Los Alamos National LaboratoryBiosurveillance Gateway
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Biosurveillance Publications

Recent and past publications and presentations in biosurveillance at the Lab

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Understanding polynomial distributed lag models: truncation lag implications for a mosquito-borne disease risk model in Brazil. Jessica Conrad; Amanda Ziemann; Randall Refeld; Nidhi Parikh; Amir Siraj; Nicholas Generous; Sara Del Valle; Geoffrey Fairchild; Carrie Manore. Proceedings Volume 10986, Algorithms, Technologies, and Applications for Multispectral and Hyperspectral Imagery XXV; 109860N (2019).

Achieving Health Security and Threat Reduction through Sharing Sequence Data. Kenneth Yeh, Jeanne Fair, Helen Cui, Carl Newman, Gavin Braunstein, Gvantsa Chanturia, Sapana Vora, Kendra Chittenden, Ashley Tseng, Corina Monagin and Jacqueline Fletcher. Tropical Medicine and Infectious Disease 2019, 4(2), 78; 

Forecasting Zoonotic Infectious Disease Response to Climate Change: Mosquito Vectors and a Changing Environment Andrew W. Bartlow, Carrie Manore, Chonggang Xu, Kimberly A. Kaufeld, Sara Del Valle, Amanda Ziemann, Geoffrey Fairchild, and Jeanne M. Fair. Vet. Sci. 2019, 6 (2), 40

Analytics for Investigation of Disease Outbreaks (AIDO) – A web-based analytic facilitating situational awareness in unfolding disease outbreaks Velappan, Nileena ; Daughton, Ashlynn Rae ; Fairchild, Geoffrey ; Rosenberger, William Earl ; Generous, Nicholas ; Chitanvis, Maneesha Elizabeth ; Altherr, Forest Michael ; Castro, Lauren A. ; Priedhorsky, Reid ; Abeyta, Esteban Luis ; Naranjo, Leslie A. ; Hollander, Attelia Dawn ; Vuyisich, Grace ; Lillo, Antonietta Maria ; Cloyd, Emily Kathryn ; Vaidya, Ashvini Rajendra; Deshpande, Alina. JMIR Public Health and Surveillance. February 25, 2019

Understanding the Significance of Biochemistry in the Storage, Handling, Purification, and Sampling of Amphiphilic Mycolactone Jessica Z. Kubicek-Sutherland, Dung M. Vu, Aaron S. Anderson, Timothy C. Sanchez, Paul J. Converse,  >Ricardo Mart-Arbona, Eric L. Nuermberger, Basil I. Swanson, and Harshini Mukundan. Toxins2019, 11(4), 202

Direct detection of bacteremia by exploiting host-pathogen interactions of lipoteichoic acid and lipopolysaccharideJessica Z. Kubicek-Sutherland, Dung M. Vu, Aneesa Noormohamed, Heather M. Mendez, Loreen R. Stromberg, Christine A. Pedersen, Astrid C. Hengartner, Katja E. Klosterman, Haley A. Bridgewater, Vincent Otieno, Qiuying Cheng, Samuel B. Anyona, Collins Ouma, Evans Raballah, Douglas J. Perkins, Benjamin H. McMahon, Harshini Mukundan. Scientific Reports volume 9, Article 6203, 2019



Epidemiological Data Challenges: Planning for a More Robust Future Through Data Standards Fairchild, Geoffrey ; Tasseff, Byron ; Khalsa, Hari ; Generous, Nicholas ; Daughton, Ashlynn R. ; Velappan, Nileena ; Priedhorsky, Reid ; Deshpande, Alina. Frontiers in Public Health, 11/23/2018, Vol.6

Summary results of the 2014-2015 DARPA Chikungunya challenge Del Valle, Sara Y ; Mcmahon, Benjamin H ; Asher, Jason ; Hatchett, Richard ; Lega, Joceline C ; Brown, Heidi E ; Leany, Mark E ; Pantazis, Yannis ; Roberts, David J ; Moore, Sean ; Peterson, A Townsend ; Escobar, Luis E ; Qiao, Huijie ; Hengartner, Nicholas W ; Mukundan, Harshini. BMC infectious diseases, 30 May 2018, Vol.18(1), pp.245



Measuring Global Disease with Wikipedia: Success, Failure, and a Research Agenda Priedhorsky, Reid ; Osthus, Dave ; Daughton, Ashlynn ; Moran, Kelly ; Generous, Nicholas ; Fairchild, Geoffrey ; Deshpande, Alina ; Del Valle, Sara. Proceedings of the 2017 ACM Conference on computer supported cooperative work and social computing, 25 February 2017, pp.1812-1834

An extensible framework and database of infectious disease for biosurveillance Ashlynn R. Daughton ; Reid Priedhorsky ; Geoffrey Fairchild ; Nicholas Generous ; Andrea Hengartner ; Esteban Abeyta ; Nileena Velappan ; Antonietta Lillo ; Karen Stark ; Alina Deshpande. BMC Infectious Diseases, 01 August 2017, Vol.17(1), pp.1-8  

An approach to and web-based tool for infectious disease outbreak intervention analysis Ashlynn R. Daughton ; Nicholas Generous ; Reid Priedhorsky ; Alina Deshpande. Scientific Reports, 2017, Vol.7  

Detection of Lipomannan in Cattle Infected with Bovine Tuberculosis Vu, Dung M. ; Sakamuri, Rama M. ; Waters, W. Ray ; Swanson, Basil I. ; Mukundan, Harshini. Analytical Sciences, 2017, Vol.33(4), pp.457-460 




The Biosurveillance Analytics Resource Directory (BARD): Facilitating the Use of Epidemiological Models for Infectious Disease Surveillance, Margevicius KJ, Generous N, Abeyta E, Althouse B, Burkom H, Castro L, Daughton A, Del Valle S, Fairchild G, Hyman J, Kiang R, Morse AP, Pancerella CM, Pullum L, Ramanathan A, Schlegelmilch J, Scott A, Taylor-McCabe KJ, Vespignani A,  Deshpande A

SPIDR-WEB: an NGS biotechnology platform for diagnostic and transcriptomic applications, Hatch A, Chain P, Gans J, Vuyisich M

Surveillance For Emerging Diseases With Multiplexed Point-Of-Care Diagnostics, Deshpande A, McMahon B, Daughton A, Abeyta E, Hodge D, Anderson K, Pillai S

Culture-Independent Diagnostics For Health Security, Doggett N, Mukundan H, Lefkowitz E, Slezak T, Chain P, Morse S, Anderson K, Hodge D, Pillai S

Reduced Parasite Burden in Children with Falciparum Malaria and Bacteremia Coinfections: Role of Mediators of Inflammation, Davenport G,  Hittner J, Otieno V, Karim Z, Mukundan H, Fenimore P, Hengartner N, McMahon B, Kempaiah P, Ong'echa J, Perkins D

Development of 11-Plex MOL-PCR Assay for the Rapid Screening of Samples for Shiga Toxin-Producing Escherichia coli, Woods T,  Mendez H, Ortega S, Shi X,  Marx D, Bai J, Moxley R, Nagaraja TG, Graves S, Deshpande A

Novel use of flu surveillance data: Evaluating potential of sentinel populations for early detection of influenza outbreaks, Daughton A, Velappan N, Abeyta E, Priedhorsky R, Deshpande A

Epidemic Forecasting is Messier Than Weather Forecasting: The Role of Human Behavior and Internet Data Streams in Epidemic Forecast, Moran K R, Fairchild G, Generous N, Hickmann KS, Osthus D, Priedhorsky R, Hyman JM, and Del Valle SY



Targeting Bacterial Persistence to Develop Therapeutics Against Infectious Disease, Hong-Geller E,  Micheva-Viteva S

Development of Forensic Assay Signatures for Ebola viruses, Song J, Doggett N, Wren M, Burr T, Fenimore PW, Hatcher EL, Bruno WJ, Li Po-E, Stubben C, Wolinsky M

Constructing Rigorous and Broad Biosurveillance Networks for Detecting Emerging Zoonotic OutbreaksBrown M, Moore L, McMahon B, Powell D, LaBute M, Hyman JM, Rivas A, Jankowski M, Berendzen J, Loeppky J, Manore C, Fair J

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures, Freitas TAK, Li Po-E, Scholz MB, Chain, PSG

Mathematical Modeling of Hepatitis C Prevalence Reduction with Antiviral Treatment Scale-Up in Persons Who Inject Drugs in Metropolitan Chicago, Echevarria D, Gutfraind A, Boodram B, Major M, Del Valle S, Cotler SJ, Dahari H

Enhancing disease surveillance with novel data streams: challenges and opportunities, Althouse BM, Scarpino S, Meyers LA, Ayers JW, Bargsten M, Baumbach J, Brownstein JS, Castro L, Clapham H, Cummings DAT, Del Valle S, Eubank S, Fairchild G, Finelli L, Generous N, George D, Harper DR, Hebert-Dufresne L, Johansson MA, Konty K, Lipsitch M, Milinovich G, Miller JD, Nsoesie EO, Olson DR, Paul M, Polgreen PM, Priedhorsky R, Read JM, Rodriguez-Barraquer I, Smith DJ, Stefansen C, Swerdlow DL, Thompson D, Vespignani A, Wesolowski A



Advancing a Framework to Enable Characterization and Evaluation of Data Streams Useful for Biosurveillance, Margevicius KJ, Generous N, Taylor-McCabe KJ, Brown M, Daniel WB, Castro L, Hengartner A, Deshpande A

Inferring the Origin Locations of Tweets with Quantitative Confidence, Priedhorsky R, Culotta A, Del Valle AY

Selecting Essential Information for Biosurveillance-A Multi-Criteria Decision Analysis, Generous N, Margevicius KJ, Taylor-McCabe KJ, Brown M, Daniel WB, Castro L, Hengartner A, Deshpande A

Global Disease Monitoring and Forecasting with Wikipedia, Generous N, Fairchild F, Deshpande A, Del Valle S, Priedhorsky R

Detection of the urban release of Bacillus anthracis simulant by air sampling, Garza A, Van Cuyk S, Brown M, Omberg K

The Surveillance Window - An Evaluation Method for Identifying Data Streams for Early Warning and Detection of Infectious Disease Outbreaks, Taylor-McCabe KJ, Castro LA, Generous N, Margevicius KJ, Brown M, Deshpande A

Forecasting the 2013-2014 Influenza Season using Wikipedia (Pre-print), Hickmann KS, Fairchild G, Priedhorsky R, Generous N, Hyman JM, Deshpande A, Del Valle S

Comparing Dengue and Chikungunya Emergence and Endemic Transmission in A. aeypti and A. albopictus, Manore CA, HIckmann KS, Xu S, Weaving HJ, Hyman JM

A Network-Patch Methodology for Adapting Agent-Based Models for Directly Transmitting Disease to Mosquite-Borne Disease (Pre-print), Manore CA, Hickmann KS, Hyman JM, Foppa IM, Davis JK, Wesson DM, Mores CN

Understanding the Impact of Face Mask Usage Through Epidemic Simulation of Large Social Networks, Mniszewski SM, Del Valle SY, Priedhorsky R, Hyman JM, Hickmann KS

Crowdsourcing rare events: Using curiosity to draw participants into science and early warning systems, Tapia AH, LaLone N, MacDonald E, Priedhorsky R, Hall M

Quantifying the impact of decay in bed-net efficacy on malaria transmission, Ngonghala CN, Del Valle SY, Zhao R, Mohammed-Awel J

Detection of stealthy small amphiphilic biomarkers, Sakamuri RM, Capek P, Dickerson TJ, Barry CE, Mukundan H, Swanson BI


An epidemiological model of spatial coupling for trips longer than the infectious periodDaniel WB, Hengartner NW, Rivera MK, Powell DR, McPherson TN

Optimizing human activity patterns using global sensitivity analysisFairchild G, Hickmann KS, Mniszewski SM, Del Valle SY, Hyman JM

How many suffice? A computational framework for sizing sentinel surveillance networksFairchild G, Polgreen PM, Foster E, Rushton G, Segre AM

Detecting laboratory DNA contamination using polyester-rayon wipes: A method validation studyRemillard M, Taylor LK, Layshock J, Van Cuyk S, Omberg K

A Systematic Evaluation of Traditional and Non-Traditional Data Streams for Integrated BiosurveillanceDeshpande A, Brown M, Castro LA, Daniel WB, Generous EN, Hengartner A, Longo JF, Margevicius KJ, McCabe KJ, Parliman ZA

Mathematical models of contact patterns between age groups for predicting the spread of infectious diseasesDel Valle SY, Hyman JM, Chitnis N

The impact of bed-net use on malaria prevalenceAgusto FB, Del Valle SY, Blayneh KW, Ngonghala CN, Goncalves MJ, Nianpeng L, Ruijun Z, Gong H

Modeling the impact of behavior changes on the spread of pandemic influenzaDel Valle SY, Mniszewski SM, Hyman JM

Novel optical strategies for biodetectionSakamuri RM, Wolfenden MS, Anderson AS, Swanson BI, Schmidt JS, Mukundan H

Integration of hyperspectral imagery and biosensors for biological and chemical facility classificationMunsky B, Yeager JD, Sellars S, Mukundan H, Nadler BR


Developing Tools to Combat Emerging Infectious DiseasesMukundan H

Primary stroke centers should be located using maximal coverage models for optimal accessLeira EC, Fairchild G, Segre AM, Rushton G, Froehler MT, Polgreen PM

Detection and tracking of a novel genetically tagged biological simulant in the environmentEmmanuel P, Edmonds J, Sutton T, Ginley W, Keiser C, Doherty R, Kim M, Kragl J, Buckley P, Bailey A, Rastogi V, Paikoff S, Leppert S, Strawbridge J, INsalac J, Ziernski M, Harvey S, Hirsch E, Bieschke KM, Harris CL, Omberg K, Van Cuyk, Gibbons SS

Reaerosolization of Bacillus spp. in Outdoor Environments: A Review of the Experimental LiteratureLayshock J, Pearson B, Crockett K, Brown M, Van Cuyk S, Daniel WB, Omberg, K

Transport of Bacillus thuringiensis var. kurstaki from an outdoor release into buildings: Pathways of infiltration and a rapid method to identify contaminated buildingsVan Cuyk S, Deshpande A, Hollander A, Duvall N, Ticknor L, Gallegos-Graves L, Omberg K

Economic analysis of the use of facemasks during the pandemicTracht SM, Del Valle SY, Edwards BK

Mixing in age-structured population models of infectious diseasesGlasser J, Feng Z, Moylan A, Del Valle SY, Castillo-Chavez C

Rapid phylogenetic and functional classification of short genomic fragments with signature peptidesBerendzen J, Bruno WJ, Cohn JD, Hengartner NW, Kuske CR, McMahon BH, Wolinksy MA, and Xie G

Using Phage and Yeast Display to Select Hundreds of Monoclonal Antibodies: Application to Antigen 85, a Tuberculosis BiomarkerFerrara F, Naranjo LA, Kumar S, Gaiotto T, Swanson BI, Mukundan H, Bradbury AS

Waveguide Biosensors for Medical DiagnosticsMukundan H


Quantitative Multiplex Detection of Pathogen Biomarkers on Multichannel WaveguidesMukundan H, Xie H, Price D, Kubicek-Sutherland J, Anderson AS, Martinez JS, Grace WK, Hartman N, Swanson BI

Can we reduce the spread of influenza in schools with face masks?Del Valle SY, Tellier R, Settles GS, Tang JW

Mathematical modeling of the effectiveness of facemasks in reducing the spread of novel influenza A (H1N1)Tracht SM, Del Valle SY, Hyman JM


Waveguide-based Sensors for Pathogen DetectionMukundan HAnderson AS, Grace WK, Grace K, Hartman N, Martinez JS, Swanson BI

Photostable Multiplex Analyte Detection on Single Mode Planar Optical WaveguidesMukundan HXie H, Anderson AS, Grace WK, Price D, Swanson BI

Robust Sensing Films for Pathogen Detection and Medical DiagnosticsAnderson AS, Dattelbaum A, Mukundan H, Grace WK, Swanson BI


Detection of Intact Influenza Viruses using Biotinylated Biantennary S-SialosidesKale R, Mukundan H, Price D, Foster-Harris J, Lewallen DM, Swanson BI, Schmidt JG, Iyer SS

Pandemic simulation of antivirals and school closures: buying time until strain specific vaccine is availableMniszewski SM, Del Valle SY, Stroud PD, Riese JM, Sydoriak SJ

EpiSimS simulation of a multi-component strategy for pandemic influenzaMniszewski SM, Del Valle SY, Stroud PD, Riese JM, Sydoriak SJ


Estimating the reproduction number from the initial phase of the Spanish Flu pandemic waves in Geneva, Switzerland, Chowell G, Ammon CE, Hengartner NW, Hyman JM

Spatial dynamics of pandemic influenza in a massive artificial societyStroud PD, Del Valle SY, Sydoriak SJ, Riese JM, Mniszewski SM

Mixing Patterns between age groups in social networksDel Valle SY, Hyman JM, Hethcote HW, Eubank SG


Critical response to post-outbreak vaccination against foot-and-mouth disease, Chowell G, Rivas AL, Hengartner NW, Hyman JM, Castillo-Chavez C

The role of spatial mixing in the spread of foot-and-mouth diseaseChowell G, Rivas AL, Hengartner NW, Hyman JM, Castillo-Chavez C

Transmission dynamics of the great influenza pandemic of 1918 in Geneva, Switzerland: Assessing the effects of hypothetical interventions, Chowell G, Ammon CE, Hengartner NW, Hyman JM

Accounting for Seasonal Patterns in Syndromic Surveillance Data for Outbreak DetectionBurr T, Graves T, Klamann R, Michalak S, Picard R, Hengartner NW

EpiSimS Los Angeles Case Study, Del Valle SY, Kubicek D, Mniszewski SM, Riese JM, Romero PR, Smith JP, Stroud PD, Sydoriak SJ

Mathematical applications associated with the deliberate release of infectious agents, Chowell G, Cintroon-Arias A, Del Valle SY, Sanchez G, Sung B, Hyman JM, Hethcote HW, Castillo-Chavez C

EpiSimS: epidemic simulation system, Del Valle SY, Stroud PD, Smith JP, Mniszewski SM, Riese JM, Sydoriak SJ, Kubicek DA


Effects of behavioral changes in a smallpox attack model, Del Valle SY, Hethcote H, Hyman JM, Castillo-Chavez C


The basic reproductive number and the effects on public health measures: the cases of Congo and UgandaChowell G, Hengartner NW, Castillo-Chavez C, Fenimore PW, Hyman JM