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<h1 class="mt-4 mb-3">Publications
<small>journals, conferences, technical reports, preprints</small>
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<h2>2025</h2>
<p><strong>S. Quinn</strong> and A. Abbadi, <strong>S. A. Vaezi</strong>, R. Karls, and F. D. Quinn. "Identifying Virulence Determinants in Pathogenic Mycobacteria via Changes in Host Cell Mitochondrial Morphology." <em>IEEE ISBI</em>. <br />
[Submitted] [<a href="https://arxiv.org/abs/2411.06035">preprint</a>]</p>
</div>
</div>
<div class="row">
<div class="col-lg-12">
<h2>2024</h2>
<p>R. Yan, <strong>S. Quinn</strong>, B. Falkenstein, J. Monkman, K. O'Bryne, S.C. Chennubhotla, F. Pullara, and A. Kulasinghe. "Multi-omic spatial data integration resolves immunometabolic heterogeneity associated with Nivolumab response in non-small cell lung cancer (NSCLC) patients." <em>Journal for ImmunoTherapy of Cancer.</em> <br />
[<a href="https://doi.org/10.1136/jitc-2024-SITC2024.0212">doi</a>]</p>
<p>A. Kulasinghe, R. Yan, <strong>S. Quinn</strong>, B. Falkenstein, J. Monkman, K.J. O'Byrne, S.C. Chennubhotla, and F. Pullara. "Unraveling functionally distinct metabolic programs to predict immunotherapy response in non-small cell lung cancer (NSCLC)." <em>Annals of Oncology</em>. <br />
[<a href="https://doi.org/10.1016/j.annonc.2024.08.142">doi</a>]</p>
<p><strong>M. Fazli</strong> and <strong>S. Quinn</strong>. "Object Tracking in a 360° View: A Novel Perspective on Bridging the Gap to Biomedical Advancements." <em>IEEE Access</em>. <br />
[Submitted] [<a href="https://arxiv.org/abs/2412.01119">preprint</a>]</p>
<p>A. Abbadi and <strong>S. A. Vaezi</strong>, R. Karls, F. D. Quinn, and <strong>S. Quinn</strong>. "Time-lapse 3D confocal microscopy videos of mitochondrial dynamics in human alveolar epithelial cells (A549-DsRed) infected with Mycobacterium marinum (Mmar) strains." <em>Zenodo</em>. <br />
[<a href="https://doi.org/10.5281/zenodo.14046983">doi</a>]</p>
<p>M. A. H. Triana, K. M. Márquez-Nogueras, <strong>M. S. Fazli</strong>, <strong>S. Quinn</strong>, and S. N. J. Moreno. "Regulation of Calcium entry by cyclic GMP signaling in <em>Toxoplasma gondii</em>." <em>J. of Biological Chemistry</em>. <br />
[<a href="https://doi.org/10.1016/j.jbc.2024.105771">doi</a>] [<a href="http://cobweb.cs.uga.edu/~squinn/articles/JBC_2024.pdf">pdf</a>]</p>
<p><strong>S. A. Vaezi</strong> and <strong>S. Quinn</strong>. "Training a Supervised Cilia Segmentation Model from Self-Supervision." <em>SciPy</em>. <br />
[<a href="https://doi.org/10.25080/HXCJ6205">doi</a>] [<a href="https://pub.curvenote.com/0192d936-72e9-7066-83c3-41104f1ef3e0/public/full_text-82be3da7e3292103166b47b1491e81da.pdf">pdf</a>]</p>
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<h2>2023</h2>
<p><strong>C. Li</strong>, K. Lechtreck, J. Eggenschwiler, A. Brinck, <strong>R. Patel</strong>, and <strong>S. Quinn</strong>. "Video Dataset of Respiratory Cilia Motion Phenotypes." <em>Zenodo</em>. <br />
[<a href="https://doi.org/10.5281/zenodo.8135892">doi</a>]</p>
</div>
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<div class="col-lg-12">
<h2>2022</h2>
<p><strong>C. Godwin</strong>, <strong>M. Zain</strong>, <strong>N. Safir</strong>, <strong>I. Humphrey</strong>, and <strong>S. Quinn</strong>. "Incorporating Task-Agnostic Information in Task-Based Active Learning Using a Variational Autoencoder." <em>SciPy</em>. <br />
[<a href="https://doi.org/10.25080/majora-212e5952-011">doi</a>] [<a href="https://conference.scipy.org/proceedings/scipy2022/pdfs/godwin_zain.pdf">pdf</a>]</p>
<p><strong>N. Jacobi</strong>, <strong>I. Mo</strong>, <strong>A. You</strong>, <strong>K. Kishore</strong>, <strong>Z. Page</strong>, T. Heckman, and <strong>S. Quinn</strong>. "Temporal Word Embeddings Analysis for Disease Prevention." <em>SciPy</em>. <br />
[<a href="https://doi.org/10.25080/majora-212e5952-01a">doi</a>] [<a href="https://conference.scipy.org/proceedings/scipy2022/pdfs/nathan_jacobi_ivan_mo_albert_you.pdf">pdf</a>]</p>
<p><strong>S. A. Vaezi</strong>, <strong>G. Orlando</strong>, <strong>M. Fazli</strong>, G. Ward, S. Moreno, and <strong>S. Quinn</strong>. "A Novel Pipeline for Cell Instance Segmentation, Tracking, and Motility Classification of <em>Toxoplasma gondii</em> in 3D." <em>SciPy</em>. <br />
[<a href="https://doi.org/10.25080/majora-212e5952-009">doi</a>] [<a href="https://conference.scipy.org/proceedings/scipy2022/pdfs/alireza_vaezi.pdf">pdf</a>]</p>
<p><strong>N. Safir</strong>, <strong>M. Zain</strong>, <strong>C. Godwin</strong>, E. Miller, <strong>I. Humphrey</strong>, and <strong>S. Quinn</strong>. "Variational Autoencoders for Semi-Supervised Deep Metric Learning." <em>SciPy</em>. <br />
[<a href="https://doi.org/10.25080/majora-212e5952-022">doi</a>] [<a href="https://conference.scipy.org/proceedings/scipy2022/pdfs/safir_zain_22.pdf">pdf</a>]</p></p>
<p><strong>M. Zain</strong>, E. Miller, C. W. Lo, and <strong>S. Quinn</strong>. "Low-Level Feature Extraction for Cilia Segmentation." <em>SciPy</em>. <br />
[<a href="https://doi.org/10.25080/majora-212e5952-026">doi</a>] [<a href="https://conference.scipy.org/proceedings/scipy2022/pdfs/zain_miller.pdf">pdf</a>]</p>
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<div class="col-lg-12">
<h2>2021</h2>
<p>M. Skaro, <strong>M. Hill</strong>, Y. Zhou, <strong>S. Quinn</strong>, M. B. Davis, A. Sboner, M. Murph, and J. Arnold. "Are we there yet? A machine learning architecture to predict organotropic metastases." <em>BMC Medical Genomics</em>. <br />
[<a href="http://doi.org/10.1186/s12920-021-01122-7">doi</a>] [<a href="https://bmcmedgenomics.biomedcentral.com/track/pdf/10.1186/s12920-021-01122-7.pdf">pdf</a>]</p>
<p><strong>N. Pulagam</strong>, <strong>M. Hill</strong>, <strong>M. Fazli</strong>, <strong>M. Zain</strong>, <strong>R. Mattson</strong>, <strong>A. Durden</strong>, F. Quinn, C. Chennubhotla, and <strong>S. Quinn</strong>. "Classification of Diffuse Subcellular Morphologies." <em>SciPy</em>. <br />
[<a href="https://doi.org/10.25080/majora-1b6fd038-00f">doi</a>] [<a href="http://conference.scipy.org/proceedings/scipy2021/pdfs/neelima_pulagam.pdf">pdf</a>]</p>
<!--<strong>B. Alaila</strong>, <strong>M. Fazli</strong>, and <strong>S. Quinn</strong>. "Weakly-supervised, Deep and Multi-domain Object Segmentation via Contrastive Coding." <em>Medical Image Computing & Computer Assisted Intervention (MICCAI)</em>. <br />
[Under Review]</p>-->
<p>A. J. Stasic, E. J. Dykes, C. D. Cordeiro, S. A. Vella, <strong>M. S. Fazli</strong>, <strong>S. Quinn</strong>, R. Docampo, and S. N. J. Moreno. "Ca<sup>2+</sup> entry at the plasma membrane and uptake by acidic stores is regulated by proton transport in <em>Toxoplasma gondii</em>." <em>Molecular Microbiology</em>. <br />
[<a href="https://doi.org/10.1111/mmi.14722">doi</a>] [<a href="https://cobweb.cs.uga.edu/~squinn/articles/17049727.pdf">pdf</a>]</p>
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<div class="col-lg-12">
<h2>2020</h2>
<p>R. Anil, G. Capan, I. Drost-Fromm, T. Dunning, E. Friedman, T. Grant, <strong>S. Quinn</strong>, P. Ranjan, S. Schelter, and Ö. Yilmazel. "Apache Mahout: Machine Learning on Distributed Dataflow Systems." <em>Journal of Machine Learning Research (JMLR)</em>. <br />
[<a href="http://jmlr.org/papers/v21/18-800.html">doi</a>] [<a href="https://jmlr.csail.mit.edu/papers/volume21/18-800/18-800.pdf">pdf</a>]</p>
<p><strong>M. Hill</strong>, <strong>M. Fazli</strong>, <strong>R. Mattson</strong>, <strong>M. Zain</strong>, <strong>A. Durden</strong>, A. T. Loy, B. Reaves, A. Courtney, F. Quinn, C. Chennubhotla, and <strong>S. Quinn</strong>. "Spectral Analysis of Mitochondrial Dynamics: A Graph-Theoretic Approach to Understanding Subcellular Pathology." <em>SciPy</em>. <br />
[<a href="https://doi.org/10.25080/Majora-342d178e-00d">doi</a>] [<a href="https://conference.scipy.org/proceedings/scipy2020/pdfs/marcus_hill.pdf">pdf</a>] [<a href="https://mybinder.org/v2/gh/marcdh3/Scipy-2020/master?filepath=notebooks%2FSpectral%20Analysis%20of%20Mitochondrial%20Dynamics%20Poster.ipynb">mybinder</a>]</p>
<p><strong>M. Zain</strong>, <strong>S. Rao</strong>, <strong>N. Safir</strong>, <strong>Q. Wyner</strong>, <strong>I. Humphrey</strong>, <strong>A. Eldridge</strong>, <strong>C. Li</strong>, <strong>B. AlAila</strong>, and <strong>S. Quinn</strong>. "Unsupervised Representation of Cilia Video Using A Modular Generative Pipeline." <em>SciPy</em>. <br />
[<a href="https://doi.org/10.25080/Majora-342d178e-017">doi</a>] [<a href="https://conference.scipy.org/proceedings/scipy2020/pdfs/zain.pdf">pdf</a>]</p>
<p><strong>M. Fazli</strong>, <strong>M. Hill</strong>, <strong>A. Durden</strong>, A. Loy, <strong>R. Mattson</strong>, B. Reaves, A. Courtney, F. Quinn, C. Chennubhotla, and <strong>S. Quinn</strong>. "OrNet: A Python Toolkit to Model the Diffuse Structure of Organelles as Social Networks." <em>Journal of Open Source Software (JOSS)</em>. <br />
[<a href="https://doi.org/10.21105/joss.01983">doi</a>] [<a href="https://joss.theoj.org/papers/10.21105/joss.01983">pdf</a>] [<a href="https://github.com/quinngroup/ornet-JOSS">code</a>]</p>
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<h2>2019</h2>
<p><strong>M. Fazli</strong>, R. Stadler, <strong>B. AlAila</strong>, S. Vella, S. Moreno, G. E. Ward, and <strong>S. Quinn</strong>. "Lightweight and Scalable Particle Tracking and Motion Clustering of 3D Cell Trajectories." <em>IEEE International Conference on Data Science and Advanced Analytics (DSAA)</em>. <br />
[<a href="https://doi.org/10.1109/DSAA.2019.00056">doi</a>] [<a href="https://arxiv.org/abs/1908.03775">preprint</a>]</p>
<p><strong>R. Sivakumar</strong>, <strong>S. Quinn</strong>. "Parkinson's Classification and Feature Extraction from Diffusion Tensor Images." <em>SciPy</em>. <br />
[<a href="https://doi.org/10.25080/Majora-7ddc1dd1-00f">doi</a>] [<a href="http://conference.scipy.org/proceedings/scipy2019/pdfs/rajeswari_sivakumar.pdf">pdf</a>] [<a href="https://github.com/quinngroup/SciPy2019-demo">code</a>]</p>
<p><strong>C. McDaniel</strong>, <strong>S. Quinn</strong>. "GCNeuro: A Graph Convolutional Network Pipeline for Preprocessing and Analyzing Multimodal Neuroimage Data." <em>SciPy</em>. <br />
[<a href="https://doi.org/10.25080/Majora-7ddc1dd1-006">doi</a>] [<a href="http://conference.scipy.org/proceedings/scipy2019/pdfs/christian_mcdaniel.pdf">pdf</a>] [<a href="https://github.com/quinngroup/GCNeuro">code</a>]</p>
<p><strong>R. Ceren</strong>, <strong>S. Quinn</strong>, and G. Rains. "Towards a Decentralized, Autonomous Multiagent Framework for Mitigating Crop Loss." <br />
[<a href="https://arxiv.org/abs/1901.02035">preprint</a>]</p>
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<div class="col-lg-12">
<h2>2018</h2>
<p><strong>M. Fazli</strong>, S. Vella, S. Moreno, G. Ward, and <strong>S. Quinn</strong>. "Toward Simple & Scalable 3D Cell Tracking." <a href="https://osbd.github.io/2018/">Open Science in Big Data (OSBD) Workshop</a>. <em>IEEE BigData Conference</em>. <br />
[<a href="https://doi.org/10.1109/BigData.2018.8622403">doi</a>] [<a href="https://github.com/osbd/osbd-2018/raw/master/proceedings/S09209_6003.pdf">pdf</a>] [<a href="https://github.com/quinngroup/toxoplasma-3DTracking">code</a>]
<p><strong>A. Durden</strong>, A. Loy, B. Reaves, <strong>M. Fazli</strong>, A. Courtney, F. D. Quinn, S. C. Chennubhotla, and <strong>S. Quinn</strong>. "Dynamic Social Network Modeling of Diffuse Subcellular Morphologies." <em>SciPy</em>. <br />
[<a href="https://doi.org/10.25080/Majora-4af1f417-000">doi</a>] [<a href="http://conference.scipy.org/proceedings/scipy2018/pdfs/Andrew_Durden.pdf">pdf</a>] [<a href="https://cobweb.cs.uga.edu/~squinn/posters/OrNet_poster_SciPy2018.pdf">poster</a>]</p>
<p><strong>C. McDaniel</strong>, <strong>S. Quinn</strong>. "Developing an LSTM Pipeline for Accelerometer Data." <em>SciPy</em>. <br />
[<a href="https://doi.org/10.25080/Majora-4af1f417-005">doi</a>] [<a href="https://conference.scipy.org/proceedings/scipy2018/pdfs/christian_mcdaniel.pdf">pdf</a>] [<a href="https://cobweb.cs.uga.edu/~squinn/posters/LSTM_poster_SciPy2018.pptx">poster</a>] [<a href="https://github.com/xtianmcd/accelstm">code</a>]</p>
<p>M. Makkie, X. Li, <strong>S. Quinn</strong>, B. Lin, J. Yi, <strong>G. Mon</strong>, and T. Liu. "A Distributed Computing Platform for fMRI Big Data Analytics." <em>IEEE Transactions on Big Data</em>. <br />
[<a href="https://dx.doi.org/10.1109/TBDATA.2018.2811508">doi</a>] [<a href="https://cobweb.cs.uga.edu/~squinn/articles/TBD_fmri_2018.pdf">pdf</a>]</p>
<p><strong>N. Pandhe</strong>, B. Rada, and <strong>S. Quinn</strong>. "Generative Spatiotemporal Modeling of Neutrophil Behavior." <em>IEEE ISBI</em>. <br />
[<a href="https://doi.org/10.1109/ISBI.2018.8363732">doi</a>] [<a href="https://arxiv.org/abs/1804.00393">preprint</a>] [<a href="https://github.com/quinngroup/neutrophil-isbi2018/blob/master/poster.pdf">poster</a>]</p>
<p><strong>M. Fazli</strong>, S. Vella, S. Moreno, and <strong>S. Quinn</strong>. "Unsupervised Discovery of <em>Toxoplasma gondii</em> Motility Phenotypes." <em>IEEE ISBI</em>. <br />
[<a href="https://doi.org/10.1109/ISBI.2018.8363735">doi</a>] [<a href="https://arxiv.org/abs/1801.02591">preprint</a>] [<a href="https://drive.google.com/file/d/17vbC1K6nZ7NuTGcnVlQAK1cL4m0nqkIy/view">poster</a>] [<a href="https://github.com/quinngroup/toxoplasma-isbi2018">code</a>]</p>
<!--<p><strong>S. Quinn</strong>, A. Ramanathan, J. Castro, and C. Chennubhotla. "Designing a Physiochemical Descriptor Based Metric for Categorizing Odors." <em>Scientific Reports</em>. <br />
[Accepted]</p>-->
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<h2>2017</h2>
<p>W. Shalaby, <strong>B. AlAila</strong>, M. Korayem, L. Pournajaf, K. Aljadda, <strong>S. Quinn</strong>, and W. Zadrozny. "Help Me Find a Job: A Graph-based Approach for Job Recommendation at Scale." <em>IEEE BigData Conference</em>. <br />
[<a href="https://doi.org/10.1109/BigData.2017.8258088">doi</a>] [<a href="https://arxiv.org/abs/1801.00377">preprint</a>] </p>
<p><strong>M. Fazli</strong>, S. Vella, S. Moreno, and <strong>S. Quinn</strong>. "Computational Motility Tracking of Calcium Dynamics in Toxoplasma gondii." <a href="http://bigdas.org/">KDD Bigdas Workshop</a>. <em>ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD)</em>. <br />
[<a href="http://bigdas.org/wp-content/uploads/2015/10/computational_motility_tracking_Final-1.pdf">pdf</a>] [<a href="https://arxiv.org/abs/1708.01871">preprint</a>]</p>
<p><strong>C. Lu</strong> and <strong>S. Quinn</strong>. "Classification of Ciliary Motion with 3D Convolutional Neural Networks." <em>ACM Southeastern Conference</em>. <br />
[<a href="https://doi.org/10.1145/3077286.3077303">doi</a>] [<a href="https://www.researchgate.net/profile/Charles_Lu7/publication/316281392_Classification_of_Ciliary_Motion_with_3D_Convolutional_Neural_Networks/links/58f94fd20f7e9ba3ba4c65ac/Classification-of-Ciliary-Motion-with-3D-Convolutional-Neural-Networks.pdf">pdf</a>]</p>
<p>Y. Zhao, X. Li, M. Makkie, <strong>S. Quinn</strong>, B. Lin, J. Ye, and T. Liu. "Template-guided Functional Network Identification via Supervised Dictionary Learning." <em>IEEE ISBI</em>. <br />
[<a href="https://doi.org/10.1109/ISBI.2017.7950471">doi</a>] [<a href="https://www.researchgate.net/profile/Shannon_Quinn7/publication/317724860_Template-guided_Functional_Network_Identification_via_Supervised_Dictionary_Learning/links/5967ce1ea6fdcc18ea66308c/Template-guided-Functional-Network-Identification-via-Supervised-Dictionary-Learning.pdf">pdf</a>]</p>
<p>B. Norman, T. Davis, <strong>S. Quinn</strong>, R. Massey, and D. Hirsh. "Automated Identification of Pediatric Appendicitis Score in Emergency Department Notes using Natural Language Processing." <em>IEEE BHI</em>. <br />
[<a href="https://doi.org/10.1109/BHI.2017.7897310">doi</a>] [<a href="https://www.researchgate.net/profile/Shannon_Quinn7/publication/316940029_Automated_identification_of_pediatric_appendicitis_score_in_emergency_department_notes_using_natural_language_processing">pdf</a>]</p>
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<h2>2016</h2>
<p>S. Schelter, A. Palumbo, <strong>S. Quinn</strong>, S. Marthi, and A. Musselman. "Samsara: Declarative Machine Learning on Distributed Dataflow Systems." <a href="https://sites.google.com/site/mlsysnips2016/">Machine Learning Systems Workshop</a>. <em>Neural Information Processing Systems (NIPS)</em>. <br />
[<a href="https://ssc.io/pdf/samsara.pdf">pdf</a>] [<a href="https://ssc.io/pdf/poster-mlsystems.pdf">poster</a>]</p>
<p><strong>G. Mon</strong>, M. Makkie, X. Li, T. Liu, and <strong>S. Quinn</strong>. "Implementing Dictionary Learning in Apache Flink, Or: How I Learned to Relax and Love Iterations." <a href="https://osbd.github.io/2016">Open Science in Big Data (OSBD) Workshop</a>. <em>IEEE BigData Conference</em>. <br />
[<a href="https://doi.org/10.1109/BigData.2016.7840869">doi</a>] [<a href="https://www.researchgate.net/publication/312119468_Implementing_Dictionary_Learning_in_Apache_Flink_Or_How_I_Learned_to_Relax_and_Love_Iterations">pdf</a>] [<a href="https://github.com/quinngroup/pyflink-r1dl">code</a>]</p>
<p>M. Makkie, X. Li, B. Lin, J. Ye, <strong>M. Fazli</strong>, T. Liu, and <strong>S. Quinn</strong>. "Distributed Rank-1 Dictionary Learning: Towards Fast and Scalable Solutions for fMRI Big Data Analytics." KDDBHI Workshop. <em>IEEE BigData Conference</em>. <br />
[<a href="https://doi.org/10.1109/BigData.2016.7841000">doi</a>] [<a href="https://arxiv.org/abs/1708.02638">preprint</a>]</p>
<p>P. Sil, C. P. Hayes, B. J. Reaves, P. Breen, <strong>S. Quinn</strong>, 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." <em>Journal of Immunology</em>. <br />
[<a href="https://dx.doi.org/10.4049/jimmunol.1600766">doi</a>] [<a href="https://cobweb.cs.uga.edu/~squinn/articles/J_Immunol-2017-Sil.pdf">pdf</a>] [<a href="https://github.com/quinngroup/JI-2016-MRS2578">code</a>]</p>
<p>P. Breen, J. Kelly, T. Heckman, and <strong>S. Quinn</strong>. "Mining Pre-Exposure Prophylaxis Trends in Social Media." <em>IEEE International Conference on Data Science and Advanced Analytics (DSAA)</em>. <br />
[<a href="https://doi.org/10.1109/DSAA.2016.29">doi</a>] [<a href="https://cobweb.cs.uga.edu/~squinn/articles/PID4438357.pdf">pdf</a>]</p>
<p><strong>[Invited Paper]</strong> J. Miller, C. Bowman, V. G. Harish, and <strong>S. Quinn</strong>. "Open Source Big Data Analytics Frameworks Written in Scala." <em>IEEE International Congress on Big Data</em>. <br />
[<a href="http://dx.doi.org/10.1109/BigDataCongress.2016.61">doi</a>] [<a href="https://cobweb.cs.uga.edu/~squinn/articles/miller_scala_2016.pdf">pdf</a>]</p>
<p>X. Li, M. Makkie, B. Lin, <strong>M. Fazli</strong>, I. Davidson, J. Ye, T. Liu, and <strong>S. Quinn</strong>. "Scalable Fast Rank-1 Dictionary Learning for fMRI Big Data Analysis." <em>ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD)</em>. <br />
[<a href="http://dx.doi.org/10.1145/2939672.2939730">doi</a>] [<a href="http://www.kdd.org/kdd2016/papers/files/adp0864-li.pdf">pdf</a>] [<a href="https://github.com/quinngroup/dr1dl-pyspark">code</a>]</p>
<p><strong>S. Quinn</strong>, A. Ramanathan, L. Pullum, and C. Steed. "Dr. Twitter: The Logistics of Practical Disease Surveillance using Social Media." <em>IEEE International Conference on Biomedical and Health Informatics (BHI)</em>. <br />
[<a href="https://cobweb.cs.uga.edu/~squinn/articles/quinn_bhi_2016.pdf">pdf</a>]</p>
<p>A. Ramanathan, <strong>S. Quinn</strong>, L. Pullum, and C. Steed. "Tracking Alcohol and Marijuana Usage and Behaviors from Social Media using Oak Ridge Bio-Surveillance Toolkit." <em>IEEE EMBS BHI</em>. <br />
[<a href="https://cobweb.cs.uga.edu/~squinn/articles/ramanathan_bhi_2016.pdf">pdf</a>]</p>
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<h2>2015</h2>
<p>A. Ramanathan, L. Pullum, T. Hobson, C. Stahl, C. Steed, <strong>S. Quinn</strong>, and C. Chennubhotla. "Discovering Multi-scale Co-occurrence Patterns of Asthma and Influenza with the Oak Ridge Bio-surveillance Toolkit." <em>Frontiers in Public Health</em>. <br />
[<a href="http://dx.doi.org/10.3389/fpubh.2015.00182">doi</a>] [<a href="http://journal.frontiersin.org/article/10.3389/fpubh.2015.00182/pdf">pdf</a>]</p>
<p><strong>S. Quinn</strong>, M. Zahid, J. Durkin, R. Francis, C. W. Lo, and C. Chennubhotla. "Automated identification of abnormal respiratory ciliary motion in nasal biopsies." <em>Science Translational Medicine</em>. <br />
[<a href="http://dx.doi.org/10.1126/scitranslmed.aaa1233">doi</a>] [<a href="https://cobweb.cs.uga.edu/~squinn/articles/quinn_stm2015.pdf">pdf</a>] [<a href="https://cobweb.cs.uga.edu/~squinn/articles/quinn_stm2015_supp.pdf">supplementary pdf</a>] [<a href="https://cobweb.cs.uga.edu/~squinn/articles/quinn_stm2015_avis.zip">supplementary zip</a>] <br />
(<a href="http://news.uga.edu/releases/article/new-techniques-diagnosing-respiratory-abnormalities-0815/">UGA Today</a>) (<a href="http://medicalxpress.com/news/2015-08-team-method-quantifying-ciliary-movement.html">Medical Xpress</a>)</p>
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<h2>2014</h2>
<p>A. Ramanathan, L. Pullum, T. Hobson, C. Steed, <strong>S. Quinn</strong>, and C. Chennubhotla. "ORBiT: Oak Ridge Bio-surveillance Toolkit for Public Health Dynamics." <em>BMC Bioinformatics</em>. <br />
[<a href="http://dx.doi.org/10.1186/1471-2105-16-S17-S4">doi</a>] [<a href="https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-16-S17-S4?site=bmcbioinformatics.biomedcentral.com">pdf</a>]</p>
<p>J. Castro, <strong>S. Quinn</strong>, 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. <em>Flavour</em>. <br />
[<a href="http://dx.doi.org/10.1186/2044-7248-3-S1-P3">doi</a>] [<a href="http://flavourjournal.biomedcentral.com/track/pdf/10.1186/2044-7248-3-S1-P3?site=flavourjournal.biomedcentral.com">pdf</a>]</p>
<p><strong>S. Quinn</strong>, 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. <em>D-Scholarship</em>, University of Pittsburgh.<br />
[<a href="http://d-scholarship.pitt.edu/23857/">d-scholarship</a>]</p>
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<h2>2013</h2>
<p>A. Ramanathan, L. Pullum, T. C. Hobson, <strong>S. Quinn</strong>, C. Chennubhotla, and S. Valkova. "Discovery of Disease Co-occurrence Patterns from Electronic Healthcare Reimbursement Claims Data." <em>Knowledge Discovery and Data Mining Big Data in Health Informatics (KDD-BHI)</em> <br />
[<a href="https://cobweb.cs.uga.edu/~squinn/articles/KDDBHI_2014.pdf">pdf</a>]</p>
<p>A. Ramanathan, L. Pullum, C. Steed, <strong>S. Quinn</strong>, T. Parker, and C. Chennubhotla. "Integrating Heterogeneous Healthcare Datasets and Visual Analytics for Disease Bio-Surveillance and Dynamics." <em>IEEE Workshop on Interactive Visual Text Analytics</em>, IEEE VIS. <br />
[<a href="http://vialab.science.uoit.ca/textvis2013/papers/Ramanathan-TextVis2013.pdf">pdf</a>]</p>
<p>A. Ramanathan, L. Pullum, C. Steed, T. Parker, <strong>S. Quinn</strong>, and C. Chennubhotla. "Oak Ridge Bio-Surveillance Toolkit (ORBiT): Integrating Big-Data Analytics with Visual Analysis for Public Health Dynamics." <em>Public Health’s Wicked Problems: Can InfoVis Save Lives?</em>, IEEE VIS. <br />
[<a href="http://www.cc.gatech.edu/gvu/ii/PublicHealthVis/Papers/OrBIT_PHDecisionMaking_F.pdf">pdf</a>]</p>
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<h2>2012</h2>
<p>"Statistical Inference for Big Data Problems in Molecular Biophysics" by A. Ramanathan, A. Savol, V. Burger, <strong>S. Quinn</strong>, P. Agarwal, and C. Chennubhotla, <em>NIPS2012 Workshop on Parallel and Large-Scale Machine Learning</em>. <br />
[<a href="http://www.biglearn.org/2012/files/papers/biglearning2012_submission_14.pdf">pdf</a>]</p>
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<h2>2011</h2>
<p><strong>S. Quinn</strong>, R. Francis, C. W. Lo, and C. Chennubhotla. "Novel Use of Differential Image Velocity Invariants to Categorize Ciliary Motion Defects." <em>Proceedings in the Biomedical Science and Engineering Conference</em>. <br />
[<a href="http://dx.doi.org/10.1109/BSEC.2011.5872328">doi</a>] [<a href="https://cobweb.cs.uga.edu/~squinn/articles/quinn_bsec2011.pdf">pdf</a>]</p>
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<h2>2010</h2>
<p>L. P. Coelho, E. Glory-Afshar, J. Kangas, <strong>S. Quinn</strong>, A. Shariff, and R. F. Murphy. "Principles of Bioimage Informatics: Focus on machine learning of cell patterns." <em>Lecture Notes in Computer Science</em>. <br />
[<a href="http://murphylab.web.cmu.edu/publications/168-coelho2010.pdf">pdf</a>]</p>
<p>A. Shariff, J. Kangas, L.P. Coelho, <strong>S. Quinn</strong>, and R.F. Murphy. "Automated Image Analysis for High Content Screening and Analysis." <em>J. Biomolec. Screening</em>. <br />
[<a href="http://dx.doi.org/10.1177/1087057110370894">doi</a>]</p>
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