Position: Home > Members > Visiting > Xiaojie Qiu




Institute for Systems Biology

401 Terry Avenue North

Seattle, WA 98109-5234

Phone: (206) 732-216

       E-mail:  xqiu@systemsbiology.org



Developmental and evolutionary systems biology


Academic Experiences and Education


Research Staff (Supervisor: Prof. Sui Huang), Institute for Systems Biology (ISB, Seattle)          Jan. 2012-

Ø  Investigating evo-devo (development recapitulates evolution) by asynchronous threshold network

Ø  Studying development and carcinogenesis by non-equilibrium statistical physics


Research Intern (Supervisor: Prof. Ping Ao), Shanghai Jiaotong Univeristy (STJU, Shanghai)       Sep. 2011-Jun. 2012

Ø  Constructing the first two-step development landscape for central nervous system development



Scholarship & Certificate

Ø  Distinguished Student Fellowship (three years in a row, ECNU)


Ø  Workshop in Advanced Biostatistics (Vanderbilt U. & STJU)                                                               2011-2010

Ø  Academic Quantification on Data Mining and Data Warehouse (IBM)


Ø  Second Prize of Mathematical Modeling in Northeast China (CCUT)

Ø  First Prize of Glory Mother Writing Competition (CCUT, Poem, Mother)




Publication & Research Experience

    Theoretical modeling on topics of development, reprogramming as well as evo-devo                  Jun.2010-

Book Chapter: Review discrete models used in systems biology   ISB, (In preparation, Joseph.Xu. Zhou, Aymeric F. d'Herouel, Xiaojie Qiu, Sui Huang, Computational Systems Biology, Academic Press)

Ø  Formulism, application of threshold, Boolean, neural network, etc.

Ø  Recent developments in discrete models for understanding the development, metabolism and evolution in systems biology

Ø  Advantages and limitations of discrete models and continual models like the Hill equations and master equation, etc.

Theoretical models over development and reprogramming: from Boolean network to stochastic simulation and to landscape construction       

ISB, (In preparation, Xiaojie Q, Shanshan D., Tieliu S., Invited Review, Science China Life Sciences)

Ø  A hierarchical, complete review over the coarse-grained models and detail models for understanding development and reprogramming

Recent theoretical developments in stochastic process, Markov chain on constructing the influential Waddington’s epigenetic landscape” and quantifying its dynamics



From understanding the development landscape of the canonical fate-switch pair to constructing a dynamic landscape for two-step neural differentiation    ECNU and STJU, (Xiaojie Q, Shanshan D, Tieliu S. PLoS one, 2012)

Ø  New findings in entropy evolution, noise effects and dominant transdifferentiation paths over development landscape of fate determination gene-pairs

Ø  Modeled the dynamics during development, reprogramming processes and firstly tested the optimal strategy for reprogramming

Ø  Constructed the first two-step “development landscape” and quantified the dominant paths for central nervous system development                             

A dynamic network of transcription during A. Thaliana pollen development                 May 2011-Oct. 2011

Ø  Utilized the Network Component Analysis (NCA) to decipher the regulatory activation of TFs over target genes

Ø  Constructed the first stage-specific dynamic regulatory network for A. Thaliana pollen development              

ECNU, (Jigang Wang, Xiaojie Qiu, Yuhua Li, Youping Deng and Tieliu Shi, BMC Sys. Bio., 2011, Citation: 1)

Transcription regulatory mechanisms governing the PGCs development and EOPD            Jan. 2010-Jun. 2010

Ø  Collected regulatory relationship for Primordia Germ Cells (PGCs) development

Ø  Analyzed microarray datasets using Bioconductor package of R, and mapped the dynamic network underling PGCs development

Ø  Constructed the interface-friendly database of EOPD

ECNU, (Website Address: http://www.megabionet.org/eopd/)

HCCNet: an integrated network database of hepatocellular carcinoma (HCC)                Jun. 2009-Sep. 2010

Ø  Collected experimental confirmed mechanisms for HCC genesis and development in different stages

Ø  Constructed the database and analyzed the time evolution network of HCC development

  ECNU, (Bing H., Xiaojie Q., Peng L., Lishan W., Qi L. and Tieliu S., Cell Research, 2010, Citation: 6)


Important Talks


Ø  Using threshold network to model evo-devo                                                                            Oct. 8st, 2012

Institute for Systems Biology, Prof. Sui Huang’s lab                                        (Research talk)

Ø  Evolution of functional specialization and division of labor                                                    Mar. 25th, 2012

Shanghai Jiaotong University, Shanghai Center for Systems Biomedicine                    (Literature review)

Ø  A Hierarchical Modeling based on Waddington Landscape for CNS Development                   Feb. 15st, 2012

University of Washington, Department of Bioengineer, Prof. Herbert Sauro’s lab              (Research talk)



Academic Abilities


Computational and modeling skills

Ø  Linux system operation and LaTex for scientific documentation

Ø  Software and languages for modeling: DDLab, Matlab,Vcell, XPPAU, R, Perl, PHP, SQL, etc.

Ø  Modeling skills for development, reprogramming and evolution problems: Random Boolean Network, Dynamic System, Stochastic Simulation, Nonequilibrium Statistical Physics and Stochastic Process

Ø  Bioinformatics capabilities: Gene Ontology, Pathway annotation and enrichment analysis, Database construction by using HTML, CSS, PHP and SQL, Network Component Analysis and other dimension reduction methods, etc.

Lab skills: PCR, DNA extraction, protein purification, HPLC, gel dialysis, vector construction, RAPD, etc.


Personal Interests:

Ø  Play violin and enjoy classic music

Ø  Write poetry and read philosophy, etc.

Ø  Cycling, running and body building


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