Chao Zhang, PhD
Assistant Professor
Boston University Chobanian & Avedisian School of Medicine
Computational Biomedicine

PhD, University of Missouri
MS, University of Missouri
BS, Beijing Institute of Technology
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As an interdisciplinary researcher, I have a background in systems biology, statistics, machine learning, software engineering, and especially in next-generation sequencing analysis, such as ChIP-Seq, WGS, WES, RRBS, RNASeq, ATACSeq, and Single-cell RNA sequencing.

My current researches are focusing on stem cell and cancer genomics.

In collaboration with Dr. Lorenz Studer’s group, I presented the surprising finding that manipulating the nutrient composition of the culture medium can dramatically alter the pluripotent state of hPSC. With the comprehensive analysis of multi-layered molecular data, we demonstrate that lipid-free culture conditions are sufficient to maintain human pluripotent stem cells in a naive-to-primed intermediate state via endogenous ERK inhibition and lipid supplementation can push the cells toward the primed cell state (Cell stem cell, 2019). I also devoted significant effort on aging and neuron degenerative diseases research.

Although studying associations between microbiota and diseases are very popular in the past few years, most studies were limited to the gut microbiome, due to the lack of access to clinical samples and technical challenges to quantify local microbiota, and the functions of them have been simply overlooked and underestimated. I demonstrated a novel computational pipeline to master the challenge of unbiased local microbiome detection from the sequencing data of small clinical endoscopic biopsy (Genome biology, 2015). I collected 50 gastric cancer samples and 106 gastric endoscopy biopsies from non-cancer population, the largest non-cancer gastric genomics study ever conducted. Besides microbiome characterization, I also quantified the immune infiltration for the above samples from bulk and single cell RNASeq data. By integrating multiple layers of data from our samples and TCGA GI-tract studies, I discovered a strong association between expression of immune markers and local microbiome diversity, showing that local microbiome could be very important for shaping tumor microenvironment.

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

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  1. Pan H, Renaud L, Chaligne R, Bloehdorn J, Tausch E, Mertens D, Fink AM, Fischer K, Zhang C, Betel D, Gnirke A, Imielinski M, Moreaux J, Hallek M, Meissner A, Stilgenbauer S, Wu CJ, Elemento O, Landau DA. Discovery of Candidate DNA Methylation Cancer Driver Genes. Cancer Discov. 2021 09; 11(9):2266-2281. PMID: 33972312; PMCID: PMC8419066; DOI: 10.1158/2159-8290.CD-20-1334;
  2. Chen X, Ashoor H, Musich R, Wang J, Zhang M, Zhang C, Lu M, Li S. epihet for intra-tumoral epigenetic heterogeneity analysis and visualization. Sci Rep. 2021 01 11; 11(1):376. PMID: 33432081; PMCID: PMC7801679; DOI: 10.1038/s41598-020-79627-x;
  3. Soyfoo DM, Doomah YH, Xu D, Zhang C, Sang HM, Liu YY, Zhang GX, Jiang JX, Xu SF. New genotypes of Helicobacter Pylori VacA d-region identified from global strains. BMC Mol Cell Biol. 2021 Jan 07; 22(1):4. PMID: 33413074; PMCID: PMC7791883; DOI: 10.1186/s12860-020-00338-2;
  4. Shah MA, Enzinger P, Ko AH, Ocean AJ, Philip PA, Thakkar PV, Cleveland K, Lu Y, Kortmansky J, Christos PJ, Zhang C, Kaur N, Elmonshed D, Galletti G, Sarkar S, Bhinder B, Pittman ME, Plotnikova OM, Kotlov N, Frenkel F, Bagaev A, Elemento O, Betel D, Giannakakou P, Lenz HJ. Multicenter Phase II Study of Cabazitaxel in Advanced Gastroesophageal Cancer: Association of HER2 Expression and M2-Like Tumor-Associated Macrophages with Patient Outcome. Clin Cancer Res. 2020 09 15; 26(18):4756-4766. PMID: 32641434; PMCID: PMC8209413; DOI: 10.1158/1078-0432.CCR-19-3920;
  5. Cederquist GY, Tchieu J, Callahan SJ, Ramnarine K, Ryan S, Zhang C, Rittenhouse C, Zeltner N, Chung SY, Zhou T, Chen S, Betel D, White RM, Tomishima M, Studer L. A Multiplex Human Pluripotent Stem Cell Platform Defines Molecular and Functional Subclasses of Autism-Related Genes. Cell Stem Cell. 2020 07 02; 27(1):35-49.e6. PMID: 32619517; PMCID: PMC7376579; DOI: 10.1016/j.stem.2020.06.004;
  6. Galletti G, Zhang C, Gjyrezi A, Cleveland K, Zhang J, Powell S, Thakkar PV, Betel D, Shah MA, Giannakakou P. Microtubule Engagement with Taxane Is Altered in Taxane-Resistant Gastric Cancer. Clin Cancer Res. 2020 07 15; 26(14):3771-3783. PMID: 32321717; PMCID: PMC7816968; DOI: 10.1158/1078-0432.CCR-19-3018;
  7. Li N, Inoue K, Sun J, Niu Y, Lalani S, Yallowitz A, Yang X, Zhang C, Shen R, Zhao B, Xu R, Greenblatt MB. Osteoclasts are not a source of SLIT3. Bone Res. 2020; 8:11. PMID: 32133214; PMCID: PMC7031526; DOI: 10.1038/s41413-020-0086-3;
  8. Cornacchia D, Zhang C, Zimmer B, Chung SY, Fan Y, Soliman MA, Tchieu J, Chambers SM, Shah H, Paull D, Konrad C, Vincendeau M, Noggle SA, Manfredi G, Finley LWS, Cross JR, Betel D, Studer L. Lipid Deprivation Induces a Stable, Naive-to-Primed Intermediate State of Pluripotency in Human PSCs. Cell Stem Cell. 2019 07 03; 25(1):120-136.e10. PMID: 31155483; PMCID: PMC7549840; DOI: 10.1016/j.stem.2019.05.001;
  9. Zhang C, Thakkar PV, Powell SE, Sharma P, Vennelaganti S, Betel D, Shah MA. A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples. Front Microbiol. 2018; 9:3246. PMID: 30671046; PMCID: PMC6331478; DOI: 10.3389/fmicb.2018.03246;
  10. Xu R, Yallowitz A, Qin A, Wu Z, Shin DY, Kim JM, Debnath S, Ji G, Bostrom MP, Yang X, Zhang C, Dong H, Kermani P, Lalani S, Li N, Liu Y, Poulos MG, Wach A, Zhang Y, Inoue K, Di Lorenzo A, Zhao B, Butler JM, Shim JH, Glimcher LH, Greenblatt MB. Targeting skeletal endothelium to ameliorate bone loss. Nat Med. 2018 06; 24(6):823-833. PMID: 29785024; PMCID: PMC5992080; DOI: 10.1038/s41591-018-0020-z;
Showing 10 of 43 results. Show More

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 43 publications over 14 distinct years, with a maximum of 7 publications in 2014


2014 Google Summer of CodeTM: mentor award
2011-2012 Google Summer of CodeTM: student developer award
2010 University of Missouri, Columbia, MO: Winner of Programming Competition
2008 University of Missouri, Columbia, MO: President of Computer Science Graduate Student Council

Available to Mentor as: (Review Mentor Role Definitions):
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  • Project Mentor
  • Research / Scholarly Mentor
Contact for Mentoring:

72 E. Concord Street
Boston MA 02118
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