Chao Zhang PhD
Assistant Professor, Computational Biomedicine
72 E. Concord Street | (617) 358-8535chz2009@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
Lu SL, Karkempetzaki AI, Huang N, Zhang C, Murphy GJ, Ravid K. Hematopoietic JAK2V617F Mutation-Induced Reprograming of Blood and Bone Marrow Megakaryocytes. Blood Adv. 2026 Feb 18. PMID: 41707101.
Published on 12/5/2025Jose A, Lu S, Zhang C, La J, Young M, Gaziano JM, Fillmore NR, Ravid K, Chitalia VC. A panel of plasma proteins associated with venous thromboembolism in patients with prostate cancer. Cancer Biomark. 2025 Dec; 42(12):18758592251390251. PMID: 41348521.
Published on 11/24/2025Vitantonio AT, Dimovasili C, Liu Y, Ye B, Lee JR, Hartigan M, Bouchard B, Ray M, Conner B, Vaughan KL, Mattison JA, Moore TL, Zhang C, Rosene DL. Calorie Restriction Attenuates Transcriptional Aging Signatures in White Matter Oligodendrocytes and Immune Cells of the Monkey Brain. Aging Cell. 2026 Jan; 25(1):e70298. PMID: 41283828.
Published on 11/3/2025Fukuda Y, Zhang C, Ksander BR, Jo VY, Lian CG, Murphy GF, Frank MH, Frank NY, Sasamoto Y. MYEOV Is a Novel Marker of Differentiated Corneal Epithelium. Invest Ophthalmol Vis Sci. 2025 Nov 03; 66(14):7. PMID: 41186354.
Published on 10/24/2025Moore SPG, Zou A, Zhang X, Jonathan OC, Lang D, Zhang C. VaMiAnalyzer: an open source, Python-based application for analysis of 3D in vitro vasculogenic mimicry assays. BMC Bioinformatics. 2025 Oct 24; 26(1):263. PMID: 41136932.
Published on 9/10/2025Oberst P, Xu N, Munguba H, Zhang C, Zhong A, Zhou T, Liston C, Levitz J, Studer L. Environmental and genetic risk factors of depression converge on neuronal dysfunction driven by changes in cholesterol homeostasis. Dev Cell. 2026 Jan 14; 61(1):102-116.e6. PMID: 40934929.
Published on 8/2/2025Raut 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, 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.