Chao Zhang PhD
Assistant Professor, Computational Biomedicine
72 E. Concord Street | (573) 289-3632chz2009@bu.edu
Sections
Computational Biomedicine
Biography
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.
Education
Computer Science, PhD, University of Missouri
Statistics, MS, University of Missouri
Computer Science, MS, University of Missouri
Automation, BS, Beijing Institute of Technology
Publications
Raut RD, Chakraborty AK, Neogi T, Albro M, Snyder B, Schaer TP, Zhang C, Grinstaff MW, Bais MV. A multi-tissue human knee single-cell atlas identifies that osteoarthritis reduces regenerative tissue stem cells while increasing inflammatory pain macrophages. Commun Biol. 2025 Aug 02; 8(1):1146. PMID: 40753276.
Published on 5/14/2025Moore SPG, Zhang X, Jonathan OC, Zou A, Lang D, Zhang C. VaMiAnalyzer: An open source, python-based application for analysis of 3D in vitro vasculogenic mimicry assays. bioRxiv. 2025 May 14. PMID: 40463128.
Published on 5/14/2025Moore SPG, Ganesh Krishnan S, Jaswanth Kothari R, Prince NB, Kenny C, Zhang C, Lang D. PAX3 Regulatory Signatures and Gene Targets in Melanoma Cells. Genes (Basel). 2025 May 14; 16(5). PMID: 40428399.
Published on 4/30/2025Zhang C, Saurat N, Cornacchia D, Chung SY, Sikder T, Nemchik A, Minotti A, Studer L, Betel D. Identifying Age-Modulating Compounds Using a Novel Computational Framework for Evaluating Transcriptional Age. Aging Cell. 2025 Jul; 24(7):e70075. PMID: 40307992.
Published on 3/28/2025Laudon A, Wang Z, Zou A, Sharma R, Ji J, Tan W, Kim C, Qian Y, Ye Q, Chen H, Henderson JM, Zhang C, Kolachalama VB, Lu W. Digital pathology assessment of kidney glomerular filtration barrier ultrastructure in an animal model of podocytopathy. Biol Methods Protoc. 2025; 10(1):bpaf024. PMID: 40223818.
Published on 9/14/2024Zhang Z, Lin W, Gan Q, Lei M, Gong B, Zhang C, Henrique JS, Han J, Tian H, Tao Q, Potempa LA, Stein TD, Emili A, Qiu WQ. The influences of ApoE isoforms on endothelial adherens junctions and actin cytoskeleton responding to mCRP. Angiogenesis. 2024 Nov; 27(4):861-881. PMID: 39276310.
Published on 10/16/2023Tao Q, Zhang C, Mercier G, Lunetta K, Ang TFA, Akhter-Khan S, Zhang Z, Taylor A, Killiany RJ, Alosco M, Mez J, Au R, Zhang X, Farrer LA, Qiu WWQ. Identification of an APOE e4-specific blood-based molecular pathway for Alzheimer's disease risk. Alzheimers Dement (Amst). 2023; 15(4):e12490. PMID: 37854772.
Published on 2/13/2023Zhou P, Lu SL, Chang L, Liao B, Cheng M, Xu X, Sui X, Liu F, Zhang M, Wang Y, Yang R, Li R, Pan H, Zhang C. The pan-cancer landscape of abnormal DNA methylation and intratumor microorganisms. Neoplasia. 2023 Mar; 37:100882. PMID: 36791577.
Published on 5/10/2021Pan 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.
Published on 1/11/2021Chen 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.