The Network Dynamics and Simulation Science Laboratory integrates informatics, analytics, and large complex system modeling across diverse domains to build synthetic information tools for real world, stakeholder-defined problems.

Highlights

People

Publications

2018

2017

  • Nath M, Ren Y, Khorramzadeh Y, Eubank S. Determining whether a class of random graphs is consistent with an observed contact network. Journal of Theoretical Biology. 2017;440:121–132. https://doi.org/10.1016/j.jtbi.2017.12.021.
  • Wattam AR, Brettin T, Davis JJ, Gerdes S, Kenyon R, Machi D, Mao C, Olson R, Overbeek R, Pusch GD, Shukla MP, Stevens R, Vonstein V, Warren A, Xia F, Yoo H. Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center. Methods in Molecular Biology (Clifton, NJ). 2017;1704:79–101. https://doi.org/10.1007/978-1-4939-7463-4_4.
  • Lewis B. Interviewed by Anderson A. Virginia Tech partners with Accuweather to forecast the flu. WSET. 2017. http://wset.com/news/local/virginia-tech-partners-with-accuweath....
  • Lewis B, Marathe M, Reynolds Z. Interviewed by Williams A. AccuWeather to offer users innovative flu forecasts from Virginia Tech's Biocomplexity Institute. Accuweather. 2017. https://www.accuweather.com/en/weather-news/accuweather-to-offer....
  • Lewis B, Marathe M, Reynolds Z. Interviewed by Accuweather. AccuWeather to offer users innovative flu forecasts from Virginia Tech’s Biocomplexity Institute. Major News. 2017. https://majornews.us/archives/9068.
  • Orr M, Pfautz J, Moody J, Barrett C. Interviewed by Rosplock D. Virginia Tech team leads federal effort to forecast the flow of information online. VT News. 2017. https://vtnews.vt.edu/articles/2017/11/bi-forecasting-info-flow-....
  • Venkatramanan S. Interviewed by WSLS. Virginia Tech flu forecasting technology to be used by AccuWeather. WSLS. 2017. https://www.wsls.com/news/virginia/new-river-valley/virginia-tec....
  • Danetz E, Marathe M. Interviewed by Staff W. Flu forecasts now accessible online, three Hampton Roads cities named top infected regions. WTKR. 2017. http://wtkr.com/2017/12/05/flu-forecasts-now-accessible-online-t....
  • Reynolds Z. Interviewed by Stewart K. Virginia Tech partners with AccuWeather to share flu outlook. WTOP. 2017. https://wtop.com/health-fitness/2017/12/predicting-the-flu-how-a....
  • Lewis B, Marathe M, Sameroff S, Reynolds Z. Interviewed by Rife L. Virginia Tech partners with AccuWeather to forecast flu season. Richmond Times Dispatch. 2017. http://www.richmond.com/life/health/virginia-tech-partners-with-....
  • Lewis B, Danetz E, Chen J, Marathe M, Sameroff S. Interviewed by Freemal R. Innovative partnership will extend cutting-edge flu forecasting research to millions. VT News. 2017. https://vtnews.vt.edu/articles/2017/11/bi-accuweather-flu-foreca....
  • NRECA.Newsletter. Where Does Solar Stand? Focus Group Results. 2017. https://www.cooperative.com/programs-services/bts/Documents/Advi....
  • Lewis B. Interviewed by sfederico. Bryan Lewis | Virginia Tech and AccuWeather Team to Forecast Flu Spread. WINA News Radio. 2017. http://wina.com/podcasts/bryan-lewis-virginia-tech-and-accuweath....
  • Jadhon J, Ward J, Reynolds Z, Lewis B. Interviewed by Ward J. Virginia Tech flu season forecasting now part of AccuWeather. WDBJ7. 2017. http://www.wdbj7.com/content/news/Virginia-Tech-flu-season-forec....
  • Lewis B, Marathe M, Sameroff S, Reynolds Z. Interviewed by richmond.com. Virginia Tech partners with AccuWeather to forecast flu season. American News. 2017. http://www.america.easybranches.com/virginia/Virginia-Tech-partn....
  • Mayorga LS, Verma M, Hontecillias R, Hoops S, Bassaganya-Riera J. Agents and networks to model the dynamic interactions of intracellular transport. Cellular Logistics. 2017;7(4):e1392401. https://doi.org/10.1080/21592799.2017.1392401.
  • Kuhlman C, Ren Y, Lewis B, Schlitt J. Hybrid Agent-Based Modeling of Zika in the United States. In: Proceedings of the Winter Simulation Conference 2017. 2017:1085–1096. https://doi.org/10.1109/WSC.2017.8247857.
  • Bodi Winn C, Bakthavatchalu V, Esmail MY, Feng Y, Dzink-Fox JA, Richey L, Perkins SE, Nordberg EK, Fox JG. Isolation and molecular characterization of group B Streptococcus from laboratory Long-Evans rats (Rattus norvegicus) with and without invasive group B streptococcal disease. Journal of Medical Microbiology. 2017;67(1):97–109. http://jmm.microbiologyresearch.org/content/journal/jmm/10.1099/....
  • Yao Z, Ramanathan A, Vullikanti A, Pullum L, Prakash AB. Data-Driven Immunization. Presented at the IEEE ICDM 2017, New Orleans, LA; 2017.
  • Zhao Z, Chen L, Avram M, Li M, Wang G, Butt AR, Khan M, Marathe M, Qiu J, Vullikanti A. Finding and counting tree-like subgraphs using MapReduce. IEEE TRANSACTIONS ON MULTI-SCALE COMPUTING SYSTEMS. 2017;PP(99). https://doi.org/10.1109/TMSCS.2017.2768426.
  • Bergmann FT, Hoops S, Klahn B, Kummer U, Mendes P, Pahle J, Sahle S. COPASI and its applications in biotechnology. Journal of Biotechnology. 2017;261:215–220. https://doi.org/10.1016/j.jbiotec.2017.06.1200.
  • Cadena J, Basak A, Deng X, Vullikanti A. Graph Scan Statistics With Uncertainty. Presented at the AAAI Conference on Artificial Intelligence, New Orleans; 2017.
  • Brownstein JS, Chu S, Marathe A, Marathe MV, Nguyen AT, Paolotti D, Perra N, Perrotta D, Santillana M, Swarup S, Tizzoni M, Vespignani A, Vullikanti AKS, Wilson ML, Zhang Q. Combining Participatory Influenza Surveillance with Modeling and Forecasting: Three Alternative Approaches. JMIR public health and surveillance. 2017;3(4):e83. https://doi.org/10.2196/publichealth.7344.
  • Eubank S, Marathe M, Stevens R, Warren A. Interviewed by Trent T. Research team creates powerful system to identify biological threats. VT News. 2017. https://vtnews.vt.edu/articles/2017/11/bi-fungcatiarpa.html.
  • Kang G, Ewing-Nelson SR, Mackey L, Schlitt J, Marathe A, Abbas K, Swarup S. Vaccine sentiment on social media: A semantic network analysis. Presented at the 145th American Public Health Association (APHA) Annual Meeting and Exposition, Atlanta, GA; 2017.
  • Lewis B, Reynolds Z, Sameroff S, Marathe M. Interviewed by Rife L. Virginia Tech partners with AccuWeather to forecast flu season. The Roanoke Times. 2017. http://www.roanoke.com/business/news/virginia-tech-partners-with....
  • Cadena J, Vullikanti A. Mining Heavy Temporal Subgraphs: Fast Algorithms and Applications. Presented at the AAAI 2018; 2017.
  • Venkatramanan S, Wu S, Shi B, Marathe A, Marathe M, Eubank S, Sah LP, Giri AP, Colavito LA, Nitin KS, Sridhar V, Asokan R, Muniappan R, Norton G, Adiga A. Towards Robust Models of Food Flows and Their Role in Invasive Species Spread. Presented at the IEEE Big Data 2017, Boston, MA, USA; 2017.
  • Chen J, Lewis BL, Marathe A, Marathe MV, Swarup S, Kumar VSA. Individual and Collective Behavior in Public Health Epidemiology. In: HS 36 Disease Modelling and Public Health. 1st ed. Elsevier; 2017.
  • Abbas K. Systems thinking to improve effectiveness, efficiency, and equity in health. Presented at the 3rd Systems and Complexity Science for Healthcare Conference, Ashburn, VA; 2017.
  • Korkmaz G, Kuhlman CJ, Ravi SS, Vega-Redondo F. Spreading of social contagions without key players. World Wide Web. 2017:1–35. https://doi.org/10.1007/s11280-017-0500-y.
  • Powell Doherty R, Müller-Demary D, Hosszu A, Duminica A, Bertke A, Lewis B, Eubank S. A survey of quality of life indicators in the Romanian Roma population following the ‘Decade of Roma Inclusion.’ F1000Research. 2017;6:1692. https://doi.org/10.12688/f1000research.12546.1.
  • Marathe M. Interviewed by USFWS. Storm Evacuations Cause Ripple Effects That Stall Transportation and Communications Infrastructure, Says Virginia Tech Expert. News Wise. 2017. https://www.newswise.com/articles/storm-evacuations-cause-ripple....
  • Marathe M. Synthetic social habitats for policy and decision making. 2017.
  • Ghosh S, Chakraborty P, Lewis BL, Majumder MS, Cohn E, Brownstein JS, Marathe MV, Ramakrishnan N. GELL: Automatic Extraction of Epidemiological Line Lists from Open Sources. In: Proceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. ACM; 2017:1477–1485. https://doi.org/10.1145/3097983.3098073.
  • Ghosh S, Chakraborty P, Lewis BL, Majumder MS, Cohn E, Brownstein JS, Marathe MV, Ramakrishnan N. Guided Deep List: Automating the Generation of Epidemiological Line Lists from Open Sources. KDD. 2017:1477–1486. http://arxiv.org/abs/1702.06663v1.
  • Lewis B, Marathe M, Vullikanti A. Mathematical and computational foundations of infectious disease epidemiology. Presented at the International Conference on Systems Biology (ICSB) 2017, Blacksburg, VA; 2017.
  • Antonopoulos DA, Assaf R, Aziz RK, Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S, Kenyon RW, Machi D, Mao C, Murphy-Olson DE, Nordberg EK, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Santerre J, Shukla M, Stevens RL, VanOeffelen M, Vonstein V, Warren AS, Wattam AR, Xia F, Yoo H. PATRIC as a unique resource for studying antimicrobial resistance. Briefings in bioinformatics. 2017. https://doi.org/10.1093/bib/bbx083.
  • Marathe M, Marathe A, Nordberg EK. Interviewed by Rosplock D. New tool could find relief for America’s overworked energy grid. VT News. 2017. https://vtnews.vt.edu/articles/2017/07/bi-energyusemodel.html.
  • Chu S, Kuhlman C, Marathe A. Disparities in Slum Health and Its Impact on Larger Urban Regions. Presented at the North American Social Networks Conference NASN2017, Washington, DC; 2017.
  • Wang L, Chen J, Marathe A. Framework for Learning Health Disparities Among Cohorts in An Influenza Epidemic. Presented at the North American Social Networks Conference NASN2017, Washington, DC; 2017.
  • Marathe M. Interviewed by Rosplock D. New Tool Could Find Relief for America’s Overworked Energy Grid . BI Website . 2017. https://www.bi.vt.edu/news/new-tool-could-find-relief-for-americ....
  • Marathe M. Interviewed by IQ NPRR. Growing Solar: Modernizing the Grid for a New Direction . NPR Radio IQ. 2017. http://wvtf.org/post/growing-solar-modernizing-grid-new-directio....
  • Lewis B, Longini I, Gilbert N, Epstein J, Hatchett R, Dunphy K, Rivers C, Telionis P, Schlitt J, Vespignani A, Del Valle S, Farmer D. Interviewed by Waldrop M. Special Agents Offer Modeling Upgrade. PNAS. 2017. https://drive.google.com/file/d/0Bz0xYBGb1yNoUFYwUGstTGYxNklsWXV....
  • Barrett C, Lewis B, Marathe M, Telionis P, Eubank S. Interviewed by Waldrop M. Special agents offer modeling upgrade. PNAS . 2017. http://www.pnas.org/content/114/28/7176.full.
  • Thorve S, Lewis B, Wilson ML. Interviewed by Rosplock D. Biocomplexity Institute’s Ebola-tested tools help set new standard for federal disease control. VT News. 2017. https://vtnews.vt.edu/articles/2017/06/bi-diseasesurveillance.ht....
  • Kang G, Swarup S. Interviewed by Rosplock D. Child safety or parental duty: New study maps out core concepts in the vaccination debate. NEWS Line. 2017. https://www.news-line.com/PA_news27664_.
  • Ziemer K, Pires B, Lancaster V, Keller S, Orr M, Shipp S. A New Lens on High School Dropout: Use of Correspondence Analysis and the Statewide Longitudinal Data System. The American Statistician. 2017. https://doi.org/https://doi.org/10.1080/00031305.2017.1322002.
  • Kang G, Swarup S. Interviewed by Rosplock D. Child safety or parental duty: New study maps out core concepts in the vaccination debate. Newscaf. 2017. http://www.newscaf.com/science/child-safety-or-parental-duty-new....
  • Kang G, Swarup S. Interviewed by Rosplock D. Child safety or parental duty: New study maps out core concepts in the vaccination debate. Science Daily. 2017. https://www.sciencedaily.com/releases/2017/06/170623100439.htm.
  • Kang G, Swarup S. Interviewed by Rosplock D. New study maps out core concepts in the vaccination debate. Medical Xpress. 2017. https://medicalxpress.com/news/2017-06-core-concepts-vaccination....
  • Kang G, Swarup S. Interviewed by Rosplock D. Child safety or parental duty: new study maps out core concepts in the vaccination debate. VT News. 2017. https://vtnews.vt.edu/articles/2017/06/bi-vaccinesentiment.html.
  • Hixson JE, Jun G, Shimmin LC, Wang Y, Yu G, Mao C, Warren AS, Howard TD, Vander Heide RS, Van Eyk J, Wang Y, Herrington DM. Whole Exome Sequencing to Identify Genetic Variants Associated with Raised Atherosclerotic Lesions in Young Persons. Scientific Reports. 2017;7. https://doi.org/10.1038/s41598-017-04433-x.
  • Tabataba FS, Hosseinipour M, Lewis BL, Tabataba FS, Venkatramanan S, Higdon D, Chen J, Marathe MV. Epidemic Forecasting by Combining Agent-Based Models and Smart Beam-Particle Filtering Framework. In: Proceedings of the IEEE International Conference on Data Mining 2017. 2017.
  • Swarup S, Dorratoltaj N, Abbas K, Marathe A. Interviewed by Science PL of. Who to vaccinate when flu season strikes. Medical Xpress. 2017. https://medicalxpress.com/news/2017-06-vaccinate-flu-season.html....
  • Parikh NK, Marathe MV, Swarup S. Contextual Ranking of Behaviors for Large-scale Multiagent Simulations. In: Proceedings of the 16th Conference on Autonomous Agents and MultiAgent Systems. 2017:1676–1678. http://www.aamas2017.org/proceedings/pdfs/p1676.pdf.
  • Wu S, Mortveit HS, Gupta S. A Framework for Validation of Large-Scale, Computer Simulation Models: An Application to Networked Epidemics. In: Proceedings of the ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS). 2017. https://doi.org/10.1145/3064911.3064922.
  • Tabataba FS, Chakraborty P, Ramakrishnan N, Venkatramanan S, Chen J, Lewis BL, Marathe MV. A framework for evaluating epidemic forecasts. BMC Infectious Diseases. 2017. https://doi.org/10.1186/s12879-017-2365-1.
  • Eubank S. Interviewed by Metzner J. Modeling Disease Pulse of the Populace. NPR. 2017. https://www.pulseplanet.com/dailyprogram/dailies.php?POP=6572.
  • Venkatramanan S, Chen J, Gupta S, Lewis BL, Marathe MV, Mortveit HS, Kumar VSA. Spatio-temporal optimization of seasonal vaccination using a metapopulation model of influenza. In: IEEE International Conference on Healthcare Informatics (ICHI). IEEE; 2017.
  • Eubank S, Swarup S, Marathe M. Interviewed by Holmes P. VT researchers help federal government prepare for catastrophic events. WFXR. 2017. http://www.virginiafirst.com/news/local-news/vt-researchers-help....
  • Swarup S, Gohlke J, Bohland J. A Multi-agent Model of Population Heat Exposure. Presented at the 2nd International Workshop on Agent-based modeling of urban systems (ABMUS), Sao Paulo, Brazil ; 2017.
  • Lewis B. Disease Simulation Extensions - Zika Hybrid & and National Influenza. Presented at the MIDAS Annual Conference, Atlanta, GA; 2017.
  • Nath M, Ren Y, Eubank SG. Determining whether a particular contact network is consistent with a network model. Journal of Theoretical Biology. 2017;400C:121–132.
  • Lum K, Eubank S, Torres J, Hawdon J, Swarup S. Interviewed by Rosplock D. “Color-blind” sentencing alone can’t cure racial bias in U.S. criminal justice system, new study suggests. VT News. 2017. https://vtnews.vt.edu/articles/2017/04/bi-incarcerationmodel.htm....
  • Dorrataltaj N, Marathe A, Lewis BL, Swarup S, Eubank SG, Abbas KM. Epidemiological and Economic Impact of Pandemic Influenza in Chicago: Priorities for Vaccine Interventions. PLoS Computational Biology. 2017;13(6). https://doi.org/10.1371/journal.pcbi.1005521.
  • Wattam R. Interviewed by Trent T. Hopping the species barrier: Harmful bacteria discovered in both amphibians and mammals. VT News. 2017. https://vtnews.vt.edu/articles/2017/03/bi-brucellainamphibians.h....
  • Kang GJ, Ewing-Nelson SR, Mackey L, Schlitt J, Marathe A, Abbas KM, Swarup S. Semantic Network Analysis of Vaccine Sentiment in Online Social Media. Vaccine. 2017;35(29):3621–3638. https://doi.org/10.1016/j.vaccine.2017.05.052.
  • Kuo C-T, Ravi SS, Dao T-B-H, Vrain C, Davidson I. A Framework for Minimal Clustering Modification via Constraint Programming. In: Proc. AAAI 2017. 2017:1389–1395.
  • Venkatramanan S, Wu S, Adiga A, Marathe A, Eubank SG, Marathe MV. Hybrid models for ecological and anthropogenic drivers of pest invasion: Case study of Tuta Absoluta in Nepal. Presented at the ICBCL 2017; 2017.
  • Venkatramanan S, Lewis BL, Chen J, Higdon D, Kumar VSA, Marathe MV. Using data-driven agent-based models for forecasting emerging infectious diseases. Epidemics - Special Issue on Ebola Challenge. 2017. https://doi.org/10.1016/j.epidem.2017.02.010.
  • Keller S, Korkmaz G, Orr M, Schroeder A, Shipp S. The Evolution of Data Quality: Understanding the Transdisciplinary Origins of Data Quality Concepts and Approaches. Annual Review of Statistics and its Application, Vof 4. 2017;4:85–108. https://doi.org/10.1146/annurev-statistics-060116-054114.
  • Wang L, Cho J-H, Chen I-R, Chen J. PDGM: Percolation-based Directed Graph Matching in Social Networks. In: Proceedings of The IEEE International Conference on Communications (ICC). 2017.
  • Bhuiyan MH, Khan M, Chen J, Marathe MV. Parallel algorithms for switching edges in heterogeneous graphs. Journal of Parallel and Distributed Computing. 2017;104:19–35. https://doi.org/10.1016/j.jpdc.2016.12.005.
  • Chu S, Swarup S, Chen J, Marathe A. A Comparison of Targeted Layered Containment Strategies for a Flu Pandemic in Three US Cities. In: Proceedings of the 16th International Conference on Autonomous Agents and Multiagent Systems (AAMAS). 2017.
  • Hawdon J, Lum K, Swarup S, Torres JA, Eubank SG. Addressing the Race Gap in Incarceration Rates: An Agent Based Model. Corrections. 2017:1–20. https://doi.org/10.1080/23774657.2016.1265472.
  • Verma M, Erwin S, Abedi V, Hontecillas R, Hoops S, Leber A, Bassaganya-Riera J, Ciupe SM. Modeling the Mechanisms by Which HIV-Associated Immunosuppression Influences HPV Persistence at the Oral Mucosa. PLOS ONE. 2017;12(1):1–20. https://doi.org/10.1371/journal.pone.0168133.
  • Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard JL, Gerdes S, Henry CS, Kenyon RW, Machi D, Mao C, Nordberg EK, Olsen GJ, Murphy-Olson DE, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Vonstein V, Warren A, Xia F, Yoo H, Stevens RL. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 2017;45(D1):D535–D542. https://doi.org/10.1093/nar/gkw1017.
  • Manogaran G, Thota C, Lopez D, Vijayakumar V, Abbas KM, Sundarsekar R. Big Data Knowledge System in Healthcare. In: Internet of Things and Big Data Technologies for Next Generation Healthcare. Vol 23. Springer International Publishing; 2017:133–157. https://doi.org/10.1007/978-3-319-49736-5_7.
  • Pal A, Mishra C, Kumar VSA, Ravi SS. A General Optimal Substation Coverage Algorithm for Phasor Measurement Unit Placement in Practical Systems. IET Generation, Transmission & Distribution. 2017;11(2):347–353. https://doi.org/10.1049/iet-gtd.2016.0553.
  • Pal A, Kumar VSA, Ravi SS. A PMU Placement Scheme Considering Realistic Costs and Modern Trends in Relaying. IEEE Transactions on Power Systems. 2017;32(1):552–561. https://doi.org/10.1109/TPWRS.2016.2551320.
  • Subbiah R, Pal A, Nordberg EK, Marathe A, Marathe MV. Energy Demand Model for Residential Sector: A First Principles Approach. IEEE Transactions on Sustainable Energy. 2017;8(3):1215–1224. https://doi.org/10.1109/TSTE.2017.2669990.

2016

  • Abedi V, Lu P, Hontecillas-Magarzo R, Verma M, Vess G, Philipson CW, Carbo A, Leber A, Juni NT, Hoops S, Bassaganya-Riera J. Phase III Placebo-Controlled, Randomized Clinical Trial with Synthetic Crohn's disease Patients to Evaluate Treatment Response. In: Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology. Elsevier/MK; 2016:441–427. https://doi.org/10.1016/B978-0-12-804203-8.00028-6.
  • Nath M, Ren Y, Khorramzadeh Y, Eubank SG. Diffusive Dynamics on a Network. Presented at the 83rd Annual Meeting of the APS Southeastern Section, Charlottesville, VA; 2016. http://meetings.aps.org/Meeting/SES16/Session/K1.57.
  • Ren Y, Eubank SG, Nath M. From network reliability to the Ising model: A parallel scheme for estimating the joint density of states. Physical Review E. 2016;94:042125. http://journals.aps.org/pre/abstract/10.1103/PhysRevE.94.042125.
  • Wang L, Chen J, Marathe A. Understanding Health Disparities in an Influenza Epidemic. In: Computational Social Science Society of the Americas Annual Conference (CSSSA). 2016.
  • Korkmaz G, Kuhlman CJ, Vega-Redondo F. Can Social Contagion Spread Without Key Players? In: The 3rd International Conference on Behavioral, Economic, and Socio-Cultural Computing (BESC). 2016.
  • Marathe A, Chen J, Chu S, Chungbaek Y, Khan M, Kuhlman CJ, Mortveit HS, Kumar VSA, Xie D. Effect of Modeling Slum Populations on Influenza Spread Delhi. BMJ Open. 2016;6(9):e011699. https://doi.org/10.1136/bmjopen-2016-011699.
  • Adiga A, Kuhlman CJ, Marathe MV, Ravi SS, Rosenkrantz DJ, Stearns RE. Inferring Local Transition Functions of Discrete Dynamical Systems From Observations of System Behavior. Theoretical Computer Science. 2016. https://doi.org/10.1016/j.tcs.2016.07.008.
  • Abdelhamid S, Kuhlman CJ, Marathe MV, Ravi SS. Interactive Exploration and Understanding of Contagion Dynamics in Networked Populations. In: The 3rd International Conference on Behavioral, Economic, and Socio-Cultural Computing (BESC). IEEE; 2016:1–6. https://doi.org/10.1109/BESC.2016.7804480.
  • Korkmaz G, Cadena JE, Kuhlman CJ, Marathe A, Kumar VSA, Ramakrishnan N. Multi-source models for civil unrest forecasting. Social Network Analysis and Mining. 2016;6(1):1–25. https://doi.org/10.1007/s13278-016-0355-8.
  • Biggerstaff M, Alper D, Dredze M, Fox S, Chun-Hai I, Hickmann K, Lewis BL, Rosenfeld R, Shaman J, Tsou M-H, Velardi P, Vespignani A, Finelli L. Results from the centers for disease control and prevention's predict the 2013-2014 Influenza Season Challenge. BMC infectious diseases. 2016;16(357):1–10. https://doi.org/10.1186/s12879-016-1669-x.
  • Korkmaz G, Kuhlman CJ, Ravi SS, Vega-Redondo F. Approximate Contagion Model of Common Knowledge on Facebook. In: Proceedings of the 27th ACM Conference on Hypertext and Social Media. ACM; 2016:231–236. https://doi.org/10.1145/2914586.2914630.
  • Zhang Y, Adiga A, Saha S, Kumar VSA, Prakash BA. Near-optimal Algorithms for Controlling Propagation at Group Scale on Networks. IEEE Transactions on Knowledge and Data Engineering. 2016;28(12):3339–3352. https://doi.org/10.1109/TKDE.2016.2605088.
  • Dorratoltaj N, Marathe A, Lewis BL, Eubank SG, Swarup S, Abbas KM. Economic Evaluation of Influenza Vaccine Intervention. In: Proceedings of the American Public Health Association Annual Meeting & Expo. 2016. https://apha.confex.com/apha/144am/meetingapp.cgi/Paper/366314.
  • Alam MM, Khan M, Kumar VSA, Marathe MV. An Efficient and Scalable Algorithmic Method for Generating Large–Scale Random Graphs. In: Proceedings of the The International Conference for High Performance Computing, Networking, Storage and Analysis. 2016.
  • Davis JJ, Boisvert S, Brettin T, Kenyon RW, Mao C, Olson R, Overbeek R, Santerre J, Shukla M, Wattam AR, Will R, Xia F, Stevens R. Antimicrobial Resistance Prediction in PATRIC and RAST. Sci Rep. 2016;6:27930. https://doi.org/10.1038/srep27930.
  • Barrett CL, Marathe M, Bisset K. Complex situation analysis system using a plurality of brokers that control access to information sources. 2016. https://patents.google.com/patent/US9367805B2.
  • Sathappan M, Butler P, Khandpur R, Saraf P, Self N, Rozovskaya A, Zhao L, Cadena J, Lu C, Vullikanti AKS, Marathe A, Summers K, Katz G, Arredondo J, Gupta D, Mares D, Ramakrishnan N. EMBERS at 4 years: Experiences operating an Open Source Indicators Forecasting System. In: Proceedings of the 22nd ACM SIGKDD Conference on Knowledge Discovery and Data Mining. 2016.
  • Parikh N, Marathe MV, Swarup S. Integrating Behavior and Microsimulation Models. Presented at the AAMAS, Singapore; 2016.
  • Kumar VSA, Marathe MV, Parthasarathy S, Srinivasan A. Distributed Algorithms for End-to-End Packet Scheduling in Wireless Ad Hoc Networks. ACM Transactions on Algorithms (TALG). 2016;12(3):28. https://doi.org/10.1145/2812811.
  • Parikh N, Marathe M, Swarup S. Summarizing Simulation Results Using Causally-Relevant States. Presented at the Conference on Autonomous Agents and Multiagent Systems (AAMAS) Workshops, Singapore, SINGAPORE; 2016. https://doi.org/10.1007/978-3-319-46840-2_6.
  • Pal A, Sanchez-Ayala GA, Thorp JS, Centeno VA. A community-based partitioning approach for PMU placement in large systems. Electric Power Components & Systems. 2016;44(12):1317–1329. https://doi.org/10.1080/15325008.2016.1167791.
  • Barrett CL, Centeno VA, Eubank SG, Evrenosoglu CY, Marathe A, Marathe MV, Mishra C, Mortveit HS, Pal A, Phadke AG, Thorp JS, Kumar VSA, Youssef M. Impact of a Surface Nuclear Blast on the Transient Stability of the Power System. Springer International Publishing; 2016:153–158.
  • Adiga A, Venkatramanan S, Kumar VSA. To delay or not: Temporal vaccination games on networks. In: Proceedings of the 35th Annual IEEE International Conference on Computer Communications. IEEE; 2016:1–9.
  • Abdelhamid S, Kuhlman CJ, Marathe MV, Ravi SS. Agent-Based Modeling and Simulation of Depression and Its Impact on Students’ Success and Academic Retention. In: Proceedings of the American Society for Engineering Education Annual Conference. 2016.
  • Bisset KR, Cadena JE, Khan M, Kuhlman CJ, Lewis BL, Telionis P. An Integrated Agent-Based Approach for Modeling Disease Spread in Large Populations to Support Health Informatics. In: Proceedings of the 2016 IEEE International Conference on Biomedical and Health Informatics. IEEE; 2016:629–632.
  • Abdelhamid S, Kuhlman CJ, Marathe MV, Ravi SS. Network Services and Their Compositions for Network Science Applications. In: Proceedings of the International Conference on Computational Science (ICCS). Vol 80. Elsevier; 2016:472–483. https://doi.org/10.1016/j.procs.2016.05.326.
  • Parikh NK, Marathe MV, Swarup S. Summarizing Simulation Results using Causally-relevant States. Proceedings of the 17th International Workshop on Multi-Agent Based Simulation (MABS), held in conjunction with AAMAS. 2016. https://doi.org/10.1007/978-3-319-46840-2_6.
  • Parikh NK, Hayatnagarkar HG, Beckman RJ, Marathe MV, Swarup S. A comparison of multiple behavior models in a simulation of the aftermath of an improvised nuclear detonation. Autonomous Agents and Multi-Agent Systems. 2016:1–27. https://doi.org/10.1007/s10458-016-9331-y.
  • Abbas KM, Dorratoltaj N, Marathe A, Swarup S, Lewis BL, Eubank SG. Economic evaluation of influenza vaccine intervention. International Journal of Infectious Diseases. 2016;45(supplement 1):159.
  • Marathe A. Interviewed by Kettlewell C. License To Ill. Virginia Living. 2016. https://issuu.com/capefear/docs/2016_04apr_issuu.
  • Leber A, Abedi V, Hontecillas R, Viladomiu M, Hoops S, Ciupe S, Caughman J, Andrew T, Bassaganya-Riera J. Bistability analyses of CD4+T follicular helper and regulatory cells during Helicobacter pylori infection. JOURNAL OF THEORETICAL BIOLOGY. 2016;398:74–84. https://doi.org/10.1016/j.jtbi.2016.02.036.
  • Abbas K, Dorratoltaj N, O'Dell M, Bordwine P, Kerkering TM, Redican KJ. Clinical Response, Outbreak Investigation, and Epidemiology of the Fungal Meningitis Epidemic in the United States: Systematic Review. Disaster Med Public Health Prep. 2016;10(1):145–151. https://doi.org/10.1056/NEJMoa1215460.
  • Marathe A, Chen J. Interviewed by Trent T. Biocomplexity Institute researchers seek to eliminate the heavy costs of flu season. VT News . 2016. https://vtnews.vt.edu/articles/2016/01/011416-bi-flu.html.
  • Adiga A, Galyean H, Kuhlman CJ, Levet M, Mortveit HS, Wu S. Activity in Boolean Networks. Presented at the Proceedings of the 21st International Workshop on Cellular Automata and Discrete Complex Systems: Automata 2015, Turku, Finland; 2016. https://doi.org/10.1007/s11047-016-9584-z.
  • Lofgren E, Kumar VSA. Hospital stockpiling problems with inventory sharing. In: Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence. AAAI Press; 2016:35–41. http://www.aaai.org/ocs/index.php/AAAI/AAAI16/paper/viewFile/124....
  • Lum K, Chungbaek Y, Eubank SG, Marathe MV. A Two-stage, Fitted Values Approach to Activity Matching. International Journal of Transportation. 2016;4(1):41–56.
  • Pal A, Sanchez-Ayala G, Thorp JS, Centeno VA. A Community-based Partitioning Approach for Phasor Measurement Unit Placement in Large Systems. Electric Power Components and Systems. 2016;(1317-1329). https://doi.org/10.1080/15325008.2016.1167791.
  • Chen J, Kumar VSA, Marathe MV, Sundaram R, Thakur M, Thulasidasan S. A study of the structure and vulnerabilities of metropolitan area networks. In: Proceedings of the 8th International Conference on COMmunication Systems & NETworkS. IEEE; 2016:1–8.
  • Lofgren E, Collins KM, Smith TC, Cartwright RA. Equations of the End: Teaching Mathematical Modeling using the Zombie Apocalypse. Journal of Microbiology and Biology Education. 2016;17(1):137–142. https://doi.org/10.1128/jmbe.v17i1.1066.
  • Dutta T, Heath L, Kumar VSA, Marathe MV. Labeled cuts in graphs. Theoretical Computer Science. 2016;648(34-39). https://doi.org/10.1016/j.tcs.2016.07.040.
  • Smith C, Stringer AM, Mao C, Palumbo MJ, Wade JT. Mapping the Regulatory Network for Salmonella enterica Serovar Typhimurium Invasion. mBio. 2016;7(5). https://doi.org/10.1128/mbio.01024-16.
  • Cadena JE, Kumar VSA, Aggarwal CC. On Dense Subgraphs in Signed Network Streams. In: Proceedings of the IEEE International Conference on Data Mining 2016. IEEE; 2016. https://doi.org/10.1109/ICDM.2016.0016.
  • Adiga A, Kumar VSA. Temporal Vaccination Games Under Resource Constraints. In: Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence. 2016.

2015

  • Mishra C, Jones KD, Pal A, Centeno VA. A binary particle swarm optimisation-based optimal substation coverage algorithm for PMU installations in practical systems. IET Generation, Transmission & Distribution. 2015;10(2):555–562. https://doi.org/10.1049/iet-gtd.2015.1077.
  • Pal A, Chatterjee P, Thorp JS, Centeno VA. On-line Calibration of Voltage Transformers Using Synchrophasor Measurements. IEEE Transactions on Power Delivery. 2015;PP(99):1–10. https://doi.org/10.1109/TPWRD.2015.2494058.
  • Althouse BM, Scarpino SV, Meyers LA, Ayers JW, Bargsten M, Baumbach J, Brownstein JS, Castro L, Clapham H, Cummings DAT, Valle SD, Eubank SG, Fairchild G, Finelli L, Generous N, George D, Harper DR, Hebert-Dufresne L, Johansson MA, Konty K, Lipsitch M, Milinovich G, Miller JD, Nsoesie EO, Olson DR, Paul M, Polgreen PM, Priedhorsky R, Read JM, Rodríguez-Barraquer I, Smith DJ, Stefansen C, Swerdlow DL, Thompson D, Vespignani A, Wesolowski A. Enhancing disease surveillance with novel data streams: challenges and opportunities. EPJ Data Science. 2015;4(17). https://doi.org/10.1140/epjds/s13688-015-0054-0.
  • Pires B, Korkmaz G, Ensor K, Higdon D, Keller S, Lewis B, Schroeder A. Towards an in silico Experimental Platform for Air Quality: Houston, TX as a Case Study. Presented at the Annual Conference of the Computational Social Science Society of the Americas (CSSSA), Santa Fe, New Mexico; 2015. http://computationalsocialscience.org/wp-content/uploads/2015/10....
  • Bassaganya-Riera J, Hontecillas R, Abedi V, Carbo A, Philipson C, Hoops S. Computational Modeling. In: Computational Immunology: Models and Tools. 1st ed. 2015:9–29.
  • Hoops S, Sobral BW, Michalak P, Abedi V, Kronsteiner B, Hontecillas R, Viladomiu M, Bassaganya-Riera J. Immunoinformatics cybernfrastructure for modeling and analytics. In: Computational Immunology: Models and Tools. 1st ed. 2015:45–61.
  • Abedi V, Hoops S, Hontecillas R, Carbo A, Philipson C, Viladomiu M, Leber A, Lu P, Bassaganya-Riera J. Modeling exercises. In: Computational Immunology: Models and Tools. 2015.
  • Hoops S, Hontecillas R, Abedi V, Leber A, Philipson C, Carbo A, Bassaganya-Riera J. Ordinary Differential Equations (ODE) based Modeling. In: Computational Immunology: Models and Tools. 2015.
  • Hontecillas-Magarzo R, Bassaganya-Riera J, Philipson C, Leber A, Viladomiu M, Carbo A, Wendelsdorf K, Hoops S. Use of Computational Modeling in Immunological Research. In: Computational Immunology: Models and Tools. 2015.
  • Ramakrishnan N, Lu C-T, Marathe MV, Marathe A, Kumar VSA, Eubank SG, Leman S, Roan M, Summers K, Getoor L, Srinivasan A, Choudhury T, Gupta D, Mares D. Model-Based Forecasting of Significant Societal Events. IEEE Intelligent Systems. 2015;30(5):86–90. https://doi.org/10.1109/MIS.2015.74.
  • Philipson CW, Bassaganya-Riera J, Viladomiu M, Kronsteiner B, Abedi V, Hoops S, Michalak P, Kang L, Girardin SE, Hontecillas R. Modeling the Regulatory Mechanisms by Which NLRX1 Modulates Innate Immune Responses to Helicobacter pylori Infection. PLOS ONE. 2015;10(9). https://doi.org/10.1371/journal.pone.0137839.
  • Adiga A, Chu S, Marathe A, Kumar VSA. Can social distancing compensate for the unvaccinated? In: Proceedings of the Computational Social Science Society of the Americas Annual Conference. 2015. https://computationalsocialscience.org/.
  • Lu P, Abedi V, Mei Y, Hontecillas R, Hoops S, Carbo A, Bassaganya-Riera J. Supervised learning methods in modeling of CD4+T cell heterogeneity. BIODATA MINING. 2015;8. https://doi.org/10.1186/s13040-015-0060-6.
  • Barrett C, Marathe M, Bisset K, Beckman R, Stretz P, Mortveit H, Eubank S, Marathe A, Vullikanti AKS, Atkins KS. Complex Situation Analysis System. 2015. https://patents.google.com/patent/AU2010236510.
  • Ross-Innes C, Becq J, Warren A, Cheetham R, Northen H, O'Donovan M, Malhotra S, Pietro M, Ivakhno S, He M, Weaver J, Lynch A, Kingsbury Z, Ross M, Humphray S, Bentley D, Fitzgerald R. Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma. Nature genetics. 2015;47(9):1038–1046.
  • Mei Y, Abedi V, Carbo A, Zhang X, Lu P, Philipson C, Hontecillas R, Hoops S, Liles N, Bassaganya-Riera J. Multiscale modeling of mucosal immune responses. BMC BIOINFORMATICS. 2015;16. https://doi.org/10.1186/1471-2105-16-S12-S2.
  • Zhang Y, Adiga A, Kumar VSA, Prakash BA. Controlling Propagation at Group Scale on Networks. In: Proceedings of the IEEE International Conference on Data Mining (ICDM 2015). 2015.
  • Deodhar S, Chen J, Wilson AL, Bisset KR, Lewis BL, Barrett CL, Marathe MV. EpiCaster: An Integrated Web Application For Situation Assessment and Forecasting of Global Epidemics. In: Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB). ACM; 2015:156–165. https://doi.org/10.1145/2808719.2808735.
  • Deodhar S, Chen J, Wilson AL, Soundarapandian M, Bisset KR, Lewis BL, Barrett CL, Marathe MV. FluCaster: A Pervasive Web Application For High Resolution Situation Assessment and Forecasting of Flu Outbreaks. In: Proceedings of the 2nd IEEE International Conference on Healthcare Informatics. IEEE; 2015:105–114. https://doi.org/10.1109/ICHI.2015.20.
  • Zhao L, Chen J, Chen F, Wang W, Lu C-T, Ramakrishnan N. SimNest: Social Media Nested Epidemic Simulation via Online Semi-supervised Deep Learning. In: Proceedings of the IEEE International Conference on Data Mining. 2015. http://icdm2015.stonybrook.edu/.
  • Adiga A, Chu S, Marathe A, Kumar VSA. Vaccination or social distancing: A public health dilemma. Presented at the INFORMS Healthcare Conference, Nashville, TN; 2015.
  • Alam MM, Abedi V, Bassaganya-Riera J, Wendelsdorf KV, Bisset KR, Deng X, Eubank SG, Hontecillas-Magarzo R, Hoops S, Marathe MV. Agent-Based Modeling and High Performance Computing. In: Computational Immunology: Models and Tools. Elsevier; 2015:79–112. http://store.elsevier.com/product.jsp?isbn=9780128036976.
  • Alam MM, Deng X, Philipson C, Bassaganya-Riera J, Bisset KR, Carbo A, Eubank SG, Hontecillas-Magarzo R, Hoops S, Mei Y, Abedi V, Marathe MV. Sensitivity Analysis of an ENteric Immunity SImulator (ENISI)-based Model of Immune Responses to Helicobacter pylori Infection. PLOS One. 2015;10(9):e0136139. https://doi.org/10.1371/journal.pone.0136139.
  • Lu P, Abedi V, Mei Y, Hontecillas R, Philipson C, Hoops S, Carbo A, Bassaganya-Riera J. Supervised Learning with Artificial Neural Network in Modeling of Cell Differentiation Process. In: Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology. Morgan Kaufmann; 2015.
  • Marathe A, Abbas KM, Swarup S. Understanding Feedback Between Behavioral Interventions and Disease Evolution. In: Proceedings of the 2015 INFORMS Annual Meeting. 2015.
  • Leber A, Viladomiu M, Hontecillas R, Abedi V, Philipson C, Hoops S, Howard B, Bassaganya-Riera J. Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection. PLOS ONE. 2015;10(7). https://doi.org/10.1371/journal.pone.0134849.
  • Korkmaz G, Cadena JE, Kuhlman CJ, Marathe A, Kumar VSA, Ramakrishnan N. Combining Heterogeneous Data Sources for Civil-Unrest Forecasting. In: Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Network Analysis and Mining (ASONAM). ACM; 2015:258–265. https://doi.org/10.1145/2808797.2808847.
  • Abdelhamid SEM, Kuhlman CJ, Korkmaz G, Marathe MV, Ravi SS. EDISON: A Web Application for Computational Health Informatics At Scale. In: Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics. ACM; 2015:413–422.
  • Abdelhamid SHE, Kuhlman CJ, Marathe MV, Mortveit HS, Ravi SS. GDSCalc: A Web-Based Application for Evaluating Discrete Graph Dynamical Systems. PLoS One. 2015;10(8):e0133660. https://doi.org/10.1371/journal.pone.0133660.
  • Kuhlman CJ, Mortveit HS. Limit Sets of Generalized, Multi-Threshold Networks. Journal of Cellular Automata. 2015;10:161–193.
  • Saha S, Adiga A, Prakash BA, Kumar VSA. Approximation algorithms for reducing the spectral radius to control epidemic spread. In: Proceedings of the 2015 International Conference on Data Mining. 2015. http://www.siam.org/meetings/sdm15/.
  • Schlitt J, Lewis BL, Eubank SG. ChatterGrabber: A Lightweight Easy to Use Social Media Surveillance Toolkit. Online Journal of Public Health Informatics. 2015;7(1). https://doi.org/10.5210/ojphi.v7i1.5717.
  • Nath M, Eubank SG, Youssef M, Khorramzadeh Y, Mowlaei S. Four Parameter Characterization of Network Reliability and Analysis of Critical Point Phenomenology. In: Bulletin of the American Physical Society. Vol 60. American Physical Society; 2015:1057P. http://meetings.aps.org/link/BAPS.2015.MAR.P1.57.
  • Lofgren E, Halloran ME, Rivers CM, Drake JM, Porco T, Lewis BL, Yang W, Vespignani A, Shaman J, Eisenberg J, Eisenberg MC, Marathe MV, Scarpino SV, Alexander KA, Meza R, Ferrari MJ, Hyman JM, Meyers LA, Eubank SG. Mathematical models: A key tool for outbreak response. Proceedings of the National Academy of Science. 2015;111(51):18095–18096. https://doi.org/10.1073/pnas.1421551111.
  • Eubank SG, Khorramzadeh Y, Youssef M, Mowlaei S, Nath M. Network Reliability As a Tool for Using Dynamics to Probe Network Structure. In: Proceedings of the 2015 Conference on Applications of Dynamical Systems. 2015. http://www.siam.org/meetings/ds15/.
  • Lofgren E. Pools versus Queues: The Variable Dynamics of Stochastic “Steady States.” PLOS One. 2015. https://doi.org/10.1371/journal.pone.0130574.
  • Pal A, Youssef M, Kumar VSA, Marathe A, Eubank SG, Marathe MV, Barrett CL, Thorp J, Phadke A, Centeno V. Role of Power System Relays in a Large Scale Physical Attack. In: Proceedings of the 6th Int. Conf. Liberalization & Modernization of Power Systems and CRIS Problems of Critical Infrastructures. 2015.
  • Adiga A, Beckman RJ, Bisset KR, Chen J, Chungbaek Y, Eubank SG, Gupta S, Khan M, Kuhlman CJ, Lofgren E, Lewis BL, Marathe A, Marathe MV, Mortveit HS, Nordberg EK, Rivers CM, Stretz PE, Swarup S, Wilson AL, Xie D. Synthetic Populations for Epidemic Modeling. In: Proceedings of the International Conference on Computational Social Sciences (ICCSS). 2015. http://www.iccss2015.eu/.
  • Abbas K, Dorratoltaj N, O'Dell ML, Bordwine P, Kerkering TM, Redican KJ. Economic Evaluation of a Fungal Meningitis Outbreak Response in New River Valley: Local Health Department Perspective. Front Public Health Serv Syst Res. 2015;4(4):21–28. https://doi.org/10.13023/FPHSSR.0404.04.
  • Marathe A. Vaccination or social distancing: A public health dilemma. 2015.
  • Arifuzzaman SM, Khan M, Marathe MV. A Space-efficient Parallel Algorithm for Counting Exact Triangles in Massive Networks. In: Proceedings of the 17th IEEE International Conference on High Performance Computing and Communications. 2015. http://cse.stfx.ca/~hpcc2015/.
  • Adiga A, Kuhlman CJ, Marathe MV, Ravi SS, Rosenkrantz DJ, Stearns RE. Complexity of Inferring Local Transition Functions of Discrete Dynamical Systems. In: 20th International Conference Implementation and Application of Automata (CIAA). 2015:21–34. http://link.springer.com/chapter/10.1007%2F978-3-319-22360-5_3.
  • Marathe M. Analysis Problems for Graphical Dynamical Systems: A United Approach Through Graph Predicates. Presented at the International Conference on Autonomous Agents & Multiagent Systems (AAMAS), Istanbul, Turkey ; 2015.
  • Adiga A, Kuhlman CJ, Mortveit HS, Wu S. Effect of Graph Structure on the Limit Sets of Threshold Dynamical Systems. In: Proceedings of the 21st International Workshop on Cellular Automata and Discrete Complex Systems. 2015. http://math.utu.fi/automata2015/abstracts/.
  • Adiga A, Galyean H, Kuhlman CJ, Levet M, Mortveit HS, Wu S. Network Structure and Activity in Boolean Networks. In: Proceedings of the 21st International Workshop on Cellular Automata and Discrete Complex Systems. Vol 8155. 2015:210–223. https://doi.org/10.1007/978-3-662-47221-7_16.
  • Rosenkrantz D, Marathe MV, III HH, Ravi SS, Sterns R. Analysis Problems for Graphical Dynamical Systems: A Unified Approach Through Graph Predicates. In: Proceedings of the 14th International Conference on Autonomous Agents and Multiagent Systems (AAMAS2015). 2015. http://www.aamas2015.com/en/.
  • Lau E, Zheng J, Tsang T, Liao Q, Lewis B, Brownstein J, Sanders S, Mekaru S, Rivers C, Leung G, Feng L, Cowling B, Yu H. Epidemiological inferences using public information, influenza H7N9 epidemic in China. Online J Public Health Inform. 2015;7(1):e143. https://doi.org/10.5210/ojphi.v7i1.5809.
  • Marathe A, Gray J, Gray L, Fan S, Norton G. Projecting the Spread of Infectious Diseases. Ebola: Predicting it, Addressing it, and Food Security Impacts. 2015.
  • Kang GJ, Culp R, Marathe A, Abbas KM. Parental Factors Associated with Influenza School Located Vaccination Program in the United States. Presented at the CUGH Global Health Conference, "Mobilizing Research for Global Health", Boston, Massachusetts; 2015.
  • Lopez D, Gunasekaran M, Murugan B, Harprett K, Abbas K. Spatial big data analytics of influenza epidemic in Vellore, India. In: 2014 IEEE International Conference on Big Data (Big Data). 2015:19–24. https://doi.org/10.1109/BigData.2014.7004422.
  • Warren AS, Aurrecoechea C, Brunk B, Desai P, Emrich S, Giraldo-Calderon GI, Harb O, Hix D, Lawson D, Machi D, Mao C, McClelland M, Nordberg E, Shukla M, Vosshall LB, Wattam AR, Will R, Yoo HS, Sobral B. RNA-Rocket: an RNA-Seq analysis resource for infectious disease research. BIOINFORMATICS. 2015;31(9):1496–1498. https://doi.org/10.1093/bioinformatics/btv002.
  • Warren A, Aurrecoechea C, Brunk B, Desai P, Emrich S, Giraldo-Calderón GI, Harb O, Hix D, Lawson D, Machi D, Mao C, McClelland M, Nordberg E, Shukla M, Vosshall LB, Wattam A, Will R, Yoo HS, Sobral B. RNA-Rocket: an RNA-Seq analysis resource for infectious disease research. Bioinformatics. 2015;31(9):1496–1498. https://doi.org/10.1093/bioinformatics/btv002.
  • Yi M, Marathe A. Fairness versus Efficiency of Vaccine Allocation Strategies. Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research. 2015;18(2):278–283. http://www.sciencedirect.com/science/article/pii/S10983015140477....
  • Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arca B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VLM, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DST, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MKN, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simao FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GWC, Tojo M, Topalis P, Tubio JMC, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu Y-C, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MAT, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJ. Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes. SCIENCE. 2015;347(6217). https://doi.org/10.1126/science.1258522.
  • Arifuzzaman SM, Khan M, Marathe MV. A Fast Parallel Algorithm for Counting Triangles in Graphs using Dynamic Load Balancing. In: Proceedings of the 2015 IEEE International Conference on Big Data. 2015.
  • Khorramzadeh Y, Youssef M, Eubank SG, Mowlaei S. Analyzing network reliability using structural motifs. Phys Rev E. 2015;91(4):042814.
  • Pyne S, Marathe MV, Kumar VSA. Big Data Applications in Health Sciences and Epidemiology, Handbook of Statistics, Volume 33: Big Data Analytics. Elsevier. Edited by V. Govindaraju, V.V. Raghavan, C.R. Rao; 2015:171–202. https://doi.org/10.1016/B978-0-444-63492-4.00008-3.
  • BW S, Wattam AR. Comparative Genomics and Phylogenomics of the Brucella. Horizon Scientific Press; 2015.
  • Kamal T, Bisset KR, Butt AR, Marathe MV. Cost Estimation of Parallel Constrained Producer-Consumer Algorithms. In: Parallel, Distributed and Network-Based Processing (PDP), 23rd Euromicro International Conference On. CPS, IEEE Computer Society; 2015:86–93.
  • Abedi V, Hontecillas R, Hoops S, Liles N, Carbo A, Lu P, Philipson C, Bassaganya-Riera J. ENISI Multiscale modeling of mucosal immune responses driven by high performance computing. Presented at the IEEE International Conference on Bioinformatics and Biomedicine, Washington, DC; 2015. https://doi.org/10.1109/BIBM.2015.7359768.
  • Mei Y, Carbo A, Hoops S, Hontecillas R, Bassaganya-Riera J. ENISI SDE: A New Web-Based Tool for Modeling Stochastic Processes. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. 2015;12(2):289–297. https://doi.org/10.1109/TCBB.2014.2351823.
  • Cadena JE, Korkmaz G, Kuhlman CJ, Marathe A, Ramakrishnan N, Kumar VSA. Forecasting Social Unrest Using Activity Cascades. PLoS One. 2015;10(6):e0128879. http://journals.plos.org/plosone/article?id=10.1371/journal.pone....
  • Barrett C, Marathe M. Interviewed by Gordon M, Adams M. Fortune-telling and other uses of big data at Virginia Tech. VT Magazine . 2015. http://www.vtmag.vt.edu/winter15/big-data-at-Virginia-Tech.html.
  • Swarup S, Ravi R, Mahmud MMH, Lum K, Ravi SS. Identifying Core Network Structure for Epidemic Simulations. In: Proceedings of the 12th International Workshop on Agents and Data-Mining Interaction. 2015.
  • Kuhlman CJ, Kumar VSA, Marathe MV, Ravi SS, Rosenkrantz DJ. Inhibiting diffusion of complex contagions in social networks: theoretical and experimental results. Data Mining and Knowledge Discovery. 2015;29(2):423–465. https://doi.org/10.1007/s10618-014-0351-4.
  • Orr M, Lewis B, Ziemer K, Keller S. Mathematical and Computational Simulation of the Behavioral and Social Drivers of Population Health in Population Health: Social and Behavioral Insights. 2015. http://www.ahrq.gov/sites/default/files/wysiwyg/professionals/ed....
  • Carbo A, Hontecillas R, Viladomiu M, Leber A, Hoops S, Bassaganya-Riera J. Modeling the Dynamics of T Helper 17 Induction and Differentiation. MOJ Immunol. 2015;2. https://doi.org/10.15406/moji.2015.02.00038.
  • Abedi V, Hontecillas R, Carbo A, Philipson C, Hoops S, Bassaganya-Riera J. Multiscale Modeling: Concepts, Technologies, and Use Cases in Immunology. In: Computational Immunology: Models and Tools. 2015.
  • Orr MG, Lewis B, Ziemer K, Keller S. Search Health Topics Health Care Delivery. Issues. 2015;2013.
  • Xia H, Nagaraj KS, Chen J, Marathe MV. Synthesis of a High Resolution Social Contact Network for Delhi With Application to Pandemic Planning. Journal of Artificial Intelligence in Medicine. 2015;65(2):113–130. https://doi.org/10.1016/j.artmed.2015.06.003.
  • Barrett CL, Eubank SG, Marathe A, Marathe MV, Swarup S. Synthetic Information Environments for Policy Informatics: A Distributed Cognition Perspective. Routledge Press; 2015:pp. 267–284. eds. Erik Johnston. http://www.routledge.com/books/details/9781138832084/.

2014

  • Times NY. Fewer Ebola Cases Go Unreported Than Thought, Study Finds . New York Times . 2014. https://www.nytimes.com/2014/12/16/science/fewer-ebola-cases-go-....
  • Lofgren E, Halloran ME, Rivers CM, Drake JM, Porco T, Lewis BL, Yang W, Vespignani A, Shaman J, Eisenberg J, Eisenberg MC, Marathe MV, Scarpino SV, Alexander KA, Meza R, Ferrari MJ, Hyman JM, Meyers LA, Eubank SG. Opinion: Mathematical models: A key tool for outbreak response. Proceedings of the National Academy of Sciences (PNAS). 2014;111(51):18095–18096. https://doi.org/10.1073/pnas.1421551111.
  • Alexander KA, Sanderson CE, Marathe MV, Lewis BL, Rivers CM, Shaman J, Drake JM, Lofgren E, Dato VM, Eisenberg MC, Eubank SG. What factors might have led to the emergence of Ebola in West Africa? PLOS Neglected Tropical Diseases. 2014:1418–1425. http://blogs.plos.org/speakingofmedicine/2014/11/11/factors-migh....
  • Guilford G. How crowdsourcing and supercomputing are helping Sierra Leone combat its Ebola epidemic. Quartz. 2014. https://qz.com/287178/how-crowdsourcing-and-supercomputing-are-h....
  • Eubank S. Interviewed by Self N to. Containing Ebola Like They Did in This Video Game. 2014. http://www.wnyc.org/story/corrupted-blood-part-our-ebola-strateg....
  • Rivers CM, Lofgren E, Marathe MV, Eubank SG, Lewis BL. Modeling the Impact of Interventions on an Epidemic of Ebola in Sierra Leone and Liberia. PLOS Currents Outbreaks. 2014;Edition 1. https://doi.org/10.1371/currents.outbreaks.fd38dd85078565450b0be....
  • Eubank SG, Youssef M, Khorramzadeh Y. Using the network reliability polynomial to characterize and design networks. Journal of Complex Networks. 2014;2(4):356–372. https://doi.org/10.1093/comnet/cnu037.
  • Internationalt P. Computer nerds are used in the fight against Ebola . Politiken Internationalt. 2014. http://politiken.dk/udland/fokus_int/Ebola/art5554269/Analyse-Co....
  • McGinty JC. Success in Modeling Ebola’s Spread Depends on Wealth of Data. The Wall Street Journal . 2014. https://www.wsj.com/articles/success-in-modeling-ebolas-spread-d....
  • Lewis B. Interviewed by IQ R. Modeling the Path of Ebola . 2014. http://wvtf.org/post/modeling-path-ebola.
  • Lewis B. Interviewed by Rehm D. Containing Ebola In The United States. 2014. http://dianerehm.org/shows/2014-10-06/containing-ebola-united-st....
  • Knox R. A Diplomat Infects A Doctor As Ebola Spreads In Nigeria. NPR Health . 2014. http://www.npr.org/sections/goatsandsoda/2014/09/05/346033875/a-....
  • Misra T. Does Ebola Spread Faster in Cities? City Lab . 2014. https://www.citylab.com/life/2014/10/does-ebola-spread-faster-in....
  • Mao C, Abraham D, Wattam AR, Wilson MJC, Shukla M, Yoo HS, Sobral BW. Curation, integration and visualization of bacterial virulence factors in PATRIC. BIOINFORMATICS. 2014;31(2):252–258. https://doi.org/10.1093/bioinformatics/btu631.
  • Elliot D. Chasing Ebola. The Atlantic . 2014. https://www.theatlantic.com/health/archive/2014/09/chasing-ebola....
  • Grady D. Ebola Cases Could Reach 1.4 Million Within Four Months, C.D.C. Estimates. The New York TImes. 2014. https://www.nytimes.com/2014/09/24/health/ebola-cases-could-reac....
  • Panas MW, Jain P, Yang H, Mitra S, Biswas D, Wattam AR, Letvin NL, Jacobs WR. Noncanonical SMC protein in Mycobacterium smegmatis restricts maintenance of Mycobacterium fortuitum plasmids. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2014;111(37):13264–13271. https://doi.org/10.1073/pnas.1414207111.
  • Barrett CL, Centeno V, Eubank SG, Evrenosoglu CY, Marathe A, Marathe MV, Mishra C, Mortveit HS, Pal A, Phadke A, Thorp J, Kumar VSA, Youssef M. Impact of a surface nuclear blast on the transient stability of the power system. In: Proceedings of the 9th International Conference on Critical Information Infrastructures Security. 2014.
  • Lewis B. Interviewed by NPR HN from. A Virtual Outbreak Offers Hints Of Ebola's Future. 2014. http://www.npr.org/sections/health-shots/2014/08/14/340346575/a-....
  • Deodhar S, Bisset KR, Chen J, Ma Y, Marathe MV. An Interactive, Web-Based High Performance Modeling Environment for Computational Epidemiology. ACM Transactions on Management Information Systems. 2014;5(2):7. https://doi.org/10.1145/2629692.
  • Rosenkrantz D, Marathe MV, Ravi SS, Kumar VSA. Bayesian inference in treewidth-bounded graphical models without indegree constraints. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (UAI). 2014.
  • Saha S, Adiga A, Kumar VSA. Equilibria in epidemic containment games. In: Twenty-Eighth AAAI Conference on Artificial Intelligence. 2014:777–783. http://www.aaai.org/ocs/index.php/AAAI/AAAI14/paper/view/8478.
  • Adiga A, Chandran SL. Representing a cubic graph as the intersection graph of axis-parallel boxes in three dimensions. SIAM Journal on Discrete Mathematics. 2014;28(3):1515–1539. http://epubs.siam.org/doi/abs/10.1137/120861795.
  • Adiga A, Kuhlman CJ, Mortveit HS, Kumar VSA. Sensitivity of diffusion dynamics to network uncertainty. Journal of Artificial Intelligence Research. 2014;51:207–226.
  • Keneshloo Y, Cadena JE, Korkmaz G, Ramakrishnan N. Detecting and Forecasting Domestic Political Crises: A Graph-based Approach. Presented at the ACM Web Science Conference 2014 (WebSci14), Indiana University, Bloomington, Indiana; 2014. https://doi.org/10.1145/2615569.2615698.
  • Youssef M, Scoglio C. Optimal Network-based Intervention in the Presence of Undetectable Viruses. IEEE Communications Letters. 2014;18:1347–1350.
  • Kuhlman CJ, Mortveit HS. Attractor Stability in Nonuniform Boolean Networks. Theoretical Computer Science. 2014;559:20–33. https://doi.org/10.1016/j.tcs.2014.08.010.
  • Lau EHY, Zheng J, Tsang TK, Liao Q, Lewis BL, Brownstein JS, Sanders S, Wong JY, Mekaru SR, Rivers CM, Wu P, Jiang H, Li Y, Yu J, Zhang Q, Chang Z, Liu F, Peng Z, Leung GM, Feng L, Cowling BJ, Yu H. Accuracy of epidemiological inferences based on publicly available information: retrospective comparative analysis of line lists of human cases infected with influenza A(H7N9) in China. BMC Medicine. 2014;12(88). https://doi.org/10.1186/1741-7015-12-88.
  • Abdelhamid SE, Alam MM, Alo R, Arifuzzaman SM, Beckman P, Bhattacharjee T, Bhuiyan MH, Bisset KR, Eubank SG, Esterline AC, Fox EA, Fox GC, Hasan SMS, Hayatnagarkar H, Khan M, Kuhlman CJ, Marathe MV, Meghanathan N, Mortveit HS, Qiu J, Ravi SS, Shams Z, Sirisaengtaksin O, Swarup S, Kumar VSA, Wu T-L. CINET 2.0: A CyberInfrastructure for Network Science. In: The 10th IEEE International Conference on EScience, 2014. 2014:324–331. https://doi.org/10.1109/eScience.2014.21.
  • Ramakrishnan N, Butler P, Muthiah S, Self N, Khandpur R, Saraf P, Wang W, Cadena JE, Kumar VSA, Korkmaz G, Kuhlman CJ, Marathe A, Zhao L, Hua T, Chen F, Lu C-T, Huang B, Srinivasan A, Trinh K, Getoor L, Katz G, Doyle A, Ackermann C, Zavorin I, Ford J, Summers K, Fayed Y, Arredondo J, Gupta D, Mares D. 'Beating the news’ with EMBERS: Forecasting Civil Unrest using Open Source Indicators. In: Proceedings of the 20th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. 2014:1799–1808. http://dl.acm.org/citation.cfm?id=2623373.
  • Beckman RJ, Bisset KR, Chen J, Lewis BL, Marathe MV, Stretz PE. ISIS: A networked-epidemiology based pervasive web app for infectious disease pandemic planning and response. In: Proceedings of the 20th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. 2014.
  • Khorramzadeh Y, Youssef M, Eubank SG. Reliability theory for diffusion processes on interconnected networks. In: Bulletin of the American Physical Society. Vol 59. American Physical Society; 2014. http://meetings.aps.org/link/BAPS.2014.MAR.Q17.9.
  • Bhuiyan MH, Chen J, Khan M, Marathe MV. Fast Parallel Algorithms for Edge-Switching to Achieve a Target Visit Rate in Heterogeneous Graphs. In: Proceedings of the International Conference on Parallel Processing (ICPP). 2014.
  • Chakraborty P, Khadivi P, Lewis BL, Mahendiran A, Chen J, Butler P, Nsoesie EO, Mekaru SR, Brownstein JS, Marathe MV, Ramakrishnan N. Forecasting a Moving Target: Ensemble Models for ILI Case Count Predictions. Presented at the 2014 SIAM International Conference on Data Mining, Philadelphia, PA; 2014. https://doi.org/10.1137/1.9781611973440.30.
  • Barrett CL, Marathe M, Bisset K, Stretz P. Complex situation analysis system that spawns/creates new brokers using existing brokers as needed to respond to requests for data. 2014. https://patents.google.com/patent/US8682828B2.
  • Young SD, Rivers CM, Lewis BL. Methods of using real-time social media technologies for detection and remote monitoring of HIV outcomes. Preventative Medicine. 2014;63(112-115). https://doi.org/10.1016/j.ypmed.2014.01.024.
  • Nsoesie EO, Mekaru SR, Ramakrishnan N, Marathe MV, Brownstein JS. Modeling to Predict Cases of Hantavirus Pulmonary Syndrome in Chile. PLOS Neglected Tropical Diseases. 2014;8(4):e2779. https://doi.org/10.1371/journal.pntd.0002779.
  • Wattam AR, Foster JT, Mane SP, Beckstrom-Sternberg SM, Beckstrom-Sternberg JM, Dickerman AW, Keim P, Pearson T, Shukla M, Ward DV, Williams KP, Sobral BW, Tsolis RM, Whatmore AM, O'Callaghan D. Comparative Phylogenomics and Evolution of the Brucellae Reveal a Path to Virulence. JOURNAL OF BACTERIOLOGY. 2014;196(5):920–930. https://doi.org/10.1128/JB.01091-13.
  • Barrett C, Marathe M, Bisset K, Beckman R, Stretz P, Mortveit H, Eubank S, Marathe A, Vullikanti AKS, Atkins KA. Complex Situation Analysis System. 2014. https://patents.google.com/patent/SG175215.
  • Parikh NK, Youssef M, Swarup S, Eubank SG, Chungbaek Y. Cover your Cough! Quantifying the Benefits of a Localized Healthy Behavior Intervention on Flu Epidemics in Washington DC. In: Social Computing, Behavioral-Cultural Modeling and Prediction, Lecture Notes in Computer Science. Vol 8393. Springer Berlin Heidelberg; 2014:137–144.
  • Rivers CM, Lewis BL. Ethical research standards in a world of big data. F1000Research. 2014;3(38). https://doi.org/10.12688/f1000research.3-38.v2.
  • Bisset KR, Chen J, Deodhar S, Feng X, Ma Y, Marathe MV. Indemics: An interactive high-performance computing framework for data-intensive epidemic modeling. ACM Transactions on Modeling and Computer Simulation (TOMACS). 2014;24(1):32. https://doi.org/10.1145/2501602.
  • Saha S, Adiga A, Kumar VSA. Equilibria in Epidemic Containment Games. In: Proceedings of the 28th AAAI Conference on Artificial Intelligence (AAAI). 2014.
  • Lum K, Swarup S, Eubank SG, Hawdon J. The Contagious Nature of Imprisonment: An agent-based model to explain racial disparities in incarceration rates. Journal of the Royal Society Interface. 2014;11(20140409). https://doi.org/10.1098/rsif.2014.0409.
  • Korkmaz G, Kuhlman CJ, Marathe A, Marathe MV, Vega-Redondo F. Collective Action Through Common Knowledge Using A Facebook Model. In: Proceedings of The Thirteenth International Conference on Autonomous Agents and Multiagent Systems (AAMAS). 2014:253–260. http://dl.acm.org/citation.cfm?id=2615774.
  • Swarup S, Eubank SG, Marathe MV. Computational Epidemiology as a Challenge Domain for Multiagent Systems. In: Proceedings of The Thirteenth International Conference on Autonomous Agents and Multiagent Systems (AAMAS). International Foundation for Autonomous Agents and Multiagent Systems; 2014:1173–1176. http://dl.acm.org/citation.cfm?id=2617434.
  • Nsoesie EO, Leman SC, Marathe MV. A Dirichlet process model for classifying and forecasting epidemic curves. BMC Infectious Diseases. 2014;14(12). https://doi.org/10.1186/1471-2334-14-12.
  • Eubank SG, Youssef M, Khorramzadeh Y. Characterizing Relevant Network Structure with Reliability Polynomials. Springer International Publishing; 2014:117–143.
  • Wattam AR, Gabbard JL, Shukla M, Sobral BW. Comparative genomic analysis at the PATRIC, a bioinformatic resource center. Methods in molecular biology (Clifton, NJ). 2014;1197:287–308. https://doi.org/10.1007/978-1-4939-1261-2_17.
  • Carbo A, Hontecillas R, Andrew T, Eden K, Mei Y, Hoops S, Bassaganya-Riera J. Computational modeling of heterogeneity and function of CD4+ T cells. Frontiers in cell and developmental biology. 2014;2:31. https://doi.org/10.3389/fcell.2014.00031.
  • Mei Y, Carbo A, Hontecillas R, Hoops S, Liles N, Lu P, Philipson C, Bassaganya-Riera J. ENISI MSM: A Novel Multi-Scale Modeling Platform for Computational Immunology. Presented at the IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), Univ Ulster, Belfast, NORTH IRELAND; 2014. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=....
  • Majumder MS, Rivers CM, Lofgren E, Fisman D. Estimation of MERS-Coronavirus Reproductive Number and Case Fatality Rate for the Spring 2014 Saudi Arabia Outbreak: Insights from Publicly Available Data. PLoS Current Outbreaks. 2014;Edition 1. https://doi.org/10.1371/currents.outbreaks.98d2f8f3382d84f390736....
  • Timoshevskiy VA, Kinney NA, deBruyn BS, Mao C, Tu Z, Severson DW, Sharakhov IV, Sharakhova MV. Genomic composition and evolution of Aedes aegypti chromosomes revealed by the analysis of physically mapped supercontigs. BMC BIOLOGY. 2014;12. https://doi.org/10.1186/1741-7007-12-27.
  • Marathe A, Chen J, Eubank SG, Liao S, Ma Y. Impact of Paid Sick Leave Policy: A Social Planner's Perspective. American Journal of Public Health. 2014;104(1):e1–e1. https://doi.org/10.2105/AJPH.2013.301639.
  • Wu S, Adiga A, Mortveit HS. Limit cycle structure for dynamic bi-threshold systems. Theoretical computer science. 2014;559:34–41. http://www.sciencedirect.com/science/article/pii/S03043975140050....
  • Kamal T, Bisset KR, Butt AR, Marathe MV. Load analysis and cost estimation of parallel constrained producer-consumer algorithms. In: Proceedings of the 2014 IEEE International Conference on Cluster Computing. IEEE Press; 2014:286–287. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6968759&tag....
  • Yeom J-S, Bhatele A, Bisset KR, Bohm E, Gupta A, Kale L, Marathe MV, Nikolopoulos D, Schulz M, Wesolowski L. Overcoming the Scalability Challenges of Epidemic Simulations on Blue Waters. In: Proceedings of the 2014 IEEE 28th International Parallel and Distributed Processing Symposium (IPDPS). IEEE; 2014:755–764. https://doi.org/10.1109/IPDPS.2014.83.
  • Marathe MV, Mortveit HS, Parikh NK, Swarup S. Prescriptive Analytics Using Synthetic Information. Emerging Methods in Predictive Analytics: Risk Management and Decision Making. William H. Hsu (ed). IGI Global; 2014:William H. Hsu (ed.). https://doi.org/10.4018/978-1-4666-5063-3.
  • Abdel-Hamid T, Akshay VS, Ankel F, Battle-Fisher M, Gibson B, Gonzalez-Parra G, Jalali MS, Kaipainen K, Kalupahana NS, Karanfil O, McKelvey KL, Marathe A, Martinson BC, Oorschot KV, Pintauro S, Poucheret P, Pronk NP, Qian Y, Sarbadhikari SN, Sazonov E, Murphy PJ. Public and Health-Professionals’ Misconceptions about Dynamics of Weight Gain/Loss. System Dynamics Review. 2014;30(1-2):58–74. https://doi.org/10.1002/sdr.1517.
  • Channakeshava K, Bisset KR, Marathe MV, Kumar VSA. Reasoning about mobile malware using high performance computing based population scale models. In: Proceedings of the 2014 Winter Simulation Conference. IEEE Press; 2014:3048–3059. http://dl.acm.org/citation.cfm?id=2694232.
  • Burns G, Gil Y, Liu Y, Villanueva-Rosales N, Risi S, Lehman J, Clune J, Lebiere C, Rosenbloom PS, Harmelen Fvan, Hitzler P, Janowic K, Swarup S, Schlitt J. Reports on the 2013 AAAI Fall Symposium Series. AI Magazine. 2014;35(2):69–74. http://www.aaai.org/ojs/index.php/aimagazine/article/view/2538/2....
  • Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). NUCLEIC ACIDS RESEARCH. 2014;42(D1):D206–D214. https://doi.org/10.1093/nar/gkt1226.

2013

  • Kuhlman CJ, Tuli G, Swarup S, Marathe MV, Ravi SS. Blocking Simple and Complex Contagion By Edge Removal. In: Proceedings of the IEEE International Conference on Data Mining. 2013:399–408. https://doi.org/10.1109/ICDM.2013.47.
  • Carbo A, Bassaganya-Riera J, Pedragosa M, Viladomiu M, Marathe MV, Eubank SG, Wendelsdorf KV, Bisset KR, Hoops S, Deng X, Alam MM, Kronsteiner B, Mei Y, Hontecillas-Magarzo R. Predictive Computational Modeling of the Mucosal Immune Responses during Helicobacter pylori Infection. PLoS One. 2013;8(9):e73365. https://doi.org/10.1371/journal.pone.0073365.
  • Arifuzzaman SM, Khan M, Marathe MV. PATRIC: A Parallel Algorithm for Counting Triangles and Computing Clustering Coefficients in Massive Networks. In: Proceedings of the 22nd ACM International Conference on Conference on Information & Knowledge Management. ACM; 2013:529–538. https://doi.org/10.1145/2505515.2505545.
  • Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJ, Yoo HS, Zhang C, Zhang Y, Sobral BW. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res. 2013;42(1):D581–91. https://doi.org/10.1093/nar/gkt1099.
  • Barrett C. Interviewed by Hatmaker K. Portland's slowdowns help advance science of transportation. KATU_News. 2013. http://katu.com/news/investigators/portlands-slowdowns-help-adva....
  • Scaria J, Mao C, Chen J-W, McDonough SP, Sobral B, Chang Y-F. Differential Stress Transcriptome Landscape of Historic and Recently Emerged Hypervirulent Strains of Clostridium difficile Strains Determined Using RNA-seq. PLoS ONE. 2013;8(11):e78489–e78489. https://doi.org/10.1371/journal.pone.0078489.
  • Parikh NK, Youssef M, Swarup S, Eubank SG. Modeling the effect of transient populations on epidemics in Washington DC. Scientific Reports. 2013;3(3152). https://doi.org/10.1038/srep03152.
  • Eubank SG, Youssef M, Khorramzadeh Y. Determining and understanding dynamically important differences between complex networks using reliability-induced structural motifs. In: Proceedings of the 2013 International Conference on Signal-Image Technology & Internet-Based Systems. Oxford University Press; 2013:641–648. https://doi.org/10.1109/SITIS.2013.105.
  • Mortveit HS, Macauley M. An atlas of limit set dynamics for asynchronous elementary cellular automata. Theoretical Computer Science. 2013;504:26–37. https://doi.org/10.1016/j.tcs.2012.09.015.
  • Eubank SG. Using network reliability polynomials to characterize contact networks for infectious disease epidemiology. In: Lecture Notes in Artificial Intelligence, a Sub Series of Lecture Notes in Computer Science. Vol 8078. Springer-Verlag Berlin Heidelberg; 2013:IX-X.
  • Adiga A, Marathe MV, Mortveit HS, Wu S, Swarup S. Modeling Urban Transportation in the Aftermath of a Nuclear Disaster: The Role of Human Behavioral Responses. In: Transportation Research: Part C (International Journal of Transportation). 2013.
  • Lum K, Chungbaek Y, Eubank SG, Marathe MV. A two-stage, fitted values approach to activity matching. In: Transportation Research: Part C (International Journal of Transportation). 2013.
  • Rivers CM, Lewis BL, Young S. Detecting the Determinants of Health in Social Media. Presented at the International Society for Disease Surveillance, San Diego, CA; 2013. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692811/.
  • Xia H, Barrett CL, Chen J, Marathe MV. Computational Methods for Testing Adequacy and Quality of Massive Synthetic Proximity Social Networks. In: Proceedings of Computational Science and Engineering (CSE), 2013 IEEE 16th International Conference On. IEEE; 2013:1113–1120. https://doi.org/10.1109/CSE.2013.162.
  • Xia H, Chen J, Marathe MV, Mortveit HS, Salathe M. Synthesizing Social Proximity Networks by Combining Subjective Surveys with Digital Traces. Presented at the The 16th IEEE International Conference on Computational Science and Engineering (CSE 2013), Sydney, Australia; 2013. https://doi.org/10.1109/CSE.2013.38.
  • Rajaraman R, Sun Z, Sundaram R, Kumar VSA. Network effects of risk behavior change following prophylactic interventions. PLoS One. 2013;8(8):e64653. https://doi.org/10.1371/journal.pone.0064653.
  • Barrett CL, Bisset KR, Chandan S, Chen J, Chungbaek Y, Eubank SG, Evrenosoglu Y, Lewis BL, Lum K, Marathe A, Marathe MV, Mortveit HS, Parikh NK, Phadke A, Reed J, Rivers CM, Saha S, Stretz PE, Swarup S, Thorpe J, Kumar VSA, Xie D. Planning and Response in the Aftermath of a Large Crisis: An Agent-based Informatics Framework. In: Proceedings of the 2013 Winter Simulation Conference: Simulation: Making Decisions in a Complex World. 2013:1515–1526. http://dl.acm.org/citation.cfm?id=2676173.
  • Yi M, Marathe A. Policy Trap and Optimal Subsidization Policy under Limited Supply of Vaccines. PLoS One. 2013;8(7):e67249. https://doi.org/10.1371/journal.pone.0067249.
  • Kuhlman CJ, Kumar VSA, Ravi SS. Controlling opinion propagation in online networks. Computer Networks. 2013;57(10):2121–2132. https://doi.org/10.1016/j.comnet.2012.11.025.
  • Adiga A, Kuhlman CJ, Mortveit HS, Kumar VSA. Sensitivity of Diffusion Dynamics to Network Uncertainty. In: Proceedings of the AAAI-2013. 2013.
  • Subbiah R, Lum K, Marathe A, Marathe MV. Activity based energy demand modeling for residential buildings. In: Innovative Smart Grid Technologies (ISGT), 2013 IEEE PES. IEEE PES; 2013:1–6. https://doi.org/10.1109/ISGT.2013.6497822.
  • Hasan SM, Bisset KR, Fox EA, Hall KD, Leidig JP, Marathe MV. An Extensible Digital Library Service to Support Network Science. In: Procedia Computer Science. Vol 18. Elsevier; 2013:419–428. https://doi.org/10.1016/j.procs.2013.05.205.
  • Xia H, Nagaraj KS, Chen J, Marathe MV. Evaluating strategies for pandemic response in Delhi using realistic social networks. In: Proceedings of the International Conference on Healthcare Informatics. IEEE Computer Society; 2013:121–130. https://doi.org/10.1109/ICHI.2013.22.
  • Bisset KR, Deodhar S, Makkapati H, Marathe MV, Stretz PE, Barrett CL. Simfrastructure: A Flexible and Adaptable Middleware Platform for Modeling and Analysis of Socially Coupled Systems. In: Proceedings of the 13th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing. 2013.
  • Rivers CM, Lum K, Lewis BL, Eubank SG. Estimating transmissibility of avian influenza A(H7N9) from poultry to humans. PLoS Currents: Outbreaks. 2013. https://doi.org/10.1371/currents.outbreaks.264e737b489bef383fbcb....
  • Carbo A, Hontecillas-Magarzo R, Kronsteiner B, Viladomiu M, Pedragosa M, Lu P, Philipson CW, Hoops S, Marathe MV, Eubank SG, Bisset KR, Wendelsdorf KV, Jarrah A, Mei Y, Bassaganya-Riera J. Systems Modeling of Molecular Mechanisms Controlling Cytokine-driven CD4+ T Cell Differentiation and Phenotype Plasticity. PLoS Computational Biology. 2013;9(4):e1003027. http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjourn....
  • Beckman RJ, Channakeshava K, Huang F, Kim J, Marathe A, Marathe MV, Saha S, Pei G, Kumar VSA. Integrated Multi-Network Modeling Environment for Spectrum Management. IEEE Journal on Selected Areas in Communication, special issue on Network Science. 2013;31(6):1158–1168. https://doi.org/10.1109/JSAC.2013.130617.
  • Marathe A, Yi M. Subsidized Vaccines A Policy Trap? Presented at the INFORMS Healthcare 2013, Chicago, IL; 2013.
  • Eubank SG, Barrett C, marathe M, Bisset K, Beckman R, Stretz P, Mortveit H, Marathe A, Vullikanti A. Complex situation analysis system that generates a social contact network, uses edge brokers and service brokers, and dynamically adds brokers. 2013. https://patents.google.com/patent/US8423494B2.
  • Rajasekaran P, Alexander JC, Seleem MN, Jain N, Sriranganathan N, Wattam AR, Setubal JC, Boyle SM. Peptide nucleic acids inhibit growth of Brucella suis in pure culture and in infected murine macrophages. INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS. 2013;41(4):358–362. https://doi.org/10.1016/j.ijantimicag.2012.11.017.
  • Driscoll T, Gillespie JJ, Nordberg EK, Azad AF, Sobral BW. Bacterial DNA Sifted from the Trichoplax adhaerens (Animalia: Placozoa) Genome Project Reveals a Putative Rickettsial Endosymbiont. GENOME BIOLOGY AND EVOLUTION. 2013;5(4):621–645. https://doi.org/10.1093/gbe/evt036.
  • Chen J-W, Scaria J, Mao C, Sobra B, Zhang S, Lawley T, Chang Y-F. Proteomic Comparison of Historic and Recently Emerged Hypervirulent Clostridium difficile Strains. JOURNAL OF PROTEOME RESEARCH. 2013;12(3):1151–1161. https://doi.org/10.1021/pr3007528.
  • Subbiah R, Lum K, Marathe A, Marathe MV. A High Resolution Energy Demand Model for Commercial Buildings. Presented at the Security in Critical Infrastructures Today, Proceedings of International ETG-Congress 2013; Symposium 1: Berlin, Germany; 2013. http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=66616....
  • Barrett CL, Eubank SG, Evrenosoglu Y, Marathe A, Marathe MV, Phadke A, Thorp J, Kumar VSA. Effects of Hypothetical Improvised Nuclear Detonation on the Electrical Infrastructure. In: Security in Critical Infrastructures Today. 2013:1–7. http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=66616....
  • Adiga A, Mortveit HS, Wu S. Route Stability in Large-Scale Transportation Models. The Workshop on Multiagent Interaction Networks (MAIN). 2013.
  • Lum K, Price ME, Banks D. Applications of Multiple Systems Estimation in Human Rights Research. The American Statistician. 2013;67(4):191–200. https://doi.org/10.1080/00031305.2013.821093.
  • Parikh NK, Swarup S, Stretz PE, Rivers CM, Lewis BL, Marathe MV, Eubank SG, Barrett CL, Lum K, Chungbaek Y. Modeling Human Behavior in the Aftermath of a Hypothetical Improvised Nuclear Detonation. In: Proceedings of The Twelfth International Conference on Autonomous Agents and Multiagent Systems (AAMAS). 2013:949–956.
  • Chandan S, Saha S, Barrett CL, Eubank SG, Marathe A, Marathe MV, Swarup S, Kumar VSA. Modeling the Interaction between Emergency Communications and Behavior in the Aftermath of a Disaster. In: Proceedings of The International Conference on Social Computing, Behavioral-Cultural Modeling, and Prediction (SBP). Vol 7812. Springer Berlin Heidelberg; 2013:476–485. https://doi.org/10.1007/978-3-642-37210-0_52.
  • Kamal T, Bisset KR, Butt AR, Chungbaek Y, Marathe MV. Load Balancing in Large-scale Epidemiological Simulations. In: Proceedings of the 22nd International Symposium on High-Performance Parallel and Distributed Computing. ACM; 2013:123–124. https://doi.org/10.1145/2462902.2462929.
  • Lewis BL, Swarup S, Bisset KR, Eubank SG, Marathe MV, Barrett CL. A Simulation Environment for the Dynamic Evaluation of Disaster Preparedness Policies and Interventions. Journal of Public Health Management and Practice. 2013;19(Suppl 5):S42–8. https://doi.org/10.1097/PHH.0b013e31829398eb.
  • Pei G, Kumar VSA. Distributed Approximation Algorithms for Maximum Link Scheduling and Local Broadcasting in the Physical Interference Model. Presented at the IEEE INFOCOM 2013, Turin, Italy; 2013. https://doi.org/10.1109/INFCOM.2013.6566927.
  • Mitchell S, Ozonoff A, Zaslavsky AM, Hedt-Gauthier B, Lum K, Coull BA. A Comparison of Marginal and Conditional Models for Capture–Recapture Data with Application to Human Rights Violations Data. Biometrics. 2013;69(4):1022–1032. https://doi.org/10.1111/biom.12089.
  • Khan M, Kumar VSA, Marathe MV, Zhao Z. Algorithms for Finding Motifs in Large Labeled Networks. Springer; 2013:243–263. https://doi.org/10.1007/978-1-4614-6729-8_12.
  • Marathe A, Pan Z, Apolloni A. Analysis of friendship network and its role in explaining obesity. ACM Transactions in Science and Technology (ACM-TIST), Special Issue on Social Computing. 2013;4(3):56:21. https://doi.org/10.1145/2483669.2483689.
  • Pei G, Parthasarathy S, Srinivasan A, Kumar VSA. Approximation algorithms for throughput maximization in wireless networks with delay constraints. In: Proceedings of IEEE INFOCOM. Vol 21. 2013:1988–2000. https://doi.org/10.1109/TNET.2013.2247415.
  • Turner H, White J, Reed J, Galindo J, Porter A, Marathe MV, Kumar VSA, Gokhale A. Building a Cloud-based Mobile Application Testbed. In: Software Testing in the Cloud: Perspectives on an Emerging Discipline. IGI Global; 2013:382–403. https://doi.org/10.4018/978-1-4666-2536-5.ch018.
  • Bisset KR, Aji AM, Kamal T, Yeom J-S, Marathe MV, Bohm EJ, Gupta A. Contagion Diffusion with EpiSimdemics. Parallel Science and Engineering Applications: The Charm++ Approach. Eds. Laxmikant V. Kale, and Abhinav Bhatele. CRC Press; 2013:211–246.
  • Lew JM, Mao C, Shukla M, Warren A, Will R, Kuznetsov D, Xenarios I, Robertson BD, Gordon SV, Schnappinger D, Cole ST, Sobral B. Database resources for the tuberculosis community. TUBERCULOSIS. 2013;93(1):12–17. https://doi.org/10.1016/j.tube.2012.11.003.
  • Mao C, Shukla M, Larrouy-Maumus G, Dix FL, Kelley LA, Sternberg MJ, Sobral BW, Carvalho LPS de. Functional assignment of Mycobacterium tuberculosis proteome revealed by genome-scale fold-recognition. TUBERCULOSIS. 2013;93(1):40–46. https://doi.org/10.1016/j.tube.2012.11.008.
  • Jimenez JM, Lewis BL, Eubank SG. Hospitals as Complex Social Systems: Agent-Based Simulations of Hospital-Acquired Infections. Complex Systems: Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering. Springer International Publishing; 2013:165–178. https://doi.org/10.1007/978-3-319-03473-7_15.
  • Sobral B, Mao C, Shukla M, Sullivan D, Zhang C. Informatics-Driven Infectious Disease Research. Springer Berlin Heidelberg; 2013:3–11. https://doi.org/10.1007/978-3-642-29752-6_1.
  • Liao S, Ma Y, Chen J, Marathe A. Paid Sick-Leave: Is It a Good Way to Control Epidemics? Complex Systems: Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering. Springer International Publishing; 2013:213–227. https://doi.org/10.1007/978-3-319-03473-7_19.
  • Adiga A, Kumar VSA, Wiggins D. Subgraph enumeration in dynamic graphs. Presented at the IEEE International Conference on Data Mining (ICDM), 2013, Dallas, TX; 2013.

2012

  • Mei Y, Hontecillas-Magarzo R, Zhang X, Bisset KR, Eubank SG, Hoops S, Marathe MV, Bassaganya-Riera J. ENISI Visual, an agent-based simulator for modeling gut immunity. In: Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE; 2012:1–5. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6392624.
  • Kuhlman CJ, Kumar VSA, Ravi SS. Controlling opinion bias in online social networks. In: Proceedings of the 3rd Annual ACM Web Science Conference. 2012:165–174. https://doi.org/10.1145/2380718.2380740.
  • Barrett CL, Channakeshava K, Huang F, Kim J, Kumar VSA, Marathe A, Marathe MV, Pei G, Subbiah BSP, Saha S. Human Initiated Cascading Failures in Societal Infrastructures. PLoS ONE 7(10). 2012:e45406. https://doi.org/10.1371/journal.pone.0045406.
  • Wendelsdorf KV, Alam MM, Bassaganya-Riera J, Bisset KR, Eubank SG, Hontecillas-Magarzo R, Hoops S, Marathe MV. ENteric Immunity SImulator: A tool for in silico study of gastroenteric infections. IEEE Trans Nanobioscience. 2012;11(3):273–288. http://www.ncbi.nlm.nih.gov/pubmed/22987134.
  • Alexander KA, Lewis BL, Marathe MV, Eubank SG, Blackburn JK. Modeling of Wildlife Associated Zoonoses: Applications and Caveats. Vector-Borne and Zoonotic Diseases. 2012;12(12):1005–1018. https://doi.org/10.1089/vbz.2012.0987.
  • Abdelhamid SE, Alo R, Arifuzzaman SM, Beckman P, Bhuiyan MH, Bisset KR, Fox EA, Fox GC, Hall KD, Hasan SMS, Joshi A, Khan M, Kuhlman CJ, Lee S, Leidig JP, Makkapati H, Marathe MV, Mortveit HS, Qiu J, Ravi SS, Shams Z, Sirisaengtaksin O, Subbiah R, Swarup S, Trebon N, Kumar VSA, Zhao Z. CINET: A CyberInfrastructure for Network Science. In: Proceedings of the 2012 IEEE 8th International Conference on E-Science (e-Science). IEEE Computer Society; 2012. https://doi.org/10.1109/eScience.2012.6404422.
  • Bisset KR, Eubank SG, Marathe MV. High Performance Informatics for Pandemic Preparedness. In: Proceedings of the 2012 Winter Simulation Conference. 2012:1–12. https://doi.org/10.1109/WSC.2012.6465211.
  • Barrett CL, Beckman RJ, Bisset KR, Chen J, Eubank SG, Kumar VSA, Lewis BL, Marathe MV, Stretz PE, DuBois T, Srinivasan A. Optimizing Epidemic Protection for Socially Essential Workers. In: 2nd ACM SIGHIT International Health Informatics Symposium. 2012:31–40. https://doi.org/10.1145/2110363.2110371.
  • DuBois T, Eubank SG, Srinivasan A. The Effect of Random Edge Removal on Network Degree Sequence. the electronic journal of combinatorics. 2012;19(#P51):1–20. http://www.combinatorics.org/ojs/index.php/eljc/article/view/v19....
  • Mortveit HS. Limit Cycle Structure for Block-Sequential Threshold Systems. In: Proceedings of the ACRI/ACA, Greece, September 24-27, 2012. Vol 7495. Springer; 2012:672–678.
  • Tuli G, Marathe MV, Ravi SS, Swarup S. Addiction Dynamics May Explain the Slow Decline of Smoking Prevalence. In: Proceedings of The International Conference on Social Computing, Behavioral-Cultural Modeling, and Prediction (SBP). 2012:114–122.
  • Khan M, Pandurangan G, Pei G, Kumar VSA. A Fast Distributed Approximation Algorithm for Minimum Spanning Trees in the SINR Model. In: Symposium on Distributed Computing (DISC). 2012.
  • Wattam AR, Inzana TJ, Williams KP, Mane SP, Shukla M, Almeida NF, Dickerman AW, Mason S, Moriyón I, O'Callaghan D, Whatmore AM, Sobral BW, Tiller RV, Hoffmaster AR, Frace MA, De Castro C, Molinaro A, Boyle SM, De BK, Setubal JC. Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway. mBio. 2012;3(5):e00246–e00211. https://doi.org/10.1128/mbio.00388-12.
  • Deodhar S, Bisset KR, Chen J, Ma Y, Marathe MV. Enhancing User-Productivity and Capability Through Integration of Distinct Software in Epidemiological Systems. In: 2nd ACM SIGHIT International Health Informatics Symposium. 2012:171–180. https://doi.org/10.1145/2110363.2110385.
  • Bisset KR, Bassaganya-Riera J, Carbo A, Eubank SG, Hontecillas-Magarzo R, Hoops S, Marathe MV, Mei Y, Wendelsdorf KV, Xie D, Yeom J-S, Alam MM. High-Performance Interaction-Based Simulation of Gut Immunopathologies with ENISI. In: Computing & Processing (Hardware/Software). Conference Publications; 2012:48–59. https://doi.org/10.1109/IPDPS.2012.15.
  • Bisset KR, Aji AM, Marathe MV, Feng W-chun. High-Performance biocomputing for simulating the spread of contagion over large contact networks. BMC Genomics. 2012;13(Suppl 2). http://www.biomedcentral.com/1471-2164/13/S2/S3.
  • Viladomiu M, Hontecillas R, Pedragosa M, Carbo A, Hoops S, Michalak P, Michalak K, Guerrant RL, Roche JK, Warren CA, Bassaganya-Riera J. Modeling the Role of Peroxisome Proliferator-Activated Receptor gamma and MicroRNA-146 in Mucosal Immune Responses to Clostridium difficile. PLOS ONE. 2012;7(10). https://doi.org/10.1371/journal.pone.0047525.
  • Pyysalo S, Ohta T, Rak R, Sullivan D, Mao C, Wang C, Sobral B, Tsujii J, Ananiadou S. Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. BMC Bioinformatics. 2012;13(Suppl 11):S2–S2. https://doi.org/10.1186/1471-2105-13-S11-S2.
  • Liao S, Ma Y, Chen J, Marathe A. Paid Sick-Leave: Is It a Good Way to Control Epidemics? Presented at the 2nd International Conference on Complex Sciences: Theory and Applications, Santa Fe, New Mexico; 2012.
  • Swarup S, McCarthy C. Representational Momentum May Explain Aspects of Vowel Shifts. In: Proceedings of Artificial Life XIII: The 13th International Conference on the Simulation and Synthesis of Living Systems. MIT Press; 2012:267–274.
  • Zhao Z, Wang G, Butt AR, Khan M, Kumar VSA, Marathe MV. SAHad: Subgraph analysis in massive networks using hadoop. In: Proceedings of the 2012 IEEE 26th International Parallel and Distributed Processing Symposium. IEEE Computer Society; 2012:390–401. https://doi.org/10.1109/IPDPS.2012.44.
  • Bisset KR, Aji AM, Bohm E, Kale LV, Kamal T, Marathe MV, Yeom J-S. Simulating the Spread of Infectious Disease over Large Realistic Social Networks using Charm++. In: Proceedings of the Parallel and Distributed Processing Symposium Workshops & PhD Forum (IPDPSW), 2012 IEEE 26th International. IEEE; 2012:507–518. https://doi.org/10.1109/IPDPSW.2012.65.

2011

  • Kim J, Kumar VSA, Marathe A, Pei G, Saha S, Subbiah BSP. Modeling Cellular Network Traffic with Mobile Call Graph Constraints. In: Proceedings of the 2011 Winter Simulation Conference. 2011:3165–3177. https://doi.org/10.1109/WSC.2011.6148015.
  • Kuhlman CJ, Kumar VSA, Marathe MV, Ravi SS, Rosenkrantz DJ. Effects of Opposition on the Diffusion of Complex Contagions in Social Networks: An Empirical Study. Lecture Notes in Computer Science. 2011;6589:188–196. http://www.springerlink.com/content/41mt14m325655775/fulltext.pd....
  • Nsoesie EO, Beckman RJ, Marathe MV, Lewis BL. Prediction of an Epidemic Curve: A Supervised Classification Approach. Statistical Communications in Infectious Diseases. 2011;3(1):Article 5. http://www.bepress.com/scid/vol3/iss1/art5.
  • Leidig JP, Barrett CL, Marathe MV. Guiding Health Care Policy Through Applied Public Health Modeling and Simulation. In: Transactions of the International Conference on Health Information Technology Advancement. Vol Paper 14. 2011. http://scholarworks.wmich.edu/ichita_transactions/14/.
  • Kuhlman CJ, Kumar VSA, Marathe MV, Mortveit HS, Swarup S, Tuli G, Ravi SS, Rosenkrantz DJ. A general-purpose graph dynamical system modeling framework. In: Proceedings of the 2011 Winter Simulation Conference. IEEE; 2011:296–308. https://doi.org/10.1109/WSC.2011.6147758.
  • Apolloni A, Marathe A, Pan Z. A longitudinal view of the relationship between social marginalization and obesity. In: Proceedings of 2011 International Conference on Social Computing, Behavioral-Cultural Modeling & Prediction. 2011.
  • Swarup S, Apolloni A, Fagyal Z. A model of norm emergence and innovation in language change. In: Proceedings of the 10th International Conference on Autonomous Agents and Multiagent Systems (AAMAS). 2011.
  • Pei G, Parthasarathy S, Srinivasan A, Kumar VSA. Approximation algorithms for throughput maximization in wireless networks with delay constraints. In: Proceedings of IEEE INFOCOM. 2011. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5934887.
  • Marathe A, Lewis BL, Barrett CL, Chen J, Marathe MV, Eubank SG, Ma Y. Comparing Effectiveness of Top-down and Bottom-up Strategies in Containing Influenza. Plos One. 2011;6(9):e25149. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.po....
  • Macauley M, McCammond J, Mortveit HS. Dynamics groups of asynchronous cellular automata. Journal of Algebraic Combinatorics. 2011;33(1):11–35. http://www.springerlink.com/content/hgv665924j44t770/.
  • Barrett CL, Bisset KR, Leidig JP, Marathe A, Marathe MV. Economic and social impact of influenza mitigation strategies by demographic class. Epidemics Journal. 2011;3(1):19–31. http://www.sciencedirect.com/science/article/pii/S17554365100007....
  • Kuhlman CJ, Kumar VSA, Marathe MV, Ravi SS, Rosenkrantz D. Effects of opposition on the diffusion of complex contagions in social networks: An empirical study. In: Proceedings of the 2011 International Conference on Social Computing, Behavioral-Cultural Modeling and Prediction. 2011 International Conference on Social Computing, Behavioral-Cultural Modeling and Prediction, (Poster Presentation); 2011:188–196.
  • Ma Y, Bisset KR, Chen J, Deodhar S, Marathe MV. Efficient Implementation of Complex Interventions in Large Scale Epidemic Simulations. In: Winter Simulation Conference. 2011.
  • Park SH, Leidig JP, Li L, Fox E, Short NJ, Hoyle K, Abott AL, Hsiao M. Experiment and Analysis Services in a Fingerprint Digital Library for Collaborative Research. In: Theory and Practices of Digital Libraries (Formerly ECDL). 2011.
  • Barrett CL, Channakeshava K, Eubank SG, Kumar VSA, Marathe MV. From biological and social network metaphors to coupled bio-social wireless networks. International Journal of Autonomous Adaptive Communications. 2011;4(2):122–144. http://www.inderscience.com/browse/index.php?journalID=263&year=....
  • Channakeshava K, Bisset KR, Marathe MV, Kumar VSA, Yardi S. High Performance Scalable and Expressive Modeling Environment to Study Mobile Malware in Large Dynamic Networks. In: Proceedings of 25th IEEE International Parallel & Distributed Processing Symposium. 2011.
  • Bisset KR, Aji AM, Marathe MV, Feng W-chun. High performance biocomputing for simulating the spread of contagion over large contact networks. In: Proceedings of 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). Presentation at 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS); 2011:26–32. http://doi.ieeecomputersociety.org/10.1109/ICCABS.2011.5729913.
  • Hontecillas-Magarzo R, Horne WT, Climent M, Guri AJ, Evans C, Zhang Y, Sobral BW, Bassaganya-Riera J. Immunoregulatory mechanisms of macrophage PPAR gamma in mice with experimental inflammatory bowel disease. Mucosal Immunology. 2011;4(3):304–314. https://doi.org/10.1038/mi.2010.75.
  • Kim J, Kumar VSA, Marathe A, Pei G, Saha S, Subbiah BSP. Impact of geographic complementarity in dynamic spectrum access. In: Proceedings of IEEE Dynamic Spectrum Access Networks (DySPAN). 2011:12. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5936235&tag....
  • Barrett CL, Eubank SG, Marathe A, Marathe MV, Pan Z, Swarup S. Information integration to support policy informatics. The Innovation Journal. 2011;16(1):Article 2. http://www.innovation.cc/volumes-issues/vol16-no1.htm.
  • Kuhlman CJ, Kumar VSA, Marathe MV, Swarup S, Tuli G, Ravi SS, Rosenkrantz DJ. Inhibiting the Diffusion of Contagions in Bi-Threshold Systems: Analytical and Experimental Results. In: Complex Adaptive Systems-AAAI Symposium Fall 2011 Symposium. 2011. http://sites.google.com/site/complexadaptivesystems2011/.
  • Bisset KR, Chen J, Kuhlman CJ, Kumar VSA, Marathe MV. Interaction-based HPC modeling of social, biological and economic contagions over large networks. In: Winter Simulation Conference. 2011.
  • Platini T. Measure of the violation of the detailed balance criterion: A possible definition of a "distance" from equilibrium. Phys Rev E. 2011;83(1):011119–011111 - 011119–011116. http://pre.aps.org/abstract/PRE/v83/i1/e011119.
  • Barrett CL, Hunt HBIII, Marathe MV, Ravi SS, Rosenkrantz D, Stearns R. Modeling and analyzing social network dynamics using stochastic discrete graphical dynamical systems. Theoretical Computer Science, Special Issue. 2011;412(30):3932–3946. http://www.sciencedirect.com/science/article/B6V1G-526SPD7-D/2/0....
  • Lee B, McGlone S, Wong K, Yilmaz L, Avery T, Song Y, Christie R, Eubank SG, Brown S, Epstein JM, Parker J, Burke D, Platt R, Huang S. Modeling the spread of methicillin-resistant staphylococcus aureus (MRSA) outbreaks throughout the hospitals in Orange County, California. Infection Control and Hospital Epidemiology. 2011;32(6):562–572. http://www.jstor.org/stable/10.1086/660014.
  • Min Y, Pan Z, Jin X, Chen M, Ge Y, Chang J. Pathway Knockout and Redundance in Metabolic Networks. Journal of Theoretical Biology. 2011;270(1):63–69.
  • Macauley M, Mortveit HS. Posets from Admissible Coxeter Sequences. The Electronic Journal of Combinatorics. 2011;18(1):#P197. http://www.combinatorics.org/Volume_18/PDF/v18i1p197.pdf.
  • Marathe A, Lewis BL, Chen J, Eubank SG. Sensitivity of Household Transmission to Household Contact Structure and Size. PLOS One. 2011;6(8):e22461. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.po....
  • Leidig JP, Fox E, Hall KD, Marathe MV, Mortveit HS. SimDL: A model ontology driven digital library for simulation systems. In: Proceedings of ACM/IEEE Joint Conference on Digital Libraries. 2011:81–84. http://dl.acm.org/citation.cfm?id=1998091.
  • Leidig JP, Fox EA, Marathe MV. Simulation Tools for Producing Metadata Description Sets Covering Simulation-Based Content Collections. In: Proceedings of the IASTED International Conference on Modelling, Simulation, and Identification (MSI). ACTA Press; 2011. https://doi.org/10.2316/P.2011.755-045.
  • Lee B, Song Y, McGlone S, Avery T, Eubank SG, Chang C-C, Bailey R, Wagner D, Burke D, Platt R, Huang S. Social network analysis of patient sharing among hospitals in Orange County, California. American Journal of Public Health. 2011;101(4):707–713.
  • Xia H, Chen J, Marathe MV, Mortveit HS. Synthesis and refinement of detailed subnetworks in a social contact network for epidemic simulations. In: Proceedings of the International Conference on Social Computing, Behavioral Modeling and Prediction (SBP11). 2011.
  • Guri AJ, Bassaganya-Riera J. Systemic effects of white adipose tissue dysregulation and obesity-related inflammation. Obesity. 2011;19. https://doi.org/10.1038/oby.2010.230.
  • Boyle KJ, Davis G, Estabrooks PA, Good DJ, King-Casas B, Marathe A, You W. Translational Economic Research: Integrating Genetics, Neurosciences & Behavioral Sciences. Association of Environmental and Resource Economists (AERE). 2011;31(1):15–25.
  • Gillespie JJ, Wattam AR, Cammer SA, Gabbard JL, Shukla MP, Dalay O, Driscoll T, Hix D, Mane SP, Mao C, Nordberg EK, Scott M, Schulman JR, Snyder EE, Sullivan DE, Wang C, Warren A, Williams KP, Xue T, Yoo HS, Zhang C, Zhang Y, Will R, Kenyon RW, Sobral BW. PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun. 2011;79(11):4286–4298. https://doi.org/IAI.00207-11. [pii] 10.1128/IAI.00207-11.
  • Driscoll T, Gabbard JL, Mao C, Dalay O, Shukla M, Freifeld CC, Hoen AG, Brownstein JS, Sobral BW. Integration and visualization of host-pathogen data related to infectious diseases. BIOINFORMATICS. 2011;27(16):2279–2287. https://doi.org/10.1093/bioinformatics/btr391.
  • Mortveit HS, Murrugarra D, Kuhlman CJ, Kumar VSA. Bifurcations in Boolean Networks. Discrete Mathematics and Theoretical Computer Science, Proceedings of the 17th International Workshop on Cellular Automata and Discrete Complex Systems. 2011;AP:29–46. http://www.automata2011.dim.uchile.cl/.
  • Mozumder P, Vasquez WF, Marathe A. Consumers' Preference for Renewable Energy in the Southwest USA. Energy Economics. 2011;33(6, November):1119–1126. https://doi.org/10.1016/j.eneco.2011.08.003.
  • Leidig JP, Fox EA, Hall KD, Marathe MV, Mortveit HS. Improving simulation management systems through ontology generation and utilization. In: Proceedings of the 11th Annual International ACM/IEEE Joint Conference on Digital Libraries. 2011:435–436. http://dl.acm.org/citation.cfm?id=1998172.
  • Ghosh A, Incel OD, Kumar VSA, Krishnamachari B. Multichannel Scheduling and Spanning Trees: Throughput–Delay Tradeoff for Fast Data Collection in Sensor Networks. IEEE/ACM Transactions on Networking. 2011;19(6):1731–1744. https://doi.org/10.1109/TNET.2011.2146273.
  • Platini T, Jia T, Kulkarni RV. Regulation by small RNAs via coupled degradation: Mean-field and variational approaches. Phys Rev E. 2011;84(2):021928–021921 - 021928–021925. https://doi.org/10.1103/PhysRevE.84.021928.
  • Marathe A, Marathe MV, Kumar VSA. Towards a Pervasive Computing Enabled Modeling Environment for Integrated Coevolving Energy. In: Proceedings of the 2011 EPU-CRIS International Conference on Science and Technology. 2011:1–8.

2010

  • Balaji P, Feng W, Lin H, Archuleta J, Matsuoka S, Warren A, Setubal J, Lusk E, Thakur R, Foster I, Katz D, Jha S, Shinpaugh K, Coghlan S, Reed D. Global-scale Distributed I/O with ParaMEDIC. Concurrency and Computation: Practice and Experience. 2010;22(16):2266–2281.
  • Arensburger P, Megy K, Waterhouse RM, Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, Camara F, Campbell CL, Campbell KS, Casola C, Castro MT, Chandramouliswaran I, Chapman SB, Christley S, Costas J, Eisenstadt E, Feschotte C, Fraser-Liggett C, Guigo R, Haas B, Hammond M, Hansson BS, Hemingway J, Hill SR, Howarth C, Ignell R, Kennedy RC, Kodira CD, Lobo NF, Mao C, Mayhew G, Michel K, Mori A, Liu N, Naveira H, Nene V, Nguyen N, Pearson MD, Pritham EJ, Puiu D, Qi Y, Ranson H, Ribeiro JMC, Roberston HM, Severson DW, Shumway M, Stanke M, Strausberg RL, Sun C, Sutton G, Tu ZJ, Tubio JMC, Unger MF, Vanlandingham DL, Vilella AJ, White O, White JR, Wondji CS, Wortman J, Zdobnov EM, Birren B, Christensen BM, Collins FH, Cornel A, Dimopoulos G, Hannick LI, Higgs S, Lanzaro GC, Lawson D, Lee NH, Muskavitch MAT, Raikhel AS, Atkinson PW. Sequencing of Culex quinquefasciatus Establishes a Platform for Mosquito Comparative Genomics. SCIENCE. 2010;330(6000):86–88. https://doi.org/10.1126/science.1191864.
  • Warren A, Anandakrishnan R, Zhang L. Functional bias in molecular evolution rate of Arabidopsis thaliana. BMC evolutionary biology. 2010;10(1):125.
  • Warren A, Archuleta J, Wu-chun F, Setubal J. Missing genes in the annotation of prokaryotic genomes. BMC bioinformatics. 2010;11(1):131.
  • Guri AJ, Misyak SA, Hontecillas-Magarzo R, Hasty A, Liu D, Si H, Bassaganya-Riera J. Abscisic acid ameliorates atherosclerosis by suppressing macrophage and CD4+ T cell recruitment into the aortic wall. The Journal of Nutritional Biochemistry. 2010;21(12):1178–1185. http://www.sciencedirect.com/science/article/B6T8P-4Y7NDK4-4/2/e....
  • Guri AJ, Hontecillas-Magarzo R, Bassaganya-Riera J. Abscisic acid ameliorates experimental IBD by downregulating cellular adhesion molecule expression and suppressing immune cell infiltration. Clinical Nutrition. 2010;29:824–831. https://doi.org/10.1016/j.clnu.2010.02.009.
  • Guri AJ, Hontecillas-Magarzo R, Bassaganya-Riera J. Abscisic acid synergizes with rosiglitazone to improve glucose tolerance and down-modulate macrophage accumulation in adipose tissue: Possible action of the cAMP/PKA/PPAR [gamma] axis. Clinical Nutrition. 2010;29(5):646–653. http://www.sciencedirect.com/science/article/B6WCM-4YJ140J-1/2/0....
  • Barrett CL, Bisset KR, Leidig JP, Marathe A, Marathe MV. An integrated modeling environment to study the co-evolution of networks, individual behavior and epidemics. AI Magazine. 2010;31(1):75–87. http://www.aaai.org/ojs/index.php/aimagazine/article/view/2283.
  • Barrett CL, Beckman RJ, Channakeshava K, Huang F, Kumar VSA, Marathe A, Marathe MV, Pei G. Cascading failures in multiple infrastructures: From transportation to communication network. In: Proceedings of Interacting Critical Infrastructures for the 21st Century. 2010:1–8. http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=05617569.
  • Han B, Hui P, Kumar VSA, Marathe MV, Pei G, Srinivasan A. Cellular traffic offloading through opportunistic communications: A case study. In: Proceedings of the 5th ACM Workshop on Challenged Networks (CHANTS). ACM; 2010:31–38. http://portal.acm.org/citation.cfm?id=1859943.
  • Fagyal Z, Swarup S, Escobar AM, Gasser L, Lakkaraju K. Centers and peripheries: Network roles in language change. Lingua. 2010;120(8):2061–2079. http://www.sciencedirect.com/science/article/B6V6H-4YK8MKV-1/2/f....
  • Kuhlman CJ, Lewis BL, Beckman RJ, Eubank SG, Dutta T. Clustering method incorporating network topology and dynamics. In: Proceedings of Society for Modeling & Simulation International. 2010.
  • Chen J, Marathe A, Marathe MV. Coevolution of Epidemics, Social Networks, and Individual Behavior: A Case Study. In: Advances in Social Computing. Springer Berlin / Heidelberg; 2010:218–227. http://www.springerlink.com/content/n28m261152650316/.
  • Chen J, Marathe A, Marathe MV. Coevolution of Epidemics, Social Networks and Individual Behaviors: A Case Study. 2010:218–227.
  • Evans NP, Misyak SA, Schmelz EM, Guri AJ, Hontecillas-Magarzo R, Bassaganya-Riera J. Conjugated Linoleic Acid Ameliorates Inflammation-Induced Colorectal Cancer in Mice through Activation of PPAR gamma. The Journal of Nutrition. 2010;140(3):515–521. http://jn.nutrition.org/content/140/3/515.abstract.
  • Kumar VSA, Marathe MV, Parthasarathy S. Cross-layer capacity estimation and throughput maximization in wireless networks. In: Algorithms for Next Generation Networks. Springer; 2010:67–98. http://www.springerlink.com/content/q4308764268h04mv/.
  • Apolloni A, Gargiulo F. Cultural fragmentation and innovation diffusion in a dynamic scenario. In: Proceedings of 5th International Workshop on Emergent Intelligence on Networked Agents. 2010.
  • Eubank SG, Barrett CL, Beckman RJ, Bisset KR, Durbeck L, Kuhlman CJ, Lewis BL, Marathe A, Marathe MV, Stretz PE. Detail in Network Models of Epidemiology: are we there yet? Journal of Biological Dynamics. 2010;4(5):446–455. http://www.informaworld.com/smpp/content~content=a921954532.
  • Bassaganya-Riera J, Hontecillas-Magarzo R. Dietary conjugated linoleic acid and n-3 polyunsaturated fatty acids in inflammatory bowel disease. Current Opinion in Clinical Nutrition and Metabolic Care. 2010;13(5):569–573. http://ovidsp.tx.ovid.com/sp-3.8.0b/ovidweb.cgi?&S=MONIFPEKJPDDA....|1|sl_10.
  • Goldstein E, Apolloni A, Lewis BL, Miller J, Macauley M, Eubank SG, Lipsitch M, Wallinga J. Distribution of vaccine/antivirals and the 'least spread line' in a stratified population. Journal of the Royal Society Interface. 2010;7(46):755–764. http://rsif.royalsocietypublishing.org/content/early/2009/10/09/....
  • Guill S, Hargens T, Nickols-Richardson S, Bassaganya-Riera J, Miller L, Zedalis D, Gregg J, Gwazdauskas F, Herbert W. Early evidence of increased risk for metabolic syndrome in young men with latent obstructive sleep apnea. Metab Syndr Relat Disord. 2010;8(1):33–38. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Pu....
  • Leidig JP, Fox E, Marathe MV, Mortveit HS. Epidemiology experiment and simulation management through schema-based digital libraries. In: Proceedings of the 2nd DL.org Workshop during the 14th European Conference on Digital Libraries. 2010.
  • Nsoesie EO, Beckman RJ, Marathe MV. Estimation of an epidemic curve during an outbreak: A classification approach. In: Proceedings of 2010 Joint Statistical Meeting. 2010.
  • Kumar VSA, Rajaraman R, Sundaram R, Sun Z. Existence theorems and approximation algorithms for generalized network security games. In: Proceedings of 30th International Conference on Distributed Computing Systems (ICDCS). 2010:348–357.
  • Kuhlman CJ, Marathe MV, Ravi SS, Rosenkrantz D. Exploiting network structure in enhancing diffusion of complex contagions. In: Proceedings of Analysis of Complex Networks (ACNE) Workshop of the ECML PKDD 2010 Conference. 2010:20–33. http://kdd.isti.cnr.it/acne/ACNE-2010-PROCEEDINGS.pdf.
  • Kuhlman CJ, Kumar VSA, Marathe MV, Ravi SS, Rosenkrantz D. Finding critical nodes for inhibiting diffusion of complex contagions in social networks. In: Proceeding of European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases. Vol LNCS 6322. Springer Berlin / Heidelberg; 2010:111–127. http://www.springerlink.com/content/b8h32020ux0571v0/.
  • Jesmin MSMR, Jamil H, Hontecillas-Magarzo R, Bassaganya-Riera J. Gene regulatory network reveals oxidative stress as the underlying molecular mechanism of type 2 diabetes and hypertension. BMC Medical Genomics. 2010;3. https://doi.org/10.1186/1755-8794-3-45.
  • Evans NP, Call JA, Bassaganya-Riera J, Robertson JL, Grange RW. Green tea extract decreases muscle pathology and NF-kappaB immunostaining in regenerating muscle fibers of mdx mice. Clin Nutr. 2010;29(3):391–398. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Pu....
  • Beckman RJ, Channakeshava K, Huang F, Marathe A, Marathe MV, Pei G, Kumar VSA. Implications of dynamic spectrum access on the efficiency of primary wireless market. In: Proceedings of IEEE International New Frontiers in Dynamic Spectrum Access Networks. 2010:1–12. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5457849.
  • Bisset KR, Chen J, Feng X, Ma Y, Marathe MV. Indemics: an interactive data intensive framework for high performance epidemic simulation. In: Proceedings of 24th International Conference on Supercomputing. 2010. http://portal.acm.org/citation.cfm?id=1810085.1810118.
  • Wendelsdorf KV, Bassaganya-Riera J, Hontecillas R, Eubank SG. Model of colonic inflammation: Immune modulatory mechanisms in inflammatory bowel disease. Journal of Theoretical Biology. 2010;264(4):1225–1239. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Pu....
  • Mohapatra SK, Cole LE, Evans C, Sobral BW, Bassaganya-Riera J, Hontecillas-Magarzo R, Vogel SN, Crasta OR. Modulation of hepatic PPAR expression during Ft LVS LPS-induced protection from Francisella tularensis LVS infection. BMC infectious diseases. 2010;10(1):10. http://www.biomedcentral.com/1471-2334/10/10.
  • Kumar VSA, Tripathi R, Valkanova E. On strategy improvement algorithms for simple stochastic games. In: Algorithms AndComplexity. Vol 6078. Springer Berlin / Heidelberg; 2010:240–251. http://www.springerlink.com/content/382627283g1486h0/.
  • Pan Z. Opinions and Networks: How Do They Effect Each Other. Computational Economics. 2010;39(2):157–171. http://link.springer.com/article/10.1007%2Fs10614-010-9241-z.
  • Bassaganya-Riera J, Song R, Roberts PC, Hontecillas-Magarzo R. PPAR-gamma activation as an anti-inflammatory therapy for respiratory virus infections. Viral Immunol. 2010;23(4):343–352. http://www.ncbi.nlm.nih.gov/pubmed/20712478.
  • Huang S, Avery T, Song Y, Elkins K, Nguyen C, Nutter S, Nafday A, Condon C, Chang M, Chrest D, Boos J, Bobashev G, Wheaton W, Frank S, Platt R, Lipsitch M, Bush R, Eubank SG, Burke D, Lee B. Quantifying inter-hospital patient sharing as a mechanism for infectious disease spread. Infection Control and Hospital Epidemiology. 2010;31(11):1160–1169. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064463/.
  • Taylor C, Marathe A, Beckman RJ. Same Influenza Vaccination Strategies but Different Outcome Across US Cities? International Journal of Infectious Diseases. 2010;14(9):e792–e795. http://www.ijidonline.com/article/S1201-9712%2810%2902405-7/abst....
  • Shawky HA, Marathe A. Stylistic differences across hedge funds as revealed by historical monthly returns. Technology and Investment. 2010;1(1):26–34.
  • Zhao Z, Khan M, Kumar VSA, Marathe MV. Subgraph enumeration in large social contact networks using parallel color coding and streaming. In: Proceedings of the 2010 39th International Conference on Parallel Processing. 2010:594–603. https://doi.org/10.1109/ICPP.2010.67.
  • Beckman RJ, Channakeshava K, Huang F, Marathe A, Marathe MV, Pei G, Kumar VSA. Synthesis and analysis of spatio-temporal spectrum demand patterns: A first principles approach. In: Proceedings of IEEE International New Frontiers in Dynamic Spectrum Access Networks. 2010. http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5457859&....
  • Swarup S, Gasser L. The classification game: Combining supervised learning and language evolution. Connection Science. 2010;22(1):1–24. http://www.tandfonline.com/doi/abs/10.1080/09540090802638766.
  • Chen J, Huang F, Khan M, Marathe MV, Stretz PE, Xia H. The effect of demographic and spatial variability on epidemics: A comparison between Beijing, Delhi, and Los Angeles. In: Proceedings of the 5th International Conference on Critical Infrastructure (CRIS). IEEE; 2010:1–8. https://doi.org/10.1109/CRIS.2010.5617584.
  • Dyer MD, Neff C, Dufford M, Rivera CG, Shattuck D, Bassaganya-Riera J, Murali TM, Sobral BW. The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PLoS One. 2010;5(8):e12089. http://www.ncbi.nlm.nih.gov/pubmed/20711500.
  • Bassaganya-Riera J, Guri AJ, Hontecillas-Magarzo R. Treatment of obesity-related complications with novel classes of naturally occurring PPAR agonists. Journal of Obesity. 2010;2011. http://www.hindawi.com/journals/jobes/2011/897894/.
  • Pan Z. Trust, influence, and convergence of behavior in social networks. Mathematical Social Sciences. 2010;60(1):69–78. http://www.sciencedirect.com/science/article/B6V88-4YT054B-2/2/3....
  • Macauley M, Mortveit HS. Update sequence stability in graph dynamical systems. Discrete and Continuous Dynamical Systems S. 2010;4(6):1533–1541.

2009

  • Mao C, Bhardwaj K, Sharkady SM, Fish RI, Driscoll T, Wower J, Zwieb C, Sobral BWS, Williams KP. Variations on the tmRNA gene. RNA BIOLOGY. 2009;6(4):355–361. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=....
  • Wattam AR, Williams KP, Snyder EE, Almeida J N. F., Shukla M, Dickerman AW, Crasta OR, Kenyon R, Lu J, Shallom JM, Yoo H, Ficht TA, Tsolis RM, Munk C, Tapia R, Han CS, Detter JC, Bruce D, Brettin TS, Sobral BW, Boyle SM, Setubal JC. Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. J Bacteriol. 2009;191(11):3569–3579. https://doi.org/JB.01767-08. [pii] 10.1128/JB.01767-08.
  • Warren A, Setubal JC. The Genome Reverse Compiler: an explorative annotation tool. BMC bioinformatics. 2009;10(1):35.
  • Almeida N, Yan S, Lindeberg M, Studholme D, Schneider D, Bradford C, Liu H, Viana C, Warren A, Evans C, Kemen E, MacLean D, Angot A, Martin G, Jones J, Collmer A, Setubal J, Vinatzer B. A Draft Genome Sequence of Pseudomonas syringae pv. tomato T1 Reveals a Type III Effector Repertoire Significantly Divergent from That of Pseudomonas syringae pv. tomato DC3000. Molecular plant-microbe interactions. 2009;22(1):52–62. https://doi.org/10.1094. / MPMI -22-1-0052.
  • Bisset KR, Marathe MV. A cyber environment to support pandemic planning and response. DOE SCIDAC Magazine. 2009:36–47. http://www.scidacreview.org/0903/html/maranthe.html.
  • Apolloni A, Channakeshava K, Durbeck L, Khan M, Kuhlman CJ, Lewis BL, Swarup S. A study of information diffusion over a realistic social network model. In: Proceeding of the IEEE International Symposium on Social Computing Applications (SCA09). 2009. https://doi.org/10.1109/CSE.2009.240.
  • Kumar VSA, Marathe MV, Parthasarathy S, Srinivasan A. A unified approach to scheduling on unrelated parallel machines. Journal of ACM. 2009;56(5). http://portal.acm.org/citation.cfm?id=1552289#.
  • Atkins K, Barrett CL, Marathe A. A web services based artificial market. In: Winter Simulation Conference (WSC). 2009:3047–3054. http://www.informs-sim.org/wsc09papers/296.pdf.
  • Khan M, Kumar VSA, Marathe MV, Pandurangan G, Ravi SS. Bi-Criteria approximation algorithms for power-efficient and low-interference topology control in unreliable ad hoc networks. In: Proceedings of the 28th Conference on Computer Communications. 2009:370–378. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5061941&tag....
  • Sriranganathan N, Seleem MN, Olsen SC, Samartino LE, Whatmore AM, Bricker B, O'Callaghan D, Halling SM, Crasta OR, Wattam AR, Purkayastha A, Sobral BW, Snyder EE, Williams K, Yu G-X, Ficht TA, Roop II CM, deFigueiredo P, Boyle SM, He O, Tsolis RM. Brucella. Springer; 2009:1–64.
  • Fagyal Z, Swarup S, Escobar AM, Gasser L, Lakkaraju K. Centers, peripheries, and popularity: The emergence of norms in simulated networks of linguistic influence. Penn Working Papers in Linguistics: Selected Papers from NWAV 37. 2009;15(2):article 10.
  • Apolloni A, Kumar VSA, Marathe MV, Swarup S. Computational epidemiology in a connected world. Computer. 2009;42(12):83–86. http://www.computer.org/portal/web/csdl/doi/10.1109/MC.2009.386.
  • Macauley M, Mortveit HS. Cycle equivalence of graph dynamical systems. Nonlinearity. 2009;22(2):421–436. https://doi.org/10.1088/0951-7715/22/2/010.
  • Khan M, Pandurangan G, Kumar VSA. Distributed algorithms for constructing approximate minimum spanning trees in wireless sensor networks. IEEE Transactions on Parallel and Distributed Systems. 2009;20(1):124–139. http://www.computer.org/portal/web/csdl/doi/10.1109/TPDS.2008.57....
  • Han B, Kumar VSA, Marathe MV, Parthasarathy S, Srinivasan A. Distributed strategies for channel allocation and scheduling in software-defined radio networks. In: Proceedings of the 28th Conference on Computer Communication (INFOCOM). 2009:1521–1529. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5062069.
  • Bisset KR, Chen J, Feng X, Kumar VSA, Marathe MV. EpiFast: A fast algorithm for large scale realistic epidemic simulations on distributed memory systems. In: Proceedings of 23rd ACM International Conference on Supercomputing (ICS'09). 2009:430–439. http://dx.doi.org/10.1145/1542275.1542336.
  • Channakeshava K, Chafekar D, Bisset KR, Kumar VSA, Marathe MV. EpiNet: A simulation framework to study the spread of malware in wireless networks. In: Proceeding of 2nd International Conference on Simulation Tools and Techniques (SIMUTools '09). 2009. https://doi.org/10.4108/ICST.SIMUTOOLS2009.5652.
  • Barrett CL, Bisset KR, Leidig JP, Marathe A, Marathe MV. Estimating the Impact of Public and Private Strategies for Controlling an Epidemic: A Multi-Agent Approach. In: Proceedings of 21st Innovative Applications of Artificial Intelligence Conference. 2009:34–39. www.aaai.org/ocs/index.php/IAAI/IAAI09/paper/download/248/1015.
  • Barrett CL, Beckman RJ, Khan M, Kumar VSA, Marathe MV, Stretz PE, Dutta T, Lewis BL. Generation and analysis of large synthetic social contact networks. In: Proceedings of Winter Simulation Conference (WSC). 2009:1003–1014. http://influenza.vbi.vt.edu/pdfs/publications/barrett-2009-proc2....
  • Feighner BH, Eubank SG, Glass RJ, Davey VJ, Chretien J-P, Gaydos JC. Infectious disease modeling and military readiness (conference summary). Emerging Infectious Diseases. 2009;15(9). http://wwwnc.cdc.gov/eid/article/15/9/09-0702_article.htm.
  • Barrett CL, Lewis BL, Chen J, Kumar VSA, Eubank SG, Marathe MV, Mortveit HS. Interactions among Human Behavior, Social Networks, and Societal Infrastructures: A Case Study in Computational Epidemiology. Vol XXII. Springer Verlag; 2009:479–507. http://www.springer.com/computer/swe/book/978-1-4020-9687-7.
  • Kumar VSA, Macauley M, Mortveit HS. Limit set reachability in asynchronous graph dynamical systems, Lecture Notes in Computer Science. In: Proceeding of Reachability Problems. Vol 5797. Springer Berlin Heidelberg; 2009:217–232. http://www.springerlink.com/content/t497v3644155p15q/.
  • Atkins K, Chen J, Kumar VSA, Macauley M, Marathe A. Locational Market Power in Network Constrained Markets. Journal of Economic Behavior & Organization. 2009;70(1-2):416–430. http://dx.doi.org/10.1016/j.jebo.2008.11.001.
  • Chen J, Macauley M, Marathe A. Network Topology and Locational Market Power. Computational Economics. 2009;34(1):21–35. http://www.springerlink.com/content/1980444351u234u6/.
  • Barrett CL, Eubank SG, Marathe MV. Policy informatics for co-evolving socio-technical networks. In: Proceedings of 4th International Conference on Critical Infrastructures. 2009. https://doi.org/10.1109/CRIS.2009.5071486.
  • Kumar VSA, Marathe MV, Parthasarathy S, Srinivasan A. Scheduling on unrelated machines under tree-like precedence constraints. Algorithmica. 2009;55(1):205–206. http://www.springerlink.com/content/p8321031hk718413/.
  • Swarup S, Gasser L. The iterated classification game: A new model of the cultural transmission of language. Adaptive Behavior. 2009;17(3):213–235. http://adb.sagepub.com/content/17/3/213.abstract.
  • Atkins K, Chen J, Kumar VSA, Marathe A. The structure of electrical networks: A graph theory based analysis. International Journal of Critical Infrastructure. 2009;5(3):265–284. http://dx.doi.org/10.1504/IJCIS.2009.024874.

2008

  • Balaji P, Feng W, Lin H, Archuleta J, Matsuoka S, Warren A, Setubal J, Lusk E, Thakur R, Foster I, Katz DS, Jha S, Shinpaugh K, Coghlan S, Reed D. Distributed I/O with ParaMEDIC: Experiences with a worldwide supercomputer. In: Proceedings of the IEEE International Supercomputing Conference. 2008.
  • Mian MAR, Zhang Y, Wang Z-Y, Zhang J-Y, Cheng X, Chen L, Chekhovskiy K, Dai X, Mao C, Cheung F, Zhao X, He J, Scott AD, Town CD, May GD. Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages. BMC PLANT BIOLOGY. 2008;8. https://doi.org/10.1186/1471-2229-8-27.
  • Khan M, Pandurangan G. A fast distributed approximation algorithm for minimum spanning trees. Distributed Computing. 2008;20(6):391–402.
  • Istrate G, Marathe MV, Ravi SS. Adversarial Analysis of Game-Theoretic Models of Norm Diffusion. 2008:273–282. https://doi.org/10.1007/978-3-540-69407-6_31.
  • Atkins K, Barrett CL, Beckman RJ, Bisset KR, Chen J, Eubank SG, Feng AC, Feng X, Harris S, Lewis BL, Kumar VSA, Marathe MV, Marathe A, Mortveit HS, Stretz PE. An Interaction Based Composable Architecture for Building Scalable Models of Large Social, Biological, Information and Technical Systems. CT Watch Quarterly. 2008;4(1):46–53. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2800380/.
  • Mortveit HS, Reidys CM. An Introduction to Sequential Dynamical Systems. Springer Verlag; 2008. https://doi.org/10.1007/978-0-387-49879-9.
  • Barrett CL, Eubank SG, Marathe MV. An interaction-based approach to computational epidemiology. In: Proceedings of 23rd Association for the Advancement of Artificial Intelligence. Vol 3. AAAI Press; 2008:1590–1593. http://www.aaai.org/Papers/AAAI/2008/AAAI08-269.pdf.
  • Chafekar D, Kumar VSA, Marathe MV, Parthasarathy S, Srinivasn A. Approximation algorithms for computing capacity of wireless networks with SINR constraints. In: Proceedings of 27th IEEE International Conference on Computer Communications (INFOCOM). IEEE; 2008:1166–1174. https://doi.org/10.1109/INFOCOM.2008.172.
  • Chafekar D, Levin D, Parthasarathy S, Kumar VSA, Marathe MV, Srinivasn A. Capacity of asynchronous random-access scheduling in wireless networks. In: Proceedings of 27th IEEE International Conference on Computer Communications (INFOCOM). INFOCOM 2008. The 27th Conference on Computer Communications. IEEE; 2008:1166–1174. https://doi.org/10.1109/INFOCOM.2008.172.
  • Swarup S. Cause and effect: The anticipatory drive and the principle of least time (Commentary). Constructivist Foundations. 2008;4(1):21–23.
  • Khan M, Kuhn F, Malkhi D, Pandurangan G, Talwar K. Efficient distributed approximation algorithms via probabilistic tree embeddings. In: Proceedings of the 27th Annual ACM SIGACT-SIGOPS Symposium on Principles of Distributed Computing (PODC 2008). 2008:263–272. http://portal.acm.org/citation.cfm?id=1400787.
  • Barrett CL, Bisset KR, Eubank SG, Feng X, Marathe MV. EpiSimdemics: an Efficient Algorithm for Simulating the Spread of Infectious Disease over Large Realistic Social Networks. In: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis. IEEE; 2008:1–12. https://doi.org/10.1109/SC.2008.5214892.
  • Barrett CL, Bisset KR, Eubank SG, Feng X, Marathe MV. EpiSimdemics: an efficient and scalable framework for simulating the spread of infectious disease on large social networks. In: Proceedings of the 2008 ACM/IEEE Conference on Supercomputing. IEEE Press; 2008. http://portal.acm.org/citation.cfm?id=1413370.1413408.
  • Eubank SG, Kumar VSA, Marathe MV. Epidemiology and Wireless Communication: Tight Analogy or Loose Metaphor. Vol 5151. Springer Verlag; 2008:91–104. http://www.springerlink.com/content/h756844635r84763/.
  • Mao C, Evans C, Jensen RV, Sobral BWS. Identification of new genes in Sinorhizobium meliloti using the genome sequencer FLX system. BMC MICROBIOLOGY. 2008;8. https://doi.org/10.1186/1471-2180-8-72.
  • Yang Y, Koopman JS, Samore MH, Eubank SG, Lewis BL. Model analysis of potential causes for pertussis secular trends. In: Epidemics Journal and Conference on Infectious Diseases Dynamics. 2008.
  • Halloran ME, Ferguson NM, Eubank SG, Longini IM, Cummings DAT, Lewis BL, Xu S, Fraser C, Kumar VSA, Germann TC, Wagener D, Beckman RJ, Kadau K, Barrett CL, Macken CA, Burke DS, Cooley P. Modeling targeted layered containment of an influenza pandemic in the United States. Proceedings of the National Academy of Sciences (PNAS). 2008;105(12):4639–4644. https://doi.org/. 10.1073/pnas.0706849105.
  • Kumar VSA, Marathe MV, Premaraju S, Pirwani I. On the complexity of minimum partition of frequency-agile radio networks. In: Proceedings of the 3rd IEEE Symposium on New Frontiers in Dynamic Spectrum Access Networks. 2008:1–10. http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4658254&....
  • Macauley M, McCammond J, Mortveit HS. Order independence in asynchronous cellular automata. Journal of Cellular Automata. 2008;3(1):37–56. http://arxiv.org/abs/0707.2360.
  • Barrett CL, Eubank SG, Lewis BL, Marathe MV. Pandemics, Detection and Management. In: Encyclopedia of Geographic Information Systems. "Springer US" # "Springer-Verlag 2008"; 2008:839–843. https://doi.org/10.1007/978-0-387-35973-1_949.
  • Chafekar D, Kumar VSA, Marathe MV, Parthasarathy S. Power efficient throughput maximization in multi-hop wireless networks. In: Proceedings of the Global Telecommunications Conference, IEEE GLOBECOM. 2008. https://doi.org/10.1109/GLOCOM.2008.ECP.937.
  • Gillespie JJ, Williams K, Shukla M, Snyder EE, Nordberg EK, Ceraul SM, Dharmanolla C, Rainey D, Soneja J, Shallom JM, Vishnubhat ND, Wattam R, Purkayastha A, Czar M, Crasta O, Setubal JC, Azad AF, Sobral BS. Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life. PLOS ONE. 2008;3(4). https://doi.org/10.1371/journal.pone.0002018.
  • Kang J, Warren AS. Thermodynamic analysis of additivity between the heavy and light chains in affinity maturation of an antibody. Molecular Immunology. 2008;45(1):304–305. https://doi.org/10.1016/j.molimm.2007.07.007.

2007

  • Zhang C, Crasta O, Cammer S, Will R, Kenyon R, Sullivan D, Yu Q, Sun W, Jha R, Liu D, Xue T, Zhang Y, Moore M, McGarvey P, Huang H, Chen Y, Zhang J, Mazumder R, Wu C, Sobral B. An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. Nucleic Acids Res. 2007;36(Database issue):D884–91. https://doi.org/gkm903. [pii] 10.1093/nar/gkm903.
  • Kang JH, Warren AS. Enthalpy-entropy compensation in the transition of a monospecific antibody towards antigen-binding promiscuity. Molecular Immunology. 2007;44(14):3623–3624.
  • Torto-Alalibo TA, Tripathy S, Smith BM, Arredondo FD, Zhou L, Li H, Chibucos MC, Qutob D, Gijzen M, Mao C, Sobral BWS, Waugh ME, Mitchell TK, Dean RA, Tyler BM. Expressed sequence tags from Phytophthora sojae reveal genes specific to development and infection. MOLECULAR PLANT-MICROBE INTERACTIONS. 2007;20(7):781–793. https://doi.org/10.1094/MPMI-20-7-0781.
  • Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, deBruyn B, DeCaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, LaButti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CFM, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'Leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers Y-H, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JMC, VanZee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW. Genome sequence of Aedes aegypti, a major arbovirus vector. SCIENCE. 2007;316(5832):1718–1723. https://doi.org/10.1126/science.1138878.
  • Barrett CL, Bisset KR, Eubank SG, Fox E, Ma Y, Marathe MV, Zhang X. A scalable data management tool to support epidemiological modeling of large urban regions. In: Research and Advanced Technology for Digital Libraries. Vol 4675. Springer Berlin/Heidelberg; 2007:546–548. https://doi.org/10.1007/978-3-540-74851-9_65.
  • Khan M, Pandurangan G, Kumar VSA. A simple randomized scheme for constructing low-weight k-connected spanning subgraphs with applications to distributed algorithms. Theoretical Computer Science. 2007;385(1-3):101–114. http://www.sciencedirect.com/science/article/B6V1G-4NXHCH1-5/2/1....
  • Mozumder P, Marathe A. Causality relationship between electricity consumption and GDP in Bangladesh. Energy Policy. 2007;35(1):395–402. http://www.sciencedirect.com/science/article/B6V2W-4J32HDR-1/2/4....
  • Barrett CL, III HBH, Marathe MV, Ravi SS, Rosenkrantz D, Stearns R, Thakur M. Computational aspects of analyzing social network dynamics. In: Proceedings of the International Joint Conference on Artificial Intelligence (IJCAI 07). 2007:2268–2273. http://www.aaai.org/Papers/IJCAI/2007/IJCAI07-365.pdf.
  • Thomas RW, DaSilva LA, Marathe MV, Wood KN. Critical design decisions for cognitive networks. In: Proceedings of IEEE International Conference of Communications. IEEE; 2007:3993–3998. https://doi.org/10.1109/ICC.2007.657.
  • Chafekar D, Kumar VSA, Marathe MV, Parthasarathy S, Srinivasan A. Cross-layer latency minimization in wireless networks with SINR constraints. In: Proceedings of the 8th ACM International Symposium on Mobile Ad Hoc Networking and Computing. ACM, New York, NY, USA; 2007:110–119. http://doi.acm.org/10.1145/1288107.1288123.
  • Barrett CL, Bisset KR, Eubank SG, Kumar VSA, Marathe MV, Mortveit HS. Modeling and Simulation of Large Biological, Information and Socio-Technical Systems: An Interaction-Based Approach. Vol 64. 2007:101–147.
  • Macauley M, Mortveit HS. On enumeration of conjugacy classes of Coxeter elements. Proceedings of the American Mathematical Society. 2007;136:4157–4165. http://www.ams.org/journals/proc/2008-136-12/S0002-9939-08-09543....
  • Barrett CL, III HBH, Marathe MV, Ravi SS, Rosenkrantz DJ, Stearns RE, Thakur M. Predecessor existence problems for finite discrete dynamical systems. Theoretical Computer Science. 2007;386(1-2):3–37.
  • Mozumder P, Marathe A. Role of Information and communication Network in Malaria Survival. Malaria Journal. 2007;6(136). https://doi.org/10.1186/1475-2875-6-136.

2006

  • Snyder EE, Kampanya N, Lu J, Nordberg EK, Karur HR, Shukla M, Soneja J, Tian Y, Xue T, Yoo H, Zhang F, Dharmanolla C, Dongre NV, Gillespie JJ, Hamelius J, Hance M, Huntington KI, Jukneliene D, Koziski J, Mackasmiel L, Mane SP, Nguyen V, Purkayastha A, Shallom J, Yu G, Guo Y, Gabbard J, Hix D, Azad AF, Baker SC, Boyle SM, Khudyakov Y, Meng XJ, Rupprecht C, Vinje J, Crasta OR, Czar MJ, Dickerman A, Eckart JD, Kenyon R, Will R, Setubal JC, Sobral BW. PATRIC: the VBI PathoSystems Resource Integration Center. Nucleic Acids Res. 2006;35(Database issue):D401–6. https://doi.org/gkl858. [pii] 10.1093/nar/gkl858.
  • Whyte B, Kenyon R. Cyberinfrastructure Underpins Infectious Disease Research. Virginia Tech Research. 2006:7–11. https://www.research.vt.edu/resmag/ResearchMagJan06/cyber.html.
  • Khan M, Pandurangan G. A fast distributed approximation algorithm for minimum spanning trees. In: Proceedings of the 20th International Symposium on Distributed Computing(DISC). Vol 20. 2006:391–402. http://staff.vbi.vt.edu/maleq/papers/disc.pdf.
  • Barrett CL, Hunt HBIII, Marathe MV, Ravi SS, Rosenkrantz D, Stearns RE. Analysis problems for sequential dynamical systems and communicating state machines. In: Proceedings of 2th Mathematical Foundations of Computer Science (MFCS 01), Lecture Notes in Computer Science. Vol 2136. 2006:159–172.
  • Barrett CL, III HH, Marathe MV, Ravi SS, Rosenkrantz D, Stearns R. Complexity of reachability problems for finite discrete dynamical systems. Journal of Computer and System Sciences. 2006;72(8):1317–1345. https://doi.org/https://doi.org/10.1016/j.jcss.2006.03.006.
  • Zhao J, Xue T, Yang B, Williams K, Wattam AR, Will R, Sharp B, Kenyon R, Crasta O, Sobral BWS. Genome Annotation and Comparison System. 2006. http://www.informatik.uni-trier.de/~ley/db/conf/biocomp/biocomp2....
  • Atkins K, Chen J, Kumar VSA, Macauley M, Marathe A. Locational Market Power in Power Markets. In: Proceedings of 29th IAEE International Conference. 2006.
  • Chen J, Rajaraman R, Sundaram R. Meet and merge:Approximation algorithms for confluent flows. Journal of Computer and Systems Sciences (JCSS), special STOC 2003 issue. 2006;72(3):468–489. http://www.sciencedirect.com/science/article/B6WJ0-4HM7S87-2/2/2....
  • Istrate G, Hansson A, Marathe MV, Thulasidasan S, Barrett CL. Semantic compression of TCP traces. In: Proceedings of IFIP Conference on Networking Conference, Lecture Notes in Computer Science. Vol 3976. Berlin/Heidelberg:Springer Verlag; 2006:123–135.
  • Barrett CL, Istrate G, Kumar VSA, Marathe MV, Thite S, Thulasidasan S. Strong edge coloring for channel assignment in wireless radio networks. In: Proceedings of the First IEEE International Workshop on Foundations and Algorithms for Wireless Networking (FAWN'06). 2006:106–110. http://www.computer.org/portal/web/csdl/doi?doc=doi/10.1109/PERC....
  • Atkins K, Chen J, Kumar VSA, Marathe A. Structural analysis of electrical power networks. In: Proceedings of 3rd International Conference on Critical Infrastructures. 2006.
  • Eubank SG, Kumar VSA, Marathe MV, Srinivasan A, Wang N. Structure of Social Contact Networks and Their Impact on Epidemics. Vol 70. 2006:181–213.
  • Chen J, Marathe MV, Rajaraman R, Sundaram R. The confluent capacity of the internet: congestion vs. dilation. In: Proceedings of the 26th International Conference on Distributed Computing Systems (ICDCS). 2006.
  • Hunt HBIII, Marathe MV, Stearns RE, Rosenkrantz DJ. Towards a predictive complexity theory of periodically specified problems: A survey. In: Computational Complexity and Statistical Physics. Oxford University Press; 2006:285–318.

2005

  • Mao C, Qiu J, Wang C, Charles TC, Sobral BWS. NodMutDB: a database for genes and mutants involved in symbiosis. Bioinformatics (Oxford, England). 2005;21(12):2927–2929. https://doi.org/10.1093/bioinformatics/bti427.
  • Toroczkai Z, Eubank SG. Agent-based modeling as a decision making tool: how to halt a smallpox epidemic. In: Proceedings of Eleventh Annual Symposium on Frontiers of Engineering Organized by National Academy of Engineering. Vol 35. 2005:22–27.
  • Toroczkai Z, Eubank SG. Agent-based modeling as a decision-making tool. The Bridge. 2005;35(4):22–27.
  • Kumar VSA, Marathe MV, Parthasarathy S, Srinivasan A. Algorithmic aspects of capacity in wireless networks. In: Proceedings of the International Conference on Measurements and Modeling of Computer Systems (Sigmetrics). ACM Press New York, NY, USA; 2005:133–144. https://doi.org/10.1145/1071690.1064228.
  • Kumar VSA, Marathe MV, Parthasarathy S, Srinivasan A. Approximation algorithms for scheduling on multiple machines. In: Proceedings of 46th Annual IEEE Symposium on Foundations of Computer Science (FOCS'05). 2005:254–263.
  • Barrett CL, Eubank SG, Smith JP. If Smallpox Strikes Portland... Scientific American, Inc. 2005;292(3):54–61. http://www.scientificamerican.com/article/if-smallpox-strikes-po....
  • Tripp J, Hansson A, Mortveit HS, Gokhale M. Metropolitan road traffic simulation on FPGAs. In: Proceedings of 13th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM'05). 2005:117–126.
  • Chen J, Jia L, Liu X, Noubir G, Sundaram R. Minimum energy accumulative routing in wireless networks. In: Proceedings of 24th Annual Joint Conference on the IEEE Computer and Communications Societies. Vol 3. 2005:1875–1886. http://ndssl.vbi.vt.edu/Publications/ChenJLNS2005.Minimum.pdf.
  • Barrett CL, Eubank SG, Marathe MV. Modeling and Simulation of Large Biological, Information and Socio-Technical Systems: An Interaction Based Approach. In: Interactive Computing: A New Paradigm. Springer Berlin Heidelberg; 2005:353–394.
  • Granich RM, Oh P, Lewis BL, Porco T, Flood J. Multidrug resistance among persons with tuberculosis in California, 1994-2003. Journal of the American Medical Association. 2005;293(22):2732–2739. http://jamanetwork.com/journals/jama/fullarticle/201036.
  • Eubank SG. Network based models of infectious disease spread. Japanese Journal of Infectious Diseases. 2005;58(6):S9–S13. http://www.ncbi.nlm.nih.gov/pubmed/16377861.
  • Hansson AAA, Mortveit HS, Reidys CM. On Asynchronous Cellular Automata. Advances in Complex Systems. 2005;8(4):521–538.
  • He YQ, Vines RR, Wattam AR, Abramochkin GV, Dickerman AW, Eckart JD, Sobral BWS. PIML: The Pathogen Information Markup Language. BIOINFORMATICS. 2005;21(1):116–121. https://doi.org/10.1093/bioinformatics/bth462.
  • Barrett CL, Eidenbenz SJ, Kroc L, Marathe MV, Smith JP. Parametric probabilistic routing in sensor networks. ACM/Baltzer J Mobile Networks and Applications (MONET). 2005;10(4):529–544. https://doi.org/10.1007/s11036-005-1565-x.
  • Tripp J, Hansson A, Gokhale M, Mortveit HS. Partitioning hardware and software for reconfigurable supercomputing applications: A case study. In: Proceedings of the 2005 ACM/IEEE Conference on Supercomputing '05 Industrial. 2005:27–38. https://doi.org/10.1109/SC.2005.54.
  • Barrett CL, Eidenbenz SJ, Kroc L, Marathe MV, Smith JP. Probabilistic multi-path vs. deterministic single-path protocols for dynamic ad-hoc network scenarios. In: Proceedings of the 2005 ACM Symposium on Applied Computing (SAC). 2005:1166–1173.
  • Kumar VSA, Parthasarathy S, Marathe MV, Srinivasan A, Zust S. Provable algorithms for parallel sweep scheduling for unstructured meshs. In: 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS-05). 2005:26.
  • Kumar VSA, Marathe MV, Parthasarathy S, Srinivasan A, Zust S. Provable algorithms for parallel sweep scheduling on unstructured meshes. In: Proceedings of International Parallel and Distributed Processing Symposium (IPDPS). 2005:26–36.
  • Barrett CL, Drozda M, Engelhart DC, Kumar VSA, Marathe MV, Morin M, Ravi SS, Smith JP. Understanding protocol performance and robustness of ad hoc networks through structural analysis. In: Proceedings of the IEEE International Conference on Wireless and Mobile Computing, Networking, and Communications (WiMob). 2005:65–72. http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=1512886&....
  • Gokhale M, Hansson A, Mortveit HS, Tripp J. Urban traffic simulation modeling for reconfigurable hardware. In: Proceedings of Industrial Simulation Conference. 2005:291–298.

2004

  • Tu ZJ, Li S, Mao CH. The changing tails of a novel short interspersed element in Aedes aegypti: Genomic evidence for slippage retrotransposition and the relationship between 3 ' tandem repeats and the poly(dA) tail. GENETICS. 2004;168(4):2037–2047. https://doi.org/10.1534/genetics.104.032045.
  • Nordberg EK. YODA: selecting signature oligonucleotides. Bioinformatics. 2004;21(8):6. https://doi.org/10.1093/bioinformatics/bti182.
  • Barrett CL, Marathe MV, Smith JP, Ravi SS. A mobility and traffic generation framework for modeling and simulating ad hoc communication networks. Scientific Programming containing selected papers presented at the 6th ACM Symposium on Applied Computing (SAC) special track on Simulations of Discrete Entities. 2004;12(1):1–23.
  • Engelhart DC, Sivasubramaniam A, Barrett CL, Marathe MV, Smith JP, Morin M. A spatial analysis of mobility models: application to wireless ad hoc network simulation. In: Proceedings of 37th Annual Simulation Symposium. Proceeding ANSS '04 Proceedings of the 37th annual symposium on Simulation; 2004:35. http://portal.acm.org/citation.cfm?id=987679.987728.
  • Tripp JL, Mortveit HS, Nassr MS, Hansson AA, Gokhale M. Acceleration of traffic simulation on reconfigurable hardware. In: Proceedings of MAPLD04. 2004.
  • Atkins K, Barrett CL, Homan C, Marathe A, Marathe MV, Thite S. Agent based economic analysis of deregulated electricity markets. In: Proceeding of 6th IAEE European Energy Conference. Zurich, Switzerland; 2004.
  • Barrett CL, Marathe MV, Engelhart DC, Sivasubramaniam A. Approximating the connectivity between nodes when simulating large-scale mobile ad hoc radio networks. The Journal of Systems and Software 73 (2004). 2004;73:63–74.
  • Atkins K, Barrett CL, Homan CM, Marathe A, Marathe MV, Thite S. Marketecture: A simulation-based framework for studying experimental deregulated power markets, LANL (2004). In: 6th IAEE European Energy Conference, September 2-3, 2004. CiteSeerx; 2004:04–2032. http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.124.6803....
  • Eubank SG. Mathematics of Epidemiological Simulations for Response Planning. In: Mathematical Science's Role In Homeland Security: Proceedings Of A Workshop. National Academies Press; 2004:166–187. http://www.nap.edu/catalog.php?record_id=10940.
  • Eubank SG, Guclu H, Kumar VSA, Marathe MV, Srinivasan A, Toroczkai Z, Wan N. Modelling disease outbreaks in realistic urban social networks. Nature. 2004;429(6988):180–184. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Pu....
  • Eubank SG, Kumar VSA, Marathe MV, Srinivasan A, Wang N. Structural and algorithmic aspects of massive social networks. In: Proceedings of the 15th ACM-SIAM Symposium on Discrete Algorithms (SODA). Society for Industrial and Applied Mathematics Philadelphia, PA, USA; 2004:718–727.
  • Eubank SG, Kumar VSA, Marathe MV, Srinivasan A, Wang N. Structural and algorithmic aspects of massive social networks. In: Proceedings of the Fifteenth Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2004:718–727. http://portal.acm.org/citation.cfm?id=982792.982902.
  • Balakrishnan H, Barrett CL, Kumar VSA, Marathe MV, Thite S. The distance-2 matching problem and its relationship to the MAC-layer capacity of ad hoc wireless networks. IEEE Journal on Selected Areas in Communications. 2004;22(6):1069–1079. http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.116.5884....

2003

  • Mao C, Cushman JC, May GD, Weller JW. ESTAP--an automated system for the analysis of EST data. Bioinformatics (Oxford, England). 2003;19(13):1720–1722. https://doi.org/10.1093/bioinformatics/btg205.
  • Barrett CL, Mortveit HS, Reidys CM. ETS IV: Sequential Dynamical Systems: fixed points, invertibility and equivalence. Appl Math and Comput. 2003;134(1):153–171.

2002

  • Mao C, Carlson NG, Little JW. Cooperative DNA-protein interactions. Effects of changing the spacing between adjacent binding sites. Journal of Molecular Biology. 2002;235(2):532–544. https://doi.org/10.1006/jmbi.1994.1011.

2001

  • Mortveit HS, Reidys CM. Discrete, Sequential Dynamical Systems. Discrete Mathematics. 2001;226(1-3):281–295.

2000

  • Czabarka E, Konjevod G, Marathe MV, Percus AG, Toney DC. Algorithms for Optimizing Production DNA Sequencing. In: Proceedings of 11th ACM-SIAM Symposium on Discrete Algorithms (SODA). Society for Industrial and Applied Mathematics Philadelphia, PA, USA ©2000; 2000:399–408. http://portal.acm.org/citation.cfm?id=338585.
  • Doddi SR, Marathe MV, Ravi SS, Taylor DS, Widmayer P. Approximation Algorithms for Clustering to Minimize the Sum of Diameters. Nordic Journal of Computing. 2000;7(3):185–203.
  • Cook D, Faber V, Hicks G, Marathe MV. Combinatorial Problems Arising in Deregulated Electrical Power Industry: Survey and Future Directions. In: Proc. Approximation and Complexity in Numerical Optimization: Continuous and Discrete Problems. Kluwer Academic Publishers; 2000:138–162.
  • Barrett CL, Mortveit HS, Reidys CM. Elements of a theory of simulation II: sequential dynamical systems. Applied Mathematics and Computation. 2000;107(2-3):121–136. https://doi.org/10.1016/S0096-3003(98)10114-5.
  • III HBH, Stearns R, Marathe MV. On the Efficient Approximability of "Hard" Problems: A Survey . Vol 42. Kluwer Academic Publishers; 2000:308–322.
  • Carr RD, Doddi S, Konjevod G, Marathe MV. On the red-blue set cover problem. In: Proceedings of the 11th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society for Industrial and Applied Mathematics; 2000:345–353.
  • Dowell L, Drozda M, Henderson D, Loose V, Marathe MV, Roberts D. Scalability of ELISIMS: comprehensive detailed simulation of the electric power industry. In: Systems, Man, and Cybernetics, 2000 IEEE International Conference. Vol 1. 2000:393–398.

1999

1998

  • Nagel K, Stretz PE, Pieck M, Leckey S, Donnelly R, Barrett CL. TRANSIMS Traffic Flow Characteristics. Transportation Research Board Annual Meeting. 1998.

1990

  • Barrett CL, Donnell ML. Real time expert advisory systems: Considerations and imperatives. Information and Decision Technologies. 1990;16:15–25.

1989

  • Barrett CL, Weisgerber SA. Workload Induced Spatio-Temporal Distortions and Safety of Flight: An Investigation of Cognitive Intrusions in Perceptual Processes. In: Situational Awareness in Aerospace Operations, NATO, AGARD. Technical Report, LA-UR-89-2895, Los Alamos National Laboratory; 1989.