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

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Submissions from 2018

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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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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

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

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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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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

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Computational Genetic Neuroanatomy of the Developing Mouse Brain: Dimensionality Reduction, Visualization, and Clustering, Shuiwang Ji

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A Method for Identifying Personalized Representations in Web Archives, Mat Kelly, Justin F. Brunelle, Michele C. Weigle, and Michael L. Nelson

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Conformational Sampling in Template Free Protein Loop Structure Modeling: An Overview, Yaohang Li

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Estimating Loop Length from CryoEM Images at Medium Resolutions, Andrew McKnight, Dong Si, Kamal Al Nasr, Andrey Chemikov, Nikos Chrisochoides, and Jing He

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Intensity-Based Skeletonization of CryoEM Gray-Scale Images Using a True Segmentation-Free Algorithm, Kamal Al Nasr, Chunmei Liu, Mugizi Rwebangira, Legand Burge, and Jing He

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GPU-optimized Code for Long-term Simulations of Beam-beam Effects in Colliders, Y. Roblin, V. Morozov, B. Terzić, M. Aturban, D. Ranjan, and M. Zubair

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Image-Level and Group-Level Models for Drosophila Gene Expression Pattern Annotation, Quian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart Newfeld, Sudhir Kumar, and Jieping Ye

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Dinosolve: A Protein Disulfide Bonding Prediction Server Using Context-Based Features to Enhance Prediction Accuracy, Ashraf Yaseen and Yaohang Li

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A Mesh Generation and Machine Learning Framework for Drosophila Gene Expression Pattern Image Analysis, Wenlu Zhang, Daming Feng, Rongjian Li, Andrey Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart Newfeld, Sudhir Kumar, and Shuiwang Ji

Submissions from 2012

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On a Versatile Stochastic Growth Model, Samiur Arif, Ismail Khalil, and Stephan Olariu

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Generalized Insertion Region Guides for Delaunay Mesh Refinement, Andrey Chernikov and Nikos Chrisochoides

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MOMCMC: An Efficient Monte Carlo Method for Multi-Objective Sampling Over Real Parameter Space, Yaohang Li

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Cooperation as a Service in VANET: Implementation and Simulation Results, Hajar Mousannif, Ismail Khalil, and Stephan Olariu

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Learning Sparse Representations for Fruit Fly Gene Expression Pattern Image Annotation and Retreival, Lei Yuan, Alexander Woodard, Shuiwang Ji, Yuan Jiang, Zhi-Hua Zhou, Sudhir Kumar, and Jieping Ye

Submissions from 2011

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Special Issue on Wireless Sensor and Actuator Networks, Jiming Chen, Karl H. Johanson, Stephan Olariu, Ioannis Ch. Paschalidis, and Ivan Stojmenovic

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Multitissue Tetrahedral Image-to-Mesh Conversion with Guaranteed Quality and Fidelity, Andrey N. Chernikov and Nikos P. Chrisochoides

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User Experiments of a Social, Faceted Multimedia Classification System, LiuLiu Fu, Kurt Maly, Elizabeth Rasnick, Harris Wu, and Mohammad Zubair

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Computational Network Analysis of the Anatomical and Genetic Organizations in the Mouse Brain, Shuiwang Ji

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Vehicular Ad Hoc Networks, Syed R. Rizvi, Stephan Olariu, Christina M. Oinotti, Shaharuddin Salleh, Mona E. Rizvi, and Zainab Zaidi

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From Isotropic to Anisotropic Side Chain Representations: Comparison of Three Models for Residue Contact Estimation, Weitao Sun and Jing He

Submissions from 2010

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Fully Generalized Two-Dimensional Constrained Delaunay Mesh Refinement, Panagiotis A. Foteinos, Andrey N. Chernikov, and Nikos P. Chrisochoides

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The 3rd Computational Structural Bioinformatics Workshop, Jing He and Di Wu

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Improving Predicted Protein Loop Structure Ranking Using a Pareto-Optimality Consensus Method, Yaohang Li, Ionel Rata, See-Wing Chiu, and Erik Jakobsson

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Structure Prediction for the Helical Skeletons Detected from the Low Resolution Protein Density Map, Kamal Al Nasr, Weitao Sun, and Jing He

Submissions from 2009

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Multicast Encryption Infrastructure for Security in Sensor Networks, Richard R. Brooks, Brijesh Pillai, Matthew Pirretti, and Michele C. Weigle

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Evaluating Multicore Algorithms on the Unified Memory Model, John E. Savage and Mohammad Zubair

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Adding eScience Assets to the Data Web, Herbert H. Van de Sompel, Carl Lagoze, Michael L. Nelson, Simeon Warner, Robert Sanderson, and Pete Johnston

Submissions from 2008

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Efficient Corona Training Protocols for Sensor Networks, Alan A. Bertossi, Stephan Olariu, and Cristina M. Pinotti

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Dedication to Pierre Lallemand on the Occasion of His Retirement, Dominque d'Humieres, Manfred Krafczyk, Li-Shi Luo, and Robert Rubinstein

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Emergent Behavior in Massively-Deployed Sensor Networks, Ekaterina Shurkova, Ruzana Ishak, Stephan Olariu, and Shaharuddin Salleh

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Creating Preservation-Ready Web Resources, Joan A. Smith and Michael L. Nelson

Submissions from 2007

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Optimal Layout of Multicast Groups Using Network Embedded Multicast Security in Ad Hoc Sensor Networks, Richard R. Brooks, Brijesh Pillai, Michele C. Weigle, and Matthew Pirretti

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All Minimal Prime Extensions of Hereditary Classes of Graphs, Vassilis Giakoumakis and Stephan Olariu

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Assessing the Format of the Presentation of Text in Developing a Reading Strategy Assessment Tool (R-SAT), Sara Gilliam, Joseph P. Magliano, Keith K. Millis, Irwin Levinstein, and Chutima Boonthum

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Hybrid Training With Binary Search Protocol for Wireless Sensor Networks, Ruzana Ishak, Qingwen Xu, Stephan Olariu, and Shaharuddin Salleh

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iSTART 2: Improvements for Efficiency and Effectiveness, Irwin B. Levinstein, Chutima Boonthum, Srinivasa P. Pillarisetti, Courtney Bell, and Danielle S. McNamara

Submissions from 2006

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SPLAI: Computational Finite Element Model for Sensor Networks, Ruzana Ishak, Shadaruddin Salleh, Stephan Olariu, and Mohd.Ismail Abdul Aziz

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FeDCOR: An Institutional CORDRA Registry, Giridhar Manepalli, Henry Jerez, and Michael L. Nelson

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Observed Web Robot Behavior on Decaying Web Subsites, Joan A. Smith, Frank McCown, and Michael L. Nelson

Submissions from 2005

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Lessons Learned with Arc, an OAI-PMH Service Provider, Xiaoming Liu, Kurt Maly, and Michael L. Nelson

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Final Report for the Development of the NASA Technical Report Server (NTRS), Michael L. Nelson

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Archive Ingest and Handling Test, Michael L. Nelson, Johan Bollen, Giridhar Manepalli, and Rabia Haq

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Introduction: Data Communication and Topology Algorithms for Sensor Networks, Stephan Olariu, David Simplot-Ryl, and Ivan Stojmenovic

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Protecting the Communication Structure in Sensor Networks, S. Olariu, Q. Xu, M. Eltoweissy, and A. Wadaa

Submissions from 2004

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Metadata and Buckets in the Smart Object, Dumb Archive (SODA) Model, Michael L. Nelson, Kurt Maly, Delwin R. Croom Jr., and Steven W. Robbins

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Resource Harvesting Within the OAI-PMH Framework, Herbert Van de Sompel, Michael L. Nelson, Carl Lagoze, and Simeon Warner

Submissions from 2003

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Report on the Third ACM/IEEE Joint Conference on Digital Libraries (JCDL), Michael L. Nelson

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Protocols for Disease Classification from Mass Spectrometry Data, Michael Wagner, Dayanand Naik, and Alex Pothen

Submissions from 2002

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Fast Inner Product Computation on Short Buses, R. Lin and S. Olariu

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A Scalable Architecture for Harvest-Based Digital Libraries, Xiaoming Liu, Tim Brody, Stevan Harnard, Les Carr, Kurt Maly, Mohammad Zubair, and Michael L. Nelson

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Federated Searching Interface Techniques for Heterogeneous OAI Repositories, Xiaoming Liu, Kurt Maly, Mohammad Zubair, Qiaoling Hong, Michael L. Nelson, Frances Knudson, and Irma Holtkamp

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Object Persistence and Availability in Digital Libraries, Michael L. Nelson and B. Danette Allen

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The Single Row Routing Problem Revisited: A Solution Based on Genetic Algorithms, Albert Y. Zomaya, Roger Karpin, and Stephan Olariu

Submissions from 2001

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Efficient Algorithms for Graphs with Few P-4’s, Luitpold Babel, Ton Kloks, Jan Kratochvíl, Dieter Kratsch, Kaiko Müller, and Stephan Olariu

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Arc - An OAI Service Provider for Digital Library Federation, Xiaoming Liu, Kurt Maly, Mohammad Zubair, and Michael L. Nelson

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Buckets: Smart Objects for Digital Libraries, Michael L. Nelson

A Survey of Complex Object Technologies for Digital Libraries, Michael L. Nelson, Brad Argue, Miles Efron, Shelia Denn, and Maria Cristina Pattuelli

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Smart Objects and Open Archives, Michael L. Nelson and Kurt Maly

Submissions from 2000

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Upper Bounds to the Clique Width of Graphs, Bruno Courcelle and Stephan Olariu

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The UPS Prototype: An Experimental End-User Service Across E-Print Archives, Herbert Van de Sompel, Thomas Krichel, Michael L. Nelson, Patrick Hochstenbach, Victor Lyapunov, Kurt Maly, Mohammad Zubair, Mohamed Kholief, Xiaoming Liu, and Heath O'Connell

Submissions from 1999

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On the p-Connectedness of Graphs – a Survey, Luitpold Babel and Stephan Olariu

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Compute as Fast as the Engineers Can Think! Utrafast Computing Team Final Report, Robert T. Biedron, P. Mehrotra, Michael L. Nelson, M. L. Preston, J. J. Rehder, J. L. Rogersm, D. H. Rudy, J. Sobieski, and O. O. Storaasli

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Reconfigurable Shift Switching Parallel Comparators, R. Lin and S. Olariu