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

Principal Investigators

Abhijin Adiga

Research Assistant Professor

Jiangzhuo Chen

Research Associate Professor

Stephen Eubank

Deputy Director and Professor, NDSSL

Sandeep Gupta

Research Scientist

Stefan Hoops

Research Assistant Professor

Ronald Kenyon

Project Director

Christopher Kuhlman

Research Scientist

Bryan Lewis

Research Associate Professor

Chunhong Mao

Research Assistant Professor

Achla Marathe

Professor

Madhav Marathe

Director and Professor, NDSSL

Henning Mortveit

Associate Professor

Sekharipuram Ravi

Research Professor

Samarth Swarup

Research Assistant Professor

Anil Vullikanti

Associate Professor

Rebecca Wattam

Research Assistant Professor

Publications

2017


Bhuiyan MH, Khan M, Chen J, Marathe M. Parallel algorithms for switching edges in heterogeneous graphs. Journal of Parallel and Distributed Computing. 2017;104:19–35.  http://www.sciencedirect.com/science/article/pii/S0743731516301800

Bhuiyan MH, Khan M, Marathe M. Efficient Algorithms for Assortative Edge Switch in Large Labeled Networks. In: Proceedings of the 25th High Performance Computing Symposium.; 2017.  

Cadena JE, Chen X, Vullikanti A. Near-Optimal and Practical Algorithms for Graph Scan Statistics. In: Proceedings of the Seventeenth SIAM International Conference on Data Mining.; 2017.  http://www.wikicfp.com/cfp/servlet/event.showcfp?eventid=56433&copyownerid=51414

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.  

Dorrataltaj N, Marathe A, Lewis B, Swarup S, Eubank S, Abbas K. Epidemiological and Economic Impact of Pandemic Influenza in Chicago: Priorities for Vaccine Interventions. PLoS Computational Biology. 2017;13(6).  http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005521

Ghosh S, Chakraborty P, Lewis B, et al. Guided Deep List: Automating the Generation of Epidemiological Line Lists from Open Sources. In: Proceedings of the 23rd SIGKDD Conference on Knowledge Discovery and Data Mining. Acm; 2017.  

Hawdon J, Lum K, Swarup S, Torres JA, Eubank S. Addressing the Race Gap in Incarceration Rates: An Agent Based Model. Corrections. 2017:1–20.  http://www.tandfonline.com/doi/abs/10.1080/23774657.2016.1265472

Kang GJ, Ewing-Nelson SR, Mackey L, et al. Semantic Network Analysis of Vaccine Sentiment in Online Social Media. Vaccine. 2017;35(29):3621–3638.  http://www.sciencedirect.com/science/article/pii/S0264410X17306886

Pal A, Mishra C, Vullikanti A, Ravi R. A General Optimal Substation Coverage Algorithm for Phasor Measurement Unit Placement in Practical Systems. IET Generation, Transmission & Distribution. 2017;11(2):347–353.  http://digital-library.theiet.org/content/journals/10.1049/iet-gtd.2016.0553

Pal A, Vullikanti A, Ravi R. A PMU Placement Scheme Considering Realistic Costs and Modern Trends in Relaying. IEEE Transactions on Power Systems. 2017;32(1):552–561.  

Saha S, Vullikanti A, Halappanavar M. FlipNet: Modeling Covert and Persistent Attacks on Networked Resources. In: Proceedings of the 37th IEEE International Conference on Distributed Computing Systems.; 2017.  http://icdcs2017.gatech.edu/

Subbiah R, Pal A, Nordberg EK, Marathe A, Marathe M. Energy Demand Model for Residential Sector: A First Principles Approach. IEEE Transactions on Sustainable Energy. 2017;8(3):1215–1224.  

Tabataba farzaneh, Chakraborty P, Ramakrishnan N, et al. A framework for evaluating epidemic forecasts. BMC Infectious Diseases. 2017.  https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-017-2365-1

Venkatramanan S, Lewis B, Chen J, Higdon D, Vullikanti A, Marathe M. Using data-driven agent-based models for forecasting emerging infectious diseases. Epidemics – Special Issue on Ebola Challenge. 2017.  http://www.sciencedirect.com/science/article/pii/S1755436517300221

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.  

Wattam AR, Davis JJ, Assaf R, et al. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 2017;45(D1):D535–D542.  http://dx.doi.org/10.1093%2Fnar%2Fgkw1017

2016


Abbas K, Dorratoltaj N, Marathe A, Swarup S, Lewis B, Eubank S. Economic evaluation of influenza vaccine intervention. International Journal of Infectious Diseases. 2016;45(supplement 1):159.  

Abdelhamid S, Kuhlman C, Marathe M, Ravi R. 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.  

Abdelhamid S, Kuhlman C, Marathe M, Ravi R. 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.  

Abdelhamid S, Kuhlman C, Marathe M, Ravi R. 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.  http://ieeexplore.ieee.org/abstract/document/7804480/

Adiga A, Galyean H, Kuhlman C, Levet M, Mortveit H, Wu S. Network Structure and Activity in Boolean Networks. Natural Computing. 2016:1–13.  http://link.springer.com/article/10.1007/s11047-016-9584-z

Adiga A, Kuhlman C, Marathe M, Ravi R, Rosenkrantz D, Stearns RE. Inferring Local Transition Functions of Discrete Dynamical Systems From Observations of System Behavior. Theoretical Computer Science. 2016.  

Adiga A, Vullikanti A. Temporal Vaccination Games Under Resource Constraints. In: Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence.; 2016.  

Alam M, Khan M, Vullikanti A, Marathe M. 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.  

Barrett C, Centeno VA, Eubank S, et al. Impact of a surface nuclear blast on the transient stability of the power system. Springer International Publishing; 2016.   http://isbn.nu/10.1007/978-3-319-31664-2%2016

Biggerstaff M, Alper D, Dredze M, et al. 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.  http://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-016-1669-x

Bisset K, Cadena JE, Khan M, Kuhlman C, Lewis B, 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.  

Cadena JE, Vullikanti A, Aggarwal CC. On Dense Subgraphs in Signed Network Streams. In: Proceedings of the IEEE International Conference on Data Mining 2016. Ieee; 2016.  http://ieeexplore.ieee.org/document/7837829/

Chen J, Vullikanti A, Marathe M, 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.  

Davis JJ, Boisvert S, Brettin T, et al. Antimicrobial Resistance Prediction in PATRIC and RAST. Sci Rep. 2016;6:27930.  http://dx.doi.org/10.1038%2Fsrep27930

Dutta T, Heath L, Vullikanti A, Marathe M. Labeled cuts in graphs. Theoretical Computer Science. 2016;648(34-39).  http://www.sciencedirect.com/science/article/pii/S0304397516303851

Korkmaz G, Cadena JE, Kuhlman C, Marathe A, Vullikanti A, Ramakrishnan N. Multi-source models for civil unrest forecasting. Social Network Analysis and Mining. 2016;6(1):1–25.  http://link.springer.com/article/10.1007/s13278-016-0355-8

Korkmaz G, Kuhlman C, Ravi R, 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.  http://dl.acm.org/citation.cfm?id=2914630

Korkmaz G, Kuhlman C, Vega-Redondo F. Can Social Contagion Spread Without Key Players? In: The 3rd International Conference on Behavioral, Economic, and Socio-Cultural Computing (BESC).; 2016.  

Leber A, Abedi V, Hontecillas R, et al. Bistability analyses of CD4+ T follicular helper and regulatory cells during Helicobacter pylori infection. Journal of Theoretical Biology. 2016;In Press.  

Lofgren E, Vullikanti A. 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/12450/11561

Lum K, Chungbaek Y, Eubank S, Marathe M. A Two-stage, Fitted Values Approach to Activity Matching. International Journal of Transportation. 2016;4(1):41–56.  

Marathe A, Chen J, Chu S, et al. Effect of Modeling Slum Populations on Influenza Spread Delhi. BMJ Open. 2016;6(9):e011699.  http://bmjopen.bmj.com/content/6/9/e011699.full

Muthiah S, Butler P, Khandpur RP, et al. 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, Hayatnagarkar HG, Beckman R, Marathe M, 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.  

Parikh N, Marathe M, Swarup S. Summarizing Simulation Results using Causally-relevant States. Springer; 2016.  http://link.springer.com/chapter/10.1007%2F978-3-319-46840-2_6

Parikh N, Marathe M, Swarup S. Integrating Behavior and Microsimulation Models. In: Proceedings of the Workshop on Agent-based Modeling of Urban Systems, held in conjunction with AAMAS. Springer; 2016:39–59.  http://www.modelling-urban-systems.com/

Ren Y, Eubank S, 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

Saha S, Vullikanti A, Halappanavar M, Chatterjee S. Identifying vulnerabilities and hardening attack graphs for networked systems. In: Proceedings of the 2016 IEEE Symposium on Technologies for Homeland Security (HST). Ieee; 2016:1–6.  ieeexplore.ieee.org/abstract/document/7568884/

Smith C, Stringer AM, Mao C, Palumbo MJ, Wade JT. Mapping the Regulatory Network for Salmonella enterica Serovar Typhimurium Invasion. MBio. 2016;7(5).  http://dx.doi.org/10.1128%2FmBio.01024-16

Swarup S, Ravi R, Mahmud MMH, Lum K. Identifying Core Network Structure for Epidemic Simulations. In: Proceedings of the Twelfth International Workshop on Agents and Data Mining Interaction.; 2016.  

Vullikanti A, Marathe M, 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.  http://dl.acm.org/citation.cfm?id=2812811

Wu S, Mortveit H, 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).; 2016.  http://www.acm-sigsim-pads.org/

Zhang Y, Adiga A, Saha S, Vullikanti A, 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.  ieeexplore.ieee.org/abstract/document/7558162/

2015


Abdelhamid S, Kuhlman C, Korkmaz G, Marathe M, Ravi R. 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 S, Kuhlman C, Marathe M, Mortveit H, Ravi R. GDSCalc: A Web-Based Application for Evaluating Discrete Graph Dynamical Systems. PLoS One. 2015;10(8):e0133660.  http://www.ncbi.nlm.nih.gov/pubmed/26263006

Abedi V, Lu P, Hontecillas R, et al. Phase III Placebo-Controlled, Randomized Clinical Trial with Synthetic Crohn's disease Patients to Evaluate Treatment Response. In: Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology ? Systems & Applications. Vol. In Press. Elsevier/MK; 2015.  

Adiga A, Beckman R, Bisset K, et al. Synthetic Populations for Epidemic Modeling. In: Proceedings of the International Conference on Computational Social Sciences (ICCSS).; 2015.  http://www.iccss2015.eu/

Adiga A, Chu S, Marathe A, Vullikanti A. Can social distancing compensate for the unvaccinated? In: Proceedings of the Computational Social Science Society of the Americas Annual Conference.; 2015.  https://computationalsocialscience.org/

Adiga A, Galyean H, Kuhlman C, Levet M, Mortveit H, Wu S. Network Structure and Activity in Boolean Networks. In: Proceedings of the 21st International Workshop on Cellular Automata and Discrete Complex Systems.; 2015.  http://math.utu.fi/automata2015/abstracts/

Adiga A, Kuhlman C, Marathe M, Ravi R, Rosenkrantz D, 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

Adiga A, Kuhlman C, Mortveit H, 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, Venkatramanan S, Vullikanti A. To delay or not: Temporal vaccination games on networks. In: Proceedings of the 35th Annual IEEE International Conference on Computer Communications. Ieee; 2015:1–9.  

Alam M, Abedi V, Bassaganya-Riera J, et al. Agent-Based Modeling and High Performance Computing. Elsevier; 2015:79–112.  http://store.elsevier.com/product.jsp?isbn=9780128036976

Alam M, Deng X, Philipson C, et al. Sensitivity Analysis of an ENteric Immunity SImulator (ENISI)-based Model of Immune Responses to Helicobacter pylori Infection. PLOS One. 2015;10(9):e0136139.  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0136139

Althouse BM, Scarpino SV, Meyers LA, et al. Enhancing disease surveillance with novel data streams: challenges and opportunities. EPJ Data Science. 2015;4(17).  http://www.epjdatascience.com/content/4/1/17

Arifuzzaman SM, Khan M, Marathe M. 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/

Arifuzzaman SM, Khan M, Marathe M. 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.  

Barrett C, Eubank S, Marathe A, Marathe M, Swarup S. Synthetic Information Environments for Policy Informatics: A Distributed Cognition Perspective. Routledge Press; 2015.  http://www.routledge.com/books/details/9781138832084/

Cadena JE, Korkmaz G, Kuhlman C, Marathe A, Ramakrishnan N, Vullikanti A. Forecasting Social Unrest Using Activity Cascades. PLoS One. 2015;10(6):e0128879.  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128879

Deodhar S, Chen J, Wilson AL, et al. 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.  

Deodhar S, Chen J, Wilson AL, et al. 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.  

Eubank S, 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/

Kamal T, Bisset K, Butt AR, Marathe M. 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.  

Khorramzadeh Y, Youssef M, Eubank S, Mowlaei S. Analyzing network reliability using structural motifs. To appear in Proceedings of Networks of Networks. 2015;91(4):042814.  

Korkmaz G, Cadena JE, Kuhlman C, Marathe A, Vullikanti A, 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.  http://dl.acm.org/citation.cfm?doid=2808797.2808847

Kuhlman C, Mortveit H. Limit Sets of Generalized, Multi-Threshold Networks. Journal of Cellular Automata. 2015;10:161–193.  

Kuhlman C, Vullikanti A, Marathe M, Ravi R, Rosenkrantz D. Inhibiting diffusion of complex contagions in social networks: theoretical and experimental results. Proceeding of European Conference on Machine Learning and Principles and Practice of Knowledge Disco. 2015;29(2):423–465.  http://link.springer.com/article/10.1007/s10618-014-0351-4

Leber A, Viladomiu M, Hontecillas R, et al. Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection. PloS one. 2015;10:e0134849.  

Lofgren E, Halloran ME, Rivers CM, et al. Mathematical models: A key tool for outbreak reaponse. Proceedings of the National Academy of Science. 2015;111(51):18095–18096.  

Lu P, Abedi V, Mei Y, et al. Supervised Learning Methods in Modeling of CD4+ T Cell Heterogeneity. BioData Mining. 2015;In Press.  

Marathe A, Abbas K, Swarup S. Understanding Feedback Between Behavioral Interventions and Disease Evolution. In: Proceedings of the 2015 INFORMS Annual Meeting.; 2015.  

Mei Y, Abedi V, Carbo A, et al. Multiscale modeling of mucosal immune responses. BMC Bioinformatics. 2015;16:S2.  

Nath M, Eubank S, 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

Nath M, Eubank S, Youssef M, Khorramzadeh Y, Mowlaei S. A two-parameter method to characterize the network reliability for diffusive processes. In: Proceedings of the 6th Workshop on Complex Networks CompleNet 2015. Vol. 597. Springer International Publishing; 2015:139–148.  

Neafsey DE, Waterhouse RM, Abai MR, et al. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science. 2015;347(6217):1258522.  http://dx.doi.org/10.1126%2Fscience.1258522

Pal A, Youssef M, Vullikanti A, et al. 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.  

Philipson C, Bassaganya-Riera J, Viladomiu M, et al. Modeling the Regulatory Mechanisms by which NLRX1 Modulates Innate Immune Responses to Helicobacter pylori infection. PLos One. 2015;In Press.  

Pyne S, Marathe M, Vullikanti A. 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.  http://www.sciencedirect.com/science/journal/01697161

Ramakrishnan N, Lu C-T, Marathe M, et al. Model-Based Forecasting of Significant Societal Events. IEEE Intelligent Systems. 2015;30(5):86–90.  

Rosenkrantz D, Marathe M, III HH, Ravi R, Sterns R. Analysis Problems for Graphical Dynamical Systems: A Unified Approach Through Graph Predicaets. In: Proceedings of the 14th International Conference on Autonomous Agents and Multiagent Systems (AAMAS2015).; 2015.  http://www.aamas2015.com/en/

Saha S, Adiga A, Prakash BA, Vullikanti A. 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 B, Eubank S. ChatterGrabber: A Lightweight Easy to Use Social Media Surveillance Toolkit. Online Journal of Public Health Informatics. 2015;7(1).  http://ojs-prod-lib.cc.uic.edu/ojs/index.php/ojphi/article/view/5717/4268

Swarup S. Generating Synthetic Populations for Computational Epidemiology. In: Workshop on the Generation of Synthetic Population, held in conjunction with The Eleventh Conference of the European Social Simulation Association.; 2015.  

Vida Abedi RH Stefan Hoops Nathan Liles Adria Carbo Pinyi Lu Cassandra Philipson and Josep Bassaganya-Riera. ENISI Multiscale modeling of mucosal immune responses driven by high performance computing. Washington, DC, USA; 2015. IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2015).  

Warren AS, Aurrecoechea C, Brunk B, et al. RNA-Rocket: an RNA-Seq analysis resource for infectious disease research. Bioinformatics. 2015;31(9):1496–1498.  http://dx.doi.org/10.1093%2Fbioinformatics%2Fbtv002

Xia H, Nagaraj KS, Chen J, Marathe M. 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.  http://www.sciencedirect.com/science/article/pii/S0933365715000822

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/S1098301514047718

Zhang Y, Adiga A, Vullikanti A, Prakash BA. Controlling Propagation at Group Scale on Networks. In: Proceedings of the IEEE International Conference on Data Mining (ICDM 2015).; 2015.  

Zhao L, Chen J, Chen X, 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/

2014


Abdel-Hamid T, Akshay VS, Ankel F, et al. Public and Health-Professionals' Misconceptions about Dynamics of Weight Gain/Loss. System Dynamics Review. 2014;30(1-2):58–74.  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300993/

Abdelhamid S, Alam M, Alo R, et al. CINET 2.0: A CyberInfrastructure for Network Science. In: The 10th IEEE International Conference on eScience, 2014.; 2014:324–331.  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6972280&tag=1

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 C, Mortveit H, Vullikanti A. Sensitivity of diffusion dynamics to network uncertainty. Journal of Artificial Intelligence Research. 2014;51:207–226.  

Alexander KA, Sanderson CE, Marathe M, et al. 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-might-led-emergence-ebola-west-africa/

Barrett C, Centeno V, Eubank S, et al. 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.  

Beckman R, Bisset K, Chen J, Lewis B, Marathe M, Stretz P. 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.  

Bhuiyan MH, Chen J, Khan M, Marathe M. 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.  

Bisset K, Chen J, Deodhar S, Feng X, Ma Y, Marathe M. Indemics: An interactive high-performance computing framework for data-intensive epidemic modeling. ACM Transactions on Modeling and Computer Simulation (TOMACS). 2014;24(1):32.  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4207128/

Burns G, Gil Y, Liu Y, et al. 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/2538/2426

Chakraborty P, Khadivi P, Lewis B, et al. Forecasting a Moving Target: Ensemble Models for ILI Case Count Predictions.; 2014.  

Channakeshava K, Bisset K, Marathe M, Vullikanti A. 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

Deodhar S, Bisset K, Chen J, Ma Y, Marathe M. An Interactive, Web-Based High Performance Modeling Environment for Computational Epidemiology. ACM Transactions on Management Information Systems. 2014;5(2):7.  

Eubank S, Youssef M, Khorramzadeh Y. Characterizing relevant network structure with reliability polynomials. Springer International Publishing; 2014:117–143.  

Eubank S, Youssef M, Khorramzadeh Y. Using the network reliability polynomial to characterize and design networks. Journal of Complex Networks. 2014;2(4):356–372.  http://comnet.oxfordjournals.org/content/early/2014/10/21/comnet.cnu037.full

Hasan SMS, Gupta S, Fox EA, Bisset K, Marathe M. Unified Digital Library and Data Access Framework For Heterogeneous and Federated Computational Epidemiology Datasets. In: Digital Libraries (JCDL), 2014 IEEE/ACM Joint Conference on.; 2014:449–450.  

Kamal T, Bisset K, Butt AR, Marathe M. 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=1

Khorramzadeh Y, Youssef M, Eubank S. 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

Korkmaz G, Kuhlman C, Marathe A, Marathe M, 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

Kuhlman C, Mortveit H. Attractor Stability in Nonuniform Boolean Networks. Theoretical Computer Science. 2014;559:20–33.  http://www.sciencedirect.com/science/article/pii/S0304397514006185

Lau EHY, Zheng J, Tsang TK, et al. 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).  http://www.biomedcentral.com/1741-7015/12/88/abstract

Lofgren E, Halloran ME, Rivers CM, et al. Opinion: Mathematical models: A key tool for outbreak response. Proceedings of the National Academy of Sciences (PNAS). 2014;111(51):18095–18096.  http://www.pnas.org/content/111/51/18095

Lum K, Swarup S, Eubank S, 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).  

Mao C, Abraham D, Wattam AR, et al. Curation, integration and visualization of bacterial virulence factors in PATRIC. Bioinformatics. 2014.  http://dx.doi.org/10.1093%2Fbioinformatics%2Fbtu631

Marathe A, Chen J, Eubank S, Liao S, Ma Y. Impact of Paid Sick Leave Policy: A Social Planner's Perspective. American Journal of Public Health. 2014;104(1):e1.  http://ajph.aphapublications.org/doi/abs/10.2105/AJPH.2013.301639

Marathe M, Mortveit H, Parikh N, Swarup S. Prescriptive Analytics Using Synthetic Information. Emerging Methods in Predictive Analytics: Risk Management and Decision Making. William H. Hsu (ed). IGI Global; 2014.  

Nsoesie EO, Leman SC, Marathe M. A Dirichlet process model for classifying and forecasting epidemic curves. BMC Infectious Diseases. 2014;14(12).  http://www.biomedcentral.com/1471-2334/14/12/abstract

Nsoesie EO, Mekaru SR, Ramakrishnan N, Marathe M, Brownstein JS. Modeling to Predict Cases of Hantavirus Pulmonary Syndrome in Chile. PLOS Neglected Tropical Diseases. 2014;8(4):e2779.  http://www.plosntds.org/article/info%3Adoi%2F10.1371%2Fjournal.pntd.0002779

Overbeek R, Olson R, Pusch GD, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42(Database issue):D206–14.  http://www.ncbi.nlm.nih.gov/pubmed/24293654

Panas MW, Jain P, Yang H, et al. Noncanonical SMC protein in Mycobacterium smegmatis restricts maintenance of Mycobacterium fortuitum plasmids. Proc Natl Acad Sci U S A. 2014;111(37):13264–13271.  http://www.ncbi.nlm.nih.gov/pubmed/25197070

Parikh N, Youssef M, Swarup S, Eubank S, 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.  

Ramakrishnan N, Butler P, Muthiah S, et al. '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

Rivers CM, Lewis B. Ethical research standards in a world of big data. F1000Research. 2014;3(38).  http://f1000research.com/articles/3-38/v2

Rivers CM, Lofgren E, Marathe M, Eubank S, Lewis B. Modeling the Impact of Interventions on an Epidemic of Ebola in Sierra Leone and Liberia. PLOS Currents Outbreaks. 2014;Edition 1.  http://currents.plos.org/outbreaks/article/obk-14-0043-modeling-the-impact-of-interventions-on-an-epidemic-of-ebola-in-sierra-leone-and-liberia/

Rosenkrantz D, Marathe M, Ravi R, Vullikanti A. 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, Vullikanti A. 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

Scaria J, Chen J-W, Useh N, et al. Comparative nutritional and chemical phenome of Clostridium difficile isolates determined using phenotype microarrays. Int J Infect Dis. 2014;27:20–25.  http://dx.doi.org/10.1016%2Fj.ijid.2014.06.018

Swarup S, Eubank S, Marathe M. 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

Timoshevskiy VA, Kinney NA, deBruyn BS, et al. Genomic composition and evolution of Aedes aegypti chromosomes revealed by the analysis of physically mapped supercontigs. BMC Biol. 2014;12:27.  http://dx.doi.org/10.1186%2F1741-7007-12-27

Wattam AR, Abraham D, Dalay O, et al. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res. 2014;42(1):D581–91.  http://dx.doi.org/10.1093%2Fnar%2Fgkt1099

Wattam AR, Foster JT, Mane SP, et al. Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence. J Bacteriol. 2014;196(5):920–930.  http://www.ncbi.nlm.nih.gov/pubmed/24336939

Wattam AR, Gabbard JL, Shukla M, Sobral BW. Comparative Genomic Analysis at the PATRIC, A Bioinformatic Resource Center. Methods Mol Biol. 2014;1197:287–308.  http://www.ncbi.nlm.nih.gov/pubmed/25172288

Wu S, Adiga A, Mortveit H. Limit cycle structure for dynamic bi-threshold systems. Theoretical computer science. 2014;559:34–41.  http://www.sciencedirect.com/science/article/pii/S0304397514005088

Yeom J-S, Bhatele A, Bisset K, et al. 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.  

Young SD, Rivers CM, Lewis B. Methods of using real-time social media technologies for detection and remote monitoring of HIV outcomes. Preventative Medicine. 2014;63(112-115).  

2013


Adiga A, Kuhlman C, Mortveit H, Vullikanti A. Sensitivity of Diffusion Dynamics to Network Uncertainty. In: Proceedings of the AAAI-2013.; 2013.  

Adiga A, Marathe M, Mortveit H, 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.  

Adiga A, Mortveit H, Wu S. Route Stability in Large-Scale Transportation Models. In: The Workshop on Multiagent Interaction Networks (MAIN).; 2013.  

Adiga A, Vullikanti A. How robust is the core of a network. In: Proceedings of ECML/PKDD.; 2013.  

Adiga A, Vullikanti A, Wiggins D. Subgraph enumeration in dynamic graphs.; 2013.  

Alam M, Khan M, Marathe M. Distributed-Memory Parallel Algorithms for Generating Massive Scale-free Networks Using Preferential Attachment Model. In: Proceedings of SC13: International Conference for High Performance Computing, Networking, Storage and Analysis. Acm; 2013.  

Apolloni A, Marathe A, Pan Z. The Spread of Obesity Among U.S. Teenagers: Causality Relation Between Marginalization and Obesity.; 2013.  

Arifuzzaman SM, Khan M, Marathe M. 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.  

Barrett C, Bisset K, Chandan S, et al. 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

Barrett C, Eubank S, Evrenosoglu Y, et al. 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=6661633

Beckman R, Channakeshava K, Fei F, et al. 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.  http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6517119

Bisset K, Aji AM, Kamal T, et al. Contagion Diffusion with EpiSimdemics. Parallel Science and Engineering Applications: The Charm++ Approach. Eds. Laxmikant V. Kale, and Abhinav Bhatele. CRC Press; 2013.  

Bisset K, Deodhar S, Makkapati H, Marathe M, Stretz P, Barrett C. 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.  

Carbo A, Bassaganya-Riera J, Pedragosa M, et al. Predictive Computational Modeling of the Mucosal Immune Responses during Helicobacter pylori Infection. PLoS One. 2013;8(9):e73365.  http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0073365

Chandan S, Saha S, Barrett C, et al. 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.  

Chen JW, Scaria J, Mao C, et al. Proteomic comparison of historic and recently emerged hypervirulent Clostridium difficile strains. Journal of Proteome Research. 2013;12:1151–1161.  http://pubs.acs.org/doi/abs/10.1021/pr3007528

Eubank S. 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.  

Eubank S, 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.  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6727255&tag=1

Hasan SMS, Bisset K, Fox EA, Hall KD, Leidig JP, Marathe M. An Extensible Digital Library Service to Support Network Science. In: Procedia Computer Science. Vol. 18. Elsevier; 2013:419–428.  

Jimenez J, Lewis B, Eubank S. 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.  http://link.springer.com/chapter/10.1007%2F978-3-319-03473-7_15

Kamal T, Bisset K, Butt AR, Chungbaek Y, Marathe M. 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.  http://dl.acm.org/citation.cfm?id=2462929

Khan M, Vullikanti A, Marathe M, Zhao Z. Algorithms for Finding Motifs in Large Labeled Networks. Springer; 2013.  http://link.springer.com/chapter/10.1007%2F978-1-4614-6729-8_12

Kuhlman C, Tuli G, Swarup S, Marathe M, Ravi R. Blocking Simple and Complex Contagion By Edge Removal. In: Proceedings of the IEEE International Conference on Data Mining.; 2013:399–408.  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6729524&tag=1

Kuhlman C, Vullikanti A, Marathe M, Ravi R, Rosenkrantz D, Stearns RE. Analysis Problems for Special Classes of Bi-threshold Dynamical Systems.; 2013.  

Kuhlman C, Vullikanti A, Ravi R. Controlling opinion propagation in online networks. Computer Networks. 2013;57(10):2121–2132.  http://www.sciencedirect.com/science/article/pii/S1389128613000893

Lewis B, Swarup S, Bisset K, Eubank S, Marathe M, Barrett C. 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.  http://journals.lww.com/jphmp/Fulltext/2013/09001/A_Simulation_Environment_for_the_Dynamic.11.aspx

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.  http://link.springer.com/chapter/10.1007%2F978-3-319-03473-7_19

Lum K, Chungbaek Y, Eubank S, Marathe M. A two-stage, fitted values approach to activity matching. In: Transportation Research: Part C (International Journal of Transportation).; 2013.  

Mao C, Shukla M, Larrouy-Maumus G, et al. Functional assignment of Mycobacterium tuberculosis proteome revealed by genome-scale fold-recognition. Tuberculosis. 2013.  http://www.sciencedirect.com/science/article/pii/S1472979212002089

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.  

Marathe A, Yi M. Subsidized Vaccines A Policy Trap?; 2013.  

Mortveit H, Macauley M. An atlas of limit set dynamics for asynchronous elementary cellular automata. Theoretical Computer Science. 2013;504:26–37.  http://www.sciencedirect.com/science/article/pii/S0304397512008651

Parikh N, Swarup S, Stretz P, et al. 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.  

Parikh N, Youssef M, Swarup S, Eubank S. Modeling the effect of transient populations on epidemics in Washington DC. Scientific Reports. 2013;3(3152).  http://www.nature.com/srep/2013/131106/srep03152/full/srep03152.html

Pei G, Parthasarathy S, Srinivasan A, Vullikanti A. Approximation algorithms for throughput maximization in wireless networks with delay constraints. Proceedings of IEEE INFOCOM. 2013;21(6):1988–2000.  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5934887

Pei G, Vullikanti A. Distributed Approximation Algorithms for Maximum Link Scheduling and Local Broadcasting in the Physical Interference Model.; 2013:1339–1347.  http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6566927

Rajaraman R, Sun Z, Sundaram R, Vullikanti A. Network effects of risk behavior change following prophylactic interventions. PLoS One. 2013;8(8):e64653.  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3731323/

Rajasekaran P, Alexander JC, Seleem MN, et al. Peptide nucleic acids inhibit growth of Brucella suis in pure culture and in infected murine macrophages. Int J Antimicrob Agents. 2013;41(4):358–362.  http://www.ncbi.nlm.nih.gov/pubmed/23305655

Rivers CM, Lewis B, Young S. Detecting the Determinants of Health in Social Media. Online Journal of Public Health Informatics. 2013;5(1):e161.  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692811/

Rivers CM, Lum K, Lewis B, Eubank S. Estimating transmissibility of avian influenza A(H7N9) from poultry to humans. PLoS Currents: Outbreaks. 2013.  http://currents.plos.org/outbreaks/article/estimating-human-cases-of-avian-influenza-ah7n9-from-poultry-exposure/

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.  http://dx.doi.org/10.1371%2Fjournal.pone.0078489

Sobral B, Mao C, Shukla M, Sullivan D, Zhang C. Informatics-Driven Infectious Disease Research. In: Fred A, Filipe J, Gamboa H, eds. Biomedical Engineering Systems and Technologies. Springer Berlin Heidelberg; 2013:3–11. Communications in Computer and Information Science 273.  http://dx.doi.org/10.1007%2F978-3-642-29752-6_1

Subbiah R, Lum K, Marathe A, Marathe M. A High Resolution Energy Demand Model for Commercial Buildings.; 2013:1–6.  http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6661639&tag=1

Subbiah R, Lum K, Marathe A, Marathe M. Activity based energy demand modeling for residential buildings. In: Innovative Smart Grid Technologies (ISGT), 2013 IEEE PES. Ieee Pes; 2013:1–6.  http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6497822

Swarup S, Lum K, Barrett C, et al. A Synthetic Information Approach to Urban-scale Disaster Modeling. In: Proceedings of Computational Science and Engineering (CSE), 2013 IEEE 16th International Conference on. Ieee; 2013:1105–1112.  

Tuli G, Kuhlman C, Marathe M, Ravi R, Rosenkrantz D. Blocking Complex Contagions Using Community Structure. In: Proceedings of the 12th International Conference on Autonomous Agents and Multiagent Systems.; 2013.  

Turner H, White J, Reed J, et al. Building a Cloud-based Mobile Application Testbed. IGI Global; 2013:382–403.  http://www.igi-global.com/chapter/building-cloud-based-mobile-application/72241

Wattam AR, Abraham D, Dalay O, et al. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res. 2013.  http://dx.doi.org/10.1093%2Fnar%2Fgkt1099

Xia H, Barrett C, Chen J, Marathe M. 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.  

Xia H, Chen J, Marathe M, Mortveit H, Salathe M. Synthesizing Social Proximity Networks by Combining Subjective Surveys with Digital Traces. Ieee; 2013:188–195.  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6755216

Xia H, Nagaraj KS, Chen J, Marathe M. 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.  

Yi M, Marathe A. Policy Trap and Optimal Subsidization Policy under Limited Supply of Vaccines. PLoS One. 2013;8(7):e67249.  http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0067249

Youssef M, Khorramzadeh Y, Eubank S. Network Reliability: A novel betweenness measure using structural motifs. In: Bulletin of the American Physical Society. Vol. 58. APS Physics; 2013.  http://meetings.aps.org/link/BAPS.2013.SES.DC.2

2012


Abdelhamid S, Alo R, Arifuzzaman SM, et al. CINET: A CyberInfrastructure for Network Science. In: Proceedings of the 2012 IEEE 8th International Conference on E-Science (e-Science). IEEE Computer Society; 2012.  http://dl.acm.org/citation.cfm?id=2470396

Alexander KA, Lewis B, Marathe M, Eubank S, Blackburn JK. Modeling of Wildlife Associated Zoonoses: Applications and Caveats. Vector-Borne and Zoonotic Diseases. 2012;12(12):1005–1018.  http://online.liebertpub.com/doi/abs/10.1089/vbz.2012.0987

Barrett C, Beckman R, Bisset K, et al. Optimizing Epidemic Protection for Socially Essential Workers. In: 2nd ACM SIGHIT International Health Informatics Symposium.; 2012:31–40.  http://dl.acm.org/citation.cfm?doid=2110363.2110371

Barrett C, Channakeshava K, Fei F, et al. Human Initiated Cascading Failures in Societal Infrastructures. PLoS ONE 7(10). 2012:e45406.  http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0045406

Bisset K, Aji AM, Bohm E, et al. 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.  

Bisset K, Aji AM, Marathe M, 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

Bisset K, Bassaganya-Riera J, Carbo A, et al. High-Performance Interaction-Based Simulation of Gut Immunopathologies with ENISI. In: Computing & Processing (Hardware/Software). Conference Publications; 2012:48–59.  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6267823&tag=1

Bisset K, Eubank S, Marathe M. High Performance Informatics for Pandemic Preparedness. In: Proceedings of the 2012 Winter Simulation Conference.; 2012:1–12.  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6465211

Deodhar S, Bisset K, Chen J, Ma Y, Marathe M. Enhancing User-Productivity and Capability Through Integration of Distinct Software in Epidemiological Systems. In: 2nd ACM SIGHIT International Health Informatics Symposium.; 2012:171–180.  

DuBois T, Eubank S, 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/v19i1p51

Khan M, Pandurangan G, Pei G, Vullikanti A. A Fast Distributed Approximation Algorithm for Minimum Spanning Trees in the SINR Model. In: Symposium on Distributed Computing (DISC).; 2012.  

Korkmaz G, Kuhlman C, Marathe A, Marathe M, Vega-Redondo F. The Role of Communication via Online Social Networks in the Dynamics of Collective Action.; 2012.  

Kuhlman C, Vullikanti A, Ravi R. Controlling opinion bias in online social networks.; 2012:165–174.  

Lew JM, Mao C, Shukla M, et al. Database resources for the tuberculosis community. Tuberculosis. 2012.  http://www.sciencedirect.com/science/article/pii/S147297921200203X

Liao S, Ma Y, Chen J, Marathe A. Paid Sick-Leave: Is It a Good Way to Control Epidemics?; 2012.  

Liu Z, Pu Y, Li F, et al. Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle. The Journal of Chemical Physics. 2012;136:034105–34111.  http://dx.doi.org/10.1063%2F1.3677190

Mei Y, Hontecillias R, Zhang X, et al. 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

Mortveit H. 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.  

Parikh N, Shirole S, Swarup S. Modeling the Effects of Transient Populations on Epidemics. In: The AAAI Fall Symposium on Social Networks and Social Contagion.; 2012.  

Pei G, Vullikanti A. Low-complexity Scheduling for Wireless Networks. ACM New York, NY; 2012:35–44.  

Pyysalo S, Ohta T, Rak R, et al. Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. BMC Bioinformatics. 2012;13 Suppl 11:S2.  http://dx.doi.org/10.1186%2F1471-2105-13-S11-S2

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.  

Tuli G, Marathe M, Ravi R, 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.  

Wattam AR, Inzana TJ, Williams KP, et al. Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway. MBio. 2012;3(5).  http://www.ncbi.nlm.nih.gov/pubmed/22930339

Zhao Z, Wang G, Butt AR, Khan M, Vullikanti A, Marathe M. 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.  http://dl.acm.org/citation.cfm?id=2358607

2011


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.  

Barrett C, Bisset K, Leidig JP, Marathe A, Marathe M. 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/S175543651000071X

Barrett C, Channakeshava K, Eubank S, Vullikanti A, Marathe M. 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=2011&vol=4&issue=2

Barrett C, Eubank S, Marathe A, Marathe M, Pan Z, Swarup S. Information integration to support policy informatics. The Innovation Journal: The Public Sector Innovation Journal. 2011;16(1):Article 2.  http://www.innovation.cc/volumes-issues/vol16-no1.htm

Barrett C, Hunt HBIII, Marathe M, Ravi R, 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/2/0dc3bb3d300be23b0d80abd70a7179bf

Bisset K, Aji AM, Marathe M, 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

Bisset K, Chen J, Kuhlman C, Vullikanti A, Marathe M. Interaction-based HPC modeling of social, biological and economic contagions over large networks. In: Winter Simulation Conference.; 2011.  

Boyle KJ, Davis G, Estabrooks PA, et al. Translational Economic Research: Integrating Genetics, Neurosciences & Behavioral Sciences. Association of Environmental and Resource Economists. 2011;31(1):15–25.  

Channakeshava K, Bisset K, Marathe M, Vullikanti A, 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.  

Driscoll T, Gabbard JL, Mao C, et al. Integration and visualization of host-pathogen data related to infectious diseases. Bioinformatics. 2011;27:2279–2287.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21712250

Ghosh A, Incel OD, Vullikanti A, 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.  

Gillespie JJ, Wattam AR, Cammer SA, et al. PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species. Infect Immun. 2011;79:4286–4298.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21896772

Kim J, Vullikanti A, 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=1

Kim J, Vullikanti A, 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.  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6148015

Kuhlman C, Vullikanti A, Marathe M, et al. A general-purpose graph dynamical system modeling framework. In: Proceedings of the 2011 Winter Simulation Conference. Ieee; 2011:296–308.  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6147758&tag=1

Kuhlman C, Vullikanti A, Marathe M, Ravi R, Rosenkrantz D. 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.pdf

Kuhlman C, Vullikanti A, Marathe M, Ravi R, 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.  

Kuhlman C, Vullikanti A, Marathe M, et al. A bi-threshold model of complex contagion and its application to the spread of smoking behavior. In: Social Network Mining and Analysis (SNA) Workshop held in conjunction with the KDD 2011.; 2011.  http://www.snakdd.com/pc.html

Kuhlman C, Vullikanti A, Marathe M, et al. 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/

Lee B, McGlone S, Wong K, et al. 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

Lee B, Song Y, McGlone S, et al. Social network analysis of patient sharing among hospitals in Orange County, California. American Journal of Public Health. 2011;101(4):707–713.  

Leidig JP, Barrett C, Marathe M. 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/

Leidig JP, Fox E, Hall KD, Marathe M, Mortveit H. 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, Hall KD, Marathe M, Mortveit H. 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

Leidig JP, Fox EA, Marathe M. 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.  http://www.actapress.com/Abstract.aspx?paperId=452925

Ma Y, Bisset K, Chen J, Deodhar S, Marathe M. Formal Specification and Experimental Analysis of an Interactive Epidemic Simulation Framework. In: ESCAPE: Extreme Scale Computing APplication Enablement – Modeling and Tools.; 2011.  http://www.cs.nthu.edu.tw/~cherung/workshop/escape/

Ma Y, Bisset K, Chen J, Deodhar S, Marathe M. Efficient Implementation of Complex Interventions in Large Scale Epidemic Simulations. In: Winter Simulation Conference.; 2011.  

Macauley M, McCammond J, Mortveit H. Dynamics groups of asynchronous cellular automata. Foundations of Computational Mathematics. 2011;33(1):11–35.  http://www.springerlink.com/content/hgv665924j44t770/

Macauley M, Mortveit H. Posets from Admissible Coxeter Sequences. Discrete Mathematics. 2011;18(1):#P197.  http://www.combinatorics.org/Volume_18/PDF/v18i1p197.pdf

Marathe A, Lewis B, Barrett C, et al. 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.pone.0025149

Marathe A, Lewis B, Chen J, Eubank S. 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.pone.0022461

Marathe A, Marathe M, Vullikanti A. 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.  

Mortveit H, Murrugarra D, Kuhlman C, Vullikanti A. Bifurcations in Boolean Networks. In: Discrete Mathematics and Theoretical Computer Science, Proceedings of the 17th International Workshop on Cellular Automata and Discrete Complex Systems. Vol. Ap.; 2011:29–46.  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.  

Nsoesie EO, Beckman R, Marathe M, Lewis B. 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

Pei G, Parthasarathy S, Srinivasan A, Vullikanti A. 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

Pyysalo S.T.O., Rak R., Sullivan D., Mao C., Wang C., Sobral B. Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011. Portland, Oregon, USA; 2011:26–35. In Proceedings of the BioNLP 2011 Workshop.  

Sobral B and AW. Comparative genomics and phylogenomics of the Brucella. In: O, ed. Brucella: Molecular microbiology and Genetics. Horizon Scientific Press; 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.  

Waltemath D, Adams R, Beard DA, et al. Minimum Information About a Simulation Experiment (MIASE). PLoS Comput Biol. 2011;7:e1001122.  http://www.ncbi.nlm.nih.gov/pubmed/21552546

Xia H, Chen J, Marathe M, Mortveit H. 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.  

2010


Arensburger P, Megy K, Waterhouse RM, et al. Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science. 2010;330:86–88.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20929810

Barrett C, Beckman R, Channakeshava K, et al. 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

Barrett C, Bisset K, Leidig JP, Marathe A, Marathe M. 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

Beckman R, Channakeshava K, Fei F, et al. 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&isnumber=5457826

Beckman R, Channakeshava K, Fei F, et al. 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 K, Chen J, Feng X, Ma Y, Marathe M. 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

Chen J, Fei F, Khan M, Marathe M, Stretz P, 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.  http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=5617584

Chen J, Marathe A, Marathe M. Coevolution of epidemics, social networks and individual behaviors: A case study.; 2010.  

Chen J, Marathe A, Marathe M. 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/

Eubank S, Barrett C, Beckman R, et al. 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

Eubank S, Vullikanti A, Khan M, Marathe M, Barrett C. Beyond Degree Distributions: Local to Global Structure of Social Contact Graphs. In: Advances in Social Computing, Third International Conference on Social Computing, Behavioral Modeling, and Prediction (SBP). Vol. 6007. Springer Berlin / Heidelberg; 2010:1.  http://www.springerlink.com/content/98592811k4k95680/

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/f91fc11461c4d052f5c14dd0c19d452a

Goldstein E, Apolloni A, Lewis B, et al. 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/rsif.2009.0393

Han B, Hui P, Vullikanti A, Marathe M, 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

Huang S, Avery T, Song Y, et al. 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/

Kuhlman C, Lewis B, Beckman R, Eubank S, Dutta T. Clustering method incorporating network topology and dynamics. In: Proceedings of Society for Modeling & Simulation International.; 2010.  

Kuhlman C, Marathe M, Ravi R, 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 C, Vullikanti A, Marathe M, Ravi R, 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/

Kummer U, Sahle S, Hoops S, Mendes P. Assessing the importance of individual players in biochemical networks in a global way. Febs Journal. 2010;277:17–18.  

Leidig JP, Fox E, Marathe M, Mortveit H. 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.  

Macauley M, Mortveit H. Update sequence stability in graph dynamical systems. Discrete and Continuous Dynamical Systems S.. 2010;4(6):1533–1541.  

Nsoesie EO, Beckman R, Marathe M. Estimation of an epidemic curve during an outbreak: A classification approach. In: Proceedings of 2010 Joint Statistical Meeting.; 2010.  

Pyysalo S, Ohta T, Cho H, et al. Towards Event Extraction from Full Texts on Infectious Diseases.; 2010. Proceedings of the 2010 Workshop on Biomedical Natural Language Processing.  

Shawky HA, Marathe A. Stylistic differences across hedge funds as revealed by historical monthly returns. Technology and Investment. 2010;1(1):26–34.  

Swarup S. The classification game: Complexity regularization through interaction. In: Coordination, Organizations, Institutions and Norms in Agent Systems V. Vol. 6069. SpringerLink; 2010:289–303.  http://www.springerlink.com/content/ex131545w3986654/

Swarup S. Computing though interaction. In: The Third International Workshop on Guided Self-Organization.; 2010.  

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

Taylor C, Marathe A, Beckman R. 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/abstract?rss=yes

Vullikanti A, Marathe M, 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/

Vullikanti A, 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.  

Vullikanti A, 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/

Wendelsdorf KV, Bassaganya-Riera J, Hontecillas R, Eubank S. 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=PubMed&dopt=Citation&list_uids=20362587

Zhao Z, Khan M, Vullikanti A, Marathe M. 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.  http://dl.acm.org/citation.cfm?id=1905247

2009


Apolloni A, Channakeshava K, Durbeck L, et al. A study of information diffusion over a realistic social network model. In: Proceeding of the IEEE International Symposium on Social Computing Applications (SCA09).; 2009.  

Apolloni A, Vullikanti A, Marathe M, 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

Atkins K, Barrett C, Marathe A. A web services based artificial market. In: Winter Simulation Conference (WSC).; 2009:3047–3054.  http://www.informs-sim.org/wsc09papers/296.pdf

Atkins K, Chen J, Vullikanti A, 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%2Fj.jebo.2008.11.001

Atkins K, Chen J, Vullikanti A, 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%2FIJCIS.2009.024874

Barrett C, Beckman R, Khan M, et al. 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-proc2009winterconf.pdf

Barrett C, Bisset K, Leidig JP, Marathe A, Marathe M. 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 C, Eubank S, Marathe M. Policy informatics for co-evolving socio-technical networks. In: Proceedings of 4th International Conference on Critical Infrastructures.; 2009.  

Barrett C, Lewis B, Chen J, et al. Interactions among human behavior, social networks, and societal infrastructures: A case study in computational epidemiology. Vol. Xxii. Springer Verlag; 2009.  http://www.springer.com/computer/swe/book/978-1-4020-9687-7

Bisset K, Chen J, Feng X, Vullikanti A, Marathe M. 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%2F1542275.1542336

Bisset K, Marathe M. A cyber environment to support pandemic planning and response. DOE SCIDAC Magazine. 2009:36–47.  http://www.scidacreview.org/0903/html/maranthe.html

Channakeshava K, Chafekar D, Bisset K, Vullikanti A, Marathe M. 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.  http://portal.acm.org/citation.cfm?id=1537622

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/

Choi Y, Khan M, Vullikanti A, Pandurangan G. Energy-Optimal distributed algorithms for minimum spanning trees. IEEE Journal on Selected Areas in Communications. 2009;27(7):1297–1304.  http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=05226979

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. 2009;15(2):article 10.  

Feighner BH, Eubank S, 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

Han B, Vullikanti A, Marathe M, 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

Khan M, Pandurangan G, Vullikanti A. 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

Khan M, Vullikanti A, Marathe M, Pandurangan G, Ravi R. 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=1

Macauley M, Mortveit H. Cycle equivalence of graph dynamical systems. Nonlinearity. 2009;22(2):421–436.  http://iopscience.iop.org/0951-7715/22/2/010

Mao C, Bhardwaj K, Sharkady SM, et al. Variations on the tmRNA gene. RNA Biol. 2009;6:355–361.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19617710

Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U. Computational modeling of biochemical networks using COPASI. Methods Mol Biol. 2009;500:17–59.  http://www.ncbi.nlm.nih.gov/pubmed/19399433

Mendes P, Messiha H, Malys N, Hoops S. Enzyme kinetics and computational modeling for systems biology. Methods Enzymol. 2009;467:583–599.  http://www.ncbi.nlm.nih.gov/pubmed/19897108

Sriranganathan N, Seleem MN, Olsen SC, et al. Brucella. In: Nene V, Kole C, eds. Genome Mapping and Genomics in Animal-Associated Microbes. Berlin: Springer; 2009:1–64.   http://isbn.nu/978-3-540-74040-7

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

Vullikanti A, Macauley M, Mortveit H. Limit set reachability in asynchronous graph dynamical systems, Lecture Notes in Computer Science. In: Reachability Problems. Vol. 5797. Springer Berlin Heidelberg; 2009:217–232.  http://www.springerlink.com/content/t497v3644155p15q/

Vullikanti A, Marathe M, 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/

Vullikanti A, Marathe M, 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#

Wattam AR, Williams KP, Snyder EE, et al. Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. J Bacteriol. 2009;191:3569–3579.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19346311

2008


Atkins K, Barrett C, Beckman R, et al. An Interaction Based Composable Architecture for Building Scalable Models of Large Social, Biological, Information and Technical Systems. CT Watch. 2008;4(1):46–53.  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2800380/

Barrett C, Bisset K, Eubank S, Feng X, Marathe M. 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

Barrett C, Bisset K, Eubank S, Feng X, Marathe M. 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.  http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=5214892

Barrett C, Bisset K, Konjevod G, Marathe M, Wagner D. Engineering label-constrained shortest-path algorithms. In: Proceedings of the Fourth International Conference on Algorithmic Aspects in Information and Management (AAIM 2008). LNCS. Springer; 2008:27–37.  

Barrett C, Eubank S, Lewis B, Marathe M. Pandemics, Detection and Management. Springer US; 2008.  http://www.springerlink.com/content/q7577h543x53k004/

Barrett C, Eubank S, Marathe M. 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, Levin D, Parthasarathy S, Vullikanti A, Marathe M, 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.  http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4509765&isnumber=4509595

Chafekar D, Vullikanti A, Marathe M, Parthasarathy S. Power efficient throughput maximization in multi-hop wireless networks. In: Proceedings of the Global Telecommunications Conference, IEEE GLOBECOM.; 2008.  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4698712&tag=1

Chafekar D, Vullikanti A, Marathe M, 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.  

Eubank S, Vullikanti A, Marathe M. Epidemiology and wireless communication: Tight Analogy or Loose Metaphor. Vol. 5151. Springer Verlag; 2008.  http://www.springerlink.com/content/h756844635r84763/

Flottmann M, Schaber J, Hoops S, Klipp E, Mendes P. ModelMage: a tool for automatic model generation, selection and management. Genome Inform. 2008;20:52–63.  http://www.ncbi.nlm.nih.gov/pubmed/19425122

Gillespie JJ, Williams K, Shukla M, et al. Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life. PLoS One. 2008;3(4):e2018.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19194535

Halloran ME, Ferguson NM, Eubank S, et al. 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.  http://www.pnas.org/content/105/12/4639.abstract

Hucka M, Hoops S, Keating SM, Le Nov. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. Nature Precedings. 2008.  

Istrate G, Marathe M, Ravi R. Adversarial analysis of game-theoretic models of norm diffusion.; 2008.  http://link.springer.com/chapter/10.1007/978-3-540-69407-6_31

Macauley M, McCammond J, Mortveit H. Order independence in asynchronous cellular automata. Journal of Cellular Automata. 2008;3(1):37–56.  http://arxiv.org/abs/0707.2360

Mao C, Evans C, Jensen RV, Sobral BW. Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system. BMC Microbiol. 2008;8:72.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18454850

Mian MA, Zhang Y, Wang ZY, et al. Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages. BMC Plant Biol. 2008;8:27.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18318913

Mortveit H, Reidys C. An Introduction to Sequential Dynamical Systems. Springer Verlag; 2008.  

Sahle S, Mendes P, Hoops S, Kummer U. A new strategy for assessing sensitivities in biochemical models. Philos Transact A Math Phys Eng Sci. 2008;366:3619–3631.  http://www.ncbi.nlm.nih.gov/pubmed/18632455

Swarup S. Cause and effect: The anticipatory drive and the principle of least time (Commentary). Constructivist Foundations. 2008;4(1):21–23.  

Vullikanti A, Marathe M, Parthasarathy S, Srinivasan A. Minimum weighted completion time. Vol. 12. Springer Verlag; 2008.  

Vullikanti A, Marathe M, 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&isnumber=4658211

Yang Y, Koopman JS, Samore MH, Eubank S, Lewis B. Model analysis of potential causes for pertussis secular trends. In: Epidemics Journal and Conference on Infectious Diseases Dynamics.; 2008.  

Zhang C, Crasta O, Cammer S, et al. An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. Nucleic Acids Res. 2008;36:D884–91.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17984082

2007


Atkins K, Marathe A, Barrett C. A computational approach to modeling commodity markets. Computational Economics. 2007;30(2):125–142.  http://www.springerlink.com/content/q664q11843775048/

Barrett C, Bisset K, Chen J, et al. Effect of public policies and individual behavior on the co-evolution of social networks and infectious disease dynamics. In: Proceedings of the DIMACS/DyDAn Workshop: Computational Methods for Dynamic Interaction Networks.; 2007.  

Barrett C, Bisset K, Eubank S, et al. 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.  http://www.springerlink.com/content/g38x1801770177g7/

Barrett C, Bisset K, Eubank S, Vullikanti A, Marathe M, Mortveit H. Modeling and simulation of large biological, information and socio-technical systems: An interaction-based approach. Vol. 64.; 2007.  

Barrett C, III HBH, Marathe M, et al. 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

Barrett C, III HBH, Marathe M, et al. Predecessor existence problems for finite discrete dynamical systems. Theoretical Computer Science. 2007;386(1-2):3–37.  

Blumer AD, Mortveit H, Patterson CD. Formal modeling of process migration. In: 17th International Conference on Field Programmable Logic and Applications.; 2007.  

Chafekar D, Vullikanti A, Marathe M, 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

Khan M, Pandurangan G, Vullikanti A. 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-4NXHCH1-5/2/14a7e5131aab110d035b338785adcdb2

Macauley M, Mortveit H. On enumeration of conjugacy classes of Coxeter elements. Proceedings of theAmerican Mathematical Society. 2007;136:4157–4165.  http://www.ams.org/journals/proc/2008-136-12/S0002-9939-08-09543-9/home.html

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-1/2/41b9331b2f8506e7b774b6ab23997873

Mozumder P, Marathe A. Role of Information and communication Network in Malaria Survival. Malaria Journal. 2007;6(136).  http://www.malariajournal.com/content/6/1/136

Nene V, Wortman JR, Lawson D, et al. Genome sequence of Aedes aegypti, a major arbovirus vector. Science. 2007;316:1718–1723.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17510324

Snyder EE, Kampanya N, Lu J, et al. PATRIC: the VBI PathoSystems Resource Integration Center. Nucleic Acids Res. 2007;35:D401–406.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17142235

Thomas RW, DaSilva LA, Marathe M, Wood KN. Critical design decisions for cognitive networks. In: Proceedings of IEEE International Conference of Communications. Ieee; 2007:3993–3998.  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4289328

Torto-Alalibo TA, Tripathy S, Smith BM, et al. Expressed sequence tags from phytophthora sojae reveal genes specific to development and infection. Mol Plant Microbe Interact. 2007;20:781–793.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17601166

2006


Atkins K, Chen J, Vullikanti A, Macauley M, Marathe A. Locational Market Power in Power Markets. In: Proceedings of 29th IAEE International Conference.; 2006.  

Atkins K, Chen J, Vullikanti A, Marathe A. Structural analysis of electrical power networks. In: Proceedings of 3rd International Conference on Critical Infrastructures.; 2006.  

Barrett C, Hunt HBIII, Marathe M, Ravi R, 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 C, III HH, Marathe M, Ravi R, Rosenkrantz D, Stearns R. Complexity of reachability problems for finite discrete dynamical systems. Journal of Computer and System Sciences. 2006;72(8):1317–1345.  

Barrett C, Istrate G, Vullikanti A, Marathe M, 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/PERCOMW.2006.129

Chen J, Rajaraman R, Sundaram R. Meet and merge:Approximation algorithms for confluent flows. Journal of Computer and Systems Sciences (J of Computer and System Science (JCSS), special STOC 2003. 2006;72(3):468–489.  http://www.sciencedirect.com/science/article/B6WJ0-4HM7S87-2/2/2eae637526a92ee376dae2bfa58fc61b

Chen J, Vullikanti A, Marathe A, Atkins K. Model Based Spatial Data Mining for Power Markets.; 2006.  

Eubank S, Vullikanti A, Marathe M, Srinivasan A, Wang N. Structure of social contact networks and their impact on epidemics. In: AMS-DIMACS Special Volume on Epidemiology. Vol. 70.; 2006:181–213.  

Hoops S, Sahle S, Gauges R, et al. COPASI--a COmplex PAthway SImulator. Bioinformatics. 2006;22:3067–3074.  http://www.ncbi.nlm.nih.gov/pubmed/17032683

Hunt HBIII, Marathe M, Stearns RE, Rosenkrantz D. Towards a predictive complexity theory of periodically specified problems: A survey. In: Computational Complexity and Statistical Physics. Oxford University Press; 2006:285–318.  

Istrate G, Hansson A, Marathe M, Thulasidasan S, Barrett C. 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.  

Zhao J, Xue T, Yang B, et al. Genome Annotation and Comparison System. Las Vegas, NV, USA; 2006. The 2006 International Conference on Bioinformatics & Computational Biology (BIOCOMP).  

2005


Barrett C, Drozda M, Engelhart DC, et al. 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&isnumber=32400

Barrett C, Eidenbenz SJ, Kroc L, Marathe M, Smith JP. Parametric probabilistic routing in sensor networks. ACM/Baltzer J. Mobile Networks and Applications (MONET). 2005;10(4):529–544.  http://www.springerlink.com/content/t65k7q865r160376/

Barrett C, Eidenbenz SJ, Kroc L, Marathe M, 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.  

Barrett C, Eubank S, Marathe M. 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.  

Barrett C, Eubank S, Smith JP. If Smallpox Strikes Portland.. Scientific American. 2005;292(3):54–61.  http://www.scientificamerican.com/article/if-smallpox-strikes-portl/

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

Eubank S. 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

Gokhale M, Hansson A, Mortveit H, Tripp J. Urban traffic simulation modeling for reconfigurable hardware. In: Proceedings of Industrial Simulation Conference.; 2005:291–298.  

Granich RM, Oh P, Lewis B, 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.  

Hansson AAA, Mortveit H, Reidys C. On Asynchronous Cellular Automata. Advances in Complex Systems. 2005;8(4):521–538.  

He Y, Vines RR, Wattam AR, et al. PIML: the Pathogen Information Markup Language. Bioinformatics. 2005;21(1):116–121.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15297293

Mao C, Qiu J, Wang C, Charles TC, Sobral BW. NodMutDB: a database for genes and mutants involved in symbiosis. Bioinformatics. 2005;21:2927–2929.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15817696

Toroczkai Z, Eubank S. 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 S. Agent-based modeling as a decision-making tool. The Bridge. 2005;35(4):22–27.  

Tripp J, Hansson A, Gokhale M, Mortveit H. 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.  

Tripp J, Hansson A, Mortveit H, 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.  

Vullikanti A, Marathe M, 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.  

Vullikanti A, Marathe M, 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.  

Vullikanti A, Marathe M, 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.  

Vullikanti A, Parthasarathy S, Marathe M, 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.  

2004


Atkins K, Barrett C, Homan C, Marathe A, Marathe M, Thite S. Agent based economic analysis of deregulated electricity markets. In: Proceeding of 6th IAEE European Energy Conference. Zurich, Switzerland; 2004.  

Atkins K, Barrett C, Homan CM, Marathe A, Marathe M, 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

Balakrishnan H, Barrett C, Vullikanti A, Marathe M, 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

Barrett C, Marathe M, Engelhart DC, Sivasubramaniam A. Approximating the connectivity between nodes when simulating large-scale mobile ad hoc radio networks. The Journal of Systems and Software. 2004;73:63–74.  

Barrett C, Marathe M, Smith JP, Ravi R. 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 Comp. 2004;12(1):1–23.  

Eubank S. 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 S, Guclu H, Vullikanti A, et al. 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=PubMed&dopt=Citation&list_uids=15141212

Eubank S, Vullikanti A, Marathe M, 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 S, Vullikanti A, Marathe M, 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

Tripp JL, Mortveit H, Nassr MS, Hansson AA, Gokhale M. Acceleration of traffic simulation on reconfigurable hardware. In: Proceedings of MAPLD04.; 2004.  

Tu Z, Li S, Mao C. 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;168:2037–2047.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15611173

2003


Barrett C, Mortveit H, Reidys C. ETS IV: Sequential Dynamical Systems: fixed points, invertibility and equivalence. Appl. Math. and Comput.. 2003;134(1):153–171.  

Hoops S, de la Fuente A, Mendes P. Partial Estimation of the Jacobian from Time Course Data. Heidelberg, Germany; 2003:93–98. 3rd Workshop on Computation of Biochemical Pathways and Genetic Networks.  

Hoops S, Eckart JD, Sobral BWS. Integration and Interoperation in Life Sciences: Examples and Challenges. New Generation Computing. 2003;22.  

Li XJ, Brazhnik O, Kamal A, et al. Databases and Visualization for Metabolomics. In: Harrigan G, Goodacre R, eds. Metabolite Profiling: Its Role in Biomarker Discovery and Gene Function Analysis. Dordrecht: Kluwer Academic Publishers; 2003:293–309.  

Mao C, Cushman JC, May GD, Weller JW. ESTAP--an automated system for the analysis of EST data. Bioinformatics. 2003;19:1720–1722.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15593407

2002


Hoops S, Chen D, Mendes P. High Performance Computing for Biochemical Network Simulations, in High Performance Computing. San Diego, CA; 2002:16–20. The Society for Modeling and Simulation International.  

Mendes P, de la Fuente A, Hoops S. Chapter One Bioinformatics and computational biology for plant functional genomics. In: John TR, Richard AD, eds. Recent Advances in Phytochemistry. Vol. Volume 36. Elsevier; 2002:1–13.  http://www.sciencedirect.com/science/article/B8GXN-4NX2MDM-2/2/8c33a98cb25a87431b0772549673d532

2001


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

2000


Barrett C, Mortveit H, Reidys C. Elements of a theory of simulation II: sequential dynamical systems. Appl. Math. Comput.. 2000;107(2-3):121–136.  http://ndssl.vbi.vt.edu/Publications/SDSIIBarrett.pdf

Carr RD, Doddi S, Konjevod G, Marathe M. 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.  

Cook S, Faber V, Hicks G, Marathe M. 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.  

Czabarka E, Konjevod G, Marathe M, 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; 2000:399–408.  http://portal.acm.org/citation.cfm?id=338585

Doddi SR, Marathe M, Ravi R, Taylor DS, Widmayer P. Approximation Algorithms for Clustering to Minimize the Sum of Diameters. Invited paper appears in the special issue of Nordic Journal of Computing, containing selected paper. 2000;7(3):185–203.  

Dowell L, Drozda M, Henderson D, Loose V, Marathe M, 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.  

III HBH, Stearns R, Marathe M. On the Efficient Approximability of. In: Approximation and Complexity in Numerical Optimization: Continuous and Discrete Problems. Vol. 42. Kluwer Academic Publishers; 2000:308–322.  

1999


Eubank S. What makes a simulation useful? [TRANSIMS]. In: Proceedings of the IEEE Systems Man and Cybernetics Conference. Vol. 4.; 1999:640–644 vol.4.  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=812479&tag=1

1998


Kidwell MG, Wattam AR. An important step forward in the genetic manipulation of mosquito vectors of human disease. Proc Natl Acad Sci U S A. 1998;95(7):3349–3350.  http://www.ncbi.nlm.nih.gov/pubmed/9520367

Mao C, Little JW. Mutations affecting cooperative DNA binding of phage HK022 CI repressor. J Mol Biol. 1998;279:31–48.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9636698

1994


Mao C, Carlson NG, Little JW. Cooperative DNA-protein interactions. Effects of changing the spacing between adjacent binding sites. J Mol Biol. 1994;235:532–544.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8289280

1992


Benguria R, Hoops S, Siedentop H. Bounds on the Excess Charge and the Ionization Energy of the Hellman-Weizs. Annales de l. 1992;45:47–65.  

Wattam AR, Christensen BM. Induced polypeptides associated with filarial worm refractoriness in Aedes aegypti. Proc Natl Acad Sci U S A. 1992;89(14):6502–6505.  http://www.ncbi.nlm.nih.gov/pubmed/1631149

Wattam AR, Christensen BM. Variation in Aedes aegypti mRNA populations related to strain, sex, and development. Am J Trop Med Hyg. 1992;47(5):702–707.  http://www.ncbi.nlm.nih.gov/pubmed/1449211

Wattam AR, Christensen BM. Further evidence that the genes controlling susceptibility of Aedes aegypti to filarial parasites function independently. J Parasitol. 1992;78(6):1092–1095.  http://www.ncbi.nlm.nih.gov/pubmed/1491306

1989


Lu G, Mao C, Wei X, Hua Z, Gu X. Crystallization and preliminary X-ray diffraction studies of Bar-headed goose (Anser indicus) methemoglobin. Acta Biophysica Sinica. 1989:259–262.  

1988


Duszynski DW, Wattam AR. Coccidian parasites (Apicomplexa: Eimeriidae) from insectivores. V. Ten forms from the moles of Japan (Euroscaptor, Mogera spp.). J Protozool. 1988;35(1):55–57.  http://www.ncbi.nlm.nih.gov/pubmed/3367320

Duszynski DW, Wattam AR. Coccidian parasites (Apicomplexa: Eimeriidae) from insectivores. IV. Four new species in Talpa europaea from England. J Protozool. 1988;35(1):58–62.  http://www.ncbi.nlm.nih.gov/pubmed/3367321