Journal Publications: (Google Scholar Profile)

  1. Kirsten Parratt, Jenny Jeong, Peng Qiu, Krishnendu Roy, "3D Material Cytometry (3DMaC): A Very High-replicate, High-throughput Analytical Method using Microfabricated, Shape-specific, Cell-material Niches", Lap on a Chip, accepted, 2017.

  2. Peng Qiu, "Toward robust and automated SPADE analysis for single-cell data", Cytometry Part A, 91(3):281-289, 2017.

  3. Dyana T. Saenz, Warren Fiskus, Yimin Qian, Taghi Manshouri, Kimal Rajapakshe, Kanak Raina, Kevin G. Coleman, Andrew P. Crew, Angela Shen, Christopher P. Mill, Baohua Sun, Peng Qiu, Tapan Kadia, Naveen Pemmaraju, Courtney DiNardo, Mi-Sun Kim, Agnieszka Nowak, Cristian Coarfa, Craig M. Crews, Srdan Verstovsek, Kapil N. Bhalla, "Novel BET protein Proteolysis Targeting Chimera (BET-PROTAC) exerts superior lethal activity than Bromodomain Inhibitor (BETi) Against Post-myeloproliferative Neoplasm (MPN) Secondary (s) AML Cells", Leukemia, accepted, 2017.

  4. Christian Spainhour, Juho Lim, Peng Qiu, "GDISC: integrative TCGA analysis to identify Gene-Drug Interaction for Survival in Cancer", Bioinformatics, 33(9):1426-1428, 2017.

  5. Nicholas J. Short, Christopher B. Benton, Hsiang-Chun Chen, Peng Qiu, Lisa Gu, Sherry Pierce, Mark Brandt, Abhishek Maiti, Taejin L. Min, Kiran Naqvi, Alfonso Quintas-Cardama, Marina Konopleva, Tapan Kadia, Jorge Cortes, Guillermo Garcia-Manero, Farhad Ravandi, Elias Jabbour, Hagop Kantarjian, Michael Andreeff, "Peripheral blood blast clearance is an independent prognostic factor for survival and response to AML induction chemotherapy", American Journal of Hematology, 91(12):1221-1226, 2016.

  6. Christian Spainhour, Peng Qiu, "Identification of gene-drug interactions that impact patient survival in TCGA", BMC Bioinformatics, 17(1):409, 2016.

  7. Dyana Saenz, Warren Fiskus, Taghi Manshouri, Kimal Rajapakshe, Stephanie Krieger, Baohua Sun, Christopher Mill, Courtney DiNardo, Naveen Pemmaraju, Tapan Kadia, Simrit Parmar, Sunil Sharma, Cristian Coarfa, Peng Qiu, Srdan Verstovsek, and Kapil Bhalla, "BET protein bromodomain inhibitor-based combinations are highly active against post-myeloproliferative neoplasm secondary AML cells", Leukemia, accepted, 2016

  8. Benedict Anchang, Tom Hart, Sean C Bendall, Peng Qiu, Zach Bjornson, Michael Linderman, Garry P Nolan and Sylvia K Plevritis, "A visualization and cellular hierarchy inference of single cell data using SPADE", Nature Protocols, 11(7):1264-79, 2016

  9. Mark Transtrum, Peng Qiu, "Bridging Mechanistic and Phenomenological Models of Complex Biological Systems", PLoS Computational Biology, 12(5):e1004915, 2016.

  10. Ankit Mahendra, Xingyu Yang, Peng Qiu, Daechan Park, Cristian Coarfa, Sandeep K Agarwal, Navin Varadarajan, "New insights into rheumatoid arthritis by whole transcriptome profiling of autoreactive B cells", Journal of Immunology, 196(supp 1):47.15, 2016.

  11. Nima Aghaeepour, Pratip Chattopadhyay, Maria Chikina, Tom Dhaene, Sofie Van Gassen, Miron Kursa, Bart N. Lambrecht, Mehrnoush Malek , Yu Qian, Peng Qiu, Yvan Saeys, Rick Stanton, Dong Tong, Celine Vens, Sławomir Walkowiak, Sam Wang, Greg Finak, Raphael Gottardo, Tim Mosmann, Garry Nolan, Richard H. Scheuermann, Ryan R. Brinkman, "A Benchmark for Evaluation of Algorithms for Identification of Cellular Correlates of Clinical Outcomes", Cytometry Part A, 89(1):16-21, 2016.

  12. Peng Qiu, "Computational prediction of manually gated rare cells in flow cytometry data", Cytometry Part A, 87(7):594-602, 2015.

  13. Lina Han+, Peng Qiu+, Zhihong Zeng, Jeffrey L. Jorgensen, Duncan H. Mak, Jared K. Burks, Wendy Schober, Teresa J. McQueen, Jorge Cortes, Scott D. Tanner, Gail J. Roboz, Hagop M. Kantarjian, Steven M. Kornblau, Monica L. Guzman, Michael Andreeff, Marina Konopleva, "Single-cell mass cytometry reveals intracellular survival/proliferative signaling in FLT3-ITD-mutated AML stem/progenitor cells", Cytometry Part A, 87(4):346-56, 2015.

  14. Yan Xu, Peng Qiu, Badrinath Roysam "Unsupervised Discovery of Subspace Trends", IEEE Trans on Pattern Analysis and Machine Intelligence, 37(10):2131-2145, 2015.

  15. Ivan Liadi, Harjeet Singh, Gabrielle Romain, Nicolas Rey-Villamizar, Amin Merouane, Jay R Adolacion, Partow Kebriaei, Helen Huls, Peng Qiu, Badrinath Roysam, Laurence J.N. Cooper, Navin Varadarajan "Individual motile CD4+ T cells can participate in efficient multi-killing through conjugation to multiple tumor cells", Cancer Immunology Research, 3(5):473-81, 2015.

  16. Pia Kvistborg, Cécile Gouttefangeas, Nima Aghaeepour, Angelica Cazaly, Pratip K. Chattopadhyay, Cliburn Chan, Judith Eckl, Greg Finak, Sine Reker Hadrup, Holden T. Maecker, Dominik Maurer, Tim Mosmann, Peng Qiu, Richard H. Scheuermann, Marij J.P. Welters, Guido Ferrari, Ryan R. Brinkman, Cedrik M. Britten, "Thinking Outside the Gate – Single Cell Assessments in Multiple Dimensions", Immunity, 42(4):591-2, 2015.

  17. Mukesh Bansal, Jichen Yang, Charles Karan, Michael P Menden, James C Costello, Hao Tang, Guanghua Xiao, Yajuan Li, Jeffrey Allen, Rui Zhong, Beibei Chen, Minsoo Kim, Tao Wang, Laura M Heiser, Ronald Realubit, Michela Mattioli, Mariano J Alvarez, Yao Shen, NCI-DREAM Community (including Peng Qiu), Daniel Gallahan, Dinah Singer, Julio Saez-Rodriguez, Yang Xie, Gustavo Stolovitzky, Andrea Califano, "A community computational challenge to predict the activity of pairs of compounds", Nature Biotechnology, 32(12):1213-22, 2014.

  18. Thomas J. Cradick, Peng Qiu, Ciaran Lee, Eli Fine, Gang Bao, "COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites", Molecular Therapy Nucleic Acids, 3:e214, 2014.

  19. Riten Mitra, Peter Mueller, Peng Qiu, Yuan Ji, "Bayesian Hierarchical Models for Protein Networks in Single Cell Mass Cytometry", Cancer Informatics, 13(Suppl 4):79-89, 2014.

  20. Mark K. Transtrum, Peng Qiu, "Coarse-graining models of emergent behavior by manifold boundaries", Physical Review Letters, 113 (9), 098701, 2014.

  21. Yitan Zhu, Peng Qiu, Yuan Ji, "TCGA-Assembler: Open-Source Software for Assembling, and Processing TCGA Data", Nature Methods, 11 (6), 599-600, 2014.

  22. James C Costello, Laura M Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P Menden, Nicholas J Wang, Mukesh Bansal, Petteri Hintsanen, Suleiman A Khan, John-Patrick Mpindi, Olli Kallioniemi, Antti Honkela, Tero Aittokallio, Krister Wennerberg, NCI DREAM Community (include Peng Qiu), James J Collins, Dan Gallahan, Dinah Singer, Julio Saez-Rodriguez, Samuel Kaski, Joe W Gray, Gustavo Stolovitzky, "A community effort to assess and improve drug sensitivity prediction algorithms", Nature Biotechnology, 32(12):1202-12, 2014.

  23. Zixing Wang, Anthony F San Lucas, Peng Qiu, Yin Liu, "Improving the Sensitivity of Sample Clustering by Leveraging Gene Co-Expression Networks in Variable Selection", BMC Bioinformatics, 15 (1):153, 2014.

  24. Peng Qiu, "Unfold high-dimensional clouds for exhaustive gating of flow cytometry data", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(6):1045-1051, 2014.

  25. Yanxun Xu, Xiaofeng Zheng, Yuan Yuan, Marcos R Estecio, Jean-Pierre Issa, Peng Qiu, Yuan Ji, Shoudan Liang, "BM-SNP: A Bayesian Model for SNP Calling using High Throughput Sequencing Data", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(6):1038-1044, 2014.

  26. Christopher B Benton, Farhad Ravandi, Michael Andreeff, Tapan Kadia, Vivian Ruvolo, Peng Qiu, David A Wheeler, Guillermo Garcia-Manero, Jorge Cortes, Hagop M Kantarjian, Marina Konopleva, "Case series of AML patients receiving hypomethylation therapy and retrospectively found to have IDH1 or IDH2 mutations", Leukemia and Lymphoma, 55(6):1431-1434, 2014.

  27. Yihua Liu, Yuan Ji, Peng Qiu, "Identification of thresholds for dichotomizing DNA methylation data", EURASIP Journal on Bioinformatics and Systems Biology, 2013(1):8, 2013.

  28. Nima Aghaeepour, Greg Finak, The FlowCAP Consortium (include Peng Qiu), The DREAM Consortium, Holger Hoos, Tim R Mosmann, Ryan Brinkman, Raphael Gottardo, Richard H Scheuermann, "Critical assessment of automated flow cytometry data analysis techniques", Nature Methods, 10(3):228-238, 2013.

  29. Peng Qiu, Sylvia K. Plevritis, "TreeVis: A MATLAB-based Tool for Tree Visualization", Computer Methods and Programs in Biomedicine, 109(1):74-76, 2013.

  30. Yuhuan Zheng, Jing Yang, Jianfei Qian, Peng Qiu, Shino Hanabuchi, Yong Lu, Zhiqiang Wang, Zhiqiang Liu, Haiyan Li, Jin He, Pei Lin, Donna Weber, Richard E. Davis, Larry Kwak, Zhen Cai, Qing Yi, "PSGL-1/Selectin and ICAM-1/CD18 interactions are involved in macrophage-induced drug resistance in myeloma", Leukemia, 27(3):702-10, 2013.

  31. Mark K. Transtrum, Peng Qiu, "Optimal Experiment Selection for Parameter Estimation in Biological Differential Equation Models", BMC Bioinformatics, 13(1):181, 2012.

  32. Peng Qiu, Li Zhang, "Identification of markers associated with global changes in DNA methylation regulation in cancers", BMC Bioinformatics, 13(suppl 13):S7, 2012.

  33. Michael D. Linderman, Zach Bjornson, Erin F. Simonds, Peng Qiu, Robert Bruggner, Ketaki Sheode, Teresa H. Meng, Sylvia K. Plevritis, Garry P. Nolan, "CytoSPADE: High-Performance Analysis and Visualization of High-Dimensional Cytometry Data", Bioinformatics, 28(18):2400-2401, 2012.

  34. Peng Qiu, "Inferring phenotypic properties from single-cell characteristics", PLoS ONE, 7(5): e37038, 2012.(PDF)

  35. Peng Qiu, Erin F. Simonds, Sean C. Bendall, Kenneth D. Gibbs Jr., Robert V. Bruggner, Michael D. Linderman, Karen Sachs, Garry P. Nolan, Sylvia K. Plevritis, "Extracting a Cellular Hierarchy from High-dimensional Cytometry Data with SPADE", Nature Biotechnology, 29(10):886-891, 2011. (PDF)(supplement)(software)

  36. Peng Qiu, Sylvia K. Plevritis, "Reconstructing Directed Signed Gene Regulatory Network from Microarray Data", IEEE Trans. on Biomedical Engineering, 58(12):3518-3521, 2011. (PDF)

  37. Sean C. Bendall, Erin F. Simonds, Peng Qiu, El-ad D. Amir, Peter O. Krutzik, Rachel Finck, Robert V. Bruggner, Rachel Melamed, Olga I. Ornatsky, Robert S. Balderas, Sylvia K. Plevritis, Karen Sachs, Dana Pe'er, Scott D. Tanner, Garry P. Nolan, "Single Cell Mass Cytometry of Differential Immune and Drug Responses Across the Human Hematopoietic Continuum", Science, 332(6030):687-696, 2011. (PDF)

  38. Peng Qiu, Andrew J. Gentles, Sylvia K. Plevritis, "Discovering Biological Progression underlying Microarray Samples", PLoS Computational Biology, 7(4):e1001123, 2011. (PDF)

  39. Peng Qiu, Andrew J. Gentles, Sylvia K. Plevritis, "Reducing the Computational Complexity of Information Theoretic Approaches for Reconstructing Gene Regulatory Networks", Journal of Computational Biology, 17(2):169-176, 2010. (PDF)

  40. Peng Qiu, Andrew J. Gentles, Sylvia K. Plevritis, "Fast Calculation of Pairwise Mutual Information for Gene Regulatory Network Reconstruction", Computer Methods and Programs in Biomedicine, 94(2):177-180, 2009. (PDF)

  41. Peng Qiu, Sylvia K. Plevritis, "Simultaneous Class Discovery and Classification of Microarray Data using Spectral Analysis", Journal of Computational Biology, 16(7):935-944, 2009. (PDF)

  42. Peng Qiu, Z. Jane Wang, K. J. Ray Liu, Zsolt Szabo, "An Activity-Subspace Approach for Estimating the Integrated Input Function and Relative Distribution Volume in PET Parametric Imaging", IEEE Trans Information Technology in Biomedicine, 13(1):25-36, 2009. (PDF)

  43. Peng Qiu, Warren D. D'Souza, Thomas J. McAvoy, K. J. Ray Liu, "Inferential Modeling and Predictive Feedback Control in Real-Time Motion Compensation Using the Treatment Couch During Radiotherapy", Physics in Medicine and Biology, 52(19):5831-5854, 2007. (PDF)

  44. Peng Qiu, Z. Jane Wang, K. J. Ray Liu, "Genomic Processing for Cancer Classification and Prediction", IEEE signal processing magazine, 24(1):100-110, Jan, 2007. (PDF)

  45. Peng Qiu, Z. Jane Wang, K. J. Ray Liu, Zhang-Zhi Hu, Cathy H. Wu, "Dependence Network Modeling for Biomarker Identification", Bioinformatics, 23(2):198-206, 2007. (PDF)

  46. Peng Qiu, Z. Jane Wang, K. J. Ray Liu,"Polynomial Model Approach for Resynchronization Analysis of Cell-cycle Gene Expression Data", Bioinformatics, 22(8):959-966, 2006. (PDF)

  47. Peng Qiu, Z. Jane Wang, K. J. Ray Liu, "Ensemble dependence model for cancer classification and prediction of cancer and normal gene expression data", Bioinformatics, 21(14):3114-3121, 2005. (PDF)

Working papers

...

Book Chapters:

  1. Peng Qiu, "Discover Trend and Progression Underlying High-Dimensional Data", Advances in Statistical Bioinformatics: Models and Integrative Inference for High-Throughput Data, Cambridge University Press, 445, 2013.

...

Conference Publications:

  1. Yan Xu, Michalis Savelonas, Peng Qiu, Kristen Trett, William Shain, and Badrinath Roysam, "Unsupervised inference of arbor morphology progression for microglia from confocal microscope images", International Symposium on Biomedical Imaging: From Nano to Macro (ISBI), 2013.

  2. Yihua Liu, and Peng Qiu, "Integrative analysis of methylation and gene expression data in TCGA", IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2012 (PDF) - best paper award.

  3. Peng Qiu, "Toward exhaustive gating of flow cytometry data", IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2012 (PDF).

  4. Peng Qiu, and Li Zhang, "Identification of markers associated with global changes in DNA methylation regulation in cancers", The 8th Annual Biotechnology and Bioinformatics Symposium, BIOT-2011 (PDF).

  5. Peng Qiu, and K. J. Ray Liu, "A Robust Method for QRS Detection based on Modified P-Spectrum", IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), pp. 501-504, 2008. (PDF)

  6. Peng Qiu, Z. Jane Wang, and K. J. Ray Liu, "Dependence Model and Network for Biomarker Identification and Cancer Classification", 14th European Signal Processing Conference (EUSIPCO) 2006. (PDF)

  7. Peng Qiu, Z. Jane Wang, and K. J. Ray Liu, "Mixture Principle Component Analysis for Distribution Volume Parametric Imaging in Brain PET Studies", IEEE International Symposium on Biomedical Imaging (ISBI), pp. 928-931, 2006. (PDF)

  8. Z. Jane Wang, Peng Qiu, and K. J. Ray Liu, "Model-based receptor quantization analysis for PET parametric imaging", IEEE International Conference of the Engineering in Medicine and Biology Society (EMBS), pp. 5908-5911, 2005. (PDF)

  9. Peng Qiu, Z. Jane Wang, and K. J. Ray Liu, "Tracking the Herd: Resynchronization Analysis of Cell-Cycle Gene Expression Data in Saccharomyces Cerevisiae", IEEE International Conference of the Engineering in Medicine and Biology Society (EMBS), pp. 4826-4829, 2005. (PDF)

  10. Peng Qiu, Z. Jane Wang, and K. J. Ray Liu, "Ensemble Dependence Model-based Cancer Classification using Gene Microarray Data", IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2005. (PDF)