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Dr. Yao has a broad background in cancer systems biology, with specific training and expertise in cancer pathway modeling and experimental testing. His Ph.D. training at UW-Madison was in cancer biology with additional emphasis on computational biology. By coupling modeling and experiments, his postdoctoral work at Duke demonstrated the first natural bistable system in mammalian cells, the Rb-E2F bistable switch that controls cell quiescence and proliferation, and help identified oncogenic pathway signatures as a guide to targeted therapies. He focuses his work at studying gene regulation and cell signaling networks by integrating experimental biology with quantitative science, to dissect complex biological systems in cancer.

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Courses
  • GMN
    Genetic and Molecular Networks

  • MG
    Molecular Genetics

  • BFGA
    Bioinformatics and Functional Genomic Analysis

  • ATCB
    Advanced Topics in Cancer Biology

  • TBC
    The Biology of Cancer

Grants
  • Funding agency logo
    Sphingolipids, Dietary Fatty Acids, and Intestinal Pathophysiology

    Co-Investigator (COI)

    2021

    $663.7K
    Active
  • Funding agency logo
    IIBR Instrumentation: All-Reflective Microscope for Biological Research

    Co-Investigator (COI)

    2021

    $466.3K
    Active
  • Funding agency logo
    IIBR Instrumentation: All-Reflective Microscope for Biological Research

    Co-Investigator (COI)

    2021

    $23.0K
    Active
  • Funding agency logo
    IIBR Multidisciplinary: Multiplexed Live Imaging with Hyperspectral Light-Sheet Microscopy

    Co-Investigator (COI)

    2020

    $780.4K
    Active
  • Funding agency logo
    IIBR Multidisciplinary: Multiplexed Live Imaging with Hyperspectral Light-Sheet Microscopy

    Co-Investigator (COI)

    2020

    $185.9K
    Active
  • Funding agency logo
    IDBR: TYPE A: Quantitative Polarization and Phase Microscope for Label-free Imaging of Live Cell and Tissue Dynamics

    Co-Investigator (COI)

    2015

    $613.8K
  • Funding agency logo
    Collaborative Research: Modeling the Coupling of Epigenetic and Transcriptional Regulation

    Principal Investigator (PI)

    2015

    $566.1K
  • Funding agency logo
    Reach: Reading and Assembling Contextual and Holistic Mechanisms From Text

    Co-Investigator (COI)

    2014

    $3.6M
  • Funding agency logo
    Collaborative Research: Semiparametric ODE Models for Complex Gene Regulatory Networks

    Principal Investigator (PI)

    2014

    $164.0K
  • Funding agency logo
    Collaborative Research on Antitumor Effective Components and Mechanisms of Ganoderma Lucidum and Coix Seed Extracts

    Principal Investigator (PI)

    2013

    $146.4K
News
  • Wake-Up Call: Cellular Sleep Isn’t As Harmless As Once Thought

    2019

  • Raising Computers to Be Good Scientists

    2015

  • Grants Support Junior Faculty, Community Outreach Projects

    2011

Publications (49)
Recent
  • Identifying Strong Modulators of Cellular Quiescence Depth Across Different Quiescent Cells and Conditions

    2022

  • Temporal Associations of Plasma Levels of the Secreted Phospholipase A2 Family and Mortality in Severe COVID-19

    2022

  • PB1992: HISPANIC ETHNICITY AS A STRONG PREDICTOR OF POOR RESPONSE TO INDUCTION THERAPY AND ASCT IN TRANSPLANT ELIGIBLE MULTIPLE MYELOMA PATIENTS

    2022

  • Cellular dormancy—State determination and plasticity

    2022

  • Group IIA Secreted Phospholipase A2 Plays a Central Role in the Pathobiology of COVID-19 (preprint)

    2021

  • Cellular Dormancy: State Determination and Plasticity

    2021

  • Extracellular Fluid Flow Induces Shallow Quiescence through Physical and Biochemical Cues

    2021

  • Group IIA Secreted Phospholipase A2 Plays a Central Role in the Pathobiology of COVID-19

    2021

  • Circadian Proteins Cry and Rev-erb Deepen Cellular Quiescence by Down-regulating Cyclin D and Cdk4, 6

    2021

  • Group IIA secreted phospholipase A2 is associated with the pathobiology leading to COVID-19 mortality

    2021

  • Quantifying E2F1 protein dynamics in single cells

    2020

  • Cell dormancy plasticity: quiescence deepens into senescence through a dimmer switch

    2020

  • Curcumin derivative C212 inhibits Hsp90 and eliminates both growing and quiescent leukemia cells in deep dormancy

    2020

  • Spatial clustering and common regulatory elements correlate with coordinated gene expression

    2019

  • Multi-wavelength quantitative polarization and phase microscope

    2019

  • ATP-Dependent Dynamic Protein Aggregation Regulates Bacterial Dormancy Depth Critical for Antibiotic Tolerance

    2018

  • Crack the state of silence: tune the depth of cellular quiescence for cancer therapy

    2018

  • Graded regulation of cellular quiescence depth between proliferation and senescence by a lysosomal dimmer switch

    2018

  • Study Quiescence Heterogeneity by Coupling Single-Cell Measurements and Computer Modeling

    2018

  • Controlling depth of cellular quiescence by an Rb-E2F network switch

    2017

  • Exit from quiescence displays a positional growth memory

    2017

  • Exit from quiescence displays a memory of cell growth and division

    2017

  • Expression level is a key determinant of E2F1-mediated cell fate

    2017

  • Controlling depth of cellular quiescence by an Rb-E2F bistable switch

    2017

  • Antitumor effects and mechanisms of Ganoderma extracts and spores oil

    2016

  • Elimination of quiescent slow-cycling cells via reducing quiescence depth by natural compounds purified from Ganoderma Lucidum

    2016

  • Ovarian serous carcinogenesis from tubal secretory cells

    2015

  • Linear population allocation by bistable switches in response to transient stimulation

    2014

  • Modelling mammalian cellular quiescence

    2014

  • Systematic reverse engineering of network topologies: A case study of resettable bistable cellular responses

    2014

  • IMP3 signatures of fallopian tube: a risk for pelvic serous cancers

    2014

  • Tubal origin of ovarian low-grade serous carcinoma

    2013

  • Origin of bistability underlying mammalian cell cycle entry

    2011

  • Using noisy gene expression mediated by engineered adenovirus to probe signaling dynamics in mammalian cells

    2011

  • Viral-Mediated Noisy Gene Expression Reveals Biphasic E2f1 Response to MYC

    2011

  • Stochastic E2F activation and reconciliation of phenomenological cell-cycle models

    2010

  • Anchorage-independent cell growth signature identifies tumors with metastatic potential

    2009

  • Sensing and integration of Erk and PI3K signals by Myc

    2008

  • A bistable Rb-E2F switch underlies the restriction point

    2008

  • Utilization of pathway signatures to reveal distinct types of B lymphoma in the Emicro-myc model and human diffuse large B-cell lymphoma

    2008

  • Oncogenic pathway signatures in human cancers as a guide to targeted therapies

    2006

  • Gene expression signatures for oncogenic pathway deregulation

    2006

  • DIG--a system for gene annotation and functional discovery

    2005

  • Sparse graphical models for exploring gene expression data

    2004

  • GraphExplore: a software tool for network visualization

    2004

  • Interaction networks in yeast define and enumerate the signaling steps of the vertebrate aryl hydrocarbon receptor

    2004

  • The Ah Receptor

    2003

  • Understanding the Ah receptor regulatory network

    2002

  • Cross-talk between the aryl hydrocarbon receptor and hypoxia inducible factor signaling pathways - Demonstration of competition and compensation

    1999

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