Yu “Max” Qian, PhD

Associate Professor



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Dr. Yu “Max” Qian is an associate professor at the J. Craig Venter Institute (JCVI). He specializes in single cell cytometry informatics. He received his Ph.D. degree in Computer Science from the University of Texas at Dallas (UT Dallas) in 2006, and an M.E. and a B.S. degree in Computer Science from Nanjing University, in 2001 and 1998, respectively. After Ph.D. graduation, he joined the University of Texas Southwestern Medical Center at Dallas (UT Southwestern) as a postdoctoral senior research associate, where he was trained on immunology informatics, bioinformatics, and clinical informatics. He was appointed as an assistant professor of Department of Clinical Sciences and Department of Pathology of UT Southwestern in 2010. Before joining JCVI in 2013, he was leading the natural language processing project at the Parkland Center for Clinical Innovation (PCCI), Parkland Health and Hospital System at Dallas on real-time disease identification for re-admission reduction.

As an informatics researcher, Dr. Qian leads and co-develops a suite of standards, models, algorithms, and software systems for computational cytometry data analysis, including FLOCK/ImmPort FLOCK, FCSTrans, FuGEFlow, MIFlowCyt, and GenePattern FCM suite. These systems have been used by informatics researchers and immunologists to improve the management of experiment metadata, explore cellular phenotypic profiles, identify novel cell subsets, and quantify immune responses to clinical treatments. Collaborating with UC San Diego, Stanford, UC Irvine, and San Diego Supercomputer Center, he is leading the technical development of a computational infrastructure for improving precision diagnostics of certain types of blood cancers through identifying cell-based biomarkers from polychromatic flow cytometry (FCM) experiment data. He was one of the previous leading developers of the FCM component of ImmPort, the NIAID/DAIT-funded immunology database and analysis portal. He has been customizing analytical pipelines and performing computational analytics of big FCM data for multiple NIH-funded research projects, including the Respiratory Pathogens Research Center (RPRC) at University of Rochester and the Human Immunology Project Consortium (HIPC) center at La Jolla Institute for Allery and Immunology. Besides research and development activities, Dr. Qian had been a teaching assistant of UT Dallas for Computer Science classes on computer graphics, machine learning and natural language processing, software architecture, and computer architecture. He had also taught classes at the Pathology Department of UT Southwestern on applied bioinformatics and DNA microarray data analysis.

Research Priorities

  • Computational methods for single cell flow, imaging, and mass cytometry data processing and analysis
  • Design and implementation of cyberinfrastructures for immunology data management and analysis
  • Integration of cytometry and RNA-seq data for cell type specific gene expression profiling
  • Text mining and data classification methods for disease identification from clinical notes
  • Computational methods to automatically scrub protected health information from clinical notes
  • Graph-based management and exploration of cell type knowledge for biomarker discovery


  • Patent US9147041 B2: Clinical dashboard user interface system and method, Parkland Center for Clinical Innovation, with Amarasingham R., et al., filed on 13 Sept 2012, granted on 29 Sept 2015.
  • Patent US9536052 B2: Clinical predictive and monitoring system and method, Parkland Center for Clinical Innovation, with Amarasingham R., et al., filed on 13 Sept 2012, granted on 03 Jan 2017.


Select Publications

Allergen-specific immunotherapy modulates the balance of circulating Tfh and Tfr cells.
The Journal of allergy and clinical immunology. 2017-05-12;
PMID: 28506846
An Integrated Workflow To Assess Technical and Biological Variability of Cell Population Frequencies in Human Peripheral Blood by Flow Cytometry.
Journal of immunology (Baltimore, Md. : 1950). 2017-02-15; 198.4: 1748-1758.
PMID: 28069807
Automated Analysis of Flow Cytometry Data to Reduce Inter-Lab Variation in the Detection of Major Histocompatibility Complex Multimer-Binding T Cells.
Frontiers in immunology. 2017-01-01; 8.858.
PMID: 28798746
A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.
Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2016-01-01; 89.1: 16-21.
PMID: 26447924
Mapping cell populations in flow cytometry data for cross-sample comparison using the Friedman-Rafsky test statistic as a distance measure.
Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2016-01-01; 89.1: 71-88.
PMID: 26274018
GenePattern flow cytometry suite.
Source code for biology and medicine. 2013-07-03; 8.1: 14.
PMID: 23822732
Critical assessment of automated flow cytometry data analysis techniques.
Nature methods. 2013-03-01; 10.3: 228-38.
PMID: 23396282
FCSTrans: an open source software system for FCS file conversion and data transformation.
Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2012-05-01; 81.5: 353-356.
PMID: 22431383
Advances in human B cell phenotypic profiling.
Frontiers in immunology. 2012-01-01; 3.302.
PMID: 23087687
Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data.
Cytometry. Part B, Clinical cytometry. 2010-01-01; 78 Suppl 1.S69-82.
PMID: 20839340
FuGEFlow: data model and markup language for flow cytometry.
BMC bioinformatics. 2009-06-16; 10.184.
PMID: 19531228