Chao Zhang | Profiles RNS

Chao Zhang, PhD

Assistant Professor

Boston University Chobanian & Avedisian School of Medicine

Medicine

Computational Biomedicine

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

Websites

ORCID : 0000-0001-8019-7998

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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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.View Related Profiles.

Taylor, Andrew
Zhang, Chao
Mercier, Gustavo
Mez, Jesse
Lunetta, Kathryn
Farrer, Lindsay
Alosco, Michael
Tao, Qiushan
Au, Rhoda
Ang, Ting Fang Alvin

PMID: 37854772; DOI: 10.1002/dad2.12490;

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; DOI: 10.1158/2159-8290.CD-20-1334;

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; DOI: 10.1038/s41598-020-79627-x;

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; DOI: 10.1186/s12860-020-00338-2;

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; DOI: 10.1158/1078-0432.CCR-19-3920;

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; DOI: 10.1016/j.stem.2020.06.004;

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; DOI: 10.1158/1078-0432.CCR-19-3018;

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; DOI: 10.1038/s41413-020-0086-3;

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; DOI: 10.1016/j.stem.2019.05.001;

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; DOI: 10.3389/fmicb.2018.03246;

Showing 10 of 44 results. Show More

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; DOI: 10.1038/s41591-018-0020-z;

Wang Q, Armenia J, Zhang C, Penson AV, Reznik E, Zhang L, Minet T, Ochoa A, Gross BE, Iacobuzio-Donahue CA, Betel D, Taylor BS, Gao J, Schultz N. Unifying cancer and normal RNA sequencing data from different sources. Sci Data. 2018 04 17; 5:180061. PMID: 29664468; DOI: 10.1038/sdata.2018.61;

Xu R, Zhang C, Shin DY, Kim JM, Lalani S, Li N, Yang YS, Liu Y, Eiseman M, Davis RJ, Shim JH, Greenblatt MB. c-Jun N-Terminal Kinases (JNKs) Are Critical Mediators of Osteoblast Activity In Vivo. J Bone Miner Res. 2017 Sep; 32(9):1811-1815. PMID: 28561373; DOI: 10.1002/jbmr.3184;

Huang LY, Wang X, Cui XF, Li H, Zhao J, Wu CC, Min L, Zhou Z, Wan L, Wang YP, Zhang C, Gao WQ, Sun Y, Han ZG. IRTKS is correlated with progression and survival time of patients with gastric cancer. Gut. 2018 08; 67(8):1400-1409. PMID: 28647685; DOI: 10.1136/gutjnl-2016-313478;

Sartaj R, Zhang C, Wan P, Pasha Z, Guaiquil V, Liu A, Liu J, Luo Y, Fuchs E, Rosenblatt MI. Characterization of slow cycling corneal limbal epithelial cells identifies putative stem cell markers. Sci Rep. 2017 06 19; 7(1):3793. PMID: 28630424; DOI: 10.1038/s41598-017-04006-y;

Wong KG, Ryan SD, Ramnarine K, Rosen SA, Mann SE, Kulick A, De Stanchina E, Müller FJ, Kacmarczyk TJ, Zhang C, Betel D, Tomishima MJ. CryoPause: A New Method to Immediately Initiate Experiments after Cryopreservation of Pluripotent Stem Cells. Stem Cell Reports. 2017 07 11; 9(1):355-365. PMID: 28602613; DOI: 10.1016/j.stemcr.2017.05.010;

Zhang C, Powell SE, Betel D, Shah MA. The Gastric Microbiome and Its Influence on Gastric Carcinogenesis: Current Knowledge and Ongoing Research. Hematol Oncol Clin North Am. 2017 06; 31(3):389-408. PMID: 28501083; DOI: 10.1016/j.hoc.2017.01.002;

Rizzo V, Touzani K, Raveendra BL, Swarnkar S, Lora J, Kadakkuzha BM, Liu XA, Zhang C, Betel D, Stackman RW, Puthanveettil SV. Encoding of contextual fear memory requires de novo proteins in the prelimbic cortex. Biol Psychiatry Cogn Neurosci Neuroimaging. 2017 Mar; 2(2):158-169. PMID: 28503670; DOI: 10.1016/j.bpsc.2016.10.002;

Wang Q, Zou Y, Nowotschin S, Kim SY, Li QV, Soh CL, Su J, Zhang C, Shu W, Xi Q, Huangfu D, Hadjantonakis AK, Massagué J. The p53 Family Coordinates Wnt and Nodal Inputs in Mesendodermal Differentiation of Embryonic Stem Cells. Cell Stem Cell. 2017 01 05; 20(1):70-86. PMID: 27889317; DOI: 10.1016/j.stem.2016.10.002;

Zhang H, Li Y, Liu Y, Liu H, Wang H, Jin W, Zhang Y, Zhang C, Xu D. Role of plant MicroRNA in cross-species regulatory networks of humans. BMC Syst Biol. 2016 08 08; 10(1):60. PMID: 27502923; DOI: 10.1186/s12918-016-0292-1;

Jin J, Kim SN, Liu X, Zhang H, Zhang C, Seo JS, Kim Y, Sun T. miR-17-92 Cluster Regulates Adult Hippocampal Neurogenesis, Anxiety, and Depression. Cell Rep. 2016 08 09; 16(6):1653-1663. PMID: 27477270; DOI: 10.1016/j.celrep.2016.06.101;

Zhang C, Wang J, Zhang C, Liu J, Xu D, Chen L. Network stratification analysis for identifying function-specific network layers. Mol Biosyst. 2016 Apr; 12(4):1232-40. PMID: 26879865; DOI: 10.1039/c5mb00782h;

Zhang C, Cleveland K, Schnoll-Sussman F, McClure B, Bigg M, Thakkar P, Schultz N, Shah MA, Betel D. Identification of low abundance microbiome in clinical samples using whole genome sequencing. Genome Biol. 2015 Nov 27; 16:265. PMID: 26614063; DOI: 10.1186/s13059-015-0821-z;

He Z, Zhang C, Xu Y, Zeng S, Zhang J, Xu D. MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis. BMC Genomics. 2014; 15 Suppl 11:S2. PMID: 25559128; DOI: 10.1186/1471-2164-15-S11-S2;

Yu D, Zhang C, Qin P, Cornish PV, Xu D. RNA-protein distance patterns in ribosomes reveal the mechanism of translational attenuation. Sci China Life Sci. 2014 Nov; 57(11):1131-9. PMID: 25326828; DOI: 10.1007/s11427-014-4753-8;

Li S, Garrett-Bakelman F, Perl AE, Luger SM, Zhang C, To BL, Lewis ID, Brown AL, D'Andrea RJ, Ross ME, Levine R, Carroll M, Melnick A, Mason CE. Dynamic evolution of clonal epialleles revealed by methclone. Genome Biol. 2014 Sep 27; 15(9):472. PMID: 25260792; DOI: 10.1186/s13059-014-0472-5;

Xu C, Ju X, Song D, Huang F, Tang D, Zou Z, Zhang C, Joshi T, Jia L, Xu W, Xu KF, Wang Q, Xiong Y, Guo Z, Chen X, Huang F, Xu J, Zhong Y, Zhu Y, Peng Y, Wang L, Zhang X, Jiang R, Li D, Jiang T, Xu D, Jiang C. An association analysis between psychophysical characteristics and genome-wide gene expression changes in human adaptation to the extreme climate at the Antarctic Dome Argus. Mol Psychiatry. 2015 Apr; 20(4):536-44. PMID: 25199918; DOI: 10.1038/mp.2014.72;

Gao J, Zhang C, van Iersel M, Zhang L, Xu D, Schultz N, R Pico A. BridgeDb app: unifying identifier mapping services for Cytoscape. F1000Res. 2014; 3:148. PMID: 25110584; DOI: 10.12688/f1000research.4521.1;

Pollock A, Bian S, Zhang C, Chen Z, Sun T. Growth of the developing cerebral cortex is controlled by microRNA-7 through the p53 pathway. Cell Rep. 2014 May 22; 7(4):1184-96. PMID: 24813889; DOI: 10.1016/j.celrep.2014.04.003;

Li J, Lao X, Zhang C, Tian L, Lu D, Xu S. Increased genetic diversity of ADME genes in African Americans compared with their putative ancestral source populations and implications for pharmacogenomics. BMC Genet. 2014 May 01; 15:52. PMID: 24884825; DOI: 10.1186/1471-2156-15-52;

Shen Z, Duan C, Zhang C, Carson A, Xu D, Zheng G. Using an intervening sequence of Faecalibacterium 16S rDNA to identify poultry feces. Water Res. 2013 Oct 15; 47(16):6415-22. PMID: 24011842; DOI: 10.1016/j.watres.2013.08.013;

Wang H, He Z, Zhang C, Zhang L, Xu D. Transmembrane protein alignment and fold recognition based on predicted topology. PLoS One. 2013; 8(7):e69744. PMID: 23894534; DOI: 10.1371/journal.pone.0069744;

Zhang C, Wang J, Hanspers K, Xu D, Chen L, Pico AR. NOA: a cytoscape plugin for network ontology analysis. Bioinformatics. 2013 Aug 15; 29(16):2066-7. PMID: 23749961; DOI: 10.1093/bioinformatics/btt334;

Liu Y, Chang Y, Zhang C, Wei Q, Chen J, Chen H, Xu D. Influence of mRNA features on siRNA interference efficacy. J Bioinform Comput Biol. 2013 Jun; 11(3):1341004. PMID: 23796181; DOI: 10.1142/S0219720013410047;

Yu D, Zhang C, Wang H, Qin P. Characterization of the weak calcium binding of trimeric globular adiponectin. Cell Biochem Funct. 2013 Jun; 31(4):338-43. PMID: 23023478; DOI: 10.1002/cbf.2906;

Wang H, Zhang C, Shi X, Zhang L, Zhou Y. Improving transmembrane protein consensus topology prediction using inter-helical interaction. Biochim Biophys Acta. 2012 Nov; 1818(11):2679-86. PMID: 22683598; DOI: 10.1016/j.bbamem.2012.05.030;

Zhang C, Xu S, Xu D. Risk assessment of gastric cancer caused by Helicobacter pylori using CagA sequence markers. PLoS One. 2012; 7(5):e36844. PMID: 22615823; DOI: 10.1371/journal.pone.0036844;

Zhang C, Hanspers K, Kuchinsky A, Salomonis N, Xu D, Pico AR. Mosaic: making biological sense of complex networks. Bioinformatics. 2012 Jul 15; 28(14):1943-4. PMID: 22576176; DOI: 10.1093/bioinformatics/bts278;

Lin GN, Zhang C, Xu D. Polytomy identification in microbial phylogenetic reconstruction. BMC Syst Biol. 2011; 5 Suppl 3:S2. PMID: 22784621; DOI: 10.1186/1752-0509-5-S3-S2;

Xu S, Zhang C, Miao Y, Gao J, Xu D. Effector prediction in host-pathogen interaction based on a Markov model of a ubiquitous EPIYA motif. BMC Genomics. 2010 Dec 01; 11 Suppl 3:S1. PMID: 21143776; DOI: 10.1186/1471-2164-11-S3-S1;

Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol. 2008; 9 Suppl 1:S2. PMID: 18613946; DOI: 10.1186/gb-2008-9-s1-s2;

Joshi T, Zhang C, Lin GN, Song Z, Xu D. GeneFAS: A tool for prediction of gene function using multiple sources of data. Methods Mol Biol. 2008; 439:369-86. PMID: 18370116; DOI: 10.1007/978-1-59745-188-8_25;

Zhang C, Joshi T, Lin GN, Xu D. An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data. Int J Comput Biol Drug Des. 2008; 1(3):254-74. PMID: 20054992; DOI: 10.1504/ijcbdd.2008.021418;

Song Z, Chen L, Zhang C, Xu D. Design and implementation of probability-based scoring function for peptide mass fingerprinting protein identification. Conf Proc IEEE Eng Med Biol Soc. 2006; 2006:4556-9. PMID: 17946250; DOI: 10.1109/IEMBS.2006.260150;

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

Bar chart showing 44 publications over 15 distinct years, with a maximum of 7 publications in 2014