Publications and Presentations on STEM

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About the Items Cited

Below we list by year publications and presentations about STEM. Many focus on the development of STEM as an open-source software tool. Others focus on its use as modeling tool. We welcome contributions to this listing by members of the scientific community who are using STEM to support their research activities and public health initiatives.

Publications and Presentations about STEM in 2021

Horn, Abigail L., et al. "An integrated risk and epidemiological model to estimate risk-stratified COVID-19 outcomes for Los Angeles County: March 1, 2020—March 1, 2021." Plos one 16.6 (2021): e0253549.

Publications and Presentations about STEM in 2019

Douglas JV, Bianco S, Edlund S, Engelhardt T, Filter M, Gunther T, Hu K, Nixon EJ, Sevilla NL, Swaid A, Kaufman JH. "STEM: An Open Source Tool for Disease Modeling." Health Security 17(4):291-306. DOI: 10.1089/hs.2019.0018.

Popescu SV. "Why we need more open-source epidemiological tools." ContagionLive: Infectious Diseases Today. https://www.contagionlive.com/contributor/saskia-v-popescu/2019/09/why-we-need-more-opensource-epidemiological-tools

Publications and Presentations about STEM in 2018

Sevilla NL. "Germs on a Plane: The Transmission and Risks of Airplane-Borne Diseases." Poster session presented at the Transportation Research Board (TRB) 97th Annual Meeting, 7-11 Jan 2018, Washington, DC. [1]

Stefan Edlund, Derryn Lovett, James Kaufman, Kezban Yagci Sokat, Johan van Wijgerden, Alan J. Poots, "Supporting decision making: Modeling and forecasting measles in a London borough" doi: https://doi.org/10.1101/497800

Publications and Presentations about STEM in 2017

Nieddu GT et al. "Extinction pathways and outbreak vulnerability in a stochastic Ebola model." Journal of The Royal Society Interface 14.127 (2017): 20160847.

Sau A. "A Simulation Study on Hypothetical Ebola Virus Transmission in India Using Spatiotemporal Epidemiological Modeler (STEM): A Way towards Precision Public Health." Journal of Environmental and Public Health Volume 2017 (2017), Article ID 7602301, https://doi.org/10.1155/2017/7602301

Co I-L, Estaur MR, Espina KE, Lara RJ, De Los Reyes VC. "Integrating health indices towards the development of a Typhoid disease model using STEM." IEEE Xplore Digital Library 16 February 2017. ieeexplore.ieee.org/document/785711/?reload=true.

Filter M, Günther T, BfR-Team. " BfR Training-STEM-Workshop". The Federal Institute for Risk Assessment, 6-7 February 2017, Berlin, Germany.

Publications and Presentations about STEM in 2016

Baldassi F, D'Amico F, Carestia M, Cenciarelli O, Mancinelli S, Gilardi F, Malizia A, Di Giovanni D, Soave P, Bellecci C, Gaudio P. May 2016. "Testing the accuracy of ratio of the Spatio-Temporal Epidemiological Modeler (STEM) through Ebola haemorrhagic fever outbreaks." Epidemiology and Infection 144(7):1463-72.

Sevilla N, "Open Source Disease Modeling: A Tool to Combat the Next Pandemic", GlobalBioDefense.com Jan. 28, 2016.

Hu K, Renly S, Edlund S, Davis M, Kaufman J. 2016. "A modeling framework to accelerate food-borne outbreak investigations." Food Control, 59, 53-58.

Publications and Presentations about STEM in 2015

Jones BA, Lessler J, Bianco S, Kaufman JH, "Statistical Mechanics and Thermodynamics of Viral Evolution", PLoS ONE 10(9): e0137482, Sept. 30, 2015. doi: 10.1371/journal.pone.0137482

Hu K. "The effect of antibody-dependent enhancement, cross immunity, and vector population on the dynamics of dengue fever." Invited talk and panel discussion at "The International Society for Neglected Tropical Diseases, ISNTD Bites: vector-control solutions for NTDs & global health", London Zoo, UK, March 2015. [2]

Hu K. "A study of environmental factors impact on the dynamics of mosquito population in modelling dengue fever." Poster at "Impact of Environmental Changes on Infectious Diseases" conference, 23-25 March 2015, Sitges, Spain

Hu K, Bianco S, Edlund S, Kaufman J. "The impact of human behavioral changes in 2014 west Africa Ebola outbreak." SBP 15, 2015 International Conference on Social Computing, Behavioral-Cultural Modeling, & Prediction, April 1, 2015, Washington, DC.

Bianco S, Hu K, Kaufman JH (IBM Research); Schwartz IB (US Naval Research Laboratory)."Predicting unobserved contacts from Ebola epidemic data." Poster presented at Ebola Modeling Workshop, January 2015. [3]

Publications and Presentations about STEM in 2014

Kaufman J, Lessler J, Harry A, Edlund S, Hu K, Douglas J, Thoens C, Appel B, Kasbohrer A, Filter M. "A likelihood-based approach to identifying contaminated food products using sales data: performance and challenges." PLoS Comput Biol 10(11): e 100399. doi: 10.1371/journal.pcbi.1003999.

Bamaiyi PH. "Simulation of the use of Yersinia pestis as a biological weapon in Nigeria." 2014. Communications in Applied Sciences 2(1):111-128.

Bamaiyi PH. "Simulation model on the potential use of Vibrio Cholerae as a biological agent of terror and simulated economic impact in Nigeria. 2014. International Journal of Tropical Medicine 3(1):3-11.

Publications and Presentations about STEM in 2013

Hu K, Thoens C, Bianco S, Edlund S, Davis M, Douglas J, Kaufman JH. "The effect of antibody-dependent enhancement, cross immunity, and vector population on the dynamics of dengue fever." Journal of Theoretical Biology, 319:62–74, 21 Feb 2013, doi:10.1016/j.jtbi.2012.11.021

Hu K, Thoens C, Bianco S, Edlund S, Davis M, Douglas J, Kaufman JH. "Modeling the dynamics of dengue fever." Proceedings of SBP 2013, the International Conference on Social Computing, Behavioral-Cultural Modeling and Prediction, LNCS 7812, pp. 486-494, April 2013, Washington DC.

Falenski A, Filter M, Thoens C, Weiser AA, Wigger JF, Davis M, Douglas JV, Edlund S, Hu K, Kaufman JH, Appel B, Kaesbohrer A. "A generic open-source software framework supporting scenario simulations in bioterrorist crises" Biosecurity and Bioterrorism 11 (SUPPL. 1):S134-S145, 2013. [4]

Publications and Presentations about STEM in 2012

Edlund S, Davis M, Douglas JV, Kershenbaum A, Waraporn N, Lessler J, Kaufman JH. "A global model of malaria climate sensitivity: comparing malaria response to historic climate data based on simulation and officially reported malaria incidence." Malaria Journal 2012, 11:331 doi:10.1186/1475-2875-11-331.

Three presentations document the ongoing collaboration between IBM Research Division, Almaden Research Center, San Jose, CA, and the Federal Institute for Risk Assessment, Department for Biological Safety, Germany.

• Kaufman JH, Davis M, Douglas JV, Edlund S, Hu K, Filter M, Wigger J-F, Thoens C, Weiser AA, Kaesbohrer A, Appel B. "The SpatioTemporal Epidemiological Modeler: an open source framework for modeling food-borne disease." ISVEE 13, Building Bridges, Crossing Borders, the annual meeting of the International Society for Veterinary Epidemiology and Economics, Masstricht, the Netherlands, August 20-24, 2012.

• Falenski A, Thoens C, Filter M, Kaesbohrer A, Appel B, Kaufman JH, Edlund S, Davis M, Douglas JV, Hu K. "A community resource for spatial, temporal and food chain epidemiological modelling to assess risks in bio-terroristic or agro-terroristic crisis situations." ISVEE 13, Building Bridges, Crossing Borders, the annual meeting of the International Society for Veterinary Epidemiology and Economics, Masstricht, the Netherlands, August 20-24, 2012.

• Falenski A, Thoens C, Filter M, Kaesbohrer A, Kaufman J, Edlund S, Davis M, Douglas J, Hu K, Appel B. "An open-source community resource for epidemiological modelling in bioterroristic or agroterroristic crisis situations." Future Security 2012, Bonn, Germany, September 4-6, 2012. 7th meeting on this topic sponsored by the Fraunhofer Institute for Communication, Information Process and Ergonomics (FKE).

• Daniel Doerr, Kun Hu, Sondra Renly, Stefan Edlund, Matthew Davis, Justin Lessler, Matthias Filter, Annemarie Käsbohrer, Bernd Appel and James Kaufman. "Accelerating investigation of food-borne disease outbreaks using pro-active geospatial modeling of food supply chains", First ACM SIGSPATIAL International Workshop on the Use of GIS in public health.

Edlund S, Davis M, Kaufman J. "Extending geospatial data to support epidemiological modeling." ACM SIGSPATIAL GIS'12

Thoens C, Filter M, Kaesbohrer A, Appel B, Kaufman JH, Edlund S, Davis M, Hu K. "The Spatiotemporal Epidemiological Modeler, an Eclipse framework for spatial and temporal modeling of infectious diseases." Eclipse Integrated Development Day 2012, Berlin, Germany, May 30, 2012.

Hu K, Thoens C, Edlund S, Davis M, Kaufman JH. "Disease dynamics in three models of dengue fever." Proceedings of the 2012 Industrial and Systems Engineering Research Conference, Orlando, FL, USA, May 2012.

Hu K, Thoens C, Edlund S, Davis M, Kaufman JH. "STEM: A platform for modeling complex zoonotic disease." Industrial and Systems Engineering Research Conference, Orlando, FL, USA, May 21, 2012.

Kaufman JH, Edlund S, Davis M, Hu K. "The SpatioTemporal Epidemiological Modeler: An open source framework for modeling infectious disease." EE2 (EPIWORK/EPIFOR) 2nd International Workshop, Facing the Challenge of Infectious Diseases, Aosta, Italy, Jan 2012.

Earlier scientific publications and presentations about STEM

Talks Online Featuring a talk at Epidemics 2009

Edlund S, Davis M, Pieper J, Kershenbaum A, Waraporn N, Kaufman J. "A global study of malaria climate susceptibility." Epidemics 3, November 29-December 2, 2011, Boston, MA.

Hu K, Thoens C, Edlund S, Davis M, Kaufman JH, "Modeling Dengue Fever: An extra large data challenge." 5th Extremely Large Databases Conference (XLDB5), SLAC National Accelerator Laboratory, October 2011, Menlo Park, CA.

Edlund S, Kaufman J, Lessler J, Douglas J, Bromberg M, Kaufman Z, Bassal R, Chodick G, Marom R, Shalev V, Mesika Y, Ram R, Leventhal A. 2011. "Comparing three basic models for seasonal influenza." Epidemics, August 2011, 3(3):135-142. doi:10.1016/j.epidem.2011.04.002 [5]

Ahued J, Morales J, Renly S, Edlund S, Kaufman J. "Improving disease surveillance capabilities through a public health information affinity domain." Proceedings of the 1st ACM International Health Informatics Symposium ACM New York, NY, USA 2010. doi 10.1145/1882992.1883079

Edlund S, Davis M, Kaufman J. "The Spatiotemporal Epidemiological Modeler." ACM Digital Library and 1st ACM International Health Informatics Symposium, November 11-2, 2010 Arlington, VA.

Renly S, Kaufman J, Ram R. "Improving disease surveillance capabilities in IHE [health information exchanges]." IADIS International Conference e-Health, June 2009, Algarve, Portugal.

Edlund S et al. "The Spatiotemporal Epidemiological Modeler." Workshop on frontiers in the computational modeling of disease spreading, ICCS 2010, May 31 - June 2, 2010, Amsterdam.

Keil WP. "Spatio-Temporal Epidemiologic Modeler (STEM)." Eclipse DemoCamp 2009, November 2009, Vienna, Austria. [6]

Edlund S, Bromberg M, Chodick G, Douglas J, Ford D, Kaufman Z, Lessler J, Marom R, Mesika Y, Ram R, Shalev V, Kaufman J. 2009. "A spatiotemporal model for influenza." HIC 2009, Frontiers of Health Informatics, Canberra, Australia, August 19-21, 2009. http://www.hisa.org.au/system/files/u2233/hic09-2_StefanEdlund.pdf

Kaufman J, Edlund S, Douglas J. 2009. "Infectious disease modeling: creating a community to respond to biological threats." Statistical Communications in Infectious Diseases, Vol 1, Issue 1, Article 1. The Berkeley Electronic Press. [7]

Kaufman J, Edlund S, Bromberg M, Chodick G, Lessler J, Mesika Yossi, Ram R, Douglas J, Kaufman Z, Levanthal A, Marom R, Shalev V. 2009. "Temporal and spatial effects of lunar calendar holidays on influenza A transmission in Israel." Epidemics 2, Athens, Greece, December 2009.

Zhang H. Modelling Pandemic Influenza Progression Using Spatiotemporal Epidemiological Modeller (STEM). Dissertation, Massachusetts Institute of Technology, 2009.

Hulse CL, Conant JL, Kaufman JH, Edlund SB, Ford DA. “Development and utilization of a spatial and temporal modeling system to investigate disease outbreaks in vermont”, PHIN 2009 [8]

Keil WP. 2009. "The spatiotemporal epidemiological modeller (STEM)." Presentation at epicenter 2009 Conference, Dublin, Ireland, Aug 28, 2009.

Ford DA, Kaufman JH, Mesika Y. "Modeling in space and time: a framework for visualization and collaboration." In D Zeng et al. (eds), Infectious Disease Informatics and Biosurveillance, Integrated Series in Information Systems, 2011, Volume 27, Part 2, 191-206, DOI: 10.1007/978-1-4419-6892-0_9

Lessler J, Kaufman JH, Ford DA, Douglas JV. 2009. "The cost of simplifying air travel when modeling disease spread." PLoS ONE 4(2): e4403. doi: 10.1371/journal.pone.004403.

Kaufman JH, Edlund S, Ford DA. "Spatio-Temporal Epidemiologic Modeler: application in Middle Eastern countries", PHIFP colloquium at U.S. Centers For Disease Control, Atlanta. May 8, 2009.

Kaufman JH, Edlund S, Ford DA, Renly S, Ram R, Mesika Y, et al. "Spatio-Temporal Epidemiologic Modeler: evaluation of 10 years of influenza data from Maccabi Healthcare." Presentation at Israel Centers for Disease Control, Tel Aviv, Israel. April 16, 2009.

Kaufman JH, Conant JL, Ford DA, Kirihata W, Jones B, Douglas JV. "Assessing the accuracy of spatiotemporal epidemiological models." In D Zeng et al. (Eds): BioSecure 2008, LNCS 5354, pp. 143-154, 2008. Also presented at BioSecure 2008, Biosurveillance and Biosecurity Workshop, Raleigh, NC, Dec 2, 2008.

Ford DA, Kaufman JH. 2008. "The spatiotemporal epidemiological modeller (STEM)." Presentation at the Joint Session Homeland/Humanitarian Preparedness for Pandemic Influenza, Washington, DC, Oct 13, 2008.

Kaufman JH, Conant JL, Ford DA, Kirihata W, Douglas JV, Jones BA. 2008 (December). "Assessing the accuracy of spatiotemporal epidemiological models. In D Zeng et al. (eds): BioSecure 2008, LNCS 5354, pp. 143-154.

Kaufman JH, Ford DA, Mesika Y, Lessler J. 2008 (December). Modeling disease spread in space and time: extending and validating an open source tool for public health. Epidemics (EPID2008): First International Conference on Infectious Disease Dynamics. Asilomar, CA, December 1-3, 2008.

Keil WP, Ford DA, Kaufman JH. 2007 (In press), "Eclipse OHF STEM", Eclipse Magazin, S&S Verlag, July 2007

Ford DA, Kaufman JH, Eiron I, "An extensible spatial and temporal epidemiological modeling system," International Journal of Health Geographics 2006, 5:4 http://www.ij-healthgeographics.com/content/5/1/4 (17Jan2006)

Keil WP. 2005. "Eclipse Open Health Framework (OHF)." Presentation at JavaPolis 2005 Conference, Antwerp, Belgium, Dec 12, 2005.