S. Quinn and A. Abbadi, S. A. Vaezi, R. Karls, and F. D. Quinn. "Identifying Virulence Determinants in Pathogenic Mycobacteria via Changes in Host Cell Mitochondrial Morphology." IEEE ISBI.
[Submitted] [preprint]
M. Fazli and S. Quinn. "Object Tracking in a 360° View: A Novel Perspective on Bridging the Gap to Biomedical Advancements." IEEE Access.
[Submitted] [preprint]
A. Abbadi and S. A. Vaezi, R. Karls, F. D. Quinn, and S. Quinn. "Time-lapse 3D confocal microscopy videos of mitochondrial dynamics in human alveolar epithelial cells (A549-DsRed) infected with Mycobacterium marinum (Mmar) strains." Zenodo.
[doi]
M. A. H. Triana, K. M. Márquez-Nogueras, M. S. Fazli, S. Quinn, and S. N. J. Moreno. "Regulation of Calcium entry by cyclic GMP signaling in Toxoplasma gondii." J. of Biological Chemistry.
[doi] [pdf]
S. A. Vaezi and S. Quinn. "Training a Supervised Cilia Segmentation Model from Self-Supervision." SciPy.
[doi] [pdf]
C. Li, K. Lechtreck, J. Eggenschwiler, A. Brinck, R. Patel, and S. Quinn. "Video Dataset of Respiratory Cilia Motion Phenotypes." Zenodo.
[doi]
C. Godwin, M. Zain, N. Safir, I. Humphrey, and S. Quinn. "Incorporating Task-Agnostic Information in Task-Based Active Learning Using a Variational Autoencoder." SciPy.
[doi] [pdf]
N. Jacobi, I. Mo, A. You, K. Kishore, Z. Page, T. Heckman, and S. Quinn. "Temporal Word Embeddings Analysis for Disease Prevention." SciPy.
[doi] [pdf]
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.
[doi] [pdf]
N. Safir, M. Zain, C. Godwin, E. Miller, I. Humphrey, and S. Quinn. "Variational Autoencoders for Semi-Supervised Deep Metric Learning." SciPy.
[doi] [pdf]
M. Zain, E. Miller, C. W. Lo, and S. Quinn. "Low-Level Feature Extraction for Cilia Segmentation." SciPy.
[doi] [pdf]
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.
[doi] [pdf]
N. Pulagam, M. Hill, M. Fazli, M. Zain, R. Mattson, A. Durden, F. Quinn, C. Chennubhotla, and S. Quinn. "Classification of Diffuse Subcellular Morphologies." SciPy.
[doi] [pdf]
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.
[doi] [pdf]
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).
[doi] [pdf]
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. Zain, S. Rao, N. Safir, Q. Wyner, I. Humphrey, A. Eldridge, C. Li, B. AlAila, and S. Quinn. "Unsupervised Representation of Cilia Video Using A Modular Generative Pipeline." SciPy.
[doi] [pdf]
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).
[doi] [preprint]
R. Sivakumar, S. Quinn. "Parkinson's Classification and Feature Extraction from Diffusion Tensor Images." SciPy.
[doi] [pdf] [code]
C. McDaniel, S. Quinn. "GCNeuro: A Graph Convolutional Network Pipeline for Preprocessing and Analyzing Multimodal Neuroimage Data." SciPy.
[doi] [pdf] [code]
R. Ceren, S. Quinn, and G. Rains. "Towards a Decentralized, Autonomous Multiagent Framework for Mitigating Crop Loss."
[preprint]
M. Fazli, S. Vella, S. Moreno, G. Ward, and S. Quinn. "Toward Simple & Scalable 3D Cell Tracking." Open Science in Big Data (OSBD) Workshop. IEEE BigData Conference.
[doi] [pdf] [code]
A. Durden, A. Loy, B. Reaves, M. Fazli, A. Courtney, F. D. Quinn, S. C. Chennubhotla, and S. Quinn. "Dynamic Social Network Modeling of Diffuse Subcellular Morphologies." SciPy.
[doi] [pdf] [poster]
C. McDaniel, S. Quinn. "Developing an LSTM Pipeline for Accelerometer Data." SciPy.
[doi] [pdf] [poster] [code]
M. Makkie, X. Li, S. Quinn, B. Lin, J. Yi, G. Mon, and T. Liu. "A Distributed Computing Platform for fMRI Big Data Analytics." IEEE Transactions on Big Data.
[doi] [pdf]
N. Pandhe, B. Rada, and S. Quinn. "Generative Spatiotemporal Modeling of Neutrophil Behavior." IEEE ISBI.
[doi] [preprint] [poster]
M. Fazli, S. Vella, S. Moreno, and S. Quinn. "Unsupervised Discovery of Toxoplasma gondii Motility Phenotypes." IEEE ISBI.
[doi] [preprint] [poster] [code]
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.
[doi] [preprint]
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).
[pdf] [preprint]
C. Lu and S. Quinn. "Classification of Ciliary Motion with 3D Convolutional Neural Networks." ACM Southeastern Conference.
[doi] [pdf]
Y. Zhao, X. Li, M. Makkie, S. Quinn, B. Lin, J. Ye, and T. Liu. "Template-guided Functional Network Identification via Supervised Dictionary Learning." IEEE ISBI.
[doi] [pdf]
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.
[doi] [pdf]
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).
[pdf] [poster]
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.
[doi] [preprint]
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]
P. Breen, J. Kelly, T. Heckman, and S. Quinn. "Mining Pre-Exposure Prophylaxis Trends in Social Media." IEEE International Conference on Data Science and Advanced Analytics (DSAA).
[doi] [pdf]
[Invited Paper] J. Miller, C. Bowman, V. G. Harish, and S. Quinn. "Open Source Big Data Analytics Frameworks Written in Scala." IEEE International Congress on Big Data.
[doi] [pdf]
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).
[pdf]
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.
[pdf]
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.
[doi] [pdf]
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)
A. Ramanathan, L. Pullum, T. Hobson, C. Steed, S. Quinn, and C. Chennubhotla. "ORBiT: Oak Ridge Bio-surveillance Toolkit for Public Health Dynamics." BMC Bioinformatics.
[doi] [pdf]
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.
[doi] [pdf]
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.
[d-scholarship]
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)
[pdf]
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.
[pdf]
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.
[pdf]
"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.
[pdf]
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.
[pdf]
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.
[doi]