S. A. Vaezi, G. Orlando, M. Fazli, G. Ward, S. Moreno, and S. Quinn. "A Novel Pipeline for Cell Instance Segmentation, Tracking, and Motility Classification of Toxoplasma gondii in 3D." SciPy.
M. Skaro, M. Hill, Y. Zhou, S. Quinn, M. B. Davis, A. Sboner, M. Murph, and J. Arnold. "Are we there yet? A machine learning architecture to predict organotropic metastases." BMC Medical Genomics.
A. J. Stasic, E. J. Dykes, C. D. Cordeiro, S. A. Vella, M. S. Fazli, S. Quinn, R. Docampo, and S. N. J. Moreno. "Ca2+ entry at the plasma membrane and uptake by acidic stores is regulated by proton transport in Toxoplasma gondii." Molecular Microbiology.
R. Anil, G. Capan, I. Drost-Fromm, T. Dunning, E. Friedman, T. Grant, S. Quinn, P. Ranjan, S. Schelter, and Ö. Yilmazel. "Apache Mahout: Machine Learning on Distributed Dataflow Systems." Journal of Machine Learning Research (JMLR).
M. Hill, M. Fazli, R. Mattson, M. Zain, A. Durden, A. T. Loy, B. Reaves, A. Courtney, F. Quinn, C. Chennubhotla, and S. Quinn. "Spectral Analysis of Mitochondrial Dynamics: A Graph-Theoretic Approach to Understanding Subcellular Pathology." SciPy.
[doi] [pdf] [mybinder]
M. Fazli, M. Hill, A. Durden, A. Loy, R. Mattson, B. Reaves, A. Courtney, F. Quinn, C. Chennubhotla, and S. Quinn. "OrNet: A Python Toolkit to Model the Diffuse Structure of Organelles as Social Networks." Journal of Open Source Software (JOSS).
[doi] [pdf] [code]
M. Fazli, R. Stadler, B. AlAila, S. Vella, S. Moreno, G. E. Ward, and S. Quinn. "Lightweight and Scalable Particle Tracking and Motion Clustering of 3D Cell Trajectories." IEEE International Conference on Data Science and Advanced Analytics (DSAA).
R. Ceren, S. Quinn, and G. Rains. "Towards a Decentralized, Autonomous Multiagent Framework for Mitigating Crop Loss."
W. Shalaby, B. AlAila, M. Korayem, L. Pournajaf, K. Aljadda, S. Quinn, and W. Zadrozny. "Help Me Find a Job: A Graph-based Approach for Job Recommendation at Scale." IEEE BigData Conference.
M. Fazli, S. Vella, S. Moreno, and S. Quinn. "Computational Motility Tracking of Calcium Dynamics in Toxoplasma gondii." KDD Bigdas Workshop. ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD).
B. Norman, T. Davis, S. Quinn, R. Massey, and D. Hirsh. "Automated Identification of Pediatric Appendicitis Score in Emergency Department Notes using Natural Language Processing." IEEE BHI.
S. Schelter, A. Palumbo, S. Quinn, S. Marthi, and A. Musselman. "Samsara: Declarative Machine Learning on Distributed Dataflow Systems." Machine Learning Systems Workshop. Neural Information Processing Systems (NIPS).
G. Mon, M. Makkie, X. Li, T. Liu, and S. Quinn. "Implementing Dictionary Learning in Apache Flink, Or: How I Learned to Relax and Love Iterations." Open Science in Big Data (OSBD) Workshop. IEEE BigData Conference.
[doi] [pdf] [code]
M. Makkie, X. Li, B. Lin, J. Ye, M. Fazli, T. Liu, and S. Quinn. "Distributed Rank-1 Dictionary Learning: Towards Fast and Scalable Solutions for fMRI Big Data Analytics." KDDBHI Workshop. IEEE BigData Conference.
P. Sil, C. P. Hayes, B. J. Reaves, P. Breen, S. Quinn, J. Sokolove, and B. Rada. "P2Y6 Receptor Antagonist MRS2578 Inhibits Neutrophil Activation and Aggregated Neutrophil Extracellular Trap Formation Induced by Gout-Associated Monosodium Urate Crystals." Journal of Immunology.
[doi] [pdf] [code]
X. Li, M. Makkie, B. Lin, M. Fazli, I. Davidson, J. Ye, T. Liu, and S. Quinn. "Scalable Fast Rank-1 Dictionary Learning for fMRI Big Data Analysis." ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD).
[doi] [pdf] [code]
S. Quinn, A. Ramanathan, L. Pullum, and C. Steed. "Dr. Twitter: The Logistics of Practical Disease Surveillance using Social Media." IEEE International Conference on Biomedical and Health Informatics (BHI).
A. Ramanathan, S. Quinn, L. Pullum, and C. Steed. "Tracking Alcohol and Marijuana Usage and Behaviors from Social Media using Oak Ridge Bio-Surveillance Toolkit." IEEE EMBS BHI.
A. Ramanathan, L. Pullum, T. Hobson, C. Stahl, C. Steed, S. Quinn, and C. Chennubhotla. "Discovering Multi-scale Co-occurrence Patterns of Asthma and Influenza with the Oak Ridge Bio-surveillance Toolkit." Frontiers in Public Health.
S. Quinn, M. Zahid, J. Durkin, R. Francis, C. W. Lo, and C. Chennubhotla. "Automated identification of abnormal respiratory ciliary motion in nasal biopsies." Science Translational Medicine.
[doi] [pdf] [supplementary pdf] [supplementary zip]
(UGA Today) (Medical Xpress)
J. Castro, S. Quinn, A. Ramanathan, and C. Chennubhotla. "Categorical, low-dimensional decomposition of human odor space with non-negative matrix factorization." Proceedings of the 1st International Workshop on Odor Spaces. Flavour.
S. Quinn, C. Chennubhotla, T. Benos, C. Lo, A. Ramanathan, R. Schwartz, and L. Taylor. "Distributed Spectral Graph Methods for Analyzing Large-Scale Unstructured Biomedical Data." Doctoral Dissertation. D-Scholarship, University of Pittsburgh.
A. Ramanathan, L. Pullum, T. C. Hobson, S. Quinn, C. Chennubhotla, and S. Valkova. "Discovery of Disease Co-occurrence Patterns from Electronic Healthcare Reimbursement Claims Data." Knowledge Discovery and Data Mining Big Data in Health Informatics (KDD-BHI)
A. Ramanathan, L. Pullum, C. Steed, S. Quinn, T. Parker, and C. Chennubhotla. "Integrating Heterogeneous Healthcare Datasets and Visual Analytics for Disease Bio-Surveillance and Dynamics." IEEE Workshop on Interactive Visual Text Analytics, IEEE VIS.
A. Ramanathan, L. Pullum, C. Steed, T. Parker, S. Quinn, and C. Chennubhotla. "Oak Ridge Bio-Surveillance Toolkit (ORBiT): Integrating Big-Data Analytics with Visual Analysis for Public Health Dynamics." Public Health’s Wicked Problems: Can InfoVis Save Lives?, IEEE VIS.
"Statistical Inference for Big Data Problems in Molecular Biophysics" by A. Ramanathan, A. Savol, V. Burger, S. Quinn, P. Agarwal, and C. Chennubhotla, NIPS2012 Workshop on Parallel and Large-Scale Machine Learning.
L. P. Coelho, E. Glory-Afshar, J. Kangas, S. Quinn, A. Shariff, and R. F. Murphy. "Principles of Bioimage Informatics: Focus on machine learning of cell patterns." Lecture Notes in Computer Science.
A. Shariff, J. Kangas, L.P. Coelho, S. Quinn, and R.F. Murphy. "Automated Image Analysis for High Content Screening and Analysis." J. Biomolec. Screening.