Yuan Qi, Ph.D.

Principal Statistical Analyst


  • Ph.D. in Computational Biology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX
  • M.A. in Biochemistry, The University of Scranton, Scranton, PA
  • B.S. in Cell Biology and Biophysics, University of Science and Technology of China (USTC), Hefei, China

Areas of Interest

  • Pharmacogenomic analysis
  • Pathway analysis
  • Clinical trial design
  • Survival analysis
  • Multivariate analysis
  • Cancer genomics study and personalized medicine


Shen K, Qi Y, Song N, Tian C, Rice SD, Gabrin MJ, Brower SL, Symmans WF, O'Shaughnessy JA, Holmes FA, Asmar L, Pusztai L. Cell line derived multi-gene predictor of pathologic response to neoadjuvant chemotherapy in breast cancer: a validation study on US Oncology 02-103 clinical trial. BMC Med Genomics. 2012; 5:51.

McGovern SL, Qi Y, Pusztai L, Symmans WF, Buchholz TA. Centromere protein-A, an essential centromere protein, is a prognostic marker for relapse in estrogen receptor-positive breast cancer. Breast Cancer Res. 2012; 14(3):R72.

Dutta B, Pusztai L, Qi Y, André F, Lazar V, Bianchini G, Ueno N, Agarwal R, Wang B, Shiang CY, Hortobagyi GN, Mills GB, Symmans WF,  Balázsi G. A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes. Br J Cancer.  2012; 106:1107–16.

Santarpia L, Qi Y, Stemke-Hale K, Wang B, Young EJ, Booser DJ, Holmes FA, O'Shaughnessy J, Hellerstedt B, Pippen J, Vidaurre T, Gomez H, Valero V, Hortobagyi GN, Symmans WF, Bottai G, Di Leo A, Gonzalez-Angulo AM, Pusztai L. Mutation profiling identifies numerous rare drug targets and distinct mutation patterns in different clinical subtypes of breast cancers. Breast Cancer Res Treat. 2012; 134(1):333–43.

Iwamoto T, Booser D, Valero V, Murray JL, Koenig K, Esteva FJ, Ueno NT, Zhang J, Shi W, Qi Y, Matsuoka J, Yang EJ, Hortobagyi GN, Hatzis C, Symmans WF, Pusztai L. Estrogen receptor (ER) mRNA and ER-related gene expression in breast cancers that are 1% to 10% ER-positive by immunohistochemistry. J Clin Oncol. 2012; 30(7):729–34.

Hess K, Wei C, Qi Y, Iwamoto T, Symmans W, Pusztai L. Lack of sufficiently strong informative features limits the potential of gene expression analysis as predictive tool for many clinical classification problems. BMC Bioinformatics. 2011; 12:463.

Coutant C, Rouzier R, Qi Y, Lehmann-Che J, Bianchini G, Iwamoto T, Hortobagyi GN, Symmans WF, Uzan S, Andre F, de Thé H, Pusztai L. Distinct p53 gene signatures are needed to predict prognosis and response to chemotherapy in ER-positive and ER-negative breast cancers. Clin Cancer Res. 2011; 17:2591–601.

Desmedt C, Azambuja E, Larsimont D, Haibe-Kains B, Selleslags J, Delaloge S, Duhem C, Kains JP, Carly B, Maerevoet M, Vindevoghel A, Rouas G, Lallemand F, Durbecq V, Cardoso F, Salgado R, Rovere R, Bontempi G, Buyse M, Nogaret JM, Qi Y, Symmans F, Pusztai L, D'Hondt V, Leo AD, Piccart-Gebhart M, Sotiriou C.  Multi-factorial approach to predicting sensitivity to anthracyclines. J Clin Oncol. 2011; 29(12):1578–86.

Iwamoto T, Bianchini G, Booser D, Qi Y, Coutant C, Shiang CYH, Santarpia L, Matsuoka J, Hortobagyi GN, Symmans WF, Holmes FA, O’Shaughnessy J, Hellerstedt B, Pippen J, Andre F, Simon R, Pusztai L. Gene pathways associated with prognosis and chemotherapy sensitivity in molecular subtypes of breast cancer. J Natl Cancer Inst. 2011; 103(3):264–72.

Iwamoto T, Bianchini G, Qi Y, Cristofanilli M, Lucci A, Woodward W, Reuben JM, Matsuoka J, Hortobagyi GN, Robertson F, Symmans W, Pusztai L, Ueno NT. Different gene expressions are associated with the different molecular subtypes of inflammatory breast cancer. Breast Cancer Res Treat. 2011; 125(3):785–95.

Bianchini G, Iwamoto T, Qi Y, Coutant C, Shiang C, Wang B, Santarpia L, Valero V, Hortobagyi GN, Symmans WF, Gianni L, Pusztai L. Prognostic and therapeutic implications of distinct kinase expression patterns in different subtypes of breast cancer. Cancer Res. 2010; 70(21):8852–62.

Tabchy A, Valero V, Vidaurre T, Lluch A, Gomez H, Martin M, Qi Y, Barajas-Figueroa LJ, Souchon E, Coutant C, Doimi F, Ibrahim N, Gong Y, Hortobagyi G, Hess K, Symmans F, Pusztai L. Evaluation of a 30-gene paclitaxel, fluorouracil, doxorubicin and cyclophosphamide chemotherapy response predictor in a multicenter randomized trial in breast cancer. Clin Cancer Res. 2010; 16(21):5351–61.

Bianchini G, Qi Y, Alvarez RH, Iwamoto T, Coutant C, Ibrahim NK, Valero V, Cristofanilli M, Green MC, Radvanyi L, Hatzis C, Hortobagyi GN, Andre F, Gianni L, Symmans WF, Pusztai L. Molecular anatomy of breast cancer stroma and its prognostic value in estrogen receptor-positive and -negative cancers. J Clin Oncol. 2010; 28(28):4316–23.

Cabanski CR*, Qi Y*, Yin X, Bair E, Hayward MC, Fan C, Li J, Wilkerson MD, Marron JS, Perou CM, Hayes DN. SWISS MADE: Standardized WithIn Class Sum of Squares to evaluate methodologies and dataset elements. PLoS One. 2010; 5(3):e9905. (*These authors contributed equally to this work.)

Lee JK, Coutant C, Kim YC, Qi Y, Theodorescu D, Symmans WF, Baggerly K, Rouzier R, Pusztai L. Prospective comparison of clinical and genomic multivariate predictors of response to neoadjuvant chemotherapy in breast cancer. Clin Cancer Res. 2010; 16(2):711–8.

Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, Alexe G, Lawrence M, O'Kelly M, Tamayo P, Weir BA, Gabriel S, Winckler W, Gupta S, Jakkula L, Feiler HS,  Hodgson JG, James CD, Sarkaria JN, Brennan C, Kahn A, Spellman PT, Wilson RK, Speed TP, Gray JW, Meyerson M, Getz G, Perou CM, Hayes DN. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010; 17(1):98–110.

Shiang CY, Qi Y, Wang B, Lazar V, Wang J, Symmans WF, Hortobagyi GN, Andre F, Pusztai L. Amplification of fibroblast growth factor receptor-1 in breast cancer and the effects of brivanib alaninate. Breast Cancer Res Treat. 2009; 123(3):747–55.

Cancer Genome Atlas Research Network (including Qi Y). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008; 455(7216):1061–8.

Qi Y, Sadreyev R, Wang Y, Kim B-H, Grishin N. A comprehensive system for evaluation of remote sequence similarity detection. BMC Bioinformatics. 2007; 8(1):314.

Qi Y, Grishin NV. Structural classification of thioredoxin-like fold proteins. Proteins. 2005; 58(2):376–88.

Cheek S, Qi Y, Krishna SS, Kinch LN, Grishin NV. SCOPmap: automated assignment of protein structures to evolutionary superfamilies. BMC Bioinformatics. 2004; 5:197.

Qi Y, Grishin NV. PCOAT: positional correlation analysis using multiple methods. Bioinformatics. 2004; 20(18):3697–9.

Kinch LN, Qi Y, Hubbard TJ, Grishin NV. CASP5 target classification. Proteins. 2003; 53(Suppl 6):340–51.

Kinch LN, Wrabl JO, Krishna SS, Majumdar I, Sadreyev RI, Qi Y, Pei J, Cheng H, Grishin NV. CASP5 assessment of fold recognition target predictions. Proteins. 2003; 53(Suppl 6):395–409.

Qi Y, Pei J, Grishin NV. C-terminal domain of gyrase A is predicted to have a beta-propeller structure. Proteins. 2002; 47(3):258–64.

Patra G, Williams LE, Qi Y, Rose S, Redkar R, Delvecchio VG. Rapid genotyping of Bacillus anthracis strains by real-time polymerase chain reaction. Ann N Y Acad Sci. 2002; 969:106–11.

Abbott JJ, Pei J, Ford JL, Qi Y, Grishin VN, Pitcher LA, Phillips MA, Grishin NV. Structure prediction and active site analysis of the metal binding determinants in gamma–glutamylcysteine synthetase. J Biol Chem. 2001; 276(45):42099–107.

Qi Y, Patra G, Liang X, Williams LE, Rose S, Redkar RJ, DelVecchio VG. Utilization of the rpoB gene as a specific chromosomal marker for real-time PCR detection of Bacillus anthracis. Appl Environ Microbiol. 2001; 67(8):3720–7.


Iwamoto T, Pusztai L, Matsuoka J, Callari M, Kelly CM, Qi Y, MotokiT, Taira N, Santarpia L, Doihara H, Gianni L, Bianchini G. ER+/HER2+ and ER-/HER2+ breast cancers are molecularly distinct but immune gene signatures are prognostic and predictive in both groups. European Society for Medical Oncology Congress, Vienna, Austria, September 2012.

Bianchini G, Pusztai L, Qi Y, Iwamoto T, Kelly CM, Zambetti M, Symmans WF, Gianni L. A dendritic metagene that predicts good prognosis but endocrine resistance in breast cancer. American Society of Clinical Oncology, Chicago, Illinois, June 2012.

Hayashi N, Iwamoto T, Qi Y, Niikura N, Santarpia L, Nakamura S, Hortobagyi GN, Pusztai L, Symmans WF, Ueno NT. Problems with identifying bone metastasis-specific genes without considering biological differences between ER-positive and ER-negative breast cancers. San Antonio Breast Cancer Symposium, December 2011.

Qi Y, Liang H, Liu C, Wang B, Symmans WF, Pusztai L. Reproducibility study of targeted kinome sequencing using SOLiD platform. Biotechnology and Bioinformatics Symposium , Houston, TX, October 2011.

Shiang CY, Qi Y, Iwamoto T, Wang B, Broom BM, Hortobagyi GN, Pusztai L. ApoE and its receptors (LRP8, VLDLR) function as growth signals for triple-negative breast cancer and represent novel therapeutic target. American Association of Cancer Research, Orlando, FL, 2011.

Shen K, Pusztai L, Qi Y, Symmans WF, Song N, Rice SD, Gabrin MJ, Holmes FA, O’Shaughnessy JA. Multi-gene predictors developed from breast cancer cell lines to predict response to chemotherapy: a validation study on US Oncology Study 02-103, CTRC-AACR San Antonio Breast Cancer Symposium, San Antonio, TX, 2010.

Pusztai L, Moulder S, Litton J, Valero V, Ueno N, Melhem-Bertrandt A, Morrow PK, Dotter K, Mattair DN, Strauss L, Qi Y, Hortobagyi GN, Symmans WF. Prospective testing of 3 different gene-signatures for patient selection for dasatinib therapy in metastatic breast cancer, San Antonio Breast Cancer Symposium, San Antonio, TX, 2010.

Santarpia L, Gonzalez-Angulo AM, Qi Y, Stemke-Hale K, Wang B, Booser DJ, Bianchini G, Iawamoto T, Hortobagyi GN, Symmans WF, Leo AD, Pusztai L. Use of mutation profiling of breast cancer using sequenom technology detects distinct mutation patterns in triple-negative compared to receptor-positive cancers, American Society of Clinical Oncology, Chicago, Illinois, 2010.

Pusztai L, Rouzier R, Qi Y, Lehmann-Che J, Bianchini G, Iwamoto T, Symmans WF, Andre F, The HD, Coutant C. Clinical Subtype-Derived p53 Gene Signature Is Predictive of Prognosis and Response to Chemotherapy in ER-Positive but Not in ER-Negative Breast Cancers, San Antonio Breast Cancer Symposium, San Antonio, TX, 2009.

Bianchini G, Alvarez RH, Qi Y, Hatzis C, Iwamoto T, Shiang C, Coutant C, Hortobagyi GN, Symmans WF, Pusztai L. The Molecular Anatomy of Breast Cancer Stroma; Independent Prognostic Role in ER-Positive and ER-Negative Cancers, San Antonio Breast Cancer Symposium, San Antonio, TX, 2009.

Tabchy A, Symmans WF, Valero V, Vidaurre T, Lluch A, Qi Y, Souchon E, Barajas-Figueroa LJ, Gomez H, Martin M, Coutant C, Hess K, Hortobagyi GN, Pusztai L. Evaluation of the Predictive Performance and Regimen Specificity of a 30-Gene Predictor of Pathologic Complete Response in a Prospective Randomized Neoadjuvant Clinical Trial for Stage I-III Breast Cancer, San Antonio Breast Cancer Symposium, San Antonio, TX, 2009.

Bianchini G, Iwamoto T, Qi Y, Shiang Y, Valero V, Hortobagyi GN, Symmans WF, Pusztai L. Prognostic and therapeutic implications of kinase expression patterns in breast cancer, American Society of Clinical Oncology Breast Cancer Symposium, San Francisco, CA, 2009.

Verhaak R, Hoadley K, Purdom E, Wang V, Qi Y, Wilkerson M, Miller C, Ding L, Golub T, Mesirov J, Gupta S, Lawrence M, O'Kelly M, Gabriel S, Winckler W, Alexa G, Kahn A, Spellman P, Wilson R, Speed T, Gray J, Meyerson M, Getz G, Perou C, Hayes N. The Cancer Genome Atlas Research. Reproducible gene expression subtypes of glioblastoma show associations with chromosomal aberrations, gene mutations, and clinical phenotypes, 100th Annual Meeting of American Association of Cancer Research, Denver, CO, 2009.

Shiang CY, Qi Y, Wang J, Pusztai L. Pharmacogenomic Approach to Anti-angiogenic Therapy of Breast Cancer, The Academy of Medicine, Engineering and Science of Texas, Frontiers of Cancer Research Symposium, Houston, TX, March 2009.

Qi Y, Hoadley K, Topal M, Perou C, Hayes D. Parallel microRNA and gene expression profiling of human glioblastomas, American Association of Cancer Research, San Diego, CA, 2008.

Qi Y, Hayes DN. 1-color vs. 2-color Experimental Designs for Gene Expression Microarrays, Scientific Retreat of the Department of Genetics at the University of North Carolina at Chapel Hill, Asheville, NC, September 2007.

Hayes DN, Qi Y, Perou CM, mRNA Expression Profiling of GBM Samples, The Cancer Genome Atlas (TCGA) Pilot Project Steering Committee Meeting by National Cancer Institute and National Human Genome Research Institute of National Institutes of Health, Gaithersburg, MD, July 2007.


American Association for Cancer Research (AACR) Annual Meeting, San Diego, CA, April 2008. “Glioblastoma (GBM) microRNA Profiling and Integrative Analysis with Gene Expression and Copy Number Variation Data.”

UT Southwestern Molecular Biophysics Retreat, Dallas, TX, June 2005. “COMPRASS: A Further Step Towards Structure Modeling And Homology Detection.”

UTSW Biochemistry Research Symposium, New Braunfels, TX, November 2005. “Using Alignments With Predicted Secondary Structure To Detect Structural Similarities From Sequence.”


Updated January 15, 2013