A selection of publications from faculty in the Computer Science Department at Old Dominion University.

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Submissions from 2022

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DeepPatent: Large Scale Patent Drawing Recognition and Retrieval, Michal Kucer, Diane Oyen, Juan Castorena, and Jian Wu

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Eye Movement and Pupil Measures: A Review, Bhanuka Mahanama, Yasith Jayawardana, Sundararaman Rengarajan, Gavindya Jayawardena, Leanne Chukoskie, Joseph Snider, and Sampath Jayarathna

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m-CUBES: An Efficient and Portable Implementation of Multi-Dimensional Integration for GPUs, Ioannis Sakiotis, Kamesh Arumugam, Marc Paterno, Desh Ranjan, Balŝa Terzić, and Mohammad Zubair

Submissions from 2021

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NPGreat: Assembly of the Human Subtelomere Regions with the Use of Ultralong Nanopore Reads and Linked Reads, Eleni Adam, Desh Ranjan, and Harold Riethman

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Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies, Maytha Alshammari and Jing He

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Smart Parking Systems: Reviewing the Literature, Architecture and Ways Forward, Can Biyik, Zaheer Allam, Gabriele Pieri, Davide Moroni, Muftah O' Fraifer, Eoin O' Connell, Stephan Olariu, and Muhammad Khalid

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fMRI Feature Extraction Model for ADHD Classification Using Convolutional Neural Network, Senuri De Silva, Sanuwani Udara Dayarathna, Gangani Ariyarathne, Dulani Meedeniya, and Sampath Jayarathna

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Adaptive Physics-Based Non-Rigid Registration for Immersive Image-Guided Neuronavigation Systems, Fotis Drakopoulos, Christos Tsolakis, Angelos Angelopoulos, Yixun Liu, Chengjun Yao, Kyriaki Rafailia Kavazidi, Nikolaos Foroglou, Andrey Fedorov, Sarah Frisken, Ron Kikinis, Alexandra Golby, and Nikos Chrisochoides

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A Survey of Enabling Technologies for Smart Communities, Amna Iqbal and Stephan Olariu

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Automated Filtering of Eye Movements Using Dynamic AOI in Multiple Granularity Levels, Gavindya Jayawardena and Sampath Jayarathna

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Understanding the Impact of Encrypted DNS on Internet Censorship, Lin Jin, Shuai Hao, Haining Wang, and Chase Cotton

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Large Scale Subject Category Classification of Scholarly Papers With Deep Attentive Neural Networks, Bharath Kandimalla, Shaurya Rohatgi, Jian Wu, and C. Lee Giles

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Extraction and Evaluation of Statistical Information from Social and Behavioral Science Papers, Sree Sai Teja Lanka, Sarah Rajtmajer, Jian Wu, and C. Lee Giles

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Vehicular Crowdsourcing for Congestion Support in Smart Cities, Stephan Olariu

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SEE-TREND: SEcurE Traffic-Related EveNt Detection in Smart Communities, Stephan Olariu and Dimitrie C. Popescu

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Cybersecurity, Technology, and Society: Developing an Interdisciplinary, Open, General Education Cybersecurity Course, Brian K. Payne, Wu He, Cong Wang, D. E. Wittkower, and Hongyi Wu

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DeapSECURE Computational Training for Cybersecurity Students: Improvements, Mid-Stage Evaluation, and Lessons Learned, Wirawan Purwanto, Yuming He, Jewel Ossom, Qiao Zhang, Liuwan Zhu, Karina Arcaute, Masha Sosonkina, and Hongyi Wu

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Ranked List Fusion and Re-Ranking With Pre-Trained Transformers for ARQMath Lab, Shaurya Rohatgi, Jian Wu, and C. Lee Giles

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Parallel Anisotropic Unstructured Grid Adaptation, Christos Tsolakis, Nikos Chrisochoides, Michael A. Park, Adrien Loseille, and Todd Michal

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De Novo Prediction of Drug–Target Interactions Using Laplacian Regularized Schatten p-Norm Minimization, Gaoyan Wu, Mengyun Yang, Yaohang Li, and Jianxin Wang

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You See What I Want You To See: Exploring Targeted Black-Box Transferability Attack for Hash-Based Image Retrieval Systems, Yanru Xiao and Cong Wang

Submissions from 2020

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SaIL: Saliency-Driven Injection of ARIA Landmarks, Ali Selman Aydin, Shirin Feiz, Vikas Ashok, and IV Ramakrishnan

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Towards Making Videos Accessible for Low Vision Screen Magnifier Users, Ali Selman Aydin, Shirin Feiz, Vikas Ashok, and IV Ramakrishnan

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A Saliency-Driven Video Magnifier For People With Low Vision, Ali Selman Aydin, Shirin Feiz, IV Ramakrishnan, and Vikas Ashok

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Outlier Profiles of Atomic Structures Derived From X-ray Crystallography and From Cryo-electron Microscopy, Lin Chen, Jing He, and Angelo Facchiano

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A Heuristic Baseline Method for Metadata Extraction from Scanned Electronic Theses and Dissertations, Muntabir H. Choudhury, Jian Wu, William A. Ingam, and Edward A. Fox

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DeepFrag-k: A Fragment-Based Deep Learning Approach for Protein Fold Recognition, Wessam Elhefnawy, Min Li, Jianxin Wang, and Yaohang Li

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Streaming Analytics and Workflow Automation for DFS, Yasith Jayawardana and Sampath Jayarathna

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MementoEmbed and Raintale for Web Archive Storytelling, Shawn M. Jones, Martin Klein, Michele C. Weigle, and Michael L. Nelson

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SHARI- An Integration of Tools to Visualize the Story of the Day, Shawn M. Jones, Alexander C. Nwala, Martin Klein, Michele C. Weigle, and Michael L. Nelson

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Rotate-and-Press: A Non-Visual Alternative to Point-and-Click, Hae-Na Lee, Vikas Ashok, and I. V. Ramakrishnan

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Repurposing Visual Input Modalities for Blind Users: A Case Study of Word Processors, Hae-Na Lee, Vikas Ashok, and I.V. Ramakrishnan

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Granulosa Cell Proliferation is Inhibited by PGE2 in the Primate Ovulatory Follicle, Patric S. Lundberg, Gil J. Moskowitz, Carmel Bellacose, Esra Demirel, Heidi A. Trau, and Diane M. Duffy

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TMVis: Visualizing Webpage Changes Over Time, Abigail Mabe, Dhruv Patel, Maheedhar Gunnam, Surbhi Shankar, Mat Kelly, Sawood Alam, Michael L. Nelson, and Michele C. Weigle

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DeepMag+ : Sniffing Mobile Apps in Magnetic Field Through Deep Learning, Rui Ning, Cong Wang, ChunSheng Xin, Jiang Li, and Hongyi Wu

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A Genome-Wide Association Study of Cocaine Use Disorder Accounting for Phenotypic Heterogeneity and Gene–Environment Interaction, Jiangwen Sun, Henry R. Kranzler, Joel Gelernter, and Jinbo Bi

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Extreme Ultraviolet Quasar Colours from GALEX Observations of the SDSS DR14Q Catalogue, Daniel E. Vanden Berk, Sarah C. Wesolowski, Mary J. Yeckley, Joseph M. Marcinik, Jean M. Quashnock, Lawrence M. Machia, and Jian Wu

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Gabapentin Drug Misuse Signals: A Pharmacovigilance Assessment Using the FDA Adverse Event Reporting System, Rachel Vickers-Smith, Jiangwen Sun, Richard J. Charnigo, Michelle R. Lofwall, Sharon L. Walsh, and Jennifer R. Havens

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Evade Deep Image Retrieval by Stashing Private Images in the Hash Space, Yanru Xiao, Cong Wang, and Xing Gao

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GangSweep: Sweep Out Neural Backdoors by GAN, Liuwan Zhu, Rui Ning, Cong Wang, Chunsheng Xin, and Hongyi Wu

Submissions from 2019

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Impact of HTTP Cookie Violations in Web Archives, Sawood Alam, Michele C. Weigle, and Michael L. Nelson

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MementoMap: An Archive Profile Dissemination Framework, Sawood Alam, Michele C. Weigle, and Michael L. Nelson

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EEG-Based Processing and Classification Methodologies for Autism Spectrum Disorder: A Review, Gunavaran Brihadiswaran, Dilantha Haputhanthri, Sahan Gunathilaka, Dulani Meedeniya, and Sampath Jayarathna

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Dormant Pathogenic CD4(+) T Cells Are Prevalent in the Peripheral Repertoire of Healthy Mice, Anna Cebula, Michal Kuczma, Edyta Szurek, Maciej Pietrzak, Natasha Savage, Wessam R. Elhefnawy, Grzegorz Rempala, Piotr Kraj, and Leszek Ignatowicz

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Multi-View Cluster Analysis With Incomplete Data to Understand Treatment Effects, Guoqing Chao, Jiangwen Sun, Jin Lu, An-Li Wang, Daniel D. Langleben, Chiang-Shan Li, and Jinbo Bi

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A Survey of Attention Deficit Hyperactivity Disorder Identification Using Psychophysiological Data, S. De Silva, S. Dayarathna, G. Ariyarathne, D. Meedeniya, and Sampath Jayarathna

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Electroencephalogram (EEG) For Delineating Objective Measure of Autism Spectrum Disorder, Sampath Jayarathna, Yasith Jayawardana, Mark Jaime, and Sashi Thapaliya

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Sec-Lib: Protecting Scholarly Digital Libraries From Infected Papers Using Active Machine Learning Framework, Nir Nissim, Aviad Cohen, Jian Wu, Andrea Lanzi, Lior Rokach, Yuval Elovici, and Lee Giles

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IEEE Access Special Section Editorial: Wirelessly Powered Networks, and Technologies, Theofanis P. Raptis, Nuno B. Carvalho, Diego Masotti, Lei Shu, Cong Wang, and Yuanyuan Yang

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Dynamics of Trophoblast Differentiation in Peri-Implantation–Stage Human Embryos, Rachel C. West, Hao Ming, Deirdre M. Logsdon, Jiangwen Sun, Sandeep K. Rajput, Rebecca A. Kile, William B. Schoolcraft, R. Michael Roberts, Rebecca L. Krisher, Zongliang Jiang, and Ye Yuan

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Drug Repositioning Based on Bounded Nuclear Norm Regularization, Mengyun Yang, Huimin Lao, Yaohang Li, and Jianxin Wang

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Overlap Matrix Completion for Predicting Drug-Associated Indications, Menhyun Yang, Huimin Luo, Yaohang Li, Fang-Xiang Wu, and Jianxin Wang

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Clinical Big Data and Deep Learning: Applications, Challenges, and Future Outlooks, Ying Yu, Liangliang Liu, Yaohang Li, and Jianxin Wang

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DeepEP: A Deep Learning Framework for Identifying Essential Proteins, Min Zeng, Min Li, Fang-Xiang Wu, Yaohang Li, and Yi Pan

Submissions from 2018

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Unobtrusive and Extensible Archival Replay Banners Using Custom Elements, Sawood Alam, Mat Kelly, Michele C. Weigle, and Michael L. Nelson

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An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains, Lin Chen, Jing He, Salim Sazzed, and Rayshawn Walker

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Quantification of Twist from the Central Lines of β-Strands, Tunazzina Islam, Michael Poteat, and Jing He

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Prediction of lncRNA-Disease Associations Based on Inductive Matrix Completion, Chengqian Lu, Mengyun Yang, Feng Luo, Fang-Xiang Wu, Min Li, Yi Pan, Yaohang Li, and Jianxin Wang

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A Survey of Matrix Completion Methods for Recommendation Systems, Andy Ramlatchan, Mengyun Yang, Quan Liu, Min Li, Jianxin Wang, and Yaohang Li

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Tracing Actin Filament Bundles in Three-Dimensional Electron Tomography Density Maps of Hair Cell Stereocilia, Salim Sazzed, Junha Song, Julio Kovacs, Willi Wriggers, Manfred Auer, and Jing He

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Non-Canonicaly Recruited TCRαβCD8αα IELs Recognize Microbial Antigens, Lukasz Wojciech, Edyta Szurek, Michal Kuczma, Anna Cebula, Wessam R. Elhefnawy, Maciej Pietrzak, Grzegorz Rempala, and Leszek Ignatowicz

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Efficient Randomized Algorithms for the Fixed Precision Low Rank Matrix Approximation, Wenjian Yu, Yu Gu, and Yaohang Li

Submissions from 2017

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An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Stephanie Zeil, Kamal Al Nasr, and Jing He

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Efficient Core Utilization in a Hybrid Parallel Delaunay Meshing Algorithm on Distributed-Memory Cluster, Daming Feng, Andrey N. Chernikov, and Nikos P. Chrisochoides

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Impact of URI Canonicalization on Memento Count, Mat Kelly, Lulwah M. Alkwai, Michael L. Nelson, Michele C. Weigle, and Herbert Van De Sompel

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An Iterative Bézier Method for Fitting Beta-Sheet Component of a Cryo-EM Density Map, Michael Poteat and Jing He

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Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps, Dong Si and Jing He

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Homeomorphic Tetrahedralization of Multi-material Images with Quality and Fidelity Guarantees, Jing Xu and Andrey N. Chernikov

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Homeomorphic Tetrahedral Tessellation for Biomedical Images, Jing Xu and Andrey N. Chernikov

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Comparing an Atomic Model or Structure to a Corresponding Cryo-Electron Microscopy Image at the Central Axis of a Helix, Stephanie Zeil, Julio Kovacs, Willy Wriggers, and Jing He

Submissions from 2016

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Leveraging Heritrix and the Wayback Machine on a Corporate Intranet: A Case Study on Improving Corporate Archives, Justin F. Brunelle, Krista Ferrante, Eliot Wilczek, Michele C. Weigle, and Michael L. Nelson

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Deep Models for Brain EM Image Segmentation: Novel Insights and improved Performance, Ahmed Fakhry, Hanchuan Peng, and Shuiwang Ji

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A Hybrid Parallel Delaunay Image-to-Mesh Conversion Algorithm Scalable on Distributed-memory Clusters, Daming Feng, Andrey N. Chernikov, and Nikos Chrisochoides

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Big Data-Enabled Multiscale Serviceability Analysis for Aging Bridges, Yu Liang, Dalei Wu, Guirong Liu, Yaohang Li, Cuilan Gao, Zhongguo John Ma, and Weidong Wu

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A Hybrid Algorithm Based on Optimal Quadratic Spline Collocation and Parareal Deferred Correction for Parabolic PDEs, Jun Liu, Yan Wang, and Rongjian Li

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RCD+: Fast Loop Modeling Server, José R. López-Blanco, Alejandro J. Canosa-Valis, Yaohang Li, and Pablo Chacón

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FLEXc: Protein Flexibility Prediction Using Context-Based Statistics, Predicted Structural Features, and Sequence Information, Ashraf Yaseen, Mais Nijim, Brandon Williams, Lei Qian, Min Li, Jianxin Wang, and Yaohang Li

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Interactively Cutting and Constraining Vertices in Meshes Using Augmented Matrices, Yu-Hong Yeung, Jessica Crouch, and Alex Pothen

Submissions from 2015

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Characteristics of Social Media Stories, Yasmin AINoamany, Michele C. Weigle, and Michael L. Nelson

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ISQuest: Finding Insertion Sequences in Prokaryotic Sequence Fragment Data, Abhishek Biswas, David T. Gauthier, Desh Ranjan, and Mohammad Zubair

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Extreme-Scale Parallel Mesh Generation: Telescopic Approach, Nikos Chrisochoides, Andrey Chernikov, Daming Feng, and Christos Tsolakis

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Tetrahedral Image-to-Mesh Conversion Software for Anatomic Modeling of Arteriovenous Malformations, Fotis Drakopoulos, Ricardo Ortiz, Andinet Enquobahrie, Deanna Sasaki-Adams, and Nikos Chrisochoides

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Scalable 3D Hybrid Parallel Delaunay Image-to-Mesh Conversion Algorithm for Distributed Shared Memory Architectures, Daming Feng, Christos Tsolakis, Andrey N. Chernikov, and Nikos P. Chrisochoides

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Making Sense of Video Analytics: Lessons Learned from Clickstream Interactions, Attitudes, and Learning Outcome in a Video-Assisted Course, Michail N. Giannakos, Konstantinos Chorianopoulos, and Nikos Chrisochoides

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Scaffolding to Improve Writing Skills in a Computer Science Literacy Course, Wu He, Harris Wu, Li Xu, and Kurt Maly

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Saccharomyces Boulardii and Bismuth Subsalicylate as Low-Cost Interventions to Reduce the Duration and Severity of Cholera, Johnathan Sheele, Jessica Cartowski, Angela Dart, Arjun Poddar, Shikha Gupta, and Ajay Gupta

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High-Performance Simulations of Coherent Synchrotron Radiation on Multicore GPU and CPU Platforms, B. Terzić, A. Godunov, K. Arumugam, D. Ranjan, and M. Zubair

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Reminiscing About 15 Years of Interoperability Efforts, Herbert Van de Sompel and Michael L. Nelson

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Numerical Geometry of Map and Model Assessment, Willy Wriggers and Jing He

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Deep Convolutional Neural Networks for Annotating Gene Expression Patterns in the Mouse Brain, Tao Zeng, Rongjian Li, Ravi Mukkamala, Jieping Ye, and Shuiwang Ji

Submissions from 2014

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Toward a Real Time Multi-Tissue Adaptive Physics Based Non-Rigid Registration Framework for Brain Tumor Resection, Fotis Drakopoulos, Panagiotis Foteinos, Yixun Liu, and Nikos Chrisochoides

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Automated Identification of Cell Type Specific Genes in the Mouse Brain by Image Computing of Expression Patterns, Rongjian Li, Wenlu Zhang, and Shuiwang Ji

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A Nonrigid Registration Method for Correcting Brain Deformation Induced by Tumor Resection, Yixun Liu, Chengjun Yao, Fotis Drakopoulos, Jinsong Wu, Liangfu Zhou, and Nikos Chrisochoides

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A Scalable Backward Chaining-Based Reasoner for a Semantic Web, Hui Shi, Kurt Maly, and Steven Zeil

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Tracing Beta Strands Using StrandTwister from Cryo-EM Density Maps at Medium Resolutions, Dong Si and Jing He

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GPU Accelerated Long-Term Simulations of Beam-Beam Effects in Colliders, B. Terzić, V. Morozov, Y. Roblin, F. Lin, H. Zhang, M. Aturban, D. Ranjan, and M. Zubair

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Automatic Curvilinear Quality Mesh Generation Driven by Smooth Boundary and Guaranteed Fidelity, Jing Xu and Andrey N. Chernikov

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Template-Based C8-Scorpion: A Protein 8 State Secondary Structure Prediction Method Using Structural Information and Context-Based Features, Ashraf Yaseen and Yaohang Li

Submissions from 2013

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The 6th Computational Structural Bioinformatics Workshop Introduction, Jing He, Amarda Shehu, Nurit Haspel, and Brian Chen

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Convergence Analysis of Markov Chain Monte Carlo Linear Solvers Using Ulam--von Neumann Algorithm, Hao Ji, Michael Mascagni, and Yaohang Li