Chao DL, Arzika AM, Abdou A, Maliki R, Karamba A, Galo N, Beidi D, Harouna N, Abarchi M, Root E, Mishra A, Lebas E, Arnold BF, Oldenburg CE, Keenan JD, Lietman TM, O'Brien KS. Distance to Health Centers and Effectiveness of Azithromycin Mass Administration for Children in Niger: A Secondary Analysis of the MORDOR Cluster Randomized Trial. JAMA Netw Open 2023 Dec 1;6(12):e2346840.
doi: 10.1001/jamanetworkopen.2023.46840.

O'Brien ML, Zimmermann M, Eitmann L, Chao DL, Proctor JL. Contraceptive adoption and changes in empowerment in Kenya, Nigeria, and Senegal. Studies in Family Planning 2023 Dec;54(4):609-623.
doi: 10.1111/sifp.12250

Chao DL, Oron AP, Chabot-Couture G, Sopekan A, Nnebe-Agumadu U, Bates I, Piel FB, Nnodu OE. Contribution of malaria and sickle cell disease to anaemia among children aged 6-59 months in Nigeria: a cross-sectional study using data from the 2018 Demographic and Health Survey. BMJ Open 2022;12:e063369. 2022.
doi: 10.1136/bmjopen-2022-063369
medRxiv version: 10.1101/2022.03.23.22272825

Nelson EJ, Khan AI, Keita AM, Brintz BJ, Keita Y, Sanogo D, Islam MT, Khan ZH, Rashid MM, Nasrin D, Watt MH, Ahmed SM, Haaland B, Pavia AT, Levine AC, Chao DL, Kotloff KL, Qadri F, Sow SO, Leung DT. Improving Antibiotic Stewardship for Diarrheal Disease With Probability-Based Electronic Clinical Decision Support: A Randomized Crossover Trial. JAMA Pediatrics. 176(10):973-979. 2022.
doi: 10.1001/jamapediatrics.2022.2535

Chao DL, Cho V, Izzo AS, Proctor JL, Zimmermann M. Quantifying behavior change during the first year of the COVID-19 pandemic in the United States. medRxiv. 2022.
doi: 10.1101/2022.01.10.22268799

Selvaraj P, Wagner BG, Chao DL, Jackson ML, Breugelmans JG, Jackson N, Chang ST. Rural prioritization may increase the impact of COVID-19 vaccines in a representative COVAX AMC country setting due to ongoing internal migration: A modeling study. PLOS Global Public Health. 2(1): e0000053. 2022.
doi: 10.1371/journal.pgph.0000053
medrxiv version: 10.1101/2021.06.18.21259164

Chao DL. Mathematical modeling of endemic cholera transmission. Journal of Infectious Diseases. 224(suppl 7):S738-S741. 2021.
doi: 10.1093/infdis/jiab472

Levin R, Chao DL, Wenger EA, Proctor JL. Insights into population behavior during the COVID-19 pandemic from cell phone mobility data and manifold learning. Nature Computational Science. 1(9):588-597. 2021.
doi: 10.1038/s43588-021-00125-9
medRxiv version: 10.1101/2020.10.31.20223776

Nnodu OE, Oron AP, Sopekan A, Akaba GO, Piel FB, Chao DL. Child mortality from sickle cell disease in Nigeria: a model-estimated, population-level analysis of data from the 2018 Demographic and Health Survey. Lancet Haematology. 8:e723-31. 2021.
doi: 10.1016/S2352-3026(21)00216-7
SSRN version: 10.2139/ssrn.3825539

Brintz BJ, Haaland B, Howard J, Chao DL, Proctor JL, Khan AI, Ahmed SM, Keegan, LT, Greene T, Keita AM, Kotloff KL, Platts-Mills, JA, Nelson EJ, Levine AC, Pavia AT, Leung DT. A modular approach to integrating multiple data sources into real-time clinical prediction for pediatric diarrhea. eLife. 10:e63009. 2021.
doi: 10.7554/eLife.63009
medRxiv version: 10.1101/2020.10.26.20210385
eLife press release

Nelson EJ, Grembi JA, Chao DL, Andrews JR, Alexandrova L, Rodriguez PH, Ramachandran VV, Sayeed MA, Wamala JF, Debes AK, Sack DA, Hryckowian AJ, Haque F, Khatun S, Rahman M, Chien A, Spormann AM, Schoolnik GK. Gold-standard diagnostics are tarnished by lytic bacteriophage. Journal of Clinical Microbiology. 58(9):e00412-20. 2020.
doi: 10.1128/JCM.00412-20
bioRxiv version: 10.1101/2020.01.30.926832v1

Lee EC, Chao DL, Lemaitre JC, Matrajt L, Pasetto D, Perez-Saez J, Finger F, Rinaldo A, Sugimoto JD, Halloran ME, Longini IM Jr, Ternier R, Vissieres K, Azman AS, Lessler J, Ivers LC. Achieving coordinated national immunity and cholera elimination in Haiti through vaccination. Lancet Glob Health. 8(8):e1081-1089. 2020.
doi: 10.1016/S2214-109X(20)30310-7
medRxiv version: 10.1101/19011072

Oron AP, Chao DL, Ezeanolue EE, Ezenwa LN, Piel FB, Ojogun OT, Uyoga S, Williams TN, Nnodu OE. Caring for Africa’s sickle cell children: will we rise to the challenge? BMC Medicine 18(1):92. 2020.
doi: 10.1186/s12916-020-01557-2

Chao DL, Oron AP, Srikrishna D, Famulare M. Modeling layered non-pharmaceutical interventions against SARS-CoV-2 in the United States with Corvid. medRxiv. 2020.
doi: 10.1101/2020.04.08.20058487

Chao DL, Roose A, Roh M, Kotloff KL, Proctor JL. The seasonality of diarrheal pathogens: A retrospective study of seven sites over three years. PLoS Negl Trop Dis. 13(8):e0007211. 2019.
doi: 10.1371/journal.pntd.0007211
bioRxiv version: 10.1101/541581

Khan AI, Levin A, Chao DL, DeRoeck D, Dimitrov DT, Khan JAM, Islam MS, Ali M, Islam MT, Sarker AR, Clemens JD, Qadri F. The impact and cost-effectiveness of controlling cholera through the use of oral cholera vaccines in urban Bangladesh: a disease modeling and economic analysis. PLoS Negl Trop Dis. 12(10):e0006652. 2018.
doi: 10.1371/journal.pntd.0006652

Fong Y, Halloran ME, Park JK, Marks F, Clemens JD, Chao DL. Efficacy of a bivalent killed whole-cell cholera vaccine over five years: A re-analysis of a cluster-randomized trial. BMC Inf Dis. 18:84. 2018.
doi: 10.1186/s12879-018-2981-4

Pastore y Piontti A, Zhang Q, Gomes MFC, Rossi L, Poletto C, Colizza V, Chao DL, Longini IM, Halloran ME, Vespignani A. Real-time assessment of the international spreading risk associated with the 2014 West African Ebola outbreak. In: Chowell G, Hyman, JM, editors. Mathematical and Statistical Modeling for Emerging and Re-emerging Infectious Diseases. Berlin: Springer-Verlag. p. 39-56. 2016.
doi: 10.1007/978-3-319-40413-4_4

Hladish TJ, Pearson CAB, Chao DL, Rojas DP, Recchia GL, Gomez Dantes H, Halloran ME, Pulliam JRC, Longini IM. Projected impact of dengue vaccination in Yucatán, Mexico. PLoS Negl Trop Dis. 10(5): e0004661. 2016.
doi: 10.1371/journal.pntd.0004661

Chao DL, Dimitrov DT. Seasonality and the effectiveness of mass vaccination. Mathematical Biosciences and Engineering. 13(2):249-259. 2016.
doi: 10.3934/mbe.2015001

Troeger C, Gaudart J, Truillet R, Sallah K, Chao DL, Piarroux R. Cholera outbreak in Grande Comore: 1998-1999. The American Journal of Tropical Medicine and Hygiene. 94(1):76-81. 2016.
doi: 10.4269/ajtmh.15-0397

Chao DL, Park JK, Marks F, Ochiai RL, Longini IM, Halloran ME. The contribution of neighbours to an individual's risk of typhoid outcome. Epidemiology and Infection. 143(16):3520--3527. 2015.
doi: 10.1017/S0950268815000692

Merler S, Ajelli M, Fumanelli L, Gomes MFC, Pastore y Pontti A, Rossi L, Chao DL, Longini IM, Halloran ME, Vespignani A. Spatio-temporal spread of the Ebola 2014 outbreak in Liberia and the effectiveness of non-pharmaceutical interventions: a computational modelling analysis. Lancet Infectious Diseases. 15(2):204-211. 2015.
doi: 10.1016/S1473-3099(14)71074-6
Aspen Institute Italia Award

Dimitrov DT, Troeger C, Halloran ME, Longini IM Jr., Chao DL. Comparative effectiveness of different strategies of oral cholera vaccination in Bangladesh: A modeling study. PLoS Negl Trop Dis. 8(12):e3343. 2014.
doi:10.1371/journal.pntd.0003343

Troeger C, Sack DA, Chao DL. Evaluation of targeted mass cholera vaccination strategies in Bangladesh: A demonstration of a new cost-effectiveness calculator. The American Journal of Tropical Medicine and Hygiene. 91(6):1181-1189. 2014.
doi:10.4269/ajtmh.14-0159

Poletto C, Gomes MFC, Pastore y Piontti A, Rossi L, Bioglio L, Chao DL, Longini IM, Halloran ME, Colizza V, Vespignani A. Assessing the impact of travel restrictions on international spread of the 2014 West African Ebola epidemic. Eurosurveillance 19(42):Article 2. 2014.
doi:10.2807/1560-7917.ES2014.19.42.20936

Gomes MFC, Pastore y Piontti A, Rossi L, Chao DL, Longini IM, Halloran ME, Vespignani A. Assessing the international spreading risk associated with the 2014 West African Ebola Outbreak. PloS Currents: Outbreaks. Version 1. 2014.

Gog JR, Ballesteros S, Viboud C, Simonsen L, Bjornstad ON, Shaman J, Chao DL, Khan F, Grenfell BT. Spatial transmission of 2009 pandemic influenza in the US. PLoS Comput Biol. 10(6):e1003635. 2014.
doi:10.1371/journal.pcbi.1003635
University of Cambridge press release

Chao DL, Longini IM Jr., Morris JG Jr. Modeling cholera outbreaks. In G. Balakrish Nair and Yoshi Takeda, editors, Cholera Outbreaks. Current Topics in Microbiology and Immunology. Berlin: Springer-Verlag. vol 379:195--209. 2014.
doi:10.1007/82_2013_307

Chao DL, Longini IM Jr., Halloran ME. The effects of vector movement and distribution in a mathematical model of dengue transmission. PLoS ONE. 8(10):e76044. 2013.
doi:10.1371/journal.pone.0076044
FHCRC publication spotlight

Chao DL. Modelling the global transmission of antiviral-resistant influenza viruses. Influenza and Other Respiratory Viruses. 7(Suppl 1):58-62. 2013.
doi:10.1111/irv.12043

Willem L, Van Kerckhove K, Chao DL, Hens N, Beutels P. A nice day for an infection? Weather conditions and social contact patterns relevant to influenza transmission. PLoS ONE. 7(11): e48695. 2012.
doi:10.1371/journal.pone.0048695

Chao DL, Halstead SB, Halloran ME, Longini IM Jr. Controlling dengue with vaccines in Thailand. PLoS Negl Trop Dis. 6(10):e1876. 2012.
doi:10.1371/journal.pntd.0001876

Chao DL, Bloom JD, Kochin BF, Antia R, Longini IM Jr. The global spread of drug-resistant influenza. Journal of the Royal Society Interface. 9(69):648-56. 2012.
doi:10.1098/rsif.2011.0427

Kenah E, Chao DL, Matrajt L, Halloran ME, Longini IM Jr. The global transmission and control of influenza. PLoS ONE. 6(5): e19515. 2011.
doi:10.1371/journal.pone.0019515

Chao DL, Matrajt L, Basta NE, Sugimoto JD, Dean B, Bagwell DA, Oiulfstad B, Halloran ME, Longini IM Jr. Planning for the control of pandemic influenza H1N1 in Los Angeles County and the United States. American Journal of Epidemiology. 173(10):1121--30. 2011.
doi:10.1093/aje/kwq497
[impact factor=5.589 (2009)]

Chao DL, Halloran ME, Longini IM Jr. Vaccination strategies for epidemic cholera in Haiti with implications for the developing world. Proceedings of the National Academy of Sciences. 108(17):7081-5. 2011.
doi:10.1073/pnas.1102149108

Wang P, Chao DL, and Hsu L. Learning oncogenic pathways from binary genomic instability data. Biometrics. 67(1):164-73. 2011.
doi:10.1111/j.1541-0420.2010.01417.x

Chao DL, Halloran ME, Longini IM Jr. School opening dates predict pandemic influenza A (H1N1) epidemics in the United States. The Journal of Infectious Diseases. 202(6):877-880. 2010.
doi:10.1086/655810
2009 school opening data available at: https://github.com/dlchao/schoolopenings-2009

Chao DL, Halloran ME, Obenchain V, Longini IM Jr. FluTE, a publicly available stochastic influenza epidemic simulation model. PLoS Computational Biology, 6(1): e1000656. 2010.
doi:10.1371/journal.pcbi.1000656

Yang Y, Sugimoto JD, Halloran ME, Basta NE, Chao DL, Matrajt L, Potter G, Kenah E, Longini IM Jr. Transmissibility and control of pandemic influenza A (H1N1) virus. Science, 326(5953): 729-733. 2009.
doi: 10.1126/science.1177373

Basta NE, Chao DL, Halloran ME, Matrajt L, Longini IM Jr. Strategies for pandemic and seasonal influenza vaccination of school children in the US. American Journal of Epidemiology, 170(6):679-686. 2009.
doi: 10.1093/aje/kwp237
[impact factor=5.589 (2009)]

Paulson TG, Maley CC, Li X, Li H, Sanchez CA, Chao DL, Odze RD, Vaughan TL, Blount PL, Reid BJ. Chromosomal instability and copy number alterations in Barrett's esophagus and esophageal adenocarcinoma. Clinical Cancer Research, 15(10):3305-14. 2009.
doi: 10.1158/1078-0432.CCR-08-2494
[impact factor=6.177 (2006)]

Chao DL, Sanchez CA, Galipeau PC, Blount PL, Paulson TG, Cowan DS, Ayub K, Odze RD, Rabinovitch PS, Reid BJ. Cell proliferation, cell cycle abnormalities, and cancer outcome in patients with Barrett's esophagus: A long-term prospective study. Clinical Cancer Research, 14(21):6988-95. 2008.
doi: 10.1158/1078-0432.CCR-07-5063
[impact factor=6.177 (2006)]

Chao DL, Eck JT, Brash DE, Maley CC, Luebeck EG. Pre-neoplastic lesion growth driven by the death of adjacent normal stem cells. Proceedings of the National Academy of Sciences, 105(39):15034-9. 2008.
doi: 10.1073/pnas.0802211105
[impact factor=9.598 (2007)]
(BibTex)
Faculty of 1000 Medicine evaluation
Nature Reviews Cancer note

Galipeau PC, Chao DL, Li X, Arnaudo JD, Kissel HD, Sanchez CA, Reid BJ. Barrett's esophagus and esophageal adenocarcinoma epigenetic biomarker discovery using Infinium methylation. iCommunity Newsletter, Illumina, Inc., San Diego, CA, 2008.
(PDF)

Ribeiro RM, Perelson AS, Chao DL, Davenport MP. HIV epidemiology and the impact of nonsterilizing vaccines. In R. P. Mondaini and Rui Dilão, editors, Proceedings of BIOMAT 2006: International Symposium on Mathematical and Computational Biology. pp 69-88. World Scientific Publishing, Singapore, 2007.

Chao DL, Maley CC, X. Wu, Farrow DC, Galipeau PC, Sanchez CA, Paulson TG, Rabinovitch PS, Reid BJ, Spitz MR, Vaughan TL. Mutagen sensitivity and neoplastic progression in patients with Barrett's esophagus: A prospective study. Cancer Epidemiology Biomarkers & Prevention, 15(10):1935-40. 2006.
doi: 10.1158/1055-9965.EPI-06-0492
[impact factor=4.289 (2006)]
(PDF, BibTex)

Chao DL, Davenport MP, Forrest S, Perelson AS. The effects of thymic selection on the range of T cell cross-reactivity. European Journal of Immunology, 35(12): 3452-9. 2005.
NIHMSID: NIHMS18092
doi: 10.1002/eji.200535098
[impact factor=4.876 (2005)]
(PDF, BibTex)

Chao DL, J. Balthrop, Forrest S. Adaptive Radio: Achieving consensus using negative preferences. In K. Schmidt, M. Pendergast, M. Ackerman, and G. Mark, editors, Group '05: Proceedings of the 2005 International ACM SIGGROUP Conference on Supporting Group Work. pp 120-3. ACM Press, New York, 2005.
doi: 10.1145/1099203.1099224
(PDF, BibTex)

Davenport MP, Ribeiro RM, Chao DL, Perelson AS. Predicting the impact of a nonsterilizing vaccine against human immunodeficiency virus. Journal of Virology, 78(20):11340-51. 2004.
doi: 10.1128/JVI.78.20.11340-11351.2004
[impact factor=5.341 (2006)]
(PDF, BibTex)

Chao DL. Computer games as interfaces. interactions, 11(5): 71-2. 2004.
doi: 10.1145/1015530.1015567
(PDF, BibTex)

Chao DL. Modeling the cytotoxic T cell response. Ph.D. dissertation. The University of New Mexico Department of Computer Science, Albuquerque, NM, 2004.
(1-sided PDF, 2-sided PDF, BibTex)

Chao DL, Davenport MP, Forrest S, Perelson AS. A stochastic model of cytotoxic T cell responses. Journal of Theoretical Biology, 228(2): 227-40. 2004.
doi: 10.1016/j.jtbi.2003.12.011
[impact factor=1.96 (2005)]
(PDF, BibTex)

Chao DL, Balthrop J, Forrest S. Adaptive Radio: Achieving consensus using negative preferences. Technical Report TR-CS-2004-08, The University of New Mexico Department of Computer Science, Albuquerque, NM, 2004.
(PDF, postscript)

Chao DL, Davenport MP, Forrest S, Perelson AS. Modelling the impact of antigen kinetics on T-cell activation and response. Immunology and Cell Biology, 82(1): 55-61. 2004.
doi: 10.1111/j.1440-1711.2004.01207.x
[impact factor=2.482 (2006)]
(PDF, BibTex)

Chao DL and Forrest S. Information immune systems. Genetic Programming and Evolvable Machines, 4(4):311-31. 2003.
doi: 10.1023/A:1026139027539
(PDF, HTML, BibTex)

Chao DL, Davenport MP, Forrest S, Perelson AS. Stochastic stage-structured modeling of the adaptive immune system. Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB 2003), pp 124-131. IEEE Press, Los Alamitos, California, 2003.
doi: 10.1109/CSB.2003.1227311
[28/151=18.5% acceptance rate]
(PDF, Postscript, gzipped postscript, Powerpoint slides, HTML, BibTex)

Chao DL and Forrest S. Generating biomorphs with an aesthetic immune system. In R. Standish, M. A. Bedau, and H. A. Abbass, editors, Artificial Life VIII: Proceedings of the Eighth International Conference on the Simulation and Synthesis of Living Systems, pages 89-92. MIT Press, Cambridge, Massachusetts, 2003.
[32+35/89=75.3% acceptance rate for papers+short papers]
(PDF, Postscript, gzipped postscript, HTML, BibTex)

Chao DL and Forrest S. Information immune systems. In J. Timmis and P. J. Bentley, editors, Proceedings of the First International Conference on Artificial Immune Systems, pages 132-40. University of Kent at Canterbury Printing Unit, Canterbury, England, 2002.
[26/34=76.5% acceptance rate]
(PDF, Postscript, gzipped postscript, HTML, BibTex)

Chao DL and D'haeseleer P. The distribution of variable-length phatic interjectives on the world wide web. Technical Report TR-CS-2001-23, The University of New Mexico Department of Computer Science, Albuquerque, NM, 2001.
(gzipped postscript, HTML)

Chao DL. Doom as an interface for process management. In Proceedings of the SIGCHI Conference on Human Factors in Computing Systems (CHI Letters 3, 1), pages 152-7. ACM Press, New York, 2001.
doi: 10.1145/365024.365078
[19.5% acceptance rate]
(PDF, Postscript, gzipped postscript, HTML, BibTex)

Chao DL and Levin SA. Herding behavior: The emergence of large-scale phenomena from local interactions. In S. Ruan, G. S. K. Wolkowicz and J. Wu., editors, Differential Equations with Applications to Biology, Fields Institute Communications 21, pages 81-95. American Mathematical Society, Providence, RI, 1999.

Wagner D, Brown MJF, Broun P, Cuevas W, Moses LE, Chao DL, Gordon DM. Task-related differences in the cuticular hydrocarbon composition of the harvester ant, Pogonomyrmex barbatus. Journal of Chemical Ecology, 24(12): 2021-37. 1998.
doi: 10.1023/A:1020781508889
[impact factor=2.03 (2005)]
(PDF, BibTex)

Pascovici A, Li C, Shu J, Chao DL. Ink reduction for cluster dot halftoning. In Proceedings of the 1997 IS&T/SPIE International Symposium on Electronic Imaging Science and Technology, volume 3018, pages 293-9, 1997.

Mathematical modeling of infectious disease transmission. The 15th Annual International Vaccine Institute International Advanced Course on Vaccinology. Seoul, Korea. May 2015.

Ebola and Influenza - Perception & reality. Seattle University PUBM 5510 guest lecture. February 2015.

Using mathematical modeling to evaluate the potential cost-effectiveness of cholera vaccination in Bangladesh. 49th U.S.-Japan Conference on Cholera and Other Enteric Bacterial Infections. Gainesville, Florida. January 2015.

Mathematical modeling of infectious disease transmission. The 14th Annual International Vaccine Institute Advanced Course on Vaccinology. Seoul, Korea. May 2014.

Mathematical modeling of cholera. 2014 Institute of Disease Modeling Symposium. Bellevue, Washington. April 2014.

Vaccination strategies for epidemic and endemic cholera control - Modeling approach. Considerations around introduction of a cholera vaccine in Bangladesh. Dhaka, Bangladesh. March 2013.

Modeling mass vaccination and other interventions: An individual-based approach. Disease Dynamics 2013: Immunization, a true multi-scale problem. Vancouver, Canada. January 2013. (Link to video)

Mathematical modeling of cholera outbreaks. Third Annual Africhol Consortium Meeting. Abidjan, Cote d'Ivoire. November 2012.

Modeling the transmission of influenza in the United States. Use of Influenza Disease Models To Quantitatively Evaluate the Benefits and Risks of Vaccines: A Technical Workshop. Bethesda, MD. August 2012.

Modeling the global circulation of influenza: Preliminary results. Facing the Challenge of Infectious Diseases. Courmayeur, Italy. January 2012.

Modelling of antiviral use and resistance emergence - implications for use. Influenza Antivirals: Efficacy and Resistance. Rio de Janeiro, Brazil. November 2011.

Modeling the spread of pandemic H1N1 in the United States: 2009 and beyond. Invited talk at ICCS 2010. May 2010.

Barrett's Oesophagus. Invited talk at Infección, Inflamación y Cáncer. Instituto de Investigaciones en Salud, Universidad de Costa Rica. November 2007.

Chao DL. Doom as a tool for system administration. Shown at the Institute for New Culture Technologies/t0 in Vienna as part of the exhibit Interface Explorer (Expanding the desktop). October 2001.

Chao DL. Color-patch sheet registration. U.S. Patent 6,404,517. Issued June 11, 2002.

Li C, Pascovici A, Shu J, Chao DL. On-line ink-duty reduction. U.S. Patent 5,799,136. Issued August 25, 1998.