Yan Yan | Publications

Epidemiological risk factors correlate of the cancer microbiome

Yan Y, Drew DA, Markowitz A, Lloyd-Price J, Abu-Ali G, Nguyen LH, Tran C, Chung DC, Gilpin KK, Meixell D, Parziale M, Schuck M, Patel Z, Richter JM, Kelsey PB, Garrett WS, Chan AT, Stadler ZK, Huttenhower C. Structure of the mucosal and stool microbiome in Lynch syndrome. Cell Host & Microbe. 2020. PMID: 32240601
Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of the human microbiome. Genome Medicine. 2020. PMID: 27098841
Young C, Wood HM, Seshadri RA, Nang PV, Vaccaro C, Melendez LC, Bose M, Doi MV, Piñero TA, Valladares CT, Arguero J, Balaguer AF, Thompson KN, Yan Y, Huttenhower C, Quirke P. The colorectal cancer (CRC)-associated faecal microbiome of developing countries resembles that of developed countries. Genome Medicine. PMID: 33593386
Young C, Wood HM, Seshadri RA, Nang PV, Vaccaro C, Melendez LC, Bose M, Doi MV, Piñero TA, Valladares CT, Arguero J, Balaguer AF, Thompson KN, Yan Y, Huttenhower C, Quirke P. Microbiome analysis of over 2000 NHS Bowel Cancer Screening Programme (NHSBCSP) samples shows the potential to improve screening accuracy. Clinical Cancer Research. PMID: 33658300
Nguyen LH, Ma W, Wang DD, Cao Y, Mallick H, Gerbaba TK, Lloyd-Price J, Abu-Ali G, Hall AB, Sikavi D, Drew DA, Mehta RS, Arze C, Joshi AD, Yan Y, Branck T, DuLong C, Ivey KL, Ogino S, Rimm EB, Song M, Garrett WS, Izard J, Huttenhower C, Chan AT. Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. Gastroenterology. PMID: 31972239
Sikavi DR, Nguyen LH, Haruki K, Ugai T, Ma WJ, Wang DD, Thompson K, Yan Y, Branck T, Wilkinson J, Akimoto N, Zhong R, Lau MC, Mima K, Kosumi K, Morikawa T, Rimm EB, Garrett WS, Izard J, Cao Y, Song MY, Huttenhower C, Ogino SJ, Chan AT. The sulfur microbial diet and risk of colorectal cancer by molecular subtypes and intratumoral microbial species in adult men. 2021. Clinical and Translational Gastroenterology. PMID: 34333506

The role of microbiome in cancer therapeutic response

Yan Y. The microbial code and cancer immunotherapy outcome. Cell Host & Microbe, 2023. PIMD: 37442095
Ya Wang, Kelsey N. Thompson, Yan Y, Meghan I.Short, Yancong Zhang, Eric A.Franzosa, Jiaxian Shen, Erica M, Hartmann and Curtis Huttenhower. RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities. Microbiome. 2023. PIMD: 37312147
Wang DD, Nguyen LH, Li YP, Yan Y, Ma WJ, Rinott E, Ivey K, Shai I, Willett WC, Hu FB, Eric B. Rimm EB, Stampfer MJ, Chan AT, Huttenhower C. The gut microbiome modifies the protective effects of a Mediterranean diet against cardiometabolic disease risk. Nature Medicine. PMID: 33574608
Spencer C. et al. Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response. Science. PMID: 34941392
Zhang YC, Thompson K, Branck T, Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Metatranscriptomics for the human microbiome and microbial community functional profiling. Annual Review of Biomedical Data Science. PMID: 34465175

Assembly and dynamics of gut microbiome in host ecological microenvironment

Yan Y, Kuramae EE, de Hollander M, Klinkhamer PGL, Van Veen JA. Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere. ISME J. 2017. PMID: 27482928
Yan Y, Klinkhamer PGL, Van Veen JA, Kuramae EE. Environmental filtering: A case of bacterial community assembly in soil. Soil Biology and Biochemistry, Volume 136, September 2019, 107531. Web of science
Yan Y, Kuramae EE, de Hollander M, Klinkhamer PGL, Van Veen JA. Revisiting the dilution procedure used to manipulate microbial biodiversity in terrestrial systems. Applied Environmental Microbiology. 2015. PMID: 25888175
Wang Y, Yan Y, Thompson K, Bae S, Shen JX, Vlamakis H, Hartman EM, Huttenhower C. Characterizing microbial community viability from built environment using propidium monoazide. Microbiome. PMID: 33478576