytic fungus Gliocladium roseum (NRRL 50072). Microbiology. 2010;156(2):3830–3833. PMID: 18957585.

4. Griffin MA, Spakowicz DJ, Gianoulis TA, Strobel SA. Volatile organic compound production by organisms in the genus Ascocoryne and a re-evaluation of myco-diesel production by NRRL 50072. Microbiology. 2010;156(Pt 12):3814. PMID: 20705658.

5. Banerjee D, Strobel GA, Booth B, Sears J, Spakowicz D, Busse S. An endophytic Myrothecium inundatum producing volatile organic compounds. Mycosphere. 2010;1(3):241–247.

2008 (3)

1. Strobel GA, Knighton B, Kluck K, Ren Y, Livinghouse T, Griffin M, Spakowicz DJ, Sears J. The production of myco-diesel hydrocarbons and their derivatives by the endophytic fungus Gliocladium roseum (NRRL 50072). Microbiology. 2008;154:3319–3328. PMID: 18957585.

2. Prochniewicz E, Spakowicz DJ, Thomas DD. Changes in Actin Structural Transitions Associated with Oxidative Inhibition of Muscle Contraction. Biochemistry. 2008;47:11811–11817. PMCID: PMC3253347. PMID: 18855423.

3. Prochniewicz E, Lowe DA, Spakowicz DJ, Higgins L, O’Conor K, Thompson LV, Ferrington DA, Thomas DD. Functional, Structural, and Chemical Changes in Myosin Associated with Hydrogen Peroxide Treatment of Skeletal Muscle Fibers. Am J Physiol Cell Physiol. 2008;294(2):C613–C626. PMCID: PMC4397896. PMID: 18003749.

Book Chapters

1. Grencewicz DJ, Jahanbakhshi S, Fulton J, Wheeler C, Chalif J, Chambers L, Spakowicz D. The Role of the Microbiome in Modulating Human Health. In: Soil Health: Food as Medicine. CRC Press/Taylor & Francis Group; 2025. ISBN: 978-1-00-346974-2

Published Abstracts and Presentations

Conference abstracts, posters, and oral presentations. Journal articles are listed under Publications.

2026 (4)

1. Nambi T, Carson A, Dhrubo D, Spakowicz D. Candida albicans, Treatment Trajectories, and Survival: A Four-Cancer Analysis of the ORIEN Cohort & A multi-objective optimizer for treatment-trajectory clustering. CREATES; 2026 Jul 24. Poster. Presenter: Tharun Nambi.

2. Jahanbakhshi S, et al. (coauthor: Spakowicz D). Dietary modulation of gut Lachnospiraceae reveals conserved microbial metabolic programs linked to host immune regulation. ASM; 2026. Poster. Presenter: Shiva Jahanbakhshi.

3. Jahanbakhshi S, et al. (coauthor: Spakowicz D). Comparative genomics of gut commensal Lachnospiraceae and their associations with cancer treatment response with immune checkpoint inhibitors. Case Comprehensive Cancer Center; 2026. Poster. Presenter: Shiva Jahanbakhshi.

4. Jahanbakhshi S, et al. (coauthor: Spakowicz D). Comparative genomics of gut commensal Lachnospiraceae and their associations with cancer treatment response with immune checkpoint inhibitors. AACR Annual Meeting; 2026. Poster. Presenter: Shiva Jahanbakhshi.

2025 (13)

1. Dravillas C, et al. (coauthor: Spakowicz D). Modeling Longitudinal Microbiome Data with Application to a Melanoma Clinical Trial Evaluating Immune Checkpoint Inhibitor Treatment Response (NCT05102773). ASA; 2025. Oral presentation. Presenter: Caroline Dravillas.

2. Loncar A, et al. (coauthor: Spakowicz D). Tumor colonization with Candida albicans increases tumor growth and decreases treatment response by influencing tumor hypoxia and immune activity. Pelotonia Scholars Symposium; 2025. Oral presentation. Presenter: Alexander Loncar. Best Undergraduate Presentation Award: Alexander Loncar.

3. Spakowicz D. Using dietary interventions to improve cancer treatment outcomes via modification of the microbiome. HMIDT; 2025. Oral presentation.

4. Jahanbakhshi S, et al. (coauthor: Spakowicz D). Gut microbiome modulation by a black raspberry nectar for improving anti-PD1 therapy effectiveness in pre-clinical cancer models. CFAES; 2025. Poster. Presenter: Shiva Jahanbakhshi.

5. Jahanbakhshi S, et al. (coauthor: Spakowicz D). Gut microbiome modulation by a black raspberry nectar for improving anti-PD1 therapy effectiveness in pre-clinical cancer models. 21st Annual Russell Klein Nutrition Research Symposium; 2025. Poster. Presenter: Shiva Jahanbakhshi.

6. Grencewicz D, et al. (coauthor: Spakowicz D). Tumor colonization with Candida albicans increases tumor growth and decreases treatment response. Case Comprehensive Cancer Center Microbiome Workshop; 2025. Oral presentation. Presenter: Dennis Grencewicz. Best Trainee Presentation Award: Dennis Grencewicz.

7. Cardova J, Jahanbakhshi S, Spakowicz D, Han C. The role of the gut microbiome in symptoms of patients undergoing chemotherapy for colorectal cancer. Poster. 2025 Jul 25.

8. Chakravarthy K, Gogineni E, Manring I, Mestres-Villanueva M, Mitchell DL, Blakaj D, Bonomi MR, Bhateja P, Baliga S, Grecula JC, Ma SJ, Zhu S, Valentin S, Majercak W, Mehra Y, Jahanbakhshi S, Daniel S, Spakowicz D, Jhawar SR. Prediction of post-treatment toxicities using the pre-treatment oral microbiome in the context of definitive chemoradiation for oropharyngeal cancer. ASCO Annual Meeting; 2025.

9. Mehra Y, LaPlante E, Flora L, Dravillas C, Kim J, Aduwo J, Korley N, Diaz A, Miller E, Pitter K, Williams N, Hoyd R, Mo X, Spakowicz D, Chambers L, Arthur EK, Quick AM. Impact of pelvic radiation on vaginal microbiome and pelvic health: Findings from the GEORGIA Trial (NCT04713618). AACR Annual Meeting; Chicago, IL; 2025 Apr 25–30. Cancer Res. 2025;85(8_Suppl_1):Abstract nr 4693.

10. Grencewicz D, Loncar A, Wu R, Hoyd R, Wu J, Mehra Y, Jahanbakhshi S, Ferrandon S, Anderson M, Benej M, Zhu J, Kalady M, Carbone D, Denko N, ORIEN Microbiome Research Interest Group, Spakowicz D. Tumor colonization with Candida albicans increases tumor growth and decreases treatment response by influencing tumor hypoxia and immune activity. AACR Annual Meeting; Chicago, IL; 2025 Apr 25–30. Cancer Res. 2025;85(8_Suppl_1):Abstract nr 6521. doi: 10.1158/1538-7445.am2025-6521.

11. Wu R, Owen D, Wei L, Dikov M, Suman S, Amann J, Guan S, Su PL, Schweitzer C, Smith MB, Ferguson S, Castro J, Spakowicz D, Bertino E, Shields P, He K, Presley CJ, Otterson GA, Carson WE, Carbone DP. Targeting adenosine A2B receptor using PBF-1129 in treating patients with metastatic non-small cell lung cancer. AACR Annual Meeting; Chicago, IL; 2025 Apr 25–30. Cancer Res. 2025;85(8_Suppl_1):Abstract nr 732.

12. Bittoni MA, Lontoc A, Soileau M, Moon J, Marin L, Hockenhull V, Lewis-Hughes A, Spakowicz D, Carbone DA, Chaplow Z. The BE FIT study: feasibility of an exercise intervention on the microbiome and immune function in a high-risk cohort for lung cancer. AACR Annual Meeting; Chicago, IL; 2025 Apr 25–30. Cancer Res. 2025;85(8_Suppl_1):Abstract nr 3729. doi: 10.1158/1538-7445.am2025-3729.

13. Jahanbakhshi S, Bibi A, Hoyd R, Dravillas C, Williams N, Zhang S, Pallerla A, Suman S, Amann J, Goruganthu M, Okimoto T, Liu Y, Bittoni MA, Shi N, Conrad B, Nevers L, Heitman K, Webb M, Grainger EM, Grogan M, Quiles C, Chen T, Presley C, Li L, Bradley P, Vodovotz Y, Carbone DP, Clinton SK, Zhu J, Spakowicz D. Gut microbiome modulation by a black raspberry nectar for improving anti-PD1 therapy effectiveness in pre-clinical cancer models. AACR Annual Meeting; Chicago, IL; 2025 Apr 25–30. Cancer Res. 2025;85(8_Suppl_1):Abstract nr 2377. doi: 10.1158/1538-7445.am2025-2377.

2024 (12)

1. Jahanbakhshi S, et al. (coauthor: Spakowicz D). Gut microbiome modulation by a black raspberry nectar for improving anti-PD1 therapy effectiveness in pre-clinical cancer models. Pelotonia Institute for Immuno-Oncology (PIIO); 2024. Poster. Presenter: Shiva Jahanbakhshi.

2. Li M, Zhao S, Cheng G, Chian K, Jones N, Su P, Khorasanchi A, Elsaid M, Gheeya J, Adeluola A, Spakowicz D, Wei L, Meara A, Coss C, Phelps M, Yang Y, Roof L, Alahmadi A, Memmott R, Kaufman J, Presley C, He K, Shields P, Carbone D, Otterson G, Prosek J, Owen D. Association between developing acute renal failure and one-year survival in patients with metastatic NSCLC who have received immune checkpoint inhibitor-based front-line treatment. SITC Annual Meeting; 2024 Nov 1. J Immunother Cancer. 2024;12(Suppl_2).

3. Li M, Rubinstein M, Wei L, Voorhes T, Meara A, Spakowicz D, Collier K, Mittra A, Sukrithan V, Hays J, Gatti-Mays M, Owen D, Mortazavi A, Li Z, Verschraegen C, Yang Y. A phase 2 trial of immune checkpoint inhibitor rechallenge in combination with siltuximab prophylaxis for patients who had prior immune-related adverse event (CIRES trial). SITC Annual Meeting; 2024 Nov 1. J Immunother Cancer. 2024;12(Suppl_2).

4. Chakravarthy K, Hoyd R, ORIEN Microbiome RIG, Jhawar S, Spakowicz D. Spatial associations between tumor microbiome and immune microenvironment within breast cancer subtypes. ORIEN Scientific Summit; Tampa, FL; 2024.

5. Chakravarthy K, Hoyd R, ORIEN Microbiome RIG, Jhawar SR, Spakowicz D. Exploring the tumor microbiome in bulkRNAseq data. ORIEN Scientific Summit; Tampa, FL; 2024.

6. Jin N, Hoyd R, Yilmaz A, Zhang S, Liu Y, Grencewicz D, Singh M, Zhu J, Liu B, Mo X, Spakowicz D, exORIEN Consortium. Microbiome signature, immune landscape and global methylation in early onset colorectal cancer. ASCO Annual Meeting; 2024 Jun 1.

7. Kwon H, Li M, Ma A, Wang C, Chian K, Gauntner T, Jones N, Khorasanchi A, Spakowicz D, He K, Alahmadi A, Memmott R, Kaufman J, Shields P, Carbone D, Otterson G, Presley C, Ma Q, Li Z, Owen D. Eosinophil-neutrophil ratio as a sex-dependent prognostic marker in immune checkpoint therapy for metastatic NSCLC and transcriptomic evaluation of intratumoral eosinophil-T cell interaction. ASCO Annual Meeting; 2024 Jun 1.

8. Grencewicz D, Loncar A, Hoyd R, Pallerla A, Williams N, Benej M, Kreamer M, Mehra Y, Jahanbakhshi S, Anderson M, Denko N, Spakowicz D. Gavage with Candida albicans leads to fungal colonization of colorectal tumors and decreased response to radiotherapy. AACR Annual Meeting; 2024 Mar 15. Cancer Res. 2024;84(6_Supplement):1282.

9. Benej M, Benejova K, Hoyd R, Wheeler C, Spakowicz D, Denko N. Validation of OXPHOS gene amplification as a driver of treatment resistance in non-small cell lung cancer. AACR Annual Meeting; 2024 Mar. Cancer Res. 2024;84(6_Supplement):7057.

10. Ear P, Hu, Shilyansky JS, Fei N, Coleman S, Hoyd R, Wheeler C, Steckly KL, Churchman ML, Denko N, Dodd R, Hardikar S, Jin N, Ma Q, McCarter M, Naqash A, Osman A, Riedlinger G, Robinson L, Schneider B, Singer E, Tarhini A, Tinoco G, Ulrich C, Zakharia Y, Spakowicz D, Tan AC, Chan C. Epithelial-mesenchymal-transition gene signature changes and poor oncological outcome in Candida-positive pancreatic ductal adenocarcinoma. AACR Annual Meeting; 2024 Mar 15. Cancer Res. 2024;84(6_Supplement):7615.

11. Loncar A, Grencewicz D, Hoyd R, Pallerla A, Williams N, Benej B, Mehra Y, Jahanbakhshi S, Anderson M, Denko N, Spakowicz D. The effect of intra-tumoral Candida albicans on host gene expression. AACR Annual Meeting; 2024 Mar 15. Cancer Res. 2024;84(6_Supplement):6842.

12. Vadehra D, Rosario S, Wang J, Zhang Y, Isenhart E, Kolesar J, Ibrahimi S, Singer E, Spakowicz D, Owen DH, Churchman ML, Mukherjee S. Sex-based differences in the transcriptomic metabolic profiling in young onset colorectal cancer (YOCRC). ASCO Gastrointestinal Cancers Symposium; 2024 Jan. J Clin Oncol. 2024;42(3_suppl):155.

2023 (13)

1. Grogan M, Hoyd R, Gheeya J, Presley C, Spakowicz D. A cost-effective way to merge Fitbit devices into clinical trials: older adults with lung cancer. J Geriatr Oncol. 2023 Nov;14(8):S14–S15.

2. Li M, Zhao S, Chian K, Chakravarthy K, Kwon H, Gauntner T, Jones N, Secor A, Das P, Surya N, Zehr B, Spakowicz D, Wei L, He K, Alahmadi A, Memmott R, Kaufman J, Shields PG, Li Z, Carbone DP, Presley CJ, Otterson GA, Owen DH. P1.21-15 Prognostic value of change in platelet volume for patients with metastatic non-small cell lung cancer treated with pembrolizumab. J Thorac Oncol. 2023 Nov;18(11 Suppl):S240–S241.

3. Li M, Das K, Giuliani G, Parwani A, Spakowicz D, Mortazavi A, Das J, Li Z, Yang Y. Associations of high toll-like receptor 3 gene expression and favorable anti-tumor immune microenvironment in metastatic clear cell renal cell carcinoma treated with immune checkpoint inhibitors. SITC Annual Meeting; 2023 Oct. J Immunother Cancer. 2023;11(Suppl 1):168.

4. Williams N, Wheeler CE, Husain M, Hoyd R, Meara AS, Lynn M, Bibi A, Conrad B, Gray S, Bodnar M, Arya N, Roberts S, Hoang P, Apparicio J, Merrill D, Wu RCH, Verschraegen CF, Burd CE, Kendra KL, Spakowicz D. De-correlating immune checkpoint inhibitor toxicity and response in melanoma via the microbiome. ASCO Annual Meeting; 2023 Jun. J Clin Oncol. 2023;41(16_suppl):9569.

5. Vadehra D, Rosario S, Wang J, Zhang Y, Hsiao H, Kolesar J, McDonald P, Spakowicz D, Ibrahimi S, Tabung F, Owen DH, Mukherjee S. Transcriptional metabolic profiling in young onset colorectal cancer. ASCO Annual Meeting; 2023 Jun. J Clin Oncol. 2023;41(16_suppl):3509.

6. Li M, Zhao S, Chian K, Kwon H, Jones N, Khorasanchi A, Gauntner T, Coss C, Phelps M, Spakowicz D, Wei L, Alahmadi A, Memmott RM, Kaufman J, He K, Shields PG, Carbone DP, Otterson GA, Presley CJ, Owen DH. Patterns of weight change and overall survival during first-line pembrolizumab treatment in patients with non-small cell lung cancer. ASCO Annual Meeting; 2023 Jun. J Clin Oncol. 2023;41(16_suppl):e21094.

7. Kwon H, Li M, Chian K, Gauntner T, Jones N, Khorasanchi A, Spakowicz D, Lopez G, Goodyear E, Secor A, He K, Alahmadi A, Memmott RM, Kaufman J, Shields PG, Carbone DP, Otterson GA, Presley CJ, Li Z, Owen DH. Sex differences in prognostic utility of peripheral eosinophil count in first-line immune checkpoint therapy against metastatic NSCLC. ASCO Annual Meeting; 2023 Jun. J Clin Oncol. 2023;41(16_suppl):9067.

8. Kaufman J, Owen DH, Memmott RM, Otterson GA, He K, Presley CJ, Spakowicz D, Shields PG, Zhang X, Boyle TA, Cress WD, Wood K, Ready NE, Li L, Li Z, Carbone DP. Novel STK11 differentiation phenotype classifier STK11-DPC: immunosuppressive tumor microenvironment and response to immune checkpoint blockade in STK11-deficient NSCLC. ASCO Annual Meeting; 2023 Jun. J Clin Oncol. 2023;41(16_suppl):2626.

9. Hoyd R, Wheeler C, Coleman S, Denko L, Chan C, Zakharia Y, Dodd R, Ulrich CM, Hardikar S, Ose J, Churchman M, Tarhini A, Robinson L, Singer E, Ikeguchi AP, McCarter M, Anderson K, Carpten J, Tinoco G, Husain M, Denko N, Liu Y, Jin N, Kim Y, Masson A, Fei N, Benej M, Kreamer M, Grencewicz D, Hussein A, Tan AC, Spakowicz D. The tumor microbiome associates with features of the tumor microenvironment, treatment outcomes, and histologies: a national collaboration of the exORIEN Consortium. AACR Annual Meeting; 2023 Apr. Cancer Res. 2023;83(7_Supplement):5907.

10. Benej M, Benejova K, Kreamer M, Wu J, Asjraf S, Wheeler C, Hoyd R, Spakowicz D, Denko NC. Copy number amplification of OXPHOS genes drives tumor hypoxia in NSCLC. AACR Annual Meeting; 2023 Apr. Cancer Res. 2023;83(7_Supplement):4832.

11. Coleman S, Wheeler C, Hoyd R, Denko L, Lin C, Fadlullah M, Hu-Lieskovan S, Chung C, Tarhini A, Spakowicz D, Tan AC. Systematic analysis of the predictive gene expression signatures of immunotherapies across multiple cancer types using IOSig. AACR Annual Meeting; 2023 Apr. Cancer Res. 2023;83(7_Supplement):6574.

12. Wheeler CE, Coleman S, Hoyd R, Osman A, Denko L, Tan AC, Spakowicz D, Tarhini A. Intra-tumor microbes identified by RNAseq associated with response to immune checkpoint blockade in metastatic melanoma. AACR Annual Meeting; 2023 Apr 1. Cancer Res. 2023;83(7_Supplement):5904.

13. Pallerla A, Conrad B, Bibi A, Williams N, Wheeler C, Hoyd R, Suman S, Amann J, Liu Y, Bittoni M, Zhang S, Grogan M, Anand A, Afrah N, Presley C, Tabung FK, Li L, Vodovotz Y, Zhu J, Carbone DP, Clinton SK, Spakowicz D. A causal modeling platform for testing lifestyle interventions on the microbiome and response to immunotherapy. AACR Annual Meeting; 2023 Apr. Cancer Res. 2023;83(7_Supplement):4435.

2022 (1)

1. Spakowicz D, Hoyd R, Wheeler CE, Williams N, Bibi A, Husain M, Rajamouli S, Suman S, Amann J, Grogan M, Vibhakar P, Owen DH, Carbone DP, Rosko A, Burd CE, Presley CJ. Older adult specific microbes correlate with treatment response and markers of T-cell senescence in NSCLC. AACR Special Conference: Aging and Cancer; 2022 Nov. Cancer Res. 2023;83(2_Suppl_1).

2021 (7)

1. Karivedu V, Hoyd R, Wheeler C, Jhawar S, Bhateja P, Bonomi M, Spakowicz D. Preliminary insights into the impact of tumor microbiome in head and neck squamous cell carcinoma. SITC Annual Meeting; 2021 Nov. J Immunother Cancer. 2021;9(Suppl 2):A878. doi: 10.1136/jitc-2021-SITC2021.837.

2. Bittoni M, Bibi A, Williams N, Mendelson M, Grainger E, Vodovotz Y, Riedl K, Clinton S, Carbone D, Spakowicz D. Report on a phytochemical-rich dietary intervention trial to prevent lung cancer: implementation in a high-risk lung screening clinic. J Thorac Oncol. 2021 Mar;16(3 Suppl):S470–S471. Abstract P40.03.

3. Byun W, Ross H, Kozono D, Urbanic J, Robb R, Talabere T, Oezkan F, Spakowicz D, Stinchcombe T, Carbone D. TCR sequencing to identify responders in patients with stage III NSCLC treated with atezolizumab with chemoradiation (AFT-16). J Thorac Oncol. 2021 Mar. Abstract P79.01. doi: 10.1016/j.jtho.2021.01.1180.

4. Malalur PG, Mo X, Hoyd R, Hays JL, Carbone DP, Spakowicz D. Investigating intra-tumor microbes, blood microbes, and CEA for development of non-invasive biomarkers in colorectal cancer. ASCO Annual Meeting; 2021 Jun 4–8. Poster.

5. Jin N, Mo X, Hoyd R, Yilmaz AS, Liu Y, Jagjit Singh M, Muniak M, Hampel H, Spakowicz D. Microbiome signature, global methylation and immune landscape in early onset colorectal cancer. ASCO Annual Meeting; 2021.

6. Tinoco G, Husain M, Hoyd R, Jagjit Singh M, Liu Y, Mo X, Chen JL, Liebner DA, Spakowicz D. The sarcoma microbiome as a diagnostic and therapeutic target. ASCO Annual Meeting; 2021. J Clin Oncol. 2021;39(15_suppl):11541. doi: 10.1200/JCO.2021.39.15_suppl.11541.

7. Arthur E, Quick A, Arnett A, Mo X, Spakowicz D. The vaginal microbiome as a biomarker of pelvic health and patient-reported outcomes in women receiving pelvic radiation. ONS/NCI/NINR Symptom Science Advances in Oncology Nursing Colloquium; 2021. Poster.

2020 (8)

1. Malalur PG, Mo X, Hoyd R, Carbone DP, Spakowicz D. Intra-tumoral microbes and overall survival in colorectal cancer patients. ASCO Annual Meeting; 2020 May 29–Jun 2. Poster.

2. Zhao S, Li M, Spakowicz D, Patel SH, Johns A, Grogan M, Miah A, Husain M, He K, Bertino EM. Neutrophil-lymphocyte score: a novel prognostic scoring system that utilized the dynamic change of neutrophil, lymphocyte, and albumin and its comparison to other indices. ASCO Annual Meeting; 2020. J Clin Oncol. 2020;38(15_suppl):3048.

3. Spakowicz D, Hoyd R, Liu Y, Sahasrabudhe J, Singh MJ, Arefi I, Denney A, Carbone D, Mo X. Abstract B30: Intratumoral microbes correlate with tumor-infiltrating lymphocytes in lung cancer RNAseq. AACR; 2020 Apr. Cancer Res. 2020;80(8_Supplement):B30.

4. Riesenberg BP, Li M, Spakowicz D, Hoyd R, Beane J, Yang Y, Oezkan F, He K, Patel SH, Johns A. Platelets impact the responsiveness of immune checkpoint blockade therapy in solid tumors. ASCO Annual Meeting; 2020. J Clin Oncol. 2020;38(15_suppl):e15023.

5. Patel SH, Li M, Zhao S, Spakowicz D, Wei L, Burkart JT, Husain M, He K, Bertino EM, Shields PG, Carbone DP. Changes in lymphocyte/monocyte ratio as a prognostic marker to predict overall survival in patients with advanced cancer treated with immune checkpoint inhibitors. ASCO Annual Meeting; 2020. J Clin Oncol. 2020;38(15_suppl):3047.

6. Li M, Zhao S, Spakowicz D, Burkart JT, Patel SH, Husain M, He K, Bertino EM, Shields PG, Wei L. Neutrophil to lymphocyte ratio, PD-L1 expression, and survival in patients with advanced non-small cell lung cancer receiving first-line immune checkpoint inhibitor therapy. ASCO Annual Meeting; 2020. J Clin Oncol. 2020;38(15_suppl):46.

7. Li M, Spakowicz D, Zhao S, Patel SH, Johns A, Grogan M, Miah A, Husain M, He K, Bertino EM. Inhaled corticosteroid use and risk of pneumonitis in patients treated with immune checkpoint inhibitors. ASCO Annual Meeting; 2020. J Clin Oncol. 2020;38(15_suppl):3140.

8. Spakowicz D, Husain M, Tinoco G, Patel SH, Burkart JT, Verschraegen CF, Kendra KL, Hoffman S, Philippon J, Quiroga DM, Otterson GA, Owen DH. Intra-tumoral microbes correlate with tumor-infiltrating lymphocytes in lung cancer biopsies. AACR Special Conference: The Microbiome, Viruses, and Cancer; Orlando, FL; 2020 Feb 23. Poster.

2019 (6)

1. Serrano J, Hoyd R, Spakowicz D, Kyriazis GA. Saccharin supplementation induces glucose intolerance conditional on sweet chemoreceptor sensing. 2019. E21–E22.

2. Johns A, Grogan M, Hoyd R, Bridges JFP, Wei L, Patel S, Li M, Husain M, Kendra KL, Otterson GA, Burkart JT, Rosko AE, Andersen BL, Carbone DP, Owen DH, Spakowicz D, Presley CJ. Is immunotherapy toxicity associated with improved overall survival among older adults with advanced cancer? ASCO Annual Meeting; Chicago, IL; 2019 Jun. J Clin Oncol. 2019;37(15_suppl):6580.

3. Johns A, Wei L, Grogan M, Spakowicz D, Patel S, Li M, Husain M, Kendra K, Otterson G, Burkart J, Rosko A, Andersen B, Carbone D, Owen D, Presley CJ. Risk factors for immunotherapy toxicity among older adults. AGS Annual Scientific Meeting; Portland, OR; 2019 May.

4. Spakowicz D, Li M, Hoyd R, Burkart JT, Patel SH, Husain M, He K, Presley CJ, Bertino EM, Shields PG, Carbone DP, Shah HA, Tinoco G, Folefac E, Bhateja P, Verschraegen CF, Otterson GA, Li L, Kendra KL, Owen DH. Re-evaluating the neutrophil-to-lymphocyte ratio: machine learning-based variable selection for predicting survival at twelve months in late-stage cancer patients receiving immunotherapy. ASCO Annual Meeting; Chicago, IL; 2019 Jun. J Clin Oncol. 2019;37(15_suppl):e18201.

5. Spakowicz D, Burkart J, Patel S, Husain M, He K, Presley C, Bertino E, Shields P, Carbone DP, Verschraegen C, Otterson G, Kendra K, Li M, Owen D. Change in neutrophil to lymphocyte ratio during treatment with immune checkpoint inhibitors predicts survival in patients with advanced cancer. ASCO-SITC Clinical Immuno-Oncology Symposium; San Francisco, CA; 2019 Feb.

6. Spakowicz D, Husain M, Tinoco G, Patel SH, Burkart JT, Verschraegen CF, Kendra KL, Hoffman S, Philippon J, Quiroga DM, Otterson GA, Owen DH. Effect of concomitant medications on overall survival in patients with cancer undergoing immunotherapy. ASCO-SITC Clinical Immuno-Oncology Symposium; San Francisco, CA; 2019 Feb.

Invited Talks

• 4/13/2026 — Case Comprehensive Cancer Center Microbiome Symposium

  “Low abundance microbes in obesity-associated cancers”

  Cleveland, OH

• 12/3/2025 — Nationwide Children’s Hospital Oral-GI Microbiology Research Affinity Group (OGM-RAG) Special Seminar

  “Translating the Cancer Microbiome: From Predictive Models to Therapeutic Interventions”

  Columbus, OH

• 10/15/2025 — The Ohio State University

  Radiation Oncology 8250: Biology of the Tumor Microenvironment

  “The Impact of the Microbiome on the Tumor Microenvironment”

  Columbus, OH

• 07/03/2025 — OSU Division of Internal Medicine Grand Round Presentation

  “Current clinical implications of the microbiome and future prospects”

  Columbus, OH

• 04/25/2025 — OSU Pelotonia Institute for Immuno-Oncology Research in Progress Meeting

  “The tumor microbiome affects the microenvironment as a function of the microbe and cancer type”

  Columbus, OH

• 03/28/2025 — The 21st Annual Meeting of the MidSouth Computational Biology and Bioinformatics Society

  “Spatial effects of the breast tumor microbiome”

  Salt Lake City, UT

• 03/01/2025 — OSU Lung SPORE PPG Research Retreat

  “Radiotherapy outcomes modification via the microbiome” (w. Nic Denko)

  Columbus, OH

• 03/01/2025 — OSU Lung SPORE PPG Research Retreat

  “Age-dependent microbiome-immune effects on irAE development and outcome” (w. Carolyn Presley)

  Columbus, OH

• 02/20/2025 — Translational Research Cancer Centers Consortium

  “The tumor microbiome affects the microenvironment as a function of the microbe and cancer type”

  Seven Springs, PA

• 05/09/2024 — Abbott Nutrition

  “Using nutrition to alter cancer treatment outcomes via the microbiome”

  Columbus, OH

• 05/07/2024 — Oncology Research Information Exchange Network Microbiome Research Interest Group Meeting

  “Update on the tumor microbiome presentations at AACR24”

  Remote - Online

• 05/06/2024 — Center of Microbiome Science Annual Retreat

  “Modification of the microbiome to improve cancer treatment outcomes”

  Columbus, OH

• 04/25/2024 — Diet, Nutrition, and Cancer: Collaborating Toward a Cancer-Free World

  “Intersections of Diet, Cancer, and the Immune System”

  Controlled Environment Agriculture Research Complex, Columbus, OH

• 04/17/2024 — National Clinical Trials Network: Phase 1 Working Group

  “The Role of the Microbiome in Cancer Treatment outcomes: use for correlative science in Phase I clinical trials”

  Columbus, OH

• 03/09/2024 — Society for Immunotherapy of Cancer: Spring Scientific; Metabolism at the Hub of Cancer and Immunity

  “Dietary modification of Lachnospiraceae abundance promotes response to immune checkpoint blockade”

  Miami, FL

• 03/04/2024 — University of New Mexico Comprehensive Cancer Center Cancer Control and Population Science Research Program Meeting

  “Exploring the tumor microbiome with ORIEN sequencing data”

  Online

• 11/17/2023 — Next Generation Lung Cancer Symposium

  “The Role of the Microbiome in Lung Cancer”

  Columbus, OH

• 11/03/2023 — Rust Belt Microbiome Conference

  “Trials using the older adult microbiome as a biomarker of treatment outcomes and a therapeutic target”

  Pittsburgh, PA

• 10/17/2023 — The Ohio State University Comprehensive Cancer Center Annual Scientific Meeting

  “Exploring the tumor microbiome with ORIEN sequencing data”

  Columbus, OH

• 09/13/2023 — Pelotonia Institute for Immuno-Oncology

  Dietary modification of the microbiome to improve cancer treatment outcomes

  Columbus, OH

• 06/29/2023 — Pelotonia Institute for Immuno-Oncology

  “Increasing response to immunotherapy through diet-based alterations of the microbiome: a mouse validation study”

  Columbus, OH

• 05/15/2023 — The Ohio State University Comprehensive Cancer Center

  “The exORIEN Consortium: Progress and Future Directions”

  Columbus, OH

• 04/25/2023 — Shared Insights Seminar Series: Biospecimen Shared Resource, Super-User

  “Shared Insights: Microbiome collection and processing through the Biospecimen Shared Resource”

  Columbus, OH

• 03/30/2023 — Donors Seminar, Pelotonia Foundation

  “Using the microbiome to alter cancer treatment outcomes”

  Columbus, OH

• 03/14/2023 — Pelotonia Institute For Immuno-Oncology Research In Progress Seminar

  “Exploring the tumor microbiome”

  Columbus, OH

• 03/02/2023 — The Oncology Research Information Exchange Network Scientific Retreat

  “The tumor microbiome associates with features of the tumor microenvironment, treatment outcomes, and histologies; a national collaboration of the exORIEN Consortium”

  Salt Lake City, UT

• 03/01/2023 — The Oncology Research Information Exchange Network Scientific Retreat, Artificial Intelligence/Machine Learning Session

  “The {exotic} tool for detecting low abundance microbes in high-throughput sequencing data: processing, decontamination, and validation”

  Salt Lake City, UT

• 02/28/2023 — Oncology Data Science Symposium

  The tumor microbiome associates with features of the tumor microenvironment, treatment outcomes, and histologies; a national collaboration of the exORIEN Consortium”

  Huntsman Cancer Institute, Salt Lake City, UT

• 02/16/2023 — Science In Action Data Science Series

  “Metatranscriptomics for the assessment of paired host and microbe activities in tumors and clinical trial swabs: data generation and processing resources through the OSU Applied Microbiology Services Lab and the Ohio Supercomputing Center”

  The Ohio State University, Columbus, OH

• 02/14/2023 — Case Comprehensive Cancer Center Microbiome Workshop

  Keynote Speaker

  “Exogenous sequences in unmapped transcriptome data”

  Cleveland, OH

• 02/06/2023 — Oncogeriatrics Program Investigators Meeting

  “Incorporating microbiome science into clinical trials involving older adults”

  The Ohio State University, Columbus, OH

• 12/09/2022 — The Oncology Research Exchange Network Scientific Committee

  “Comparison of the Oral and Tumor Microbiomes Between Appalachian and non-Appalachian patients”

  Online

• 11/17/2022 — American Association for Cancer Research Aging and Cancer Conference

  Older adult-specific microbes correlate with treatment response and markers of T-cell senescence in NSCLC”

  San Diego, CA

• 10/14/2022 — The Ohio State University Comprehensive Cancer Center Annual Meeting

  “The older adult microbiome as a biomarker of treatment outcomes and a therapeutic target”

  Columbus, OH

• 04/14/2022 — Ohio SuperComputing StateWide User’s Group Annual Meeting

  “Exogenous sequences in unmapped tumor transcriptome data”

  Columbus, OH

• 09/08/2021 — Lung Cancer Foundation of America /Bristol Myers Squibb /International Lung Cancer

  Foundation Young Investigator Research Grant Update

  “Modifiable biomarkers of immunotherapy treatment response lung cancer”

• 08/31/2021 — The Scientist Symposium: Cancer and Aging

  Online

• 08/15/2021 — Cultivating a Cure

  “Modifying the gut microbiome with dietary interventions”

  Columbus, OH

• 06/22/2021 — International Society of Geriatric Oncology

  “Immunotherapy toxicity and steroids use in older cancer patients”

  Online

• 06/10/2021 — QIAGEN Human Microbiome Days series

  Online

• 05/06/2021 — Symposium on World Cancer Research 2022

  “The microbiome and response to immunotherapy in older adults”

  Online

• 10/13/2020 — Biological big data: the of the microbiome in cancer treatment

  Big Data Analytics Association, Columbus, OH

• 09/18/2020 — The role of the gut and tumor microbiomes in cancer treatment

  PIIO, Columbus, OH

• 05/02/2020 — Melanoma Research Foundation

  Columbus, Ohio

  “Understanding Melanoma: From Prevention to Treatment”

• 04/01/2020 — Innovator of the Year

  The Ohio State University, Columbus, Ohio

• 09/01/2019 — Big Ten Cancer Research Consortium Correlative Science Clinical Trial

  Chicago, Illinois

  “Practical considerations for incorporating microbiome collection into clinical trials”

• 04/17/2017 — Department of Biomedical Informatics Seminar

  Cleveland Clinic Foundation Cleveland, Ohio

  “From Microbiomes to Molecules: Natural Product Discovery through Community Sequencing”

• 02/27/2017 — Division of Medical Oncology Seminar

  The Ohio State University Columbus, Ohio

  “From Microbiomes to Molecules: Natural Product Discovery through Community Sequencing”

• 02/13/2017 — Asthma From Pathway Biology to Precision Therapeutics Conference

  Keystone, Colorado

  “Using microbial composition within sputum transcriptome data to stratify patients by asthma severity”

• 01/05/2017 — Department of Biostatistics and Data Science Seminar

  City of Hope, Duarte, California

  “From Microbiomes to Molecules: Natural Product Discovery through Community Sequencing”

Educational Activities

• 2022 — Lecturer, Biochemical Mechanisms of Carcinogenesis (BCG8270), The Ohio State University, Columbus, OH

• 2022 — Lecturer, Biology of the Tumor Microenvironment (NSGY8250) , The Ohio State University, Columbus, OH

• 2019 — Lecturer, Clinical Informatics (CBB470), The Ohio State University, Columbus, OH

• 2013-2014 — Instructor, Molecular Biophysics and Biochemistry 230: Rainforest Expedition and Laboratory, Yale University, New Haven, CT

Mentorship

Postdocs

• Mohamed Mohssen — 2026–Present

• Hiroshi Nishiwaki — 2025–Present. Current Position: Visiting Fellow.

• Yogita Mehra — 2023–Present

Medical Students/Residents/Fellows

• Reed O’Conner — 2025–Present. Honors: Gynecology Oncology Fellow.

• Julia Chalif — 2025–Present. Honors: Gynecology Oncology Fellow.

• Ahmad Hussein — 2022–2025. Honors: Medical Student; Current Position: Resident, Internal Medicine, OSU.

• Dennis Grencewicz — 2022–2026. Honors: Samuel J. Roessler Memorial Scholarship Medical Student – Research Scholar, Carolyn Kuckein AOA Fellow; President Landacre Honor Society; Current Position: Case Comprehensive Cancer Center Harrington Physician Scientist Training Program.

• Bailey Conrad — 2022–2023. Honors: Medical Student.

Graduate Students

• Tanisha Mukherjee — 2025–Present. Current Position: Microbiology Masters.

• Lynn Marcho — 2025–Present. Current Position: BSGP PhD.

• Julia Zalewski — 2025–2026. Current Position: Biostats Masters.

• Elham Mirtaheri — 2025–Present. Current Position: OSUN PhD.

• Anna Petouhoff — 2025–Present. Current Position: BSGP PhD.

• Karthik Chakravarthy — 2024–2025. Honors: MD/PhD Student.

• Shiva Jahanbakhshi — 2023–Present. Honors: Graduate Research Assistant (Food Science and Technology).

• Caroline Dravillas — 2020–Present. Honors: Masters Student, Public Health (OSU); Current Position: Data Analyst.

• Rebecca Hoyd — 2018–Present. Honors: Data Analyst, Graduate Research Assistant; Current Position: PhD Candidate in Biostatistics (OSU).

Full time staff

• Lane Nevers — 2025–Present. Honors: Pelotonia Research Scholar.

• Alexander Loncar — 2025–2026. Honors: Pelotonia Research Scholar; Current Position: Medical Student (Univ of Cincinnati).

• YunZhou Liu — 2019–2023. Honors: Pelotonia Research Scholar; Current Position: Graduate School (Johns Hopkins).

• Nyelia Williams — 2019–2023. Honors: Research Assistant; Current Position: Lab Manager, OSU.

• Mitch Muniak — 2019–2021. Honors: Research Assistant; Current Position: Medical Student (Ohio University).

• Malven Singh — 2019–2024. Honors: Undergraduate Researcher; Current Position: Research Tech, Tessera Theraputics, Boston, MA.

• Amna Bibi — 2019–2024. Honors: Research Assistant.

Undergraduate Students

• Ian Sander — 2024–Present. Honors: Barry Goldwater Scholar; Current Position: Ohio-5 Fellow.

• Bemnet Worku — 2025–Present. Honors: Undergraduate Researcher Apprenticeship Fellow.

• Raymond Nahhas — 2025–Present

• Caitlin O’Malley — 2025–Present

• Jacqueline Hudak — 2024–2025

• Jonah Bukovac — 2025–Present. Honors: Undergraduate Researcher Apprenticeship Fellow.

• Aspen Carson — 2025–Present. Honors: Undergraduate Researcher Apprenticeship Fellow.

• Ridha Pandey — 2023–2025. Honors: Undergraduate Researcher Apprenticeship Fellow.

• Idara Ntukidem — 2023–2024

• Matthew Drozda — 2023–2024

• Justin Simmons — 2023–2023. Honors: CREATES Fellow.

• Naa Dromo Korley — 2023–2023. Honors: ASPIRE Undergraduate Fellow; Current Position: Medical Student (Univ. Of Cincinnati).

• Carol Mensah-Bonsu — 2023–2023. Honors: CREATES Fellow.

• Alexander Loncar — 2022–Present. Honors: Pelotonia Research Scholar.

• Lane Nevers — 2022–Present. Honors: URAP, Undergraduate Fellow, Pelotonia Research Scholar.

• Louis Denko — 2022–2024. Honors: Undergraduate Researcher.

• Owen Snyder — 2021–2024. Honors: Undergraduate Researcher; Current Position: Medical Student (Univ. Of Cincinnati).

• Mari Lynn — 2021–2023. Honors: CREATES Undergraduate Fellow.

• Yangyang Liu — 2021–2022. Honors: Pelotonia Undergraduate Research Fellow.

• Alvin Anand — 2021–2021. Honors: Undergraduate Researcher.

• Aadi Pallerla — 2020–2022. Honors: Pelotonia Undergraduate Research Fellow; Current Position: Medical Student (Univ. Of Cincinnati).

• Isaac Arefi — 2019–2022. Honors: Undergraduate Researcher.

• Andy Denny — 2019–2021. Honors: Undergraduate Researcher.

• Mark Isom — 2019–2020. Honors: Undergraduate Researcher.

• Janhavi Sahasrabudhe — 2019–2020. Honors: Undergraduate Researcher.

• Linda Antwi — 2019–2020. Honors: Undergraduate Researcher.

• J.T. Bassett — 2019–2019. Honors: Undergraduate Researcher; Current Position: Olive Consulting.

High School Students

• Jennifer Carmona Cordova — 2025–Present. Position in Lab: CREATES Fellow; Current Position: High School Student.

• Justin A. Suppogu — 2025–Present. Current Position: High School Student.

• Camille Croom — 2025–2025. Current Position: High School Student.

• Jaleea Gamble — 2023–2023. Position in Lab: ASPIRE Fellow; Current Position: High School Student.

• Najma Afrah — 2022–2022. Position in Lab: CREATES High School Fellow; Current Position: High School Student.

Thesis Committee

• Claire Cornellier — 2025–Present. Department: Graduate Research Associate.

• Yinjie Li — 2023–Present. Department: Thesis Committee.

• Noah Lepola — 2023–Present. Department: Thesis Committee.

• Sushma Nepal — 2023–Present. Department: Thesis Committee.

• Dharti Shantaram — 2022–Present. Department: Thesis Committee.

• Shiqi Zhang — 2021–2024. Department: Thesis Committee; Current Position: Postdoc, MD Anderson.

• Connor Geraghty — 2017–2019. Department: Thesis Committee; Current Position: Postdoc, Harvard.

Faculty Mentoring

• Claire Han — College of Nursing — Mentor on Oncology Nursing Fund Early Investigator Award

• Gabriel Tinoco, MD — Division of Medical Oncology — Mentor on K08 application

• Laura Chambers, DO — Division of Gynecologic Oncology — Mentor on K12 application, DoD Career Development Award

Professional Memberships and Activities

• 2026–Present — Scientific Advisory Board Member, Lung Cancer Research Foundation (LCRF)

• 2026 - 2028 — Editor, Genome Biology

• 2026-05-01 – 2028-04-30 — Editorial Board Member, AACR Cancer Research Communications

• 2023 – Present — Infectious Disease Institute Applied Microbiology Services Lab Strategic Advisory Committee

• 2023 - Present — Leader, Oncology Research Information Exchange Network Microbiome Research Interest Group

• 2023 - 2026 — Chair, OSU Culturomics Interest Group

• 2021 - Present — Center of Microbiome Science

  College of Medicine Representative to the Executive Advisory Committee

• 2021 - Present — Cancer in Aging Research Group

• 2021 – Present — Leader, Oncology Research Information Exchange Network (ORIEN) Tumor Microbiome Inter-Member Project

• 2021 – Present — ORIEN Immuno-oncology Research Interest Group

• 2020 – Present — Alliance Care of the Older Adult Committee

• 2019 – Present — OSU Onco-geriatrics Research Group

• 2019 – Present — Big10 Cancer Research Consortium Correlative Science Working Group

• 2019 – Present — American Association for Cancer Research

• 2019 – Present — International Society for Study of Lung Cancer

• 2019 – Present — Pelotonia Institute for Immuno-Oncology

• 2018 – Present — Translational Data Analytics Institute

• 2018 – 2025 — Society for Immunotherapy of Cancer

• 2016 – 2020 — International Society for Computational Biology

• 2015 – 2020 — American Society for Microbiology

• 2012 – 2015 — Mycological Society of America

• 2006 – 2013 — Biophysical Society

• 2025 — Guest Editor, Genome Biology, “Microbiome and cancer” collection

• 2021 — Assistant Editor, Journal of Clinical Investigation (JCI)

Ad hoc reviewer

• (12) BMC Cancer 2019-2025

• (4) Cell, Host & Microbe 2024, 2025

• (4) Nature Cancer 2024-2025

• (4) Cancer Research Communications 2023-2025

• (2) Cancer Epidemiology, Biomarkers & Prevention 2025

• (2) Gut Microbes 2024

• (2) Journal of Pharmacology and Experimental Therapeutics 2023

• (2) Metabolites 2022

• (2) Microbial Biotechnology 2021

• (2) International Journal of Radiation Oncology Biology Physics 2021

• (2) Journal of Fungi 2018

• (1) eBioMedicine 2025

• (1) Lancet Oncology 2025

• (1) Cancer Cell 2025

• (1) Nutrition and Cancer 2024

• (1) Oncotarget 2024

• (1) Cell Reports 2024

• (1) Cancer Medicine 2023

• (1) Clinical Lung Cancer 2023

• (1) Proceedings of the National Academy of Sciences 2023

• (1) Annals of Translational Medicine 2022

• (1) Molecular Physiology 2022

• (1) Heliyon 2022

• (1) Current probiotics 2022

• (1) Journal of Geriatric Oncology 2022

• (1) Journal of Gastrointestical Cancer 2021

• (1) Current Biotechnology 2020

• (1) International Journal of Molecular Sciences 2020

• (1) Cancer drug resistance 2020

• (1) Genes 2019

• (1) High-Throughput 2017

Service

• 2026-11-20 (scheduled) — OSUCCC Intramural Research Program Clinical Translational Science Reviewer (Fall 2026)

• 2026-11-02 (scheduled) — OSUCCC Intramural Research Program Basic Science Reviewer (Fall 2026)

• 2026-09-23 (scheduled) — Center for Cancer Prevention and Survivorship Works in Progress R21 Grant Reviewer

• 2026 — OSU Aging Research Initiative Pilot Program Reviewer

• 2026 — CTSI R Grant Mock Study Section Reviewer

• 2026-04-29 — OSUCCC Intramural Research Program Basic Science Reviewer

• 2026 — American Cancer Society CTPS Application Reviewer

• 2025-12-16 — CTSI R Grant Mock Study Section Reviewer

• 2025 — Infectious Diseases Institute Seed Grant Reviewer

• 2025-04-07; 2025-10-31 — OSUCCC Intramural Research Program Clinical/Translational Science Reviewer

• 2025 — Graduate Faculty Representative: Mathematics defense

• 2025 — FAMRI Grant Reviewer

• 2024, 2025 — Pelotonia Graduate Fellowship Reviewer

• 2024 — European Science Foundation External Grant Reviewer

• 2022 — Division of Medical Oncology Division-Chief Search Committee Member

• 2027-01-01 – 2029-12-31 — American Cancer Society term member on the Postdoctoral Fellowship-Clinical & Population Sciences (PF-CPS) Peer Review Committee in the Career Growth and Research Excellence Program

• 2026-04-13 — Case Comprehensive Cancer Center Microbiome Symposium Poster Judge

• 2026-04-01 — Center of Microbiome Science Travel Award Reviewer

• 2025-03-03 — National Cancer Institute Translational Immuno-Oncology Study Section ad hoc reviewer

• 2025-02-26 — Small Animal Imaging Shared Resource User Committee

• 2024-02-14 – 2025-12-31 — Department of Microbial Infection and Immunity Search Committee (2 positions)

• 2024-10-29 — Moderator, Oncology Research Information Exchange Network Scientific Summit, Microbiome session

• 2024-10-28 — Moderator, Oncology Data Science Research Symposium session

• 2024-05-17 — Graduate Faculty Representative: Statistics defense

• 2024-04-11 — Pelotonia Basic Science Study Section

• 2024-01-01 – Present — ORIEN Clinical Quality Assurance Working Group

• 2024-01-01 – Present — IDI GEMS Strategic Advisory Committee

• 2024-01 – 2024-08 — OSU Microbial Infection and Immunity Faculty Search Committee

• 2023-12-08 — OSU Medical Student Research Day Judge

• 2023-10-25 — Pelotonia Translational Science Study Section

• 2023-10-16 — Pelotonia Basic Science Study Section

• 2023-06-27 — T32 Predoctoral Mentored Research Training Program Study Section

• 2023-05-11 — Foods For Health Innovator Awards Study Section

• 2023-05-03 — Center for Clinical and Translational Science Launch to Success Mock Study Section Reviewer

• 2023-04-05 — Pelotonia Basic Science Study Section

• 2023-02-24 — OSU Medical Student Research Scholarship Reviewer

• 2023-02-16 — National Cancer Institute Translational Immuno-Oncology Study Section

• 2023-02-06 — OSU Center of Microbiome Science Proposal Cohort Reviewer

• 2022-11-30 — OSU Infection Disease Institute Interdisciplinary Research Seed Grant Reviewer

• 2022-04-28 — OSU Foods For Health Seed Grant Review Panel

• 2022-03-14 — Pelotonia Basic Science Study Section

• 2022-03-07 — OSU Medical Student Research Scholarship Reviewer

• 2021-09-23 — OSUCCC RISSR User Committee Meeting

• 2021-04-28 – Present — Pelotonia Institute for Immuno-Oncology (PIIO) Center for Cancer Immuno-Microbiomics (CCIM)

• 2021-05 – 2023-01 — Data Safety Monitoring Committee (Beating Lung Cancer in Ohio)

• 2021-03-03 - 2024 — Pelotonia Institute for Immuno-Oncology Center for Cancer Immuno-Microbiomics Planning Committee

• 2021-04-22 — International Association for the Study of Lung Cancer (IASLC 2021) World Conference on Lung Cancer Abstract Grader

• 2021-05-21 — Clinical Translational Science Shared Resource (CTSSR) Oversight Committee

• 2021-04-21 — Pelotonia Postdoctoral Fellowship Study Section

• 2021-03-18 — OSU-CCC Trainee Research Day Poster Judge

• 2021-02-18 — National Cancer Institute (NCI) Clinician Science Training Grant (KL2) Study Section

• 2020-04-08 — Pelotonia Basic Science Study section

• 2019-10-24 — Pelotonia Basic Science Study section

• 2019-04-02 — OSU-CCC Trainee Research Day Poster Judge

Other Creative Products

Public Software Releases

Latest verified GitHub release per project, checked September 28, 2026. Dates are shown in US Eastern time. Study code includes published papers, preprints, submitted manuscripts, and conference work.

Reusable tools and packages

• mec-tx v1 — released 2026-04-30. Encoding and comparison of oncology treatment timelines, patient clustering, and survival analysis.

• tmesig v1 — released 2026-03-04. Tumor microenvironment expression signatures, including hypoxia and mitochondrial scores.

• mt.surv v1.1.1 — released 2025-05-20. Multi-threshold survival analysis of count and expression data.

• exotic v2.0 — released 2024-04-01. Processing and contaminant filtering of exogenous sequences in tumors and immune cells.

• microsig v1.0 — released 2023-09-29. Microbial signature scoring, including signatures from BugSigDB.

• mhealth-iit v0.1.0 — released 2023-03-12. R Shiny application supporting consent and Fitbit data collection in clinical trials.

Manuscript and study analysis code

• OCRscore v1.0.0 — released 2026-09-26. Analysis code accompanying the mitochondrial oxygen consumption and lung tumor hypoxia preprint.

• bewell-mice v1.0.0 — released 2026-09-25. Analysis code for the submitted BE WELL mouse-model manuscript.

• bewell v1.0.0 — released 2026-09-24. Analysis code for the submitted BE WELL black raspberry nectar clinical trial manuscript.

• ppiio v1.0.0 — released 2026-09-18. Proton pump inhibitors, immunotherapy, and microbiome–immune cell analyses.

• mitox v1.0 — released 2026-08-20. Melanoma clinical trial manuscript analyses and the original power calculations (NCT05102773).

• adjing v1 — released 2026-08-07. Pretreatment T-cell transcriptional signatures and melanoma immunotherapy outcomes.

• staph-brca v1.0 — released 2025-12-19. Breast tumor microbiome, anti-tumor immunity, and T-cell-associated metabolites.

• keto-rev v1.0 — released 2025-09-30. Code and analyses supporting the ketogenic diet and cancer immunotherapy review.

• exorien-exogieo v1.0 — released 2025-08-26. Early-onset colorectal cancer epigenetics, intratumoral microbiome, and immunity.

• exorien-recrad v1.0 — released 2024-05-20. Tumor microbiome, hypoxia, and radiation response in colorectal cancer.

• fitness v1.0 — released 2024-05-15. Longitudinal geriatric assessment and functional disability in lung cancer.

• atbac v2.0 — released 2024-04-01. Obesity-associated microbiomes and visceral adipose tissue inflammation.

• exorien-melio v0.1 — released 2023-05-26. Tumor microbiome and immunotherapy outcomes in metastatic melanoma.

• exohnsc v1 — released 2022-12-19. Tumor microbiome and hypoxia across head and neck cancer subsites.

• exotic-manuscript 1.0 — released 2022-08-10. Analyses accompanying the exotic methods manuscript.

• co-mo-io v1.0.0 — released 2022-06-24. Medical comorbidities and immune checkpoint inhibitor outcomes.

• mageio v1.0.1 — released 2021-02-05. Aging microbiome and response to immunotherapy.

• aacrmv20 v.10 — released 2020-12-17. Analysis code for the AACR microbiome conference presentation.

• diacomp20 v0.1 — released 2020-07-09. Analyses of diabetic complications in preclinical models.

• decoasthma v1.0 — released 2020-03-09. Integration of microbial and host RNA-seq signals in asthma.

• co-med-io v1.0.1 — released 2019-11-06. Concomitant medications and immune checkpoint inhibitor outcomes.

Additional public software

• MEGA — Intratumoral microbiome analysis; public version tag 0.0.5.

• mhealthCI — Bayesian structural time series for estimating intervention effects in mobile health data. The prior CV records v0.1 dated 2021-05-23; the repository currently lists no GitHub releases.

Historical release records

These entries are retained from the prior CV; their original repositories are no longer publicly accessible at the recorded addresses as of September 28, 2026.

• respondersig v0.1 — 2021-12-10. Microbiome responder/non-responder signatures and meta-analysis (formerly spakowiczlab/respondersig).

• LDA-link v1.0 — 2020-04-13. Integration of microbial and host RNA-seq signals in asthma (formerly Gersteinlab/lda-link).

I attest that this information is accurate.

Signature:

Date: 2026-09-10