photo credit: Rebecca Allen Dennis L. Chao
Institute for Disease Modeling
3150 139th Ave SE
Bellevue, WA 98005
http://www.dennischao.com
dennisc @ intven.com

download CV (with full list of publications)

Recent employment
2015-present Senior research scientist
Institute for Disease Modeling
Bellevue, WA
2012-2015 Senior staff scientist
Vaccine and Infectious Disease Division/Public Health Sciences Division
Fred Hutchinson Cancer Research Center, Seattle, WA
2008-2011 Staff scientist
Vaccine and Infectious Disease Division/Public Health Sciences Division
Fred Hutchinson Cancer Research Center, Seattle, WA
2004-2008 Postdoctoral fellow
Fred Hutchinson Cancer Research Center, Seattle, WA
1999-2004 Research assistant
UNM Computer Science Department, Albuquerque, NM
1998-1999 Teaching assistant
UNM Computer Science Department, Albuquerque, NM
1994-1998 Technical staff
Epson Palo Alto Laboratory, Palo Alto, CA
Education
December 2004 Ph.D. in Computer Science
University of New Mexico, Albuquerque, NM
Dissertation: Modeling the cytotoxic T cell response. (1-sided PDF or 2-sided PDF)
June 1994 B.S.E. Computer Science
Princeton University, Princeton, NJ
Honors, awards, and funding
2016 Award for scientific research and collaboration between Italy and the United States
Aspen Institute Italia
2014-2015 Models of Infectious Disease Agent Study (MIDAS) (NIH U54 GM111274)
National Institutes of Health/National Institute of General Medical Sciences
2012-2015 Mathematical modeling for the optimal control of cholera with vaccine
Bill & Melinda Gates Foundation
2011-2012, 2013-2015 Development and Testing of Dengue Vaccines
Dengue Vaccine Initiative/Bill & Melinda Gates Foundation
2008-2014 Models of Infectious Disease Agent Study (MIDAS) (NIH U01 GM070749)
National Institutes of Health/National Institute of General Medical Sciences
2012-2013 Analysis and modeling of typhoid epidemiology and vaccination
Sabin Vaccine Institute/Bill & Melinda Gates Foundation
2008 Fellowship
Ryan Hill Research Foundation
2006-2008 Multi-Scale Modeling Initiative (NIH R01 CA119224)
National Institutes of Health/National Cancer Institute
2005 SPAC course scholarship ($500)
Fred Hutchinson Cancer Research Center
2004-2006 Dual Mentor Fellowship
Fred Hutchinson Cancer Research Center
2002 Research, Project, and Travel grant ($500)
UNM Office of Graduate Studies
2002 Student Research Allocations Committee grant ($300)
UNM Graduate and Professional Student Association
2002 Outstanding graduate student award
UNM Computer Science Department
1999-2001 Graduate Fellow
NSF BIO Research Training Group in Ecological Complexity, UNM
1993 Elected to membership in the Society of Sigma Xi
Professional activities
2014-present Advisor, Scientific Advisory Process for Optimal Research on Typhoid (SAPORT) Burden of Disease Project
2014-2016 Instructor, Vaccinology course
2009-2015 Instructor, Summer Institute in Statistics and Modeling in Infectious Diseases
2013 Symposium organizer, The global burden and control of cholera (May 15, 2013)
2012 Workshop participant, NIMBioS investigative workshop: Modeling dengue fever
2012 Consultant, First meeting on typhoid transmission, intervention, disease burden and cost-effectiveness/cost-utility modeling
2012 Advisory Board, Center for Ecogenetics and Environmental Health, Community Outreach and Ethics Core
2011 Participant, WHO Consultation on oral cholera vaccine (OCV) stockpile strategic framework: potential objectives and possible policy options
2010 Symposium organizer, The Future of Flu (September 27, 2010)
2007 Symposium organizer, Biological networks: From measurements to modeling (September 10, 2007)
2007 Planning committee, 2007 FHCRC Ethics Colloquium
2005-2007 Co-manager, FHCRC Interdisciplinary Club
2005 Attendee, Pathobiology of Cancer: The Edward A. Smuckler Memorial Workshop, American Association for Cancer Research
2000 Attendee, Complex Systems Summer School, Santa Fe Institute
1999 Founder, UNM Computer Science Graduate Student Association
Publications

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

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.

Selected posters and talks

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.

Patents
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.

Software
Dengue transmission model for Ratchaburi, Thailand. 2012.
Transmission of antiviral resistant influenza model. 2011.
Global transmission of influenza model. 2011.
Haitian cholera epidemic model. 2011.
LogitNet. 2009.
FluTE influenza epidemic simulator. 2009.
Pre-cancerous lesion growth simulation. 2008.
T cell simulation. 2003.
Adaptive Radio. 2003.
PSDoom. 1999. (available on Sourceforge)
Articles about my work
How H1N1 flu escaped Tamiflu. Fred Hutchinson's Center News. October 2011.
Researchers map the global spread of drug-resistant influenza. University of Florida press release. September 2011.
The quake that brought back cholera. NIGMS Inside Life Science. August 2011.
Oral vaccine could have halved Haiti's cholera epidemic. Fred Hutchinson's Center News. April 2011.
Vaccination would curb Haitian cholera. Nature news. April 2011.
Haiti cholera epidemic could have been blunted with use of mobile stockpile of oral vaccine. Fred Hutchinson Cancer Research Center press release. April 2011.
   F. Hwang. Commando line interface. Wired 8(2), page 52. February 2000.
J. Brockmeier. A SysAdmin's dream. Linux Magazine, page 76. January 2000.
J. Schmidt. Systemverwaltung nach Hackerart. c't: Magazin für Computer Technik 23, page 68. 1999.
Systemadministration mit dem Colt. IX: Magazin für professionelle Informationstechnik 12, page 44. 1999.
Kill -9 with a Doom shotgun. Slashdot, October 20, 1999.
M. Gagné. A Process Smörgåsbord. Linux Journal 104:26-29. December 2002.