Spakowicz Lab

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Publications

Browse publications by year, or visit Daniel Spakowicz’s Google Scholar profile for citation counts and additional records.

This bibliography brings together entries from Daniel’s CV and linked publication records. Where identified, final journal articles replace earlier preprints and duplicate online-first entries. Conference abstracts are listed separately on the conference abstracts page. Counts beside each year reflect the entries listed for that year, including labeled software releases. Software links beside citations lead to the associated repositories. Where available, click the hex sticker to open the repository; browse the software page for descriptions and documentation.

Explore the original exORIEN Consortium collection and subsequent tumor-microbiome studies from the ORIEN Microbiome RIG.

Abstract word cloud

Word size reflects how often a term appears in PubMed abstracts for the papers listed below. Common English and methods language is omitted.

patientpatient: 204cancercancer: 187microbiomemicrobiome: 113tumortumor: 106iciici: 90treatmenttreatment: 84survivalsurvival: 80cellcell: 64genegene: 63outcomeoutcome: 60immuneimmune: 58microbemicrobe: 57microbialmicrobial: 49responseresponse: 49clinicalclinical: 48changechange: 40treatedtreated: 40adultadult: 37riskrisk: 36gutgut: 36scorescore: 36olderolder: 36diseasedisease: 35baselinebaseline: 34metabolicmetabolic: 34inhibitorinhibitor: 33expressionexpression: 33iraeirae: 33impactimpact: 32immunotherapyimmunotherapy: 32diversitydiversity: 30toxicitytoxicity: 30productionproduction: 29interventionintervention: 28checkpointcheckpoint: 27chemotherapychemotherapy: 27obesityobesity: 26lunglung: 26relationshiprelationship: 25researchresearch: 25dietarydietary: 25microbiotamicrobiota: 25therapytherapy: 24healthhealth: 24sequencingsequencing: 24stoolstool: 24compositioncomposition: 23factorfactor: 23therapeutictherapeutic: 23ppippi: 23receivedreceived: 22provideprovide: 22dietdiet: 22qualityquality: 22differencedifference: 21hypoxiahypoxia: 21humanhuman: 20mechanismmechanism: 20populationpopulation: 20pathwaypathway: 20signaturesignature: 20biomarkerbiomarker: 20gradegrade: 20agingaging: 20compoundcompound: 20deathdeath: 19statusstatus: 19reviewreview: 19trialtrial: 19retrospectiveretrospective: 19efficacyefficacy: 19novelnovel: 19datasetdataset: 19fungalfungal: 19receivingreceiving: 18metastaticmetastatic: 18hazardhazard: 18carecare: 18interactioninteraction: 18lmrlmr: 18melanomamelanoma: 17abundanceabundance: 17colorectalcolorectal: 17t-cellt-cell: 17fungifungi: 17hosthost: 17typetype: 16profileprofile: 16stagestage: 16functionfunction: 16
Based on 86 PubMed abstracts from this bibliography. Word size scales with frequency.

Author network

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2026 (12)

  1. Li M, Spakowicz DJ, Zhao S, Kwon H, Chian K, Khorasanchi A, Guo Y, Wei L, Meng L, Yang Y, et al. Association between obesity, sex, medical comorbidities, and survival in cancer patients treated with immune checkpoint inhibitors. J Cancer. 2026;17(6):1117–1124. DOI. PubMed. Full text.

  2. Zhou Q, Lu Y, Wang L, Zhou W, Oba H, Zhou Y, Shen M, Qu X, De Souza C, Rayner A, et al. Power and sample-size estimation in human microbiome research. Med. 2026 Jul 10;7(7):101174. DOI. PubMed.

  3. 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. PubMed.

  4. Chambers LM, Spakowicz D, Chalif J, et al. 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. Gynecologic Oncology. 2026;211:74–78. DOI. PubMed.

  5. Bukovac J, Husain M, Sapper T, et al. How the Ketogenic Diet Shapes the Microbiome to Influence Cancer Immunotherapy Outcomes: An Exploration of Clinical Trials and Their Results. Nutrition and Cancer. 2026. DOI. PubMed.

    Graphical abstract
    Review of ketogenic diet cancer trials connecting dietary intervention, microbiome changes, and immune checkpoint blockade.
    View full size · Repository source

  6. Petouhoff A, Hicks R, Husain M, et al. Impact of proton pump inhibitors on immunotherapy is modulated by prior chemotherapy and linked to gut microbiome-immune cell signatures. Cancer Immunology, Immunotherapy. 2026. DOI. PubMed.

    Graphical abstract
    Proton pump inhibitor use, prior chemotherapy, gut microbiome, and circulating immune-cell signatures are examined in relation to immunotherapy outcomes.
    View full size · Repository source

  7. 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;18(3):438. DOI. PubMed.

  8. 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. Epub ahead of print. PubMed.

  9. 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. Epub 2025 Oct 9. PubMed; Full text.

  10. 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. PubMed; Full text.

  11. Jhawar SR, Spakowicz D. Tumor bacterial burden dictates immunotherapy fate in head and neck cancer. Nat Cancer. 2026 Jan 2. DOI. Epub ahead of print. PubMed.

  12. 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. Scientific Reports. 2026;16:17587. DOI. PubMed.

    Graphical abstract
    Human breast-tumor analyses and mouse experiments connect intratumoral Staphylococcus, CD8 T-cell activity, NAD metabolism, and tumor growth.
    View full size · Repository source

2025 (13)

  1. Chalif J, Goldstein N, Mehra Y, Spakowicz D, Chambers LM. The Role of the Microbiome in Cancer Therapies: Current Evidence and Future Directions. Hematology/Oncology Clinics of North America. 2025;39(2):269–294. DOI. PubMed.

  2. 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. PubMed; Full text.

  3. 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. Epub ahead of print. PubMed.

  4. 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. Epub ahead of print. PubMed.

  5. 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. Epub ahead of print. PubMed.

  6. 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. Epub 2025 Oct 10. PubMed.

  7. 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. PubMed; Full text.

  8. Chalif J, Morton M, McLaughlin E, Gonzales G, Fulton J, Sciuva J, Ioana M, Bixel KL, Cohn DE, Cosgrove CM, Copeland LJ, Nagel CI, Backles F, O’Malley DM, Spakowicz DJ, Chambers LM. Exploratory evaluation of immunotherapy response and medication use in endometrial and cervical carcinoma. Gynecologic Oncology Reports, 2025-08-01, Volume 60, Article 101782. PubMed.

  9. 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. Epub ahead of print. PubMed.

  10. 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. Nature Methods. 2025;22:1788–1799. DOI. PubMed.

  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. Epub 2025 Apr 28. PubMed.

  12. Jin N, Hoyd R, Yilmaz AS, Zhu J, Liu Y, Singh MJ, Grencewicz D, Mo X, Kalady M, Rosenberg D, Dravillas CE, Singer EA, Carpten JD, Chan CH, Churchman ML, Denko NC, Di Clemente F, Dodd RD, Eljilany I, Fei N, Hardikar S, Ikeguchi AP, Ma A, Ma Q, McCarter MD, Osman AE, Riedlinger G, Robinson LA, Schneider BP, Tarhini AA, Tinoco G, Figueiredo J, Zakharia Y, Ulrich CM, Tan AC, Spakowicz D. Epigenetic Modulation, Intratumoral Microbiome, and Immunity in Early-Onset Colorectal Cancer. Cancer Research Communications. 2025;5(11):1985–1997. DOI. PubMed.

    Graphical abstract
    Early-onset colorectal tumors show accelerated epigenetic aging and stronger positive microbe–immune correlations, without a consistent microbial marker across datasets.
    View full size · Repository source

  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. Epub 2025 Mar 17. PubMed.

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. Epub ahead of print. PubMed.

  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. PubMed; Full text.

  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. PubMed; Full text.

  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. Epub ahead of print. PubMed.

  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. Epub ahead of print. PubMed.

  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. PubMed.

  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. PubMed; Full text.

    Graphical abstract
    Baseline RNA sequencing of 71 metastatic melanomas combines exotic tumor microbial profiles with host immune signatures to predict outcomes after immune checkpoint inhibition; the combined model has an AUROC of 0.805.
    View full size · Repository source

  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. PubMed; Full text.

  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. PubMed; Full text.

  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. PubMed; Full text.

    Graphical abstract
    Colorectal tumor RNA sequencing links hypoxia scores and microbes to survival and radiation response; mouse experiments examine changes in microbial activity with altered oxygenation.
    View full size · Repository source

  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. PubMed; Full text. atbac

  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. PubMed; Full text.

    Graphical abstract
    The FITNESS study links repeated geriatric assessments, treatment toxicity, stool microbiome, and blood T-cell measurements in older adults with lung cancer.
    View full size · Repository source

  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. Epub 2024 May 9. PubMed; Full text.

  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. Epub 2024 Mar 12. PubMed; Full text.

  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. Epub 2023 Oct 28. PubMed.

  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. PubMed; Full text.

  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. PubMed; Full text.

  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. PubMed.

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. PubMed; Full text.

  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. PubMed; Full text.

  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. Epub ahead of print. PubMed. exotic-manuscript

  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. Epub ahead of print. PubMed.

  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. PubMed; Full text.

  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. PubMed; Full text.

  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. PubMed; Full text.

  8. Software release · 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. PubMed.

  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. Epub ahead of print. PubMed. co-mo-io

2022 (6)

  1. Presley, C.J., Mohamed, M.R., Culakova, E., Flannery, M., Vibhakar, P.H., Hoyd, R., Amini, A., VanderWalde, N., Wong, M.L., Tsubata, Y. and Spakowicz, D.J., and Supriya Mohile. 2022. A Geriatric Assessment Intervention to Reduce Treatment Toxicity Among Older Adults With Advanced Lung Cancer: A Subgroup Analysis From a Cluster Randomized Controlled Trial. Frontiers in Oncology, p.1203. PubMed.

  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. Clinical Lung Cancer. 2022 Jan 8. PubMed.

  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. International Journal of Molecular Sciences. Multidisciplinary Digital Publishing Institute; 2022 Jan;23(24):15531. PubMed.

  4. Software release · Hoyd R, Liu Y, Wheeler C, Spakowicz D. spakowiczlab/mt.surv: Multi-threshold survival analysis, initial release [Internet]. Zenodo; 2022 [cited 2023 Apr 16]. 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. Journal of Cancer Research and Clinical Oncology. Springer; 2022;1–8. PubMed.

  6. 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. Full text. PubMed.

2021 (4)

  1. 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 computational biology. Public Library of Science San Francisco, CA USA; 2021;17(8):e1009303. PubMed.

  2. 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. Epub ahead of print. PubMed.

  3. 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. Epub ahead of print. PubMed.

  4. 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. Epub ahead of print. PubMed.

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. PubMed.

  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. Epub 2020 Jul 29. PubMed; Full text.

  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. PubMed; Full text.

  4. Commentary · 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. Epub 2020 May 14. PubMed.

  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. PubMed; Full text. decoasthma

  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. PubMed.

  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. PubMed; Full text.

    Graphical abstract
    Concomitant medication classes and timing are analyzed in relation to survival during immune checkpoint inhibitor treatment, with causal models exploring the microbiome.
    View full size · Repository source

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. PubMed.

    Graphical abstract
    A moderate decrease in neutrophil-to-lymphocyte ratio during immunotherapy is associated with longer survival than large decreases or increases.
    View full size · Repository source

  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. 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. Nature Communications (2019) 10:5029. PubMed.

  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. PubMed.

2018 (1)

  1. Piening, B.D., Zhou, W., Contrepois, K., Röst, H., Urban, G.J.G, Mishra, T., Hanson, B.M., Bautista, E.J., Leopold, S., Yeh, C.Y., Spakowicz, D.J., Kukurba, K., Perelman, D., Craig, C., Colbert, E., Salins, D., Rego, S., Lee, S., Zhang, C., Wheeler, J., Sailani, M.R., Liang, L., Abbott, C., Gerstein, M., Mardinoglu, A., Smith, U., Pitteri, E, Sodergren, E., McLaughlin, T.L., Weinstock, G.M., and Snyder, M.P. Integrative Personal Omics Profiles During Periods of Weight Gain and Loss. Cell Systems (2018) 6, 1–14. Full text. PubMed.

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. PubMed. Full text.

2016 (2)

  1. Muir, P., Li, S., Lou, S., Wang, D., Spakowicz, D. J., Salichos, L., Zhang, J., Weinstock, G. M., Isaacs, F., Rozowsky, J., and Gerstein, M. The Real Cost of Sequencing: Scaling Computation to Keep Pace with Data Generation. Genome Biology 17, (2016) Full text. PubMed.

  2. Sena Filho, J. G. de, Quin, M. B., Spakowicz, D. J., Shaw, J. J., Kucera, K., Dunican, B., Strobel, S. A., and Schmidt-Dannert, C. Genome of Diaporthe Sp. Provides Insights into the Potential Inter-Phylum Transfer of a Fungal Sesquiterpenoid Biosynthetic Pathway Fungal Biology (2016) Full text. PubMed.

2015 (6)

  1. Shaw, J.J., Spakowicz, D.J., Dalal, R.S., Davis, J.H., Lehr, N.A., Dunican, B.F., Orellana, E.A., Narváez-Trujillo, A., and Strobel, S.A. (2015). Biosynthesis and genomic analysis of medium-chain hydrocarbon production by the endophytic fungal isolate Nigrograna mackinnonii E5202H. Appl. Microbiol. Biotechnol. Full text These authors contributed equally. PubMed.

  2. Shaw, J.J., Berbasova, T., Sasaki, T., Jefferson-George, K., Spakowicz, D.J., Dunican, B.F., Portero, C.E., Narvaez-Trujillo, A., and Strobel, S.A. (2015). Identification of a Fungal 1,8-cineole Synthase from Hypoxylon sp. with Common Specificity Determinants to the Plant Synthases. J. Biol. Chem. jbc.M114.636159. Full text. PubMed.

  3. Patridge, E. V., Darnell, A., Kucera, K., Phillips, G. M., Bokesch, H. R., Gustafson, K. R., Spakowicz, D. J., Zhou, L., Hungerford, W. M., 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. Natural product communications 10, no. 10 (2015): 1649–1654. PubMed

  4. Forcina, G. C., Castro, A., Bokesch, H. R., Spakowicz, D. J., Legaspi, M. E., Kucera, K., Villota, S., Narváez-Trujillo, A., McMahon, J. B., Gustafson, K. R., and others. Stelliosphaerols A and B, Sesquiterpene–Polyol Conjugates from an Ecuadorian Fungal Endophyte Journal of natural products (2015) PubMed

  5. Rundell, S. M., Spakowicz, D. J., Narváez-Trujillo, A., and Strobel, S. A. The Biological Diversity and Production of Volatile Organic Compounds by Stem-Inhabiting Endophytic Fungi of Ecuador Journal of Fungi 1, no. 3 (2015): 384–396. Full text. PubMed.

  6. Spakowicz, D. J. and Strobel, S. A. Biosynthesis of Hydrocarbons and Volatile Organic Compounds by Fungi: Bioengineering Potential Applied microbiology and biotechnology 99, no. 12 (2015): 4943–4951. Full text. PubMed.

2012 (1)

  1. Gianoulis, T.A., Griffin, M.A., Spakowicz, D.J, Dunican, B.F., Alpha, C.J., Sboner, A., Sismour, A.M., Kodira, C., Egholm, M., Church, G.M., and Strobel, S.A. (2012). Genomic Analysis of the Hydrocarbon-Producing, Cellulolytic, Endophytic Fungus Ascocoryne sarcoides. PLoS Genet 8, e1002558. Full text. PubMed.

2010 (5)

  1. Tomsheck, A.R., Strobel, G.A., Booth, E., Geary, B., Spakowicz, D.J., Knighton, B., Floerchinger, C., Sears, J., Liarzi, O., and Ezra, D. (2010). Hypoxylon sp., an endophyte of Persea indica, producing 1, 8-cineole and other bioactive volatiles with fuel potential. Microbial Ecology 60, 903–914. PubMed

  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. Taylor & Francis; 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. PubMed.

  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. Microbiology Society; 2010;156(Pt 12):3814. PubMed.

  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, G.A., Knighton, B., Kluck, K., Ren, Y., Livinghouse, T., Griffin, M., Spakowicz, D.J., and Sears, J. (2008). The production of myco-diesel hydrocarbons and their derivatives by the endophytic fungus Gliocladium roseum (NRRL 50072). Microbiology 154, 3319–3328. PubMed.

  2. Prochniewicz, E., Spakowicz, D.J., and Thomas, D.D. Changes in Actin Structural Transitions Associated with Oxidative Inhibition of Muscle Contraction†. Biochemistry 47, (2008):11811–11817. Full text. PubMed.

  3. Prochniewicz, E., Lowe, D. A., Spakowicz, D. J., Higgins, L., O’Conor, K., Thompson, L. V., Ferrington, D. A., and Thomas, D. D. Functional, Structural, and Chemical Changes in Myosin Associated with Hydrogen Peroxide Treatment of Skeletal Muscle Fibers. American Journal of Physiology-Cell Physiology 294, no. 2 (2008): C613–C626. Full text. PubMed.

Book chapters

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