Journal Publications

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2018

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RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis, Xin Chen, Anjun Ma, Adam McDermaid, Hanyuan Zhang, Chao Liu, Huansheng Cao, and Qin Ma

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Holistic and component plant phenotyping using temporal image sequence, Sruti Das Choudhury, Srinidhi Bashyam, Yumou Qiu, Ashok Samal, and Tala Awada

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CROP HEIGHT ESTIMATION WITH UNMANNED AERIAL VEHICLES, Carrick Detweiler, David Anthony, and Sebastian Elbaum

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A systematic approach to RNA-associated motif discovery, Tian Gao, Jiang Shu, and Juan Cui

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Genome-scale MicroRNA target prediction through clustering with Dirichlet process mixture model, Zeynep M. Hakguder, Jiang Shu, Chunxiao Liao, Kaiyue Pan, and Juan Cui

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Astrocyte EV-Induced lincRNA-Cox2 Regulates Microglial Phagocytosis: Implications for Morphine-Mediated Neurodegeneration, Guoku Hu, Ke Liao, Fang Niu, Lu Yang, Blake W. Dallon, Shannon E. Callen, Changhai Tian, Jiang Shu, Juan Cui, Zhiqiang Sun, Yuri L. Lyubchenko, Minhan Ka, Xian-Ming Chen, and Shilpa Buch

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THE RHETORIC OF SCIENCE EDUCATION AND TECHNOLOGY, Iwasan D. Kejawa

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miRDis: a Web tool for endogenous and exogenous microRNA discovery based on deep-sequencing data analysis, Hanyuan Zhang, Bruno Vieira Resende e Silva, and Juan Cui

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Expression of the microRNA-143/145 cluster is decreased in hepatitis B virus-associated hepatocellular carcinoma and may serve as a biomarker for tumorigenesis in patients with chronic hepatitis B, Qi Zhao, Xiangfei Sun, Chao Liu, Tao Li, Juan Cui, and Chengyong Qin

2017

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ScienceSDS: A Novel Software Defined Security Framework for Large-scale Data-intensive Science, Deepak Nadig Anantha and Byrav Ramamurthy

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A Survey on Automated Food Monitoring and Dietary Management Systems, Vieira Bruno, Silva Resende, and Juan Cui

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Automated Stem Angle Determination for Temporal Plant Phenotyping Analysis, Sruti Das Choudhury, Saptarsi Goswami, Srinidhi Bashyam, Ashok Samal, and Tala Awada

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Affine-Invariant Triangulation of Spatio-Temporal Data with an Application to Image Retrieval, Sofie Haesevoets, Bart Kuijpers, and Peter Z. Revesz

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COMPUTER SCIENCE TECHNOLOGY EDUCATION: AN INCREDIBLE EXPLOSION, Iwasan D. Kejawa

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A Dynamic Data Structure to Efficiently Find the Points below a Line and Estimate Their Number, Bart Kuijpers and Peter Z. Revesz

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Extending Wireless Rechargeable Sensor Network Life without Full Knowledge, Najeeb W. Najeeb and Carrick Detweiler

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Testing the independence hypothesis of accepted mutations for pairs of adjacent amino acids in protein sequences, Jyotsna Ramanan and Peter Revesz

2016

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The Importance of Computing Education Research, Steve Cooper, Armando Fox, Susanne Hambrusch, Andrew Ko, and Beth Simon

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Converting Heterogeneous Statistical Tables on the Web to Searchable Databases, David W. Embley, Mukkai Krishnamoorthy, George Nagy, and Sharad C. Seth

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Enhancement of ELDA Tracker Based on CNN Features and Adaptive Model Update, Changxin Gao, Huizhang Shi, Jin-Gang Yu, and Nong Sang

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Wireless Communication in Data Centers: A Survey, Abdelbaset S. Hamza, Jitender Deogun, and Dennis R. Alexander

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An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes, Bingqiang Liu, Hanyuan Zhang, Chuan Zhou, Guojun Li, Anne Fennell, Guanghui Wang, Yu Kang, Qi Liu, and Qin Ma

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Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses, Bingqiang Liu, Chuan Zhou, Guojun Li, Hanyuan Zhang, Erliang Zeng, Qi Liu, and Qin Ma

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Use of a Small Unmanned Aerial System for the SR-530 Mudslide Incident near Oso, Washington, Robin Murphy, Brittany Duncan, Tyler Collins, Justin Kendrick, Patrick Lohman, Tamara Palmer, and Frank Sanborn

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Modeling Changes in Measured Conductance of Thin Boron Carbide Semiconducting Films Under Irradiation, George G. Peterson, Yongqiang Wang, Natale J. Ianno, and Michael Nastasi

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A mitochondrial DNA-based computational model of the spread of human populations, Peter Revesz

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Incremental phylogenetics by repeated insertions: An evolutionary tree algorithm, Peter Revesz and Zhiqiang Li

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Dynamic and Modularized MicroRNA Regulation and Its Implication in Human Cancers, Jiang Shu, Bruno Vieira Resende e Silva, Tian Gao, Zheng Xu, and Juan Cui

2015

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Optimization and Control of Cyber-Physical Vehicle Systems, Justin M. Bradley and Ella M. Atkins

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Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs, Kevin Chiang, Jiang Shu, Janos Zempleni, and Juan Cui

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A Rayleigh Quotient-Based Recursive Total-Least-Squares Online Maximum Capacity Estimation for Lithium-Ion Batteries, Taesic Kim, Yebin Wang, Zafer Sahinoglu, Toshihiro Wada, Satoshi Hara, and Wei Qiao

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A prototype on-line AOTF hyperspectral image acquisition system for tenderness assessment of beef carcasses, Govindarajan Konda Naganathan, Kim Cluff, Ashok Samal, Chris Calkins, David D. Jones, Carol Lorenzen, and Jeyamkondan Subbiah

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Revisiting operons: an analysis of the landscape of transcriptional units in E. coli, Xizeng Mao, Qin Ma, Bingqiang Liu, Xin Chen, Hanyuan Zhang, and Ying Xu

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Cluster-Based Boosting, L. Dee Miller and Leen-Kiat Soh

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Computational Characterization of Exogenous MicroRNAs that Can Be Transferred into Human Circulation, Jiang Shu, Kevin Chiang, Janos Zempleni, and Juan Cui

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Human Absorbable MicroRNA Prediction based on an Ensemble Manifold Ranking Model, Jiang Shu, Kevin Chiang, Dongyu Zhao, and Juan Cui

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Development of ListeriaBase and comparative analysis of Listeria monocytogenes, Mui Fern Tan, Cheuk Chuen Siow, Avirup Dutta, Naresh V.R. Mutha, Wei Yee Wee, Hamed Heydari, Shi Yang Tan, Mia Yang Ang, Guat Jah Wong, and Siew Woh Choo

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Development of ListeriaBase and comparative analysis of Listeria monocytogenes, Mui Fern Tan, Cheuk Chuen Siow, Avirup Dutta, Naresh VR Mutha, Wei Yee Wee, Hamed Heydari, Shi Yang Tan, Mia Yang Ang, Guat Jah Wong, and Siew Woh Choo

2014

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Adaptive Decentralized Control of Mobile Underwater Sensor Networks and Robots for Modeling Underwater Phenomena, Carrick Detweiler, Sreeja Banerjee, Marek Doniec, Mingshun Jiang, Francesco Peri, Robert F. Chen, and Daniela Rus

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Autonomous Capabilities for Small Unmanned Aerial Systems Conducting Radiological Response: Findings from a High-fidelity Discovery Experiment, Brittany Duncan and Robin Murphy

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Network Innovation using OpenFlow: A Survey, Adrian Lara, Anisha Kolasani, and Byrav Ramamurthy

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A phylogenetic model for understanding the effect of gene duplication on cancer progression, Qin Ma, Jaxk H. Reeves, David A. Liberles, Lili Yu, Zheng Chang, Jing Zhao, Juan Cui, Ying Xu, and Liang Liu

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A Statistical–Physical Model of Interference in Diffusion-Based Molecular Nanonetworks, Massimiliano Pierobon and Ian F. Akyildiz

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Balancing Cost and Reliability in the Design of Internet Protocol Backbone Using Agile Optical Networking, Byrav Ramamurthy, Rakesh K. Sinha, and K. K. Ramakrishnan

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Cooperative Spectrum Sensing in Cognitive Radio Networks Using Multidimensional Correlations, Dongyue Xue, Eylem Ekici, and Mehmet C. Vuran

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TCP Congestion Avoidance Algorithm Identification, Peng Yang, Juan Shao, Wen Luo, Lisong Xu, Jitender S. Deogun, and Ying Lu

2013

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The endothelial lipase protein is promising urinary biomarker for diagnosis of gastric cancer, Xueyan Dong, Guoqing Wang, Guoqing Zhang, Zhaohui Ni, Jian Suo, Juan Cui, Ai Cui, Qing Yang, Ying Xu, and Fan Li

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A Survey on Inter-Cell Interference Coordination Techniques in OFDMA-Based Cellular Networks, Abdelbaset S. Hamza, Shady S. Khalifa, Haitham S. Hamza, and Khaled Elsayed

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Reliable Peak Selection for Multisample Analysis with Comprehensive Two-Dimensional Chromatography, Stephen E. Reichenbach, Xue Tian, Akwasi A. Boateng, Charles A. Mullen, Chiara Cordero, and Qingping Tao

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Data mining the functional characterizations of proteins to predict their cancer-relatedness, Peter Revesz and Christopher Assi

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Computational Prediction of Human Salivary Proteins from Blood Circulation and Application to Diagnostic Biomarker Identification, Jiaxin Wang, Yanchun Liang, Yan Wang, Juan Cui, Ming Liu, Wei Du, and Ying Xu

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Articulatory Distinctiveness of Vowels and Consonants: A Data-Driven Approach, Jun Wang, Jordan R. Green, Ashok Samal, and Yana Yunusova

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Exploring the Design Space of Multichannel Peer-to-Peer Live Video Streaming Systems, Miao Wang, Lisong Xu, and Byrav Ramamurthy

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Elucidation of How Cancer Cells Avoid Acidosis through Comparative Transcriptomic Data Analysis, Kun Xu

2012

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Systems biology in the frontier of cancer research: a report of the Second International Workshop of Cancer Systems Biology, Juan Cui, Yan-Chun Liang, and Ying Xu

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Redistricting Using Constrained Polygonal Clustering, Deepti Joshi, Leen-Kiat Soh, and Ashok Samal

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Reconsideration of In-Silico siRNA Design Based on Feature Selection: A Cross-Platform Data Integration Perspective, Qi Liu, Han Zhou, Juan Cui, Zhiewi Cao, and Ying Xu

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Applications of Cognitive Radio Networks, Jordi Perez-Romero, Linda Doyle, and Mehmet C. Vuran

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Features for non-targeted cross-sample analysis with comprehensive two-dimensional chromatography, Stephen E. Reichenbach, Xue Tian, Chiara Cordero, and Qingping Tao

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Palantir: Early Detection of Development Conflicts Arising from Parallel Code Changes, Anita Sarma, D F. Redmiles, and Andre van der Hoek

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Exploring the Design Space of Multichannel Peer-to-Peer Live Video Streaming Systems, Miao Wang, Lisong Xu, and Byrav Ramamurthy

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Cross-Layer Analysis of the End-to-End Delay Distribution in Wireless Sensor Networks, Yunbo Wang, Mehmet C. Vuran, and Steve Goddard

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A Comparative Study of Gene-Expression Data of Basal Cell Carcinoma and Melanoma Reveals New Insights about the Two Cancers, Kun Xu, Xizeng Mao, Minesh Mehta, Juan Cui, Chi Zhang, and Ying Xu

2011

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An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer, Juan Cui, Yunbo Chen, Wen-Chi Chou, Liankun Sun, Li Chen, Jian Suo, Zhaohui Ni, Ming Zhang, Xiaoxia Kong, Lisabeth L. Hoffman, Jinsong Kang, Yingying Su, Victor Olman, Darryl Johnson, Daniel W. Tench, I. Jonathan Amster, Ron Orlando, David Puett, Fan Li, and Ying Xu

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MicroRNA Expression and Regulation in Human Ovarian Carcinoma Cells by Luteinizing Hormone, Juan Cui, Joanna B. Eldredge, Ying Xu, and David Puett

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Gene-Expression Signatures Can Distinguish Gastric Cancer Grades and Stages, Juan Cui, Fan Li, Guoqing Wang, Xuedong Fang, J. David Puett, and Ying Xu

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Regulation of gene expression in ovarian cancer cells by luteinizing hormone receptor expression and activation, Juan Cui, Brooke M. Miner, Joanna B. Eldredge, Susanne W. Warrenfeltz, Phuongan Dam, Ying Xu, and David Puett

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Reclaiming Spare Capacity and Improving Aperiodic Response Times in Real-Time Environments, Sathich Gopalakrishnan and Xue Liu

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A Computational Method for Prediction of Excretory Proteins and Application to Identification of Gastric Cancer Markers in Urine, Celine S. Hong, Juan Cui, Zhaohui Ni, Yingying Su, David Puett, Fan Li, and Ying Xu

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SimCoL: A Simulation Tool for Computer-Supported Collaborative Learning, Nobel Khandaker and Leen-Kiat Soh

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Lessons Learned from Comprehensive Deployments of Multiagent CSCL Applications I-MINDS and ClassroomWiki, Nobel Khandaker, Leen-Kiat Soh, L.D. Miller, Adam D. Eck, and Hong Jiang

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Comparative analysis of peak-detection techniques for comprehensive two-dimensional chromatography, Indu Latha, Stephen E. Reichenbach, and Qingping Tao

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A Midsummer Night’s Dream (with flying robots), Robin Murphy, Dylan Shell, Amy Guerin, Brittany Duncan, Benjamin Fine, Kevin Pratt, and Takis Zourntos

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A Comparative Analysis of Gene-Expression Data of Multiple Cancer Types, Kun Xu, Juan Cui, Victor Olman, Qing Yang, David Puett, and Ying Xu

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A Reliable Energy-Efficient Multi-Level Routing Algorithm for Wireless Sensor Networks Using Fuzzy Petri Nets, Zhenhua Yu, Xiao Fu, Yuanli Cai, and Mehmet C. Vuran

2010

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Wireless Heterogeneous Networks and Next Generation Internet, Eylem Ekici and Mehmet C. Vuran

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A Novel Weighted-Graph-Based Grouping Algorithm for Metadata Prefetching, Peng Gu, Jun Wang, Yifeng Zhu, Hong Jiang, and Pengju Shang

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ClassroomWiki: A Collaborative Wiki for Instructional Use with Multiagent Group Formation, Nobel Khandaker and Leen-Kiat Soh

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In-silico prediction of blood-secretory human proteins using a ranking algorithm, Qi Liu, Juan Cui, Qiang Yang, and Ying Xu

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A study of health effects of long-distance ocean voyages on seamen using a data classification approach, Yunmei Lu, Yanhong Gao, Zhongbo Cao, Juan Cui, Zhennan Dong, Yaping Tian, and Ying Xu

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Communication-Aware Load Balancing for Parallel Applications on Clusters, Xiao Qin, Hong Jiang, Adam Manzanares, Xiaojun Ruan, and Shu Yin

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Development of a Testbed for Wireless Underground Sensor Networks, Agnelo R. Silva and Mehmet C. Vuran

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XLP: A Cross-Layer Protocol for Efficient Communication in Wireless Sensor Networks, Mehmet C. Vuran and Ian F. Akyildiz

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The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development, Xiaobai Zhang, Juan Cui, Daniel Nilsson, Kapila Gunasekera, Astrid Chanfon, Xiaofeng Song, Huinan Wang, Ying Xu, and Torsten Ochsenreiter

2009

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Efficient MaxCount and threshold operators of moving objects, Scot Anderson and Peter Revesz

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Carving and Replaying Differential Unit Test Cases from System Test Cases, Sebastian Elbaum, Hui Nee Chin, Matthew B. Dwyer, and Matthew Jorde

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Projection Methods Require Black Border Removal, George Nagy, Sharad C. Seth, and Mahesh Viswanathan

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Dynamic Load Balancing for I/O-Intensive Applications on Clusters, Xiao Qin, Hong Jiang, Adam Manzanares, Xiaojun Ruan, and Shu Yin

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Smart Templates for peak pattern matching with comprehensive two-dimensional liquid chromatography, Stephen E. Reichenbach, Peter W. Carr, Dwight R. Stoll, and Qingping Tao

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Error Control in Wireless Sensor Networks: A Cross Layer Analysis, Mehmet C. Vuran and Ian F. Akyildiz

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Upstream-Downstream Relationships in Terms of Annual Streamflow Discharges and Drought Events in Nebraska, Hong Wu, Leen-Kiat Soh, Ashok Samal, Tao Hong, David B. Marx, and Xunhong Chen

2008

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A Survey on Spectrum Management in Cognitive Radio Networks, Ian F. Akyildiz, Won-Yeol Lee, Mehmet C. Vuran, and Shantidev Mohanty

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Techniques for Computing Fitness of Use (FoU) for Time Series Datasets with Applications in the Geospatial Domain, Lei Fu, Leen-Kiat Soh, and Ashok Samal

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Efficient Selection of Observation Points for Functional Tests, Jian Kang, Sharad C. Seth, Yi-Shing Chang, and Vijay Gangaram

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Visible/Near-Infrared Hyperspectral Imaging for Beef Tenderness Prediction, Govindarajan Konda Naganathan, Lauren M. Grimes, Jeyamkondan Subbiah, Chris R. Calkins, Ashok Samal, and George E. Meyer

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Computation of a Face Attractiveness Index Based on Neoclassical Canons, Symmetry, and Golden Ratios, Kendra Schmid, David Marx, and Ashok Samal

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Considering operational issues for multiagent conceptual inferencing in a distributed information retrieval application, Leen-Kiat Soh

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I-MINDS: A Multiagent System for Intelligent Computer- Supported Collaborative Learning and Classroom Management, Leen-Kiat Soh, Nobel Khandaker, and Hong Jiang

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Investigating adaptive, confidence-based strategic negotiations in complex multiagent environments, Leen-Kiat Soh and Xin Li

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Multidomain Optical Networks: Issues and Challenges, Chava Vijaya Saradhi, Byrav Ramamurthy, Dominic A. Schupke, and Eiji Oki