Chao Zhang, PhD

Assistant Professor, Boston University Chobanian & Avedisian School of Medicine

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.

Publications

  • Published 4/30/2025

    Zhang 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 Apr 30; e70075. PMID: 40307992.

    Read at: PubMed

  • Published 3/29/2025

    Mathur S, Beauvais M, Giribet A, Barrero NA, Zhang CT, Rahman T, Wang S, Huang J, Nouri N, Kurlovs A, Bar-Joseph Z, Passban P. PyEvoCell: an LLM-augmented single-cell trajectory analysis dashboard. Bioinformatics. 2025 Mar 29; 41(4). PMID: 40209077.

    Read at: PubMed

  • Published 10/16/2023

    Tao 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.

    Read at: PubMed

  • Published 5/10/2021

    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.

    Read at: PubMed

  • Published 1/11/2021

    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.

    Read at: PubMed

Education

  • University of Missouri, PhD
  • University of Missouri, MS
  • University of Missouri, MS
  • Beijing Institute of Technology, BS