Computational methods and challenges in analyzing intratumoral microbiome data

Trimmomatic: a flexible trimmer for Illumina sequence data

Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548 · see citing works

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works

STAR: ultrafast universal RNA-seq aligner

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works

fastp: an ultra-fast all-in-one FASTQ preprocessor

(2018) · doi:10.1093/bioinformatics/bty560 · Cited by 29,721 · see citing works

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · see citing works

A human gut microbial gene catalogue established by metagenomic sequencing

MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624 · see citing works

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Li, D., Liu, C.-M., Luo, R., Sadakane, K., & Lam, T. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv033 · Cited by 9,781 · see citing works

The human microbiome project

Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007) · Nature · doi:10.1038/nature06244 · Cited by 6,091 · see citing works

Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors

Routy, B., Le Chatelier, E., Derosa, L., Duong, C. P. M., Alou, M. T., Daillère, R., Fluckiger, A., Messaoudene, M., Rauber, C., Roberti, M. P., et al. (2018) · Science · doi:10.1126/science.aan3706 · Cited by 5,671 · see citing works

Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients

Gopalakrishnan, V., Spencer, C. N., Nezi, L., Reuben, A., Andrews, M. C., Karpinets, T. V., Prieto, P. A., Vicente, D., Hoffman, K., Wei, S. C., et al. (2018) · Science · doi:10.1126/science.aan4236 · Cited by 4,812 · see citing works

Kraken: ultrafast metagenomic sequence classification using exact alignments

Wood, D. E., & Salzberg, S. L. (2014) · Genome Biology · doi:10.1186/gb-2014-15-3-r46 · Cited by 4,521 · see citing works

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

Snyder, A., Makarov, V., Merghoub, T., Yuan, J., Zaretsky, J. M., Desrichard, A., Walsh, L. A., Postow, M. A., Wong, P., Ho, T. S., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1406498 · Cited by 4,286 · see citing works

Commensal <i>Bifidobacterium</i> promotes antitumor immunity and facilitates anti–PD-L1 efficacy

Sivan, A., Corrales, L., Hubert, N., Williams, J. B., Aquino-Michaels, K., Earley, Z. M., Benyamin, F. W., Man Lei, Y., Jabri, B., Alegre, M.-L., et al. (2015) · Science · doi:10.1126/science.aac4255 · Cited by 3,888 · see citing works

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., & Callahan, B. J. (2018) · Microbiome · doi:10.1186/s40168-018-0605-2 · Cited by 3,493 · see citing works

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota

Vétizou, M., Pitt, J. M., Daillère, R., Lepage, P., Waldschmitt, N., Flament, C., Rusakiewicz, S., Routy, B., Roberti, M. P., Duong, C. P. M., et al. (2015) · Science · doi:10.1126/science.aad1329 · Cited by 3,488 · see citing works

The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients

Matson, V., Fessler, J., Bao, R., Chongsuwat, T., Zha, Y., Alegre, M.-L., Luke, J. J., & Gajewski, T. F. (2018) · Science · doi:10.1126/science.aao3290 · Cited by 3,107 · cited 2× · see citing works

Mapping short DNA sequencing reads and calling variants using mapping quality scores

Li, H., Ruan, J., & Durbin, R. (2008) · Genome Research · doi:10.1101/gr.078212.108 · Cited by 2,638 · see citing works

Fusobacterium nucleatum Promotes Colorectal Carcinogenesis by Modulating E-Cadherin/β-Catenin Signaling via its FadA Adhesin

Rubinstein, M. R., Wang, X., Liu, W., Hao, Y., Cai, G., & Han, Y. W. (2013) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2013.07.012 · Cited by 2,476 · see citing works

The human tumor microbiome is composed of tumor type–specific intracellular bacteria

Nejman, D., Livyatan, I., Fuks, G., Gavert, N., Zwang, Y., Geller, L. T., Rotter-Maskowitz, A., Weiser, R., Mallel, G., Gigi, E., et al. (2020) · Science · doi:10.1126/science.aay9189 · Cited by 2,464 · see citing works

Differential abundance analysis for microbial marker-gene surveys

Paulson, J. N., Stine, O. C., Bravo, H. C., & Pop, M. (2013) · Nature Methods · doi:10.1038/nmeth.2658 · Cited by 2,393 · see citing works

Shotgun metagenomics, from sampling to analysis

Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017) · Nature Biotechnology · doi:10.1038/nbt.3935 · Cited by 2,202 · see citing works

Fusobacterium nucleatum Promotes Chemoresistance to Colorectal Cancer by Modulating Autophagy

Yu, T., Guo, F., Yu, Y., Sun, T., Ma, D., Han, J., Qian, Y., Kryczek, I., Sun, D., Nagarsheth, N., et al. (2017) · Cell · doi:10.1016/j.cell.2017.07.008 · Cited by 2,198 · see citing works

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

Truong, D. T., Franzosa, E. A., Tickle, T. L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C., & Segata, N. (2015) · Nature Methods · doi:10.1038/nmeth.3589 · Cited by 2,185 · see citing works

Normalization and microbial differential abundance strategies depend upon data characteristics

Weiss, S. J., Xu, Z. Z., Peddada, S. D., Amir, A., Bittinger, K. L., González, A., Lozupone, C., Zaneveld, J., Vázquez‐Baeza, Y., Birmingham, A., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0237-y · Cited by 2,123 · see citing works

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracyPreprint

Smith, T. S., Heger, A., & Sudbery, I. M. (2017) · Genome Research · doi:10.1101/gr.209601.116 · Cited by 2,072 · see citing works

The Intestinal Microbiota Modulates the Anticancer Immune Effects of Cyclophosphamide

Viaud, S., Saccheri, F., Mignot, G., Yamazaki, T., Daillère, R., Hannani, D., Enot, D. P., Pfirschke, C., Engblom, C., Pittet, M. J., et al. (2013) · Science · doi:10.1126/science.1240537 · Cited by 2,050 · see citing works

Bayesian community-wide culture-independent microbial source tracking

Knights, D., Kuczynski, J., Charlson, E. S., Zaneveld, J., Mozer, M. C., Collman, R. G., Bushman, F. D., Knight, R. D., & Kelley, S. T. (2011) · Nature Methods · doi:10.1038/nmeth.1650 · Cited by 1,839 · see citing works

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine

Geller, L. T., Barzily-Rokni, M., Danino, T., Jonas, O. H., Shental, N., Nejman, D., Gavert, N., Zwang, Y., Cooper, Z. A., Shee, K., et al. (2017) · Science · doi:10.1126/science.aah5043 · Cited by 1,817 · see citing works

Fecal microbiota transplant overcomes resistance to anti–PD-1 therapy in melanoma patients

Davar, D., Dzutsev, A. K., McCulloch, J. A., Rodrigues, R. R., Chauvin, J.-M., Morrison, R. M., Deblasio, R. N., Menna, C., Ding, Q., Pagliano, O., et al. (2021) · Science · doi:10.1126/science.abf3363 · Cited by 1,781 · cited 1× · see citing works

Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients

Baruch, E. N., Youngster, I., Ben-Betzalel, G., Ortenberg, R., Lahat, A., Katz, L., Adler, K., Dick-Necula, D., Raskin, S., Bloch, N., et al. (2021) · Science · doi:10.1126/science.abb5920 · Cited by 1,757 · see citing works

Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes

Riquelme, E., Zhang, Y., Zhang, L., Montiel, M., Zoltan, M., Dong, W., Quesada, P., Sahin, I., Chandra, V., San Lucas, A., et al. (2019) · Cell · doi:10.1016/j.cell.2019.07.008 · Cited by 1,577 · see citing works

Gut microbiome–mediated bile acid metabolism regulates liver cancer via NKT cells

Ma, C., Han, M., Heinrich, B., Fu, Q., Zhang, Q., Sandhu, M., Agdashian, D., Terabe, M., Berzofsky, J. A., Fako, V., et al. (2018) · Science · doi:10.1126/science.aan5931 · Cited by 1,508 · see citing works

Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy

Mager, L. F., Burkhard, R., Pett, N., Cooke, N. C. A., Brown, K., Ramay, H., Paik, S., Stagg, J., Groves, R. A., Gallo, M., et al. (2020) · Science · doi:10.1126/science.abc3421 · Cited by 1,407 · see citing works

The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression

Pushalkar, S., Hundeyin, M., Daley, D., Zambirinis, C. P., Kurz, E., Mishra, A., Mohan, N., Aykut, B., Usyk, M., Torres, L. E., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-1134 · Cited by 1,400 · see citing works

The microbiome and human cancer

Sepich-Poore, G. D., Zitvogel, L., Straussman, R., Hasty, J., Wargo, J. A., & Knight, R. (2021) · Science · doi:10.1126/science.abc4552 · Cited by 1,332 · see citing works

Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma

Peng, J., Sun, B.-F., Chen, C.-Y., Zhou, J.-Y., Chen, Y.-S., Chen, H., Liu, L., Huang, D., Jiang, J., Cui, G.-S., et al. (2019) · Cell Research · doi:10.1038/s41422-019-0195-y · Cited by 1,321 · see citing works

Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli

Pleguezuelos-Manzano, C., Puschhof, J., Rosendahl Huber, A., van Hoeck, A., Wood, H. M., Nomburg, J., Gurjao, C., Manders, F., Dalmasso, G., Stege, P. B., et al. (2020) · Nature · doi:10.1038/s41586-020-2080-8 · Cited by 1,208 · see citing works

Comparing the Pearson and Spearman correlation coefficients across distributions and sample sizes: a tutorial using simulations and empirical data

de Winter, J. C. F., Gosling, S. D., & Potter, J. (2016) · Psychological Methods · doi:10.1037/met0000079 · Cited by 1,201 · see citing works

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma

Ji, A. L., Rubin, A. J., Thrane, K., Jiang, S., Reynolds, D. L., Meyers, R. M., Guo, M. G., George, B. M., Mollbrink, A., Bergenstråhle, J., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.039 · Cited by 1,117 · see citing works

Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria

Dejea, C. M., Fathi, P., Craig, J. M., Boleij, A., Taddese, R., Geis, A. L., Wu, X., DeStefano Shields, C. E., Hechenbleikner, E. M., Huso, D. L., et al. (2018) · Science · doi:10.1126/science.aah3648 · Cited by 1,105 · see citing works

Alleviating Cancer Drug Toxicity by Inhibiting a Bacterial Enzyme

Wallace, B. D., Wang, H., Lane, K. T., Scott, J. E., Orans, J., Koo, J. S., Venkatesh, M., Jobin, C., Yeh, L.-A., Mani, S., et al. (2010) · Science · doi:10.1126/science.1191175 · Cited by 1,080 · see citing works

Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer

Fu, A., Yao, B., Dong, T., Chen, Y., Yao, J., Liu, Y., Li, H., Bai, H., Liu, X., Zhang, Y., et al. (2022) · Cell · doi:10.1016/j.cell.2022.02.027 · Cited by 981 · see citing works

Commensal Microbiota Promote Lung Cancer Development via γδ T Cells

Jin, C., Lagoudas, G. K., Zhao, C., Bullman, S., Bhutkar, A., Hu, B., Ameh, S., Sandel, D., Liang, X. S., Mazzilli, S., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.040 · Cited by 964 · see citing works

Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer

Lee, H., Hong, Y., Etlioglu, H. E., Cho, Y. B., Pomella, V., den Bosch, B. V., Vanhecke, J., Verbandt, S., Hong, H.-K., Min, J.-W., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0636-z · Cited by 916 · see citing works

Enterococcus hirae and Barnesiella intestinihominis Facilitate Cyclophosphamide-Induced Therapeutic Immunomodulatory Effects

Daillère, R., Vétizou, M., Waldschmitt, N., Yamazaki, T., Isnard, C., Poirier-Colame, V., Duong, C. P. M., Flament, C., Lepage, P., Roberti, M. P., et al. (2016) · Immunity · doi:10.1016/j.immuni.2016.09.009 · Cited by 897 · see citing works

Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer

Galeano Niño, J. L., Wu, H., LaCourse, K. D., Kempchinsky, A. G., Baryiames, A., Barber, B., Futran, N., Houlton, J., Sather, C., Sicinska, E., et al. (2022) · Nature · doi:10.1038/s41586-022-05435-0 · Cited by 887 · see citing works

The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL

Aykut, B., Pushalkar, S., Chen, R., Li, Q., Abengozar, R., Kim, J. I., Shadaloey, S. A., Wu, D., Preiss, P., Verma, N., et al. (2019) · Nature · doi:10.1038/s41586-019-1608-2 · Cited by 883 · see citing works

Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation

Peled, J. U., Gomes, A. L. C., Devlin, S. M., Littmann, E. R., Taur, Y., Sung, A. D., Weber, D., Hashimoto, D., Slingerland, A. E., Slingerland, J. B., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa1900623 · Cited by 765 · see citing works

Breast cancer colonization by Fusobacterium nucleatum accelerates tumor growth and metastatic progression

Parhi, L., Alon-Maimon, T., Sol, A., Nejman, D., Shhadeh, A., Fainsod-Levi, T., Yajuk, O., Isaacson, B., Abed, J., Maalouf, N., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16967-2 · Cited by 716 · see citing works

Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing

Maynard, A., McCoach, C. E., Rotow, J. K., Harris, L., Haderk, F., Kerr, D. L., Yu, E. A., Schenk, E. L., Tan, W., Zee, A., et al. (2020) · Cell · doi:10.1016/j.cell.2020.07.017 · Cited by 697 · see citing works

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

Namiki, T., Hachiya, T., Tanaka, H. L., & Sakakibara, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks678 · Cited by 677 · see citing works

FEAST: fast expectation-maximization for microbial source tracking

Shenhav, L., Thompson, M., Joseph, T., Briscoe, L., Furman, O., Bogumil, D. D., Mizrahi, I., Pe’er, I., & Halperin, E. (2019) · Nature Methods · doi:10.1038/s41592-019-0431-x · Cited by 650 · see citing works

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

Morgan, M. T., Anders, S., Lawrence, M. F., Aboyoun, P., Pagès, H., & Gentleman, R. C. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp450 · Cited by 545 · see citing works

Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions

Narunsky-Haziza, L., Sepich-Poore, G. D., Livyatan, I., Asraf, O., Martino, C., Nejman, D., Gavert, N., Stajich, J. E., Amit, G., González, A., et al. (2022) · Cell · doi:10.1016/j.cell.2022.09.005 · Cited by 538 · see citing works

The gut microbiota is associated with immune cell dynamics in humans

Schluter, J., Peled, J. U., Taylor, B. P., Markey, K. A., Smith, M., Taur, Y., Niehus, R., Staffas, A., Dai, A., Fontana, E., et al. (2020) · Nature · doi:10.1038/s41586-020-2971-8 · Cited by 534 · see citing works

Nivolumab plus ipilimumab with or without live bacterial supplementation in metastatic renal cell carcinoma: a randomized phase 1 trial

Dizman, N., Meza, L., Bergerot, P., Alcantara, M., Dorff, T., Lyou, Y., Frankel, P., Cui, Y., Mira, V., Llamas, M., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01694-6 · Cited by 515 · see citing works

Biological agents.

(2012) · PubMed Central · Cited by 502 · see citing works

Evaluating the Information Content of Shallow Shotgun Metagenomics

Hillmann, B., Al-Ghalith, G. A., Shields-Cutler, R. R., Zhu, Q., Gohl, D. M., Beckman, K. B., Knight, R., & Knights, D. (2018) · mSystems · doi:10.1128/msystems.00069-18 · Cited by 474 · see citing works

Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients

Bost, P., Giladi, A., Liu, Y., Bendjelal, Y., Xu, G., David, E., Blecher-Gonen, R., Cohen, M., Medaglia, C., Li, H., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.006 · Cited by 471 · see citing works

scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

Wang, J., Ma, A., Chang, Y., Gong, J., Jiang, Y., Qi, R., Wang, C., Fu, H., Ma, Q., & Xu, D. H. (2021) · Nature Communications · doi:10.1038/s41467-021-22197-x · Cited by 454 · see citing works

A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors

Dohlman, A. B., Klug, J., Mesko, M., Gao, I. H., Lipkin, S. M., Shen, X., & Iliev, I. D. (2022) · Cell · doi:10.1016/j.cell.2022.09.015 · Cited by 420 · see citing works

<i>Campylobacter jejuni</i> promotes colorectal tumorigenesis through the action of cytolethal distending toxin

He, Z., Gharaibeh, R. Z., Newsome, R. C., Pope, J. L., Dougherty, M. W., Tomkovich, S., Pons, B., Mirey, G., Vignard, J., Hendrixson, D. R., et al. (2019) · Gut · doi:10.1136/gutjnl-2018-317200 · Cited by 409 · see citing works

Control of lymphocyte functions by gut microbiota-derived short-chain fatty acids

Kim, C. H. (2021) · Cellular &amp; Molecular Immunology · doi:10.1038/s41423-020-00625-0 · Cited by 404 · see citing works

Critical Assessment of Metagenome Interpretation: the second round of challenges

Meyer, F., Fritz, A., Deng, Z.-L., Koslicki, D., Lesker, T. R., Gurevich, A. A., Robertson, G., Alser, M., Antipov, D., Beghini, F., et al. (2022) · Nature Methods · doi:10.1038/s41592-022-01431-4 · Cited by 371 · see citing works

Helicobacter pylori CagA Phosphorylation-Independent Function in Epithelial Proliferation and Inflammation

Suzuki, M., Mimuro, H., Kiga, K., Fukumatsu, M., Ishijima, N., Morikawa, H., Nagai, S., Koyasu, S., Gilman, R. H., Kersulyte, D., et al. (2009) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2008.11.010 · Cited by 338 · see citing works

Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice

Lee, S.-H., Cho, S.-Y., Yoon, Y., Park, C., Sohn, J., Jeong, J.-J., Jeon, B.-N., Jang, M., An, C., Lee, S., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-020-00831-6 · Cited by 325 · see citing works

Gut microbiome, big data and machine learning to promote precision medicine for cancer

Cammarota, G., Ianiro, G., Ahern, A., Carbone, C., Temko, A., Claesson, M. J., Gasbarrini, A., & Tortora, G. (2020) · Nature Reviews Gastroenterology &amp; Hepatology · doi:10.1038/s41575-020-0327-3 · Cited by 324 · see citing works

Lower Airway Dysbiosis Affects Lung Cancer Progression

Tsay, J.-C. J., Wu, B. G., Sulaiman, I., Gershner, K., Schluger, R., Li, Y., Yie, T.-A., Meyn, P., Olsen, E., Perez, L., et al. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-0263 · Cited by 322 · see citing works

Talimogene Laherparepvec (T-VEC): An Intralesional Cancer Immunotherapy for Advanced Melanoma

Ferrucci, P. F., Pala, L., Conforti, F., & Cocorocchio, E. (2021) · Cancers · doi:10.3390/cancers13061383 · Cited by 322 · see citing works

PathSeq: software to identify or discover microbes by deep sequencing of human tissue

Kostic, A. D., Ojesina, A. I., Pedamallu, C. S., Jung, J., Verhaak, R. G. W., Getz, G. A., & Meyerson, M. M. (2011) · Nature Biotechnology · doi:10.1038/nbt.1868 · Cited by 317 · see citing works

Gut microbiota modulate dendritic cell antigen presentation and radiotherapy-induced antitumor immune response

Uribe-Herranz, M., Rafail, S., Beghi, S., Gil-de-Gómez, L., Verginadis, I., Bittinger, K., Pustylnikov, S., Pierini, S., Perales-Linares, R., Blair, I. A., et al. (2019) · Journal of Clinical Investigation · doi:10.1172/jci124332 · Cited by 316 · see citing works

Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution

Dar, D., Dar, N., Cai, L., & Newman, D. K. (2021) · Science · doi:10.1126/science.abi4882 · Cited by 296 · see citing works

A faecal microbiota signature with high specificity for pancreatic cancer

Kartal, E., Schmidt, T. S. B., Molina-Montes, E., Rodríguez-Perales, S., Wirbel, J., Maistrenko, O. M., Akanni, W. A., Alashkar Alhamwe, B., Alves, R. J., Carrato, A., et al. (2022) · Gut · doi:10.1136/gutjnl-2021-324755 · Cited by 290 · see citing works

Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface

Hunter, M. V., Moncada, R. M., Weiss, J. M., Yanai, I., & White, R. M. (2021) · Nature Communications · doi:10.1038/s41467-021-26614-z · Cited by 288 · see citing works

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

Zheng, W., Zhao, S., Yin, Y., Zhang, H., Needham, D. M., Evans, E. D., Dai, C. L., Lu, P. J., Alm, E. J., & Weitz, D. A. (2022) · Science · doi:10.1126/science.abm1483 · Cited by 283 · see citing works

Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA

Paulson, K. G., Voillet, V., McAfee, M. S., Hunter, D. S., Wagener, F. D., Perdicchio, M., Valente, W. J., Koelle, S., Church, C. D., Vandeven, N. A., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06300-3 · Cited by 282 · see citing works

The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants

Dohlman, A. B., Mendoza, D. A., Ding, S., Gao, M. C., Dressman, H. K., Iliev, I. D., Lipkin, S. M., & Shen, X. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2020.12.001 · Cited by 279 · see citing works

Integrative Methods and Practical Challenges for Single-Cell Multi-omics

Ma, A., McDermaid, A., Xu, J., Chang, Y., & Ma, Q. (2020) · Trends in biotechnology · doi:10.1016/j.tibtech.2020.02.013 · Cited by 272 · see citing works

Modulation of Pulmonary Microbiota by Antibiotic or Probiotic Aerosol Therapy: A Strategy to Promote Immunosurveillance against Lung Metastases

Le Noci, V., Guglielmetti, S., Arioli, S., Camisaschi, C., Bianchi, F., Sommariva, M., Storti, C., Triulzi, T., Castelli, C., Balsari, A., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.08.090 · Cited by 270 · see citing works

Simulation-based comprehensive benchmarking of RNA-seq aligners

Baruzzo, G., Hayer, K. E., Kim, E. J., Camillo, B. D., FitzGerald, G., & Grant, G. (2016) · Nature Methods · doi:10.1038/nmeth.4106 · Cited by 261 · see citing works

Host-microbe co-metabolism dictates cancer drug efficacy in C. elegans

Scott, T. A., Quintaneiro, L. M., Norvaisas, P., Lui, P. P., Wilson, M. P., Leung, K.-Y., Herrera-Dominguez, L., Sudiwala, S., Pessia, A., Clayton, P. T., et al. (2017) · Cell · doi:10.1016/j.cell.2017.03.040 · Cited by 254 · see citing works

Highly multiplexed spatial mapping of microbial communities

Shi, H., Shi, Q., Grodner, B., Lenz, J. S., Zipfel, W. R., Brito, I., & Vlaminck, I. D. (2020) · Nature · doi:10.1038/s41586-020-2983-4 · Cited by 248 · see citing works

Bacterial metabolism affects the C. elegans response to cancer chemotherapeutics

García-González, A. P., Ritter, A. D., Shrestha, S., Andersen, E. C., Yilmaz, L. S., & Walhout, A. J. M. (2017) · Cell · doi:10.1016/j.cell.2017.03.046 · Cited by 243 · see citing works

Comparing and evaluating metagenome assembly tools from a microbiologist's perspective - not only size matters!

Vollmers, J., Wiegand, S., & Kaster, A.-K. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169662 · Cited by 240 · see citing works

Fusobacterium nucleatum in Colorectal Cancer Relates to Immune Response Differentially by Tumor Microsatellite Instability Status

Hamada, T., Zhang, X., Mima, K., Bullman, S., Sukawa, Y., Nowak, J. A., Kosumi, K., Masugi, Y., Twombly, T. S., Cao, Y., et al. (2018) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-18-0174 · Cited by 232 · see citing works

Gut microbiota dependent anti-tumor immunity restricts melanoma growth in Rnf5−/− mice

Li, Y., Tinoco, R., Elmén, L., Segota, I., Xian, Y., Fujita, Y., Sahu, A., Zarecki, R., Marie, K., Feng, Y., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09525-y · Cited by 212 · see citing works

Effects of Rare Microbiome Taxa Filtering on Statistical Analysis

Cao, Q., Sun, X., Rajesh, K., Chalasani, N., Gelow, K., Katz, B. P., Shah, V. H., Sanyal, A. J., & Smirnova, E. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.607325 · Cited by 202 · see citing works

Prebiotic-Induced Anti-tumor Immunity Attenuates Tumor Growth

Li, Y., Elmén, L., Segota, I., Xian, Y., Tinoco, R., Feng, Y., Fujita, Y., Segura Muñoz, R. R., Schmaltz, R., Bradley, L. M., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.01.035 · Cited by 189 · see citing works

Tumor microbiome links cellular programs and immunity in pancreatic cancer

Ghaddar, B., Biswas, A., Harris, C., Omary, M. B., Carpizo, D. R., Blaser, M. J., & De, S. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.09.009 · Cited by 181 · see citing works

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease

Aldars‐García, L., Chaparro, M., & Gisbert, J. P. (2021) · Microorganisms · doi:10.3390/microorganisms9050977 · Cited by 177 · see citing works

Intratumoral Injection of Clostridium novyi -NT Spores in Patients with Treatment-refractory Advanced Solid Tumors

Jankú, F., Zhang, H. H., Pezeshki, A., Goel, S., Murthy, R., Wang‐Gillam, A., Shepard, D. R., Helgason, T., Masters, T., Hong, D. S., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-2065 · Cited by 176 · see citing works

White paper on microbial anti-cancer therapy and prevention

Forbes, N. S., Coffin, R. S., Deng, L., Evgin, L., Fiering, S., Giacalone, M. J., Gravekamp, C., Gulley, J. L., Gunn, H., Hoffman, R. M., et al. (2018) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-018-0381-3 · Cited by 170 · see citing works

The gut microbiome: what the oncologist ought to know

Lee, K. A., Luong, M., Shaw, H. M., Nathan, P., Bataille, V. A., & Spector, T. D. (2021) · British Journal of Cancer · doi:10.1038/s41416-021-01467-x · Cited by 151 · see citing works

Bacterial Therapy of Cancer: Promises, Limitations, and Insights for Future Directions

Kramer, M. G., Masner, M., Ferreira, F. A., & Hoffman, R. M. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00016 · Cited by 145 · see citing works

Technology dictates algorithms: recent developments in read alignment

Alser, M., Rotman, J., Deshpande, D., Taraszka, K., Shi, H., Baykal, P. I., Yang, H. T., Xue, V., Knyazev, S., Singer, B. D., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02443-7 · Cited by 144 · see citing works

Abiraterone acetate preferentially enriches for the gut commensal Akkermansia muciniphila in castrate-resistant prostate cancer patients

Daisley, B. A., Chanyi, R. M., Abdur-Rashid, K., Al, K. F., Gibbons, S., Chmiel, J. A., Wilcox, H., Reid, G., Anderson, A., Dewar, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18649-5 · Cited by 128 · see citing works

A Gut Microbial Mimic that Hijacks Diabetogenic Autoreactivity to Suppress Colitis

Nanjundappa, R. H., Ronchi, F., Wang, J., Clemente‐Casares, X., Yamanouchi, J., Umeshappa, C. S., Yang, Y., Blanco, J., Bassolas-Molina, H., Salas, A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.022 · Cited by 116 · see citing works

Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing

Lind, A., & Pollard, K. S. (2021) · Microbiome · doi:10.1186/s40168-021-01015-y · Cited by 113 · see citing works

Mutagenesis by Microbe: the Role of the Microbiota in Shaping the Cancer Genome

Barrett, M., Hand, C. K., Shanahan, F., Murphy, T., & O’Toole, P. W. (2020) · Trends in Cancer · doi:10.1016/j.trecan.2020.01.019 · Cited by 108 · see citing works

Interaction of bacterial genera associated with therapeutic response to immune checkpoint PD-1 blockade in a United States cohort

Newsome, R. C., Gharaibeh, R. Z., Pierce, C. M., da Silva, W. V., Paul, S., Hogue, S. R., Yu, Q., Antonia, S., Conejo-Garcia, J. R., Robinson, L. A., et al. (2022) · Genome Medicine · doi:10.1186/s13073-022-01037-7 · Cited by 104 · see citing works

Spatial meta-transcriptomics reveal associations of intratumor bacteria burden with lung cancer cells showing a distinct oncogenic signature

Wong-Rolle, A., Dong, Q., Zhu, Y., Divakar, P., Hor, J. L., Kedei, N., Wong, M., Tillo, D., Conner, E. A., Rajan, A., et al. (2022) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2022-004698 · Cited by 96 · see citing works

Choosing statistical test

Bhalerao, S. S., & Parab, S. (2010) · International Journal of Ayurveda Research · doi:10.4103/0974-7788.72494 · Cited by 92 · see citing works

Intratumor microbiome in cancer progression: current developments, challenges and future trends

Liu, J., & Zhang, Y. (2022) · Biomarker Research · doi:10.1186/s40364-022-00381-5 · Cited by 84 · see citing works

Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions

Sudhakar, P., Machiels, K., Verstockt, B., Korcsmaros, T. D., & Vermeire, S. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.618856 · Cited by 65 · see citing works

What Is a Spurious Correlation?

Haig, B. D. (2003) · Understanding Statistics · doi:10.1207/s15328031us0202_03 · Cited by 56 · see citing works

Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning

Chang, Y., He, F., Wang, J., Chen, S., Li, J., Liu, J., Yu, Y., Su, L., Ma, A., Allen, C., et al. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.08.029 · Cited by 54 · see citing works

Effects of gut microbiota on host adaptive immunity under immune homeostasis and tumor pathology state

Li, Y., Ye, Z., Zhu, J., Fang, S., Meng, L., & Zhou, C. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.844335 · Cited by 45 · see citing works

Polymorphic microbes: a new emerging hallmark of cancer

Lythgoe, M. P., Mullish, B. H., Frampton, A. E., & Krell, J. (2022) · Trends in Microbiology · doi:10.1016/j.tim.2022.08.004 · Cited by 44 · see citing works

Physiological and metagenomic strategies uncover the rhizosphere bacterial microbiome succession underlying three common environmental stresses in cassava

Zeng, H., Xu, H., Liu, G., Wei, Y., Zhang, J., & Shi, H. (2021) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2021.125143 · Cited by 29 · see citing works

Statistical procedures for corrosion studies

Wysock, B. M., Sandvig, A. M., Schock, M. R., Frebis, C. P., & Prokop, B. (1995) · American Water Works Association · doi:10.1002/j.1551-8833.1995.tb06397.x · Cited by 27 · see citing works

mDrop-Seq: Massively Parallel Single-Cell RNA-Seq of Saccharomyces cerevisiae and Candida albicans

Dohn, R., Xie, B., Back, R., Selewa, A., Eckart, H., Rao, R. P., & Basu, A. (2021) · Vaccines · doi:10.3390/vaccines10010030 · Cited by 26 · see citing works

Application of fast expectation-maximization microbial source tracking to discern fecal contamination in rivers exposed to low fecal inputs

Xu, Y., Han, G., Zhang, H., Yu, Z., & Liu, R. (2022) · The Journal of Microbiology · doi:10.1007/s12275-022-1651-9 · Cited by 15 · see citing works

The potential of fecal microbiota transplantation in oncology

Lythgoe, M. P., Ghani, R., Mullish, B. H., Marchesi, J. R., & Krell, J. (2021) · Trends in Microbiology · doi:10.1016/j.tim.2021.10.003 · Cited by 14 · see citing works

Preventing Cancer and Other Diseases Caused by Human Papillomavirus Infection: 2017 Lasker-DeBakey Clinical Research Award

Lowy, D. R., & Schiller, J. T. (2017) · JAMA · doi:10.1001/jama.2017.11706 · Cited by 11 · see citing works

The Microbiome in Immuno-oncology

Toker, J. S., Arora, R., & Wargo, J. A. (2020) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-41008-7_19 · Cited by 9 · see citing works

Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine

(2011) · doi:10.1145/2147805 · Cited by 8 · see citing works

543P Neoadjuvant MRx0518 treatment is associated with significant gene and metagene signature changes in solid tumours

Lythgoe, M. P., Adriani, M., Stebbing, J., Clark, J., Pickford, E., Frampton, A. E., Liu, D., Kyrgiou, M., Rees, E., Fyvie, G., et al. (2021) · Annals of Oncology · doi:10.1016/j.annonc.2021.08.1065 · Cited by 5 · see citing works

Single-cell sequencing to multi-omics: technologies and applications

Wu, X., Yang, X., Dai, Y., Zhao, Z., Zhu, J., Guo, H., & Yang, R. (2024) · Biomarker Research · doi:10.1186/s40364-024-00643-4 · Cited by 195 · see citing works

The Role of the Microbiome in the Etiopathogenesis of Colon Cancer

Tekle, G. E., Andreeva, N., & Garrett, W. S. (2024) · Annual Review of Physiology · doi:10.1146/annurev-physiol-042022-025619 · Cited by 75 · see citing works

Spatiotemporal metabolomic approaches to the cancer-immunity panorama: a methodological perspective

Xiao, Y., Li, Y., & Zhao, H. (2024) · Molecular Cancer · doi:10.1186/s12943-024-02113-9 · Cited by 59 · see citing works

The dynamic oral–gastric microbial axis connects oral and gastric health: current evidence and disputes

Xia, M., Lei, L., Zhao, L.-Y., Xu, W., Zhang, H., Li, M., Hu, J., Cheng, R., & Hu, T. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-024-00623-4 · Cited by 52 · see citing works

The emerging tumor microbe microenvironment: From delineation to multidisciplinary approach-based interventions

Fu, Y., Li, J., Cai, W., Huang, Y., Liu, X., Ma, Z., Tang, Z., Bian, X., Zheng, J., Jiang, J., et al. (2024) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2023.11.018 · Cited by 48 · see citing works

Unveiling the intratumoral microbiota within cancer landscapes

Che, S., Yan, Z., Feng, Y., & Hai, Z. (2024) · iScience · doi:10.1016/j.isci.2024.109893 · Cited by 40 · see citing works

The mycobiome in human cancer: analytical challenges, molecular mechanisms, and therapeutic implications

Ding, T., Liu, C., & Li, Z. (2025) · Molecular Cancer · doi:10.1186/s12943-025-02227-8 · Cited by 44 · see citing works

Molecular crosstalk between polyphenols and gut microbiota in cancer prevention

Zeb, F., Naqeeb, H., Osaili, T. M. I., Faris, M. E., Ismail, L. C., Obaid, R. S., Naja, F., Radwan, H. M., Hasan, H. A., Hashim, M. S., et al. (2024) · Nutrition Research · doi:10.1016/j.nutres.2024.01.012 · Cited by 37 · see citing works

Oleocanthal as a Multifunctional Anti-Cancer Agent: Mechanistic Insights, Advanced Delivery Strategies, and Synergies for Precision Oncology

Jannati, S., Patel, A., Patnaik, R., & Banerjee, Y. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26125521 · Cited by 33 · see citing works

Artificial Intelligence Virtual Organoids (AIVOs)

Bai, L., & Su, J. (2025) · Bioactive Materials · doi:10.1016/j.bioactmat.2025.12.030 · Cited by 34 · see citing works

The new microbiome on the block: challenges and opportunities of using human tumor sequencing data to study microbes

Li, Y., Ma, A., Johnson, W. E., Eng, C., De, S., Jiang, S., Li, Z., Spakowicz, D. J., & Ma, Q. (2025) · Nature Methods · doi:10.1038/s41592-025-02807-y · Cited by 25 · see citing works

Untangling the web of intratumor microbiota in lung cancer

Liu, W. L., Xu, J., Pi, Z., Chen, Y., Jiang, G., Wan, Y., & Mao, W. (2023) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2023.189025 · Cited by 23 · see citing works

Tissue-resident microbiota impacts colorectal cancer progression and prognosis

Shi, Z., Ren, H., Lin, C., Li, F., Wu, M., Yang, F., Luo, T., Nunes, L., Isaksson, A., Hammarström, K., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-67047-2 · Cited by 19 · see citing works

Dissecting the intratumoral microbiome landscape in lung cancer

Zhao, Y. G., Yang, Z., Wu, D., & Hai, Z. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1614731 · Cited by 13 · see citing works

Identification of HPV oncogene and host cell differentiation associated cellular heterogeneity in cervical cancer via single‐cell transcriptomic analysis

Li, Y., Wang, C., Ma, A., Rani, A. Q., Luo, M., Li, J., Liu, X., & Ma, Q. (2023) · Journal of Medical Virology · doi:10.1002/jmv.29060 · Cited by 14 · see citing works

An Explainable Graph Neural Framework to Identify Cancer‐Associated Intratumoral Microbial Communities

Liu, Z., Sun, Y., Li, Y., Ma, A., Willaims, N. F., Jahanbahkshi, S., Hoyd, R., Wang, X., Zhang, S., Zhu, J., et al. (2024) · Advanced Science · doi:10.1002/advs.202403393 · Cited by 15 · see citing works

The Microbiome Matters: Its Impact on Cancer Development and Therapeutic Responses

Chung, I.-Y., Kim, J. H., & Koh, A. (2024) · The Journal of Microbiology · doi:10.1007/s12275-024-00110-7 · Cited by 13 · see citing works

Microbes in the tumor microenvironment: New additions to break the tumor immunotherapy dilemma

Zhou, L., Fan, S., Zhang, W., Wang, D., & Tang, D. (2024) · Microbiological Research · doi:10.1016/j.micres.2024.127777 · Cited by 12 · see citing works

Single Cell Transcriptomics Reveals the Hidden Microbiomes of Human TissuesPreprint

Mahmoudabadi, G., Crasta, S., & Quake, S. R. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.11.511790 · Cited by 8 · see citing works

Unraveling the potential of bioengineered microbiome-based strategies to enhance cancer immunotherapy

Hamza, M., Wang, S., Liu, Y., Li, K., Zhu, M., & Chen, L. (2025) · Microbiological Research · doi:10.1016/j.micres.2025.128156 · Cited by 6 · see citing works

Decoding Microbiome’s Role in Prostate Cancer Progression and Treatment Response

Sakellakis, M., Resta, P., Papagianni, E. D., Procter, K. A., Belouka, I., Gioti, K., Anthouli-Anagnostopoulou, F., Chaniotis, D. I., & Beloukas, A. I. (2025) · Diseases · doi:10.3390/diseases13090294 · Cited by 5 · see citing works

Tumor‑associated microbiota: Multi‑cancer landscape, mechanistic insights and clinical translation (Review)

Yang, J., Dong, Y., Chen, Y., Liang, H., Rong, S., Liu, Z., & Lang, Q. (2025) · Oncology Letters · doi:10.3892/ol.2025.15273 · Cited by 6 · see citing works

From mechanisms to precision medicine: the role of organoids in studying the gut microbiota-tumor microenvironment axis

Zheng, S., Su, Y.-Y., Cai, F.-L., Xu, D.-F., & Xu, Y. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1669482 · Cited by 5 · see citing works

Emerging Insights into the Role of the Microbiome in Brain Gliomas: A Systematic Review of Recent Evidence

Dubiński, P., Odzimek, M., Podlewski, S., & Brola, W. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms27010444 · Cited by 5 · see citing works

Host–microbiota interaction during cancer progression from bulk to single‐cell level

Ma, Y., Zhu, R., & Liu, N. (2024) · Clinical and Translational Discovery · doi:10.1002/ctd2.263 · Cited by 5 · see citing works

Intratumoral microbiota in cancer: molecular mechanism and therapeutic strategies

Yu, Y., Guo, Z., Luo, Z., Dian, Y., Yang, X., Chen, X., Zeng, F., & Deng, G. (2026) · Molecular Biomedicine · doi:10.1186/s43556-026-00473-w · Cited by 4 · see citing works

HGMT: a database of human gut microbiota for tumors and immunotherapy response

Liu, J., Wang, M., Xu, C., Jia, L., Lai, S., Zhang, Z.-C., Zhang, J., Chen, W., Yang, Y., & Zhao, X. (2025) · Genome biology · doi:10.1186/s13059-025-03865-3 · Cited by 3 · see citing works

MetaMDA: explainable prediction of microbe–drug association utilizing random walks on a microbe–metabolite–drug heterogeneous network

Wang, Q., Chen, S., Miao, X., Liu, Y., & Liu, B. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf649 · Cited by 1 · see citing works

Deciphering the intratumor microbiota in malignant gastrointestinal tumors: multifaceted interplay and clinical implications

Tang, B., Lin, Y. N., Jiang, T., Chen, Y., Zhao, Q., Wang, S., Shen, Y., Wang, S., Wu, Q., Xie, P., et al. (2026) · Cell Communication and Signaling · doi:10.1186/s12964-025-02303-y · Cited by 1 · see citing works

Intratumoral microbiota-based designing strategies for precision cancer therapeutics

Chen, Y. J., & Wu, Q. (2026) · Chemical Engineering Journal · doi:10.1016/j.cej.2026.173636

Systematic evaluation of TCGA tumor microbiota reveals context-dependent reliability

Ma, C., Su, C., Li, J., Wang, J., Liao, J., Cheng, L., Qu, J., Zhang, G., Jiang, J., & Shuai, S. (2026) · mSystems · doi:10.1128/msystems.00180-26

Fluorescence in situ hybridization for visualizing microbiome-based markers in cancer

Habib, S., & Moinuddin (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-40551-8.00020-2

Global research trends and emerging frontiers of intratumoral microbiota in cancer immunotherapy: a bibliometric and visualization analysis

Zhou, J., Tao, H., Zou, F., Guo, H., Ding, R., Lei, Q., Zhou, X. Y., & Mei, S. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1865305

Microbiome—pancreatic cancer crosstalk: From tumor biology to therapeutic intervention

薛玉芹, Ye, J., Wang, S., Liu, M., Dai, F., Bai, M., Wang, Y., Savoji, A., Wang, Y., Hylemon, P. B., et al. (2026) · iMetaOmics. · doi:10.1002/imo2.70126

Multi-omics decodes how microbiota-residing spatial niches mediate cancer progression and therapy response

Dong, H., Ma, W., & Liu, S. (2026) · Molecular and Digital Medicine · doi:10.1016/j.mdmed.2026.100012

Decoding the cancer microbiome: multi-omics, AI, and translational opportunities

Sun, Y., Cheng, O., Ma, A., Shabnaz, S., Huang, X., Zhao, J., Tan, A. C., & Ma, Q. (2026) · Genome biology · doi:10.1186/s13059-026-04284-8

Intratumoral Microbiota in Fueling Cancer and Steering Treatment Response

Xu, M., Yu, J., Chen, Y., Ge, S., Ye, L., Wang, Y., 周一雄, & Jia, R. (2026) · MedComm · doi:10.1002/mco2.71052

Multi‐level insights into the immuno‐oncology‐microbiome axis: From biotechnology to novel therapies

Pi, Z., Liu, W. L., Song, C., Zhu, C., Liu, J., Wang, L., Zhao, H., Yang, C., Wu, L., Liu, T., et al. (2024) · iMeta · doi:10.1002/imt2.240 · Cited by 17 · see citing works

Intratumoral Microorganisms in Tumors: Current Understanding and Emerging Therapeutic Strategies

Zhang, H., Du, Z., Lu, P., Jiang, A., Guo, Y., Liu, Y., Song, Z., Dai, B., & Zhang, W. (2026) · MedComm · doi:10.1002/mco2.70754 · Cited by 3 · see citing works

The new microbiome on the block: challenges and opportunities of using human tumor sequencing data to study microbes

Li, Y., Ma, A., Johnson, W. E., Eng, C., De, S., Jiang, S., Li, Z., Spakowicz, D. J., & Ma, Q. (2025) · Nature Methods · doi:10.1038/s41592-025-02807-y · Cited by 25 · see citing works

The intratumoral microbiome as an emerging hub in cancer pathogenesis and precision oncology

Sun, J., Song, S., Luo, S., Fan, Q., Li, X., Liu, H., & Wu, G. (2026) · Molecular Cancer · doi:10.1186/s12943-026-02762-y

The intratumoral microbiota: Orchestrating metabolic-immune crosstalk and shaping the therapeutic landscape in cancer

Wang, S., Liu, Z., Jiang, C., Wei, Y., Liu, G., & Pan, Y. (2026) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2026.168316 · Cited by 1 · see citing works