Publications

Journal Papers:

  1. Lim HS, Qiu P. “Quantifying the clusterness and trajectoriness of single-cell RNA-seq data“, PLoS Computational Biology, 6(1):749, 2023.
  2. Hymel LA, Anderson SE, Turner TC, York WY, Zhang H, Liversage AR, Lim HS, Qiu P, Mortensen LJ, Jang YC, Willett NJ, Botchwey EA. “Identifying dysregulated immune cell subsets following volumetric muscle loss with pseudo-time trajectories“, Communications Biology, 6(1):749, 2023.
  3. Wang Z, Emmel G, Lim HS, Zhu W, Kosters A, Ghosn EEB, Qiu P*, Bunting KD*. “Stromal STAT5-mediated trophic activity regulates hematopoietic niche factors“, Stem Cells, sxad055, 2023.
  4. Poorna R, Chen WW, Qiu P, Cicerone MT. “Toward Gene-Correlated Spatially Resolved Metabolomics with Fingerprint Coherent Raman Imaging“, Journal of Physical Chemistry B, 127(25):5576-5587, 2023.
  5. Li X, Gibson G, Qiu P. “Gene representation in scRNA-seq is correlated with common motifs at the 3′ end of transcripts“, Frontiers in Bioinformatics, 3:1120290, 2023.
  6. Young KM, Xu C, Ahkee K, Mezencev R, Swingle S, Yu T, Paikeday A, Kim C, McDonald J, Qiu P, Sulchek, T. “Correlating mechanical and gene expression data on the single cell level to investigate metastatic phenotypes“, iScience, 26(4):106393, 2023.
  7. Lim HS, Qiu P. “Quantifying Cell-Type-Specific Differences of Single-Cell Datasets Using Uniform Manifold Approximation and Projection for Dimension Reduction and Shapley Additive exPlanations“, Journal of Computational Biology, 30(7):738-750, 2023.
  8. Sun Y, Qiu P. “Domain adaptation for supervised integration of scRNA-seq data“, Communications Biology, 6(1):274, 2023.
  9. Zhao X, Du A, Qiu P. “scMODD: a model-driven algorithm for doublet identification in single-cell RNA-sequencing data“, Frontiers in Systems Biology, 2:1082309, 2023.
  10. Holt BA*, Lim HS*, Sivakumar A, Phuengkham H, Su M, Tuttle M, Liakakos H, Qiu P*, Kwong GA*. “Embracing enzyme promiscuity with activity-based compressed biosensing“, Cell Reports Methods, 3(1):100372, 2023.
  11. Lin S, Yi S, Qiu P. “Comprehensive analysis of TCGA data reveals correlation between DNA methylation and alternative splicing“, BMC Genomics, 23, 785, 2022.
  12. Neary B, Lin S, Qiu P. “Methylation of CpG Sites as Biomarkers Predictive of Drug-Specific Patient Survival in Cancer“, Cancer Informatics, 21:11769351221131124, 2022.
  13. Xu C, Lu H, Qiu P. “Comparison of cell type annotation algorithms for revealing immune response of COVID-19“, Frontiers in Systems Biology, 2:1026686, 2022.
  14. Maddipatla S, Kolachala VL, Venkateswaran S, Dodd AF, Pelia RS, Geem D, Yin H, Sun Y, Xu C, Mo A, Kosters A, Yang J, Matthews JD, Ghosn EEB, Kugathasan S*, Qiu P*. “Assessing Cellular and Transcriptional diversity of IIeal Mucosa amongst Treatment Naïve and Treated Crohn’s disease“, Inflammatory Bowel Diseases, 29(2):274-285, 2023.
  15. Xu C*, Yang J*, Kosters A, Babcock BR, Qiu P*, Ghosn EEB*. “Comprehensive multi-omics single-cell data integration reveals greater heterogeneity in the human immune system“, iSciences, 25(10):105123, 2022.
  16. Margaroli C, Horati H, Garratt LW, Giacalone VD, Schofield C, Dittrich AS, Rosenow T, Dobosh BS, Lim HS, Frey DL, Veltman M, Silva GL, Brown MR, Schultz C, Tiddens HA, Ranganathan S, Chandler JD, Qiu P, Peng L, Scholte BJ, Mall MA, Kicic A, Guglani L, Stick SM, Janssens HM, Tirouvanziam R. “Macrophage PD-1 associates with neutrophilia and reduced bacterial killing in early cystic fibrosis airway disease“, Journal of Cystic Fibrosis, S1569-1993(22)00588-4, 2022.
  17. Lin S, Zhou J, Xiao Y, Neary B, Teng Y, Qiu P. “Integrative analysis of TCGA data identifies miRNAs as drug-specific survival biomarkers“, Scientific Reports, 12(1):6785, 2022.
  18. Mac QD*, Sivakumar A*, Phuengkham H, Xu C, Bowen JR, Su FY, Stentz SZ, Sim H, Harris AM, Li TT, Qiu P, Kwong GA. “Urinary detection of early responses to checkpoint blockade and discrimination of refractory tumours via antibody-conjugated protease sensors“, Nature Biomedical Engineering, 6(3):310-324, 2022.
  19. Fernandez-Yague MA, Hymel LA, Olingy CE, McClain C, Ogle ME, García JR, Minshew D, Vyshnya S, Lim HS, Qiu P, García AJ, Botchwey EA. “Analyzing Immune Response to Engineered Hydrogels by Hierarchical Clustering of Inflammatory Cell Subsets“, Science Advances, 8(8):eabd8056, 2022.
  20. Lang L, Wang F, Ding Z, Zhao X, Loveless R, Xie J, Shay C, Qiu P, Ke Y, Saba NF, Teng Y. “Blockade of glutamine-dependent cell survival augments antitumor efficacy of CPI-613 in head and neck cancer“, Journal of Experimental & Clinical Cancer Research, 40(1):393, 2021.
  21. Tarca AL, Pataki BA, Romero R, Sirota M, Guan Y, Kutum R, Gomez-Lopez N, Done B, Bhatti G, Yu T, Andreoletti G, Chaiworapongsa T, The DREAM Preterm Birth Prediction Challenge Consortium (including Qiu P), Hassan SS, Hsu CD, Aghaeepour N, Stolovitzky G, Csabai I, Costello JC. “Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth“, Cell Reports Medicine, 2(6):100323, 2021.
  22. Gabor A, Tognetti M, Driessen A, Tanevski J, Guo B, Cao W, Shen H, Yu T, Chung V, Single Cell Signaling in Breast Cancer DREAM Consortium members (including Qiu P), Bodenmiller B, Saez-Rodriguez J. “Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd.“, Molecular Systems Biology, 17(10):e10402, 2021.
  23. Hymel LA, San Emeterio CL, Turner TC, Ogle ME, Pendleton EG, York WY, Olingy CE, Liu SY, Lim HS, Sulchek TA, Warren GL, Mortensen LJ, Qiu P, Jang YC, Willett NJ, Botchwey EA. “Nanofiber-Based Delivery of Bioactive Lipids Promotes Pro-Regenerative Inflammation and Enhances Muscle Fiber Growth After Volumetric Muscle Loss“, Frontiers in Bioengineering and Biotechnology, section Tissue Engineering and Regenerative Medicine, 9:650289, 2021.
  24. Lim HS, Qiu P. “JSOM: Jointly-evolving self-organizing maps for alignment of biological datasets and identification of related clusters“, PLoS Computational Biology, 17(3):e1008804, 2021. (highlighted in Nature Computational Science)
  25. Neary B, Zhou J, Qiu P. “Identifying gene expression patterns associated with drug-specific survival in cancer patients“, Scientific Reports, 11(1):5004, 2021.
  26. Sok MCP, Baker N, McClain C, Lim HS, Turner T, Hymel L, Ogle M, Olingy C, Palacios JI, Garcia JR, Srithar K, García AJ, Qiu P, Botchwey EA. “Dual delivery of IL-10 and AT-RvD1 from PEG hydrogels polarize immune cells towards pro-regenerative phenotypes“, Biomaterials, 268:120475, 2021.
  27. Hymel LA, Ogle ME, Anderson SE, San Emeterio CL, Turner TC, York WY, Liu AY, Olingy CE, Sridhar S, Lim HS, Sulchek T, Qiu P, Jang YC, Willett NJ, Botchwey E. “Modulating local S1P receptor signaling as a regenerative immunotherapy after volumetric muscle loss injury“, Journal of Biomedical Materials Research Part A, doi: 10.1002/jbm.a.37053, 109(5):695-712, 2021.
  28. Turner TC, Sok MCP, Hymel LA, Pittman F, York WY, Mac QD, Vishna S, Lim HS, Kwong GA, Qiu P, Botchwey EA. “Harnessing lipid signaling pathways to target specialized pro-angiogenic neutrophil subsets for regenerative immunotherapy“, Science Advances, 6(44):eaba7702, 2020.
  29. Coronel MM, Martin KE, Hunckler MD, Barber G, O’Neill EB, Medina JD, Opri E, McClain CA, Batra L, Weaver JD, Lim HS, Qiu P, Botchwey EA, Yolcu ES, Shirwan H, García AJ. “Immunotherapy via PD-L1-presenting biomaterials leads to long-term islet graft survival“, Science Advances, 6(35):eaba5573, 2020.
  30. Tanevski J, Nguyen T, Truong B, Karaiskos N, Ahsen ME, Zhang X, Shu C, Xu K, Liang X, Hu Y, Pham HV, Xiaomei L, Le TD, Tarca AL, Bhatti G, Romero R, Karathanasis N, Loher P, Chen Y, Ouyang Z, Mao D, Zhang Y, Zand M, Ruan J, Hafemeister C, Qiu P, Tran D, Nguyen T, Gabor A, Yu T, Guinney J, Glaab E, Krause R, Banda P; DREAM SCTC Consortium, Stolovitzky G, Rajewsky N, Saez-Rodriguez J, Meyer P. “Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data“, Life Science Alliance, 3(11):e202000867, 2020.
  31. Clayton EA, Pujol TA, McDonald JF, Qiu P. “Leveraging TCGA gene expression data to build predictive models for cancer drug response“, BMC Bioinformatics, 21(Suppl 14):364, 2020.
  32. Yang X, Tipton CM, Woodruff MC, Zhou E, Lee FE, Sanz I, Qiu P. “GLaMST: grow lineages along minimum spanning tree for b cell receptor sequencing data“, BMC Genomics, 21(Suppl 9):583, 2020.
  33. Pilcher W, Yang X, Zhurikhina A, Chernaya O, Xu Y, Qiu P, Tsygankov D. “Shape-to-graph Mapping Method for Efficient Characterization and Classification of Complex Geometries in Biological Images“, PLoS Computational Biology, 16(9):e1007758, 2020.
  34. Bailur JK, McCachren SS, Pendleton KE, Vasquez JC, Lim HS, Duffy A, Doxie D, Kaushal A, Foster C, DeRyckere D, Castellino SM, Kemp ML, Qiu P, Dhodapkar M, Dhodapkar K. “Risk associated alterations in marrow T cells in pediatric leukemia“, JCI Insight, 140179, 2020.
  35. Qiu P. “Embracing the dropouts in single-cell RNA-seq analysis“, Nature Communications, 11(1):1169, 2020.
  36. Youmans M, Spainhour C, Qiu P. “Classification of Antibacterial Peptides using Long Short-Term Memory Recurrent Neural Networks“, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17(4):1134-1140, 2020.
  37. Guo T, Luna A, Rajapakse V, Koh C, Wu Z, Liu W, Sun Y, Gao H, Menden M, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Ori A, Iskar M, Gillet L, Bi R, Zhang J, Zhang H, Yu C, Zhong Q, Varma S, Schmitt U, Qiu P, Zhang Q, Zhu Y, Wild P, Garnett M, Bork P, Beck M, Liu K, Saez-Rodriguez J, Elloumi F, Reinhold W, Sander C, Pommier Y, Aebersold R. “Quantitative proteome landscape of the NCI-60 cancer cell lines“, iScience, 21:664-680, 2019.
  38. Xu C, Zhu H, Qiu P. “Aging progression of human gut microbiota“, BMC Microbiology, 19(1):236, 2019.
  39. Zhuang Q*, Holt B*, Kwong G*, Qiu P*. “Deconvolving multiplexed protease signatures with substrate reduction and activity clustering“, PLoS Computational Biology, 15(9):e1006909, 2019.
  40. Spainhour C*, Lim HS*, Yi S, Qiu P. “Correlation Patterns Between DNA Methylation and Gene Expression in The Cancer Genome Atlas“, Cancer Informatics, 18:1176935119828776, 2019.
  41. Mahendra A, Yang X, Abnouf S, Adolacion JRT, Park D, Soomro S, Roszik J, Coarfa C, Romain G, Wanzeck K, Louis Bridges S Jr, Aggarwal A, Qiu P, Agarwal SK, Mohan C, Varadarajan N. “Beyond autoantibodies: Biological roles of human autoreactive B cells in rheumatoid arthritis revealed by RNA-sequencing“, Arthritis & Rheumatology, 71(4):529-541, 2019.
  42. Saenz D, Fiskus W, Manshouri T, Mill C, Qian Y, Raina K, Rajapakshe K, Coarfa C, Soldi R, Bose P, Borthakur G, Kadia T, Khoury J, Masarova L, Nowak A, Sun B, Saenz D, Kornblau S, Horrigan S, Sharma S, Qiu P, Crews C, Verstovsek S, Bhalla K. “Targeting Nuclear β-catenin as therapy for post-myeloproliferative neoplasm secondary AML“, Leukemia, 33(6):1373-1386, 2019.
  43. Jeong J, Qiu P. “Quantifying the relative importance of experimental data points in parameter estimation“, BMC Systems Biology, 12(Suppl 6):103, 2018.
  44. Yang X, Qiu P. “Automatically Generate Two-Dimensional Gating Hierarchy from Clustered Cytometry Data“, Cytometry A, 93(10):1039-1050, 2018.
  45. Jeong J, Zhuang Q, Transtrum MK, Zhou E, Qiu P. “Experimental design and model reduction in systems biology“, Quantitative Biology, 6(4):287-306, 2018.
  46. Jeong J, Frohberg NJ, Zhou E, Sulchek T, Qiu P. “Accurately tracking single-cell movement trajectories in microfluidic cell sorting devices“, PLoS One, 13(2):e0192463, 2018
  47. Bongiorno T, Gura J, Talwar P, Chambers D, Young KM, Arafat D, Wang G, Jackson-Holmes EL, Qiu P, McDevitt TC, Sulchek T. “Biophysical subsets of embryonic stem cells display distinct phenotypic and morphological signatures“, PLoS One. 13(3):e0192631, 2018.
  48. Liu A, Islam M, Stone N, Varadarajan V, Jeong J, Bowie S, Qiu P, Waller EK, Alexeev A, Sulchek T. “Microfluidic generation of transient cell volume exchange for convectively driven intracellular delivery of large macromolecules“, Materials Today, 21(7):703-712, 2018.
  49. Caicedo JC, Cooper S, Heigwer F, Warchal S, Qiu P, Molnar C, Vasilevich AS, Barry JD, Bansal HS, Kraus O, Wawer M, Paavolainen L, Herrmann MD, Rohban M, Hung J, Hennig H, Concannon J, Smith I, Clemons PA, Singh S, Rees P, Horvath P, Linington RG, Carpenter AE. “Data-analysis strategies for image-based cell profiling“, Nature Methods, 14(9):849-863, 2017.
  50. Rubelt F, Busse CE, Bukhari SAC, Bürckert JP, Mariotti-Ferrandiz E, Cowell LG, Watson CT, Marthandan N, Faison WJ, Hershberg U, Laserson U, Corrie BD, Davis MM, Peters B, Lefranc MP, Scott JK, Breden F AIRR Community (including Qiu P), Luning Prak ET, Kleinstein SH. “Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data“, Nature Immunology, 18(12):1274-1278, 2017.
  51. Parratt K, Jeong J, Qiu P, Roy K. “3D Material Cytometry (3DMaC): A Very High-replicate, High-throughput Analytical Method using Microfabricated, Shape-specific, Cell-material Niches“, Lap on a Chip, 17(16):2861-2872, 2017.
  52. Qiu P. “Toward robust and automated SPADE analysis for single-cell data“, Cytometry Part A, 91(3):281-289, 2017.
  53. Saenz DT, Fiskus W, Qian Y, Manshouri T, Rajapakshe K, Raina K, Coleman KG, Crew AP, Shen A, Mill CP, Sun B, Qiu P, Kadia TM, Pemmaraju N, DiNardo C, Kim MS, Nowak AJ, Coarfa C, Crews CM, Verstovsek S, Bhalla KN. “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, 31(9):1951-1961, 2017.
  54. Spainhour C, Lim J, Qiu P. “GDISC: integrative TCGA analysis to identify Gene-Drug Interaction for Survival in Cancer“, Bioinformatics, 33(9):1426-1428, 2017.
  55. Short NJ, Benton CB, Chen HC, Qiu P, Gu L, Pierce S, Brandt M, Maiti A, Min TL, Naqvi K, Quintas-Cardama A, Konopleva M, Kadia T, Cortes J, Garcia-Manero G, Ravandi F, Jabbour E, Kantarjian H, Andreeff M. “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.
  56. Spainhour C, Qiu P. “Identification of gene-drug interactions that impact patient survival in TCGA“, BMC Bioinformatics, 17(1):409, 2016.
  57. Saenz DT, Fiskus W, Manshouri T, Rajapakshe K, Krieger S, Sun B, Mill CP, DiNardo C, Pemmaraju N, Kadia T, Parmar S, Sharma S, Coarfa C, Qiu P, Verstovsek S, Bhalla KN. “BET protein bromodomain inhibitor-based combinations are highly active against post-myeloproliferative neoplasm secondary AML cells“, Leukemia, 31(3):678-687, 2016
  58. Anchang B, Hart TD, Bendall SC, Qiu P, Bjornson Z, Linderman M, Nolan GP, Plevritis SK. “A visualization and cellular hierarchy inference of single cell data using SPADE“, Nature Protocols, 11(7):1264-79, 2016
  59. Transtrum MK, Qiu P. “Bridging Mechanistic and Phenomenological Models of Complex Biological Systems“, PLoS Computational Biology, 12(5):e1004915, 2016.
  60. Mahendra A, Yang X, Qiu P, Park D, Coarfa C, Agarwal SK, Varadarajan N. “New insights into rheumatoid arthritis by whole transcriptome profiling of autoreactive B cells“, Journal of Immunology, 196(supp 1):47.15, 2016.
  61. Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, McLachlan GJ, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, Wang K, Finak G, Gottardo R, Mosmann T, Nolan GP, Scheuermann RH, Brinkman RR. “A Benchmark for Evaluation of Algorithms for Identification of Cellular Correlates of Clinical Outcomes“, Cytometry Part A, 89(1):16-21, 2016.
  62. Qiu P. “Computational prediction of manually gated rare cells in flow cytometry data“, Cytometry Part A, 87(7):594-602, 2015.
  63. Han L+, Qiu P+, Zeng Z, Jorgensen JL, Mak DH, Burks JK, Schober W, McQueen TJ, Cortes J, Tanner SD, Roboz GJ, Kantarjian HM, Kornblau SM, Guzman ML, Andreeff M, Konopleva M. “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.
  64. Xu Y, Qiu P, Roysam B. “Unsupervised Discovery of Subspace Trends“, IEEE Trans on Pattern Analysis and Machine Intelligence, 37(10):2131-2145, 2015.
  65. Liadi I, Singh H, Romain G, Rey-Villamizar N, Merouane A, Adolacion JR, Kebriaei P, Huls H, Qiu P, Roysam B, Cooper LJ, Varadarajan N. “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.
  66. Kvistborg P, Gouttefangeas C, Aghaeepour N, Cazaly A, Chattopadhyay PK, Chan C, Eckl J, Finak G, Hadrup SR, Maecker HT, Maurer D, Mosmann T, Qiu P, Scheuermann RH, Welters MJ, Ferrari G, Brinkman RR, Britten CM. “Thinking Outside the Gate – Single Cell Assessments in Multiple Dimensions“, Immunity, 42(4):591-2, 2015.
  67. Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y, NCI-DREAM Community (including Qiu P), Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A. “A community computational challenge to predict the activity of pairs of compounds“, Nature Biotechnology, 32(12):1213-22, 2014.
  68. Cradick TJ, Qiu P, Lee C, Fine E, Bao G. “COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites“, Molecular Therapy Nucleic Acids, 3:e214, 2014.
  69. Mitra R, Mueller P, Qiu P, Ji Y. “Bayesian Hierarchical Models for Protein Networks in Single Cell Mass Cytometry“, Cancer Informatics, 13(Suppl 4):79-89, 2014.
  70. Transtrum MK, Qiu P. “Coarse-graining models of emergent behavior by manifold boundaries“, Physical Review Letters, 113 (9), 098701, 2014.
  71. Zhu Y, Qiu P, Ji Y. “TCGA-Assembler: Open-Source Software for Assembling, and Processing TCGA Data“, Nature Methods, 11 (6), 599-600, 2014.
  72. Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, NCI DREAM Community (include Qiu P), Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G. “A community effort to assess and improve drug sensitivity prediction algorithms“, Nature Biotechnology, 32(12):1202-12, 2014.
  73. Wang Z, Lucas A, Qiu P, Liu Y. “Improving the Sensitivity of Sample Clustering by Leveraging Gene Co-Expression Networks in Variable Selection“,BMC Bioinformatics, 15 (1):153, 2014.
  74. Qiu P. “Unfold high-dimensional clouds for exhaustive gating of flow cytometry data“, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(6):1045-1051, 2014.
  75. Xu Y, Zheng X, Yuan Y, Estecio MR, Issa J, Qiu P, Ji Y, Liang S. “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.
  76. Benton CB, Ravandi F, Andreeff M, Kadia T, Ruvolo V, Qiu P, Wheeler DA, Garcia-Manero G, Cortes G, Kantarjian HM, Konopleva M. “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.
  77. Liu Y, Ji Y, Qiu P. “Identification of thresholds for dichotomizing DNA methylation data“, EURASIP Journal on Bioinformatics and Systems Biology, 2013(1):8, 2013.
  78. Aghaeepour N, Finak G, FlowCAP Consortium (include Qiu P), DREAM Consortium, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH. “Critical assessment of automated flow cytometry data analysis techniques“, Nature Methods, 10(3):228-238, 2013.
  79. Qiu P, Plevritis SK. “TreeVis: A MATLAB-based Tool for Tree Visualization“, Computer Methods and Programs in Biomedicine, 109(1):74-76, 2013.
  80. Zheng Y, Yang J, Qian J, Qiu P, Hanabuchi S, Lu Y, Wang Z, Liu Z, Li H, He J, Lin P, Weber D, Davis RE, Kwak L, Cai Z, Yi Q. “PSGL-1/Selectin and ICAM-1/CD18 interactions are involved in macrophage-induced drug resistance in myeloma“, Leukemia, 27(3):702-10, 2013.
  81. Transtrum MK, Qiu P. “Optimal Experiment Selection for Parameter Estimation in Biological Differential Equation Models“, BMC Bioinformatics, 13(1):181, 2012.
  82. Qiu P, Zhang L. “Identification of markers associated with global changes in DNA methylation regulation in cancers“, BMC Bioinformatics, 13(suppl 13):S7, 2012.
  83. Linderman MD, Bjornson Z, Simonds EF, Qiu P, Bruggner R, Sheode K, Meng TH, Plevritis SK, Nolan GP. “CytoSPADE: High-Performance Analysis and Visualization of High-Dimensional Cytometry Data“, Bioinformatics, 28(18):2400-2401, 2012.
  84. Qiu P. “Inferring phenotypic properties from single-cell characteristics“, PLoS ONE, 7(5): e37038, 2012.(PDF)
  85. Qiu P, Simonds EF, Bendall SC, Gibbs KD Jr, Bruggner RV, Linderman MD, Sachs K, Nolan GP, Plevritis SK. “Extracting a Cellular Hierarchy from High-dimensional Cytometry Data with SPADE“, Nature Biotechnology, 29(10):886-891, 2011. (PDF)(supplement)(software)
  86. Qiu P, Plevritis SK. “Reconstructing Directed Signed Gene Regulatory Network from Microarray Data“, IEEE Trans. on Biomedical Engineering, 58(12):3518-3521, 2011. (PDF)
  87. Bendall SC, Simonds EF, Qiu P, Amir ED, Krutzik PO, Finck R, Bruggner RV, Melamed R, Ornatsky OI, Balderas RS, Plevritis SK, Sachs K, Pe’er D, Tanner SD, Nolan GP. “Single Cell Mass Cytometry of Differential Immune and Drug Responses Across the Human Hematopoietic Continuum“, Science, 332(6030):687-696, 2011. (PDF)
  88. Qiu P, Gentles AJ, Plevritis SK. “Discovering Biological Progression underlying Microarray Samples“, PLoS Computational Biology, 7(4):e1001123, 2011. (PDF)
  89. Qiu P, Gentles AJ, Plevritis SK. “Reducing the Computational Complexity of Information Theoretic Approaches for Reconstructing Gene Regulatory Networks“, Journal of Computational Biology, 17(2):169-176, 2010. (PDF)
  90. Qiu P, Gentles AJ, Plevritis SK. “Fast Calculation of Pairwise Mutual Information for Gene Regulatory Network Reconstruction“, Computer Methods and Programs in Biomedicine, 94(2):177-180, 2009. (PDF)
  91. Qiu P, Plevritis SK. “Simultaneous Class Discovery and Classification of Microarray Data using Spectral Analysis“, Journal of Computational Biology, 16(7):935-944, 2009. (PDF)
  92. Qiu P, Wang ZJ, Liu KJR, Szabo Z. “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)
  93. Qiu P, D’Souza WD, McAvoy TJ, Liu KJR. “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)
  94. Qiu P, Wang ZJ, Liu KJR. “Genomic Processing for Cancer Classification and Prediction“, IEEE signal processing magazine, 24(1):100-110, Jan, 2007. (PDF)
  95. Qiu P, Wang ZJ, Liu KJR, Hu Z, Wu CH. “Dependence Network Modeling for Biomarker Identification“, Bioinformatics, 23(2):198-206, 2007. (PDF)
  96. Qiu P, Wang ZJ, Liu KJR. “Polynomial Model Approach for Resynchronization Analysis of Cell-cycle Gene Expression Data“, Bioinformatics, 22(8):959-966, 2006. (PDF)
  97. Qiu P, Wang ZJ, Liu KJR. “Ensemble dependence model for cancer classification and prediction of cancer and normal gene expression data“, Bioinformatics, 21(14):3114-3121, 2005. (PDF)

Conference Papers:

  1. Lin S, Zhou J, Xiao Y, Neary B, Teng Y, Qiu P. “Identification of protein markers predictive of drug-specific survival outcome in cancers“, International Symposium on Bioinformatics Research and Applications (ISBRA), In: Wei Y., Li M., Skums P., Cai Z. (eds) Bioinformatics Research and Applications. ISBRA 2021. Lecture Notes in Computer Science, vol 13064, pp. 58-67, 2021.  
  2. Xu C, Mac QD, Jia Q, Qiu P. “Immune-microbiota crosstalk underlying inflammatory bowel disease“, International Symposium on Bioinformatics Research and Applications (ISBRA), In: Wei Y., Li M., Skums P., Cai Z. (eds) Bioinformatics Research and Applications. ISBRA 2021. Lecture Notes in Computer Science, vol 13064, pp. 11-21, 2021.  
  3. Lim HS, Smerchansky M, Zhou J, Chatterjee P, Jimenez A, Yang X, Roy K, Qiu P. “Image-based early predictions of functional properties in cell manufacturing“, Machine Learning for Biological and Medical Image Big Data Workshop at IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2020.  
  4. Carreño Martínez J, Qiu P. “Feature selection algorithms for predicting preeclampsia: A comparative approach“, Third Workshop in Artificial Intelligence Techniques for BioMedicine and HealthCare (AIBH) at IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2020. 
  5. Jeong J, Qiu P. “The relative importance of data points in systems biology and parameter estimation“, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2017. 
  6. Youmans M, Spainhour C, Qiu P. “Long Short-Term Memory Recurrent Neural Networks for Antibacterial Peptide Identification“, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2017.
  7. Zhao A, Tsygankov D, Qiu P. “Graph-based extraction of shape features for leaf classification“, IEEE Global Conference on Signal and Information Processing (GlobalSIP), 2017.
  8. Rhee C, Zhou E, Qiu P. “An iterative algorithm for sampling from manifolds“, Proceedings of the 2014 Winter Simulation Conference, 574-585, 2014.
  9. Wang Z, Qiu P, Xu W, Liu Y. “Spectral feature selection and its application in high dimensional gene expression studies“, Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 2014. 
  10. Xu Y, Savelonas M, Qiu P, Trett K, Shain W, Roysam B. “Unsupervised inference of arbor morphology progression for microglia from confocal microscope images“, International Symposium on Biomedical Imaging: From Nano to Macro (ISBI), 2013.
  11. Liu Y, Qiu P. “Integrative analysis of methylation and gene expression data in TCGA“, IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2012. – best paper award
  12. Qiu P. “Toward exhaustive gating of flow cytometry data“, IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2012.
  13. Qiu P, Zhang L. “Identification of markers associated with global changes in DNA methylation regulation in cancers”, The 8th Annual Biotechnology and Bioinformatics Symposium, BIOT-2011. 
  14. Qiu P, Liu KJR. “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.
  15. Qiu P, Wang ZJ, Liu KJR. “Dependence Model and Network for Biomarker Identification and Cancer Classification”, 14th European Signal Processing Conference (EUSIPCO) 2006.
  16. Qiu P, Wang ZJ, Liu KJR. “Mixture Principle Component Analysis for Distribution Volume Parametric Imaging in Brain PET Studies”, IEEE International Symposium on Biomedical Imaging (ISBI), pp. 928-931, 2006.
  17. Wang ZJ, Qiu P, Liu KJR. “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.
  18. Qiu P, Wang ZJ, Liu KJR. “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.
  19. Qiu P, Wang ZJ, Liu KJR. “Ensemble Dependence Model-based Cancer Classification using Gene Microarray Data”, IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2005.

Book Chapters:

  1. Zhang Q, Xu C, Qiu P. “Inference of Networks from Large Datasets“, Systems Medicine: Integrative, Qualitative and Computational Approaches, 3:17-25, 2021.
  2. Solís-Lemus C, Ma X, Hostetter M, Kundu S, Qiu P, Pimentel-Alarcon D. “Prediction of Functional Markers of Mass Cytometry Data via Deep Learning“, Statistical Modeling in Biomedical Research, 95-104, 2020.
  3. Qiu P. “Discover Trend and Progression Underlying High-Dimensional Data”, Chapter in book Advances in statistical bioinformatics: models and integrative inference for high-throughput data, edited by Do K-A, Qin ZS, Vannucci M, Cambridge University Press, 2013.