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See here for a complete list of publications.

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Control of Inflammatory Response by Tissue Microenvironment

Wu Z*, Pope SD*, Ahmed NS, Leung DL, Hajjar S, Yue Q, Anand DM, Kopp EB, Okin D, Ma W, Kagan JC, Hargreaves DC, Medzhitov R#, Zhou X#

TBiorxiv. doi:

BRD4-containing transcriptional condensates function as a novel intracellular pH sensing pathway to regulate inflammatory based on severity of inflammation.

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pH sensing at the Intersection of Tissue Homeostasis and Inflammation

Hajjar S, Zhou X

Trends in Immunology. 2023 Oct;44(10):807-825. doi: 10.1016/ Epub 2023 Sep 14.

By expressing various intracellular (pHi) and extracellular pH (pHe)-sensing receptors, the immune system may integrate information on tissue and cellular states into the regulation of homeostatic and inflammatory programs.

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Microenvironmental Sensing by fibroblasts controls tissue composition

Zhou X*, Franklin RA*, Adler M, Carter T, Condiff E, Adams TS, Pope SD, Philip NH, Meizlish ML, Kaminski N, and Medzhitov R.

Proc Natl Acad Sci U S A. 2022 Aug 9;119(32):e2205360119. Epub 2022 Aug 5.

Biorxiv. 2022.

Sensing tissue microenvironment through fibroblast controls population size of macrophages through Hippo-Yap signaling.

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Tissue Homeostasis and Inflammation

Meizlish M*, Franklin R*, Zhou X*, Medzhitov R.


Annual Review Immunology. 2021 Apr 26;39:557-581.

We discuss how tissues are organized from a functional perspective and how this helps understand homeostasis, stress and inflammation at tissue level.

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Principles of Cell Circuits for Tissue Repair and Fibrosis

Adler M, Mayo A, Zhou X, Franklin R, Meizlish M, Medzhitov R, Kallenberger S, Alon U.


iScience. 2020 Feb 21; 23(2).

Myeloid and stromal communication circuitry drives irreversible switch between homeostatic and fibrotic states.

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Siglec-15 As an Immune Suppressor and Potential Target for Normalization Cancer Immunotherapy

Wang J, Sun JW, Liu L, Flies D, Nie XX, Zhang JP, Song C, Zarr M, Zhou X, Han X, Archer K, O’Neill T, Boto A, Chen LP.

Nature Medicine. 2019 Apr; 25(4):565-666.

Myeloid expression of Siglec15 is a  immune suppressor and provides a novel target for cancer immunotherapy.

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Desynchronization of the Molecular Clock Contributes to the Heterogeneity of the Inflammatory Response, 

Allen NC, Philip NH, Hui L, Zhou X, Franklin RA, Kong Y, Medzhitov R.

Science Signaling. 2019 Mar 5; 12(571).

Mammalian circadian clock regulates the the heterogeneity of an inflammatory response at single cell level.

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Adipocyte OGT Governs Diet-Induced Hyperphagia and Obesity,

Li MD, Vera NB, Yang YF, Zhang BC, Ni WM, Ziso-Qejvanaj E, Ding S, Zhang KS, Yin RN, Wang SM, Zhou X, Fang EX, Xu T, Erion DM, Yang XY.

Nature Communications. 2018 Nov 30; 9(1):5103


O-GlcNAc transferase promotes transcriptional activation of de novo lipid desaturation in adipose tissue.

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Circuit Design Features of a Stable Two-cell System

Zhou X*, Franklin RA*, Adler M*, Jacox JB, Bailis W, Shyer JA, Flavell RA, Mayo A, Alon U#, Medzhitov R#.

Cell. 2018 Feb 8; 172(4):744-757.


Growth factor communication cell circuit between macrophages and fibroblast can maintain proper population ratios through feedback mechanisms.

See preview by Nicholas Frankel and Windell lim

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Circuits for Homeostasis of Cell-type Ratios Using Growth-factor Endocytosis as a Feedback Mechanism. 

Adler M, Mayo A, Zhou X, Franklin RA, Jacox JB, Medzhitov R, Alon U.

PNAS. 2018 Feb 20; 115(8):E1926-E1935.

Circuit modeling reveals endocytosis as a general strategy to achieve a stable two-cell system.

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Inflammation-dependent Cerebrospinal Fluid Hypersecretion by the Choroid Plexus Epithelium in Posthemorrhagic Hydrocephalus.

Karimy JK, Zhang J, Kurland DB, Theriault BC, Duran D, Stokum JA, Furey CG, Zhou X, Mansuri MS, Montejo J, Vera A, DiLuna ML, Delpire E, Alper SL, Gunel M, Gerzanich V, Medzhitov R, Simard JM, Kahle KT.

Nature Medicine. 2017 Aug; 23(8):997-1003.

Intraventricular hemorrhage triggers Toll-like receptor 4-dependent inflammatory response in choroid plexus epithelium.

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Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway.

He B, Zhou X, O’Shea EK.

eLife. 2017 May 9;6:e25157.

Rewiring of transcriptional network markedly altered the spectrum of a cellular response.

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A Computational Approach to Map Nucleosome Positions and Alternative Chromatin States with Base Pair Resolution.

Zhou X*, Blocker AW*, Airoldi EM#, O'Shea EK#.

eLife. 2016 Sep 13;5:e16970.

A bayesian template-based model reveals eukaryotic chromatin landscape at base-pair resolution.

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Two-signal Requirement for Growth-promoting Function of Yap in Hepatocytes.

Su T*, Bondar T*, Zhou X, Zhang C, He H, Medzhitov R.

eLife. 2015 Feb 10;4:e02948.

Inflammatory signals synergize with the Hippo-signaling pathway to drive liver cancer.

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Integrated Approaches Reveal Determinants of Genome-wide Binding and Function of the Transcription Factor Pho4.

Zhou X, O’Shea EK.


Molecular Cell. 2011 Jun 1;52(3):318-27.

Specificity of transcription program not only requires DNA sequence, but also involves combinatorial epigenetic mechanisms that include restriction by chromatin, competitive and cooperative binding transcription factors. ​

Featured as cover story


Molecular Cell

June 1st, 2011.

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