Recent Submissions

  • Multi-scale immunoepidemiological modeling of within-host and between-host HIV dynamics: systematic review of mathematical models 

    Dorratoltaj, Nargesalsadat; Nikin-Beers, Ryan; Ciupe, Stanca M.; Eubank, Stephen G.; Abbas, Kaja M. (PeerJ, 2017-09-28)
    Objective The objective of this study is to conduct a systematic review of multi-scale HIV immunoepidemiological models to improve our understanding of the synergistic impact between the HIV viral-immune dynamics at the ...
  • A Simulation Optimization Approach to Epidemic Forecasting 

    Nsoesie, Elaine O.; Beckman, Richard J.; Shashaani, Sara; Nagaraj, Kalyani S.; Marathe, Madhav V. (PLOS, 2013-06-27)
    Reliable forecasts of influenza can aid in the control of both seasonal and pandemic outbreaks. We introduce a simulation optimization (SIMOP) approach for forecasting the influenza epidemic curve. This study represents ...
  • What Factors Might Have Led to the Emergence of Ebola in West Africa? 

    Alexander, Kathleen A.; Sanderson, Claire E.; Marathe, Madav; Lewis, Bryan L.; Rivers, Caitlin M.; Lofgren Eric; Eubank, Stephen; et al. (PLOS, 2015-06-04)
    An Ebola outbreak of unprecedented scope emerged in West Africa in December 2013 and presently continues unabated in the countries of Guinea, Sierra Leone, and Liberia. Ebola is not new to Africa, and outbreaks have been ...
  • Using data-driven agent-based models for forecasting emerging infectious diseases 

    Venkatramanan, Srinivasan; Lewis, Bryan; Chen, Jiangzhuo; Higdon, Dave; Vullikanti, Anil; Marathe, Madhav (Elsevier, 2017-02-22)
    Producing timely, well-informed and reliable forecasts for an ongoing epidemic of an emerging infectious disease is a huge challenge. Epidemiologists and policy makers have to deal with poor data quality, limited understanding ...
  • Modeling Commodity Flow in the Context of Invasive Species Spread: Study of Tuta absoluta in Nepal 

    Venkatramanan, S.; Wu, S.; Shi, B.; Marathe, A.; Sah, L.P.; Giri, A.P.; Colavito, L.A.; Nitin, K.S.; Sridhar, V.; Asokan, R.; Muniappan, R.; Norton, G.; Adiga, A.; Eubank, S. (Virginia Tech, 2017)
    Trade and transport of goods is widely accepted as a primary pathway for the introduction and dispersal of invasive species. However, understanding commodity flows remains a challenge owing to its complex nature, unavailability ...
  • Characterizing the Genetic Basis for Nicotine Induced Cancer Development: A Transcriptome Sequencing Study 

    Bavarva, Jasmin H.; Tae, Hongseok; Settlage, Robert E.; Garner, Harold R. (PLOS, 2013-06-18)
    Nicotine is a known risk factor for cancer development and has been shown to alter gene expression in cells and tissue upon exposure. We used Illumina® Next Generation Sequencing (NGS) technology to gain unbiased biological ...
  • High Resolution Discovery Proteomics Reveals Candidate Disease Progression Markers of Alzheimer’s Disease in Human Cerebrospinal Fluid 

    Hendrickson, Ronald C.; Lee, Anita Y.H.; Song, Qinghua; Liaw, Andy; Winer, Matt; Paweletz, Cloud P.; Seeburger, Jeffrey L.; Li, Jenny; Meng, Fanyu; Deyanova, Ekaterina G.; Mazur, Matthew T.; Settlage, Robert E.; Zhao, Xuemei; Southwick, Katie; Du, Yi; Holder, Dan; Sachs, Jeffrey R.; Laterza, Omar F.; Dallob, Aimee; Chappell, Derek L.; Snyder, Karen; Modur, Vijay; King, Elizabeth; Joachim, Catharine; Bondarenko, Andrey Y.; Shearman, Mark; Soper, Keith A.; Smith, A. David; Potter, William Z.; Koblan, Ken S.; Sachs, Alan B.; Yates, Nathan A. (PLOS, 2015-08-13)
    Disease modifying treatments for Alzheimer’s disease (AD) constitute a major goal in medicine. Current trends suggest that biomarkers reflective of AD neuropathology and modifiable by treatment would provide supportive ...
  • Gene Expression Profiling of Human Vaginal Cells In Vitro Discriminates Compounds with Pro-Inflammatory and Mucosa-Altering Properties: Novel Biomarkers for Preclinical Testing of HIV Microbicide Candidates 

    Zalenskaya, Irina A.; Joseph, Theresa; Bavarva, Jasmin; Yousefieh, Nazita; Jackson, Suzanne S.; Fashemi, Titilayo; Yamamoto, Hidemi S.; Settlage, Robert; Fichorova, Raina N.; Doncel, Gustavo F. (PLOS, 2015-06-08)
    Background Inflammation and immune activation of the cervicovaginal mucosa are considered factors that increase susceptibility to HIV infection. Therefore, it is essential to screen candidate anti-HIV microbicides for ...
  • Enhancing disease surveillance with novel data streams: challenges and opportunities 

    Althouse, Benjamin M.; Scarpino, Samuel V.; Meyers, Lauren Ancel; Ayers, John W.; Bargsten, Marisa; Baumbach, Joan; Brownstein, John S.; Castro, Lauren; Clapham, Hannah; Cummings, Derek AT; Del Valle, Sara; Eubank, Stephen; Fairchild, Geoffrey; Finelli, Lyn; Generous, Nicholas; George, Dylan; Harper, David R.; Hebert-Dufresne, Laurent; Johansson, Michael A.; Konty, Kevin; Lipsitch, Marc; Millinovich, Gabriel; Miller, Joseph D.; Nsoesie, Elaine O.; Olson, Donald R.; Paul, Michael|Polgreen, Philip M.; Priedhorsky, Reid; Read, Jonathan M.; Rodriguez-Barraquer, Isabel; Smith, Derek J.; Stefansen, Christian; Swerdlow, David L.; Thompson, Deborah; Vespignani, Alessandro; Wesolowski, Amy (Springer, 2015)
    Novel data streams (NDS), such as web search data or social media updates, hold promise for enhancing the capabilities of public health surveillance. In this paper, we outline a conceptual framework for integrating NDS ...
  • Detail in network models of epidemiology: are we there yet? 

    Eubank, Stephen; Barrett, Christopher L.; Beckman, Richard J.; Bisset, Keith R.; Durbeck, L.; Kuhlman, Christopher J.; Lewis, Bryan; Marathe, Achla; Marathe, Madhav; Stretz, P. (Taylor & Francis, 2010)
    Network models of infectious disease epidemiology can potentially provide insight into how to tailor control strategies for specific regions, but only if the network adequately reflects the structure of the region’s contact ...
  • Estimating Human Cases of Avian Influenza A(H7N9) from Poultry Exposure 

    Rivers, Caitlin; Lum, Kristian; Lewis, Bryan; Eubank, Stephen (PLOS, 2013-05-15)
    In March 2013 an outbreak of avian influenza A(H7N9) was first recognized in China. To date there have been 130 cases in human, 47% of which are in men over the age of 55.The influenza strain is a novel subtype not seen ...
  • Modeling to Predict Cases of Hantavirus Pulmonary Syndrome in Chile 

    Nsoesie, Elaine O.; Mekaru, Sumiko R.; Ramakrishnan, Naren; Marathe, Madhav V.; Brownstein, John S. (PLOS, 2014-04-24)
    Background: Hantavirus pulmonary syndrome (HPS) is a life threatening disease transmitted by the rodent Oligoryzomys longicaudatus in Chile. Hantavirus outbreaks are typically small and geographically confined. Several ...
  • Forecasting Social Unrest Using Activity Cascades 

    Cadena, Jose; Korkmaz, Gizem; Kuhlman, Chris J.; Marathe, Achla; Ramakrishnan, Naren; Vullikanti, Anil (PLOS, 2015-06-19)
    Social unrest is endemic in many societies, and recent news has drawn attention to happenings in Latin America, the Middle East, and Eastern Europe. Civilian populations mobilize, sometimes spontaneously and sometimes in ...
  • Towards an in silico Experimental Platform for Air Quality: Houston, TX as a Case Study 

    Pires, Bianica; Korkmaz, Gizem; Ensor, Katherine; Higdon, David; Keller, Sallie; Lewis, Bryan; Schroeder, Aaron (CSSSA, 2015)
    In this paper we couple a spatiotemporal air quality model of ozone concentration levels with the synthetic information model of the Houston Metropolitan Area. While traditional approaches often aggregate the population, ...
  • Can Administrative Housing Data Replace Survey Data? 

    Molfino, Emily; Korkmaz, Gizem; Keller, Sallie A.; Schroeder, Aaron; Shipp, Stephanie; Weinberg, Daniel H. (HUD, 2017)
    This article examines the feasibility of using local administrative data sources for enhancing and supplementing federally collected survey data to describe housing in Arlington County, Virginia. Using real estate assessment ...
  • Modeling targeted layered containment of an influenza pandemic in the United States 

    Halloran, Elizabeth M.; Ferguson, Neil M.; Eubank, Stephen; Longini Jr., Ira M.; Cummings, Derek A.T.; Lewis, Bryan; Xu, Shufu; Fraser, Christophe; Vullikanti, Anil; Germann, Timothy C.; Wagener, Diane; Beckman, Richard; Kadau, Kai; Barrett, Chris; Macken, Catherine A.; Burke, Donald S.; Cooley, Philip (NAS, 2008-03-25)
    Planning a response to an outbreak of a pandemic strain of influenza is a high public health priority. Three research groups using different individual-based, stochastic simulation models have examined the consequences of ...
  • Human Initiated Cascading Failures in Societal Infrastructures 

    Barrett, Chris; Channakeshava, Karthik; Huang, Fei; Kim, Junwhan; Marathe, Achla; Marathe, Madhav V.; Pei, Guanhong; Saha, Sudip; Subbiah, Balaaji S.P.; Vullikanti, Anil Kumar S. (PLOS, 2012-10-31)
    In this paper, we conduct a systematic study of human-initiated cascading failures in three critical inter-dependent societal infrastructures due to behavioral adaptations in response to a crisis. We focus on three closely ...
  • Structural, thermodynamic, and phosphatidylinositol 3-phosphate binding properties of Phafin2 

    Tang, T-X; Jo, A; Deng, J; Ellena, JF; Lazar, IM; Davis, RM; Capelluto, DGS (WILEY, 2017-04-01)
  • Building Capacity for Data Driven Governance - Creating a New Foundation for Democracy 

    Keller, SA; Lancaster, VA; Shipp, SS
    Existing data flows at the local level, public and administrative records, geospatial data, social media, surveys, as well as other federal, state, and local databases, are ubiquitous in our everyday life. These data, when ...
  • STRATEGY FOR A NATIONAL COMMUNITY LEARNING NETWORK: COMMUNITY LEARNING DATA DRIVEN DISCOVERY - Building Capacity for Evidence-Based Decision Making 

    Keller, SA (2016-12-19)
    The Social and Decision Analytics Laboratory (SDAL) of the Biocomplexity Institute of Virginia Tech received a planning grant from the Laura and John Arnold Foundation (LJAF) to develop a strategy for a national community ...

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