Heterogeneity in pre-vaccination population immunity can contribute to variability in vaccine effectiveness estimates, medRxiv
Alexander N. Pillai, Sang Woo Park, Marc Lipsitch, Benjamin J. Cowling and Sarah Cobey
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Time-varying transmission heterogeneity of SARS and COVID-19 in Hong Kong, Research Square
Dillon Adam, Katelyn Gostic, Tim Tsang, Peng Wu, Wey Wen Lim, Amy Yeung, Jessica Wong, Eric Lau, Zhanwei Du, Dongxuan Chen, Lai-Ming Ho, Mario Martín-Sánchez, Simon Cauchemez, Sarah Cobey, Gabriel Leung and Benjamin Cowling
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pdf
Cross-reactive human antibody responses to H5N1 influenza virus neuraminidase are shaped by immune history, Nature Communications
Jordan T. Ort, Ashley Sobel Leonard, Shuk Hang Li, Reilly K. Atkinson, Lydia M. Mendoza, Marcos Costa Vieira, Sydney Gang, Sarah Cobey and Scott E. Hensley
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Susceptible host dynamics explain pathogen resilience to perturbations, PNAS
Sang Woo Park, Bjarke Frost Nielsen, Emily Howerton, Bryan Grenfell and Sarah Cobey
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pdf
Immune history shapes human antibody responses to H5N1 influenza viruses, Nature Medicine
Tyler A. Garretson, Jiaojiao Liu, Shuk Hang Li, Gabrielle Scher, Jefferson J.S. Santos, Glenn Hogan, Marcos Costa Vieira, Colleen Furey, Reilly K. Atkinson, Naiqing Ye, Jordan Ort, Kangchon Kim, Kevin A. Hernandez, Theresa Eilola, David C. Schultz, Sara Cherry, Sarah Cobey and Scott E. Hensley
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pdf
Interplay between climate, childhood mixing, and population-level susceptibility explains a sudden shift in RSV seasonality in Japan, Nature Communications
Sang Woo Park, Inga Holmdahl, Emily Howerton, Wenchang Yang, Rachel E. Baker, Gabriel A. Vecchi, Sarah Cobey, C. Jessica E. Metcalf and Bryan T. Grenfell
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Measures of population immunity can predict the dominant clade of influenza A (H3N2) in the 2017–2018 season and reveal age-associated differences in susceptibility and antibody-binding specificity, Influenza and Other Respiratory Viruses
Kangchon Kim, Marcos C. Vieira, Sigrid Gouma, Madison E. Weirick, Scott E. Hensley and Sarah Cobey
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Predicting pathogen mutual invasibility and co-circulation, Science
Sang Woo Park, Sarah Cobey, C. Jessica E. Metcalf, Jonathan M. Levine and Bryan T. Grenfell
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High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains, Journal of Virology
Andrea N. Loes, Rosario Araceli L. Tarabi, John Huddleston, Lisa Touyon, Sook San Wong, Samuel M.S. Cheng, Nancy H.L. Leung, William W. Hannon, Trevor Bedford, Sarah Cobey, Benjamin J. Cowling and Jesse D. Bloom
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Vaccination against rapidly evolving pathogens and the entanglements of memory, Nature Immunology
Sarah Cobey
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Preliminary findings from the Dynamics of the Immune Responses to Repeat Influenza Vaccination Exposures (DRIVE I) Study: a randomized controlled trial, Clinical Infectious Diseases
Benjamin J. Cowling, Sook-san Wong, Jefferson J. S. Santos, Lisa Touyon, Jordan Ort, Naiqing Ye, Natalie K. M. Kwok, Faith Ho, Samuel M. S. Cheng, Dennis K. M. Ip, Malik Peiris, Richard J. Webby, Patrick C. Wilson, Sophie A. Valkenburg, John S. Tsang, Nancy H. L. Leung, Scott E. Hensley and Sarah Cobey
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A speed limit on serial strain replacement from original antigenic sin, Proceedings of the National Academy of Sciences
Lauren McGough and Sarah Cobey
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Reduced effectiveness of repeat influenza vaccination: distinguishing among within-season waning, recent clinical infection, and subclinical infection, The Journal of Infectious Diseases
Qifang Bi, Barbra A. Dickerman, Huong Q. McLean, Emily T. Martin, Manjusha Gaglani, Karen J. Wernli, G.K. Balasubramani, Brendan Flannery, Marc Lipsitch, Sarah Cobey and the US Flu Vaccine Effectiveness Network Investigators
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Germline-encoded specificities and the predictability of the B cell response, PLOS Pathogens
Marcos C. Vieira, Anna-Karin E. Palm, Christopher T. Stamper, Micah E. Tepora, Khoa D. Nguyen, Tho D. Pham, Scott D. Boyd, Patrick C. Wilson and Sarah Cobey
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Investigation of impact of childhood immune imprinting on birth year-specific risk of clinical infection during influenza A virus epidemics in Hong Kong, The Journal of Infectious Diseases
Tim K Tsang, Katelyn M. Gostic, Sijie Chen, Yifan Wang, Philip Arevalo, Eric H. Y. Lau, Sarah Cobey and Benjamin J Cowling
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Getting the most out of noisy surveillance data, Nature Computational Science
Lauren McGough
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pdf
Original antigenic sin and childhood immune responses against SARS-CoV-2, Science
Sarah Cobey and Scott E. Hensley
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pdf
PARIS and SPARTA: Finding the Achilles’ Heel of SARS-CoV-2, mSphere
Viviana Simon, Vamsi Kota, Ryan F. Bloomquist, Hannah B. Hanley, David Forgacs, Savita Pahwa, Suresh Pallikkuth, Loren G. Miller, Joanna Schaenman, Michael R. Yeaman, David Manthei, Joshua Wolf, Aditya H. Gaur, Jeremie H. Estepp, Komal Srivastava, Juan Manuel Carreño, Frans Cuevas, Ali H. Ellebedy, Aubree Gordon, Riccardo Valdez, Sarah Cobey, Elaine F. Reed, Ravindra Kolhe, Paul G. Thomas, Stacey Schultz-Cherry and Ted M. Ross
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pdf
Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA, Nature Communications
Reese Richardson, Emile Jorgensen, Philip Arevalo, Tobias M. Holden, Katelyn M. Gostic, Massimo Pacilli, Isaac Ghinai, Shannon Lightner, Sarah Cobey and Jaline Gerardin
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SARS-CoV-2 infection among pregnant people at labor and delivery and changes in Infection rates in the general population: lessons learned from Illinois, Public Health Reports
Sonal Goyal, Jaline Gerardin, Sarah Cobey, Crystal Son, Owen McCarthy, Arielle Dror, Shannon Lightner, Ngozi O. Ezike, Wayne A. Duffus and Amanda C. Bennett
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Incorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmission, Nature Communications
Yun Lin, Bingyi Yang, Sarah Cobey, Eric H. Y. Lau, Dillon C. Adam, Jessica Y. Wong, Helen S. Bond, Justin K. Cheung, Faith Ho, Huizhi Gao, Sheikh Taslim Ali, Nancy H. L. Leung, Tim K. Tsang, Peng Wu, Gabriel M. Leung and Benjamin J. Cowling
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Modeling comparative cost-effectiveness of SARS-CoV-2 vaccine dose fractionation in India, Nature Medicine
Zhanwei Du, Lin Wang, Abhishek Pandey, Wey Wen Lim, Matteo Chinazzi, Ana Pastore Y. Piontti, Eric H. Y. Lau, Peng Wu, Anup Malani, Sarah Cobey and Benjamin J. Cowling
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The potential beneficial effects of vaccination on the evolution of antigenically evolving pathogens, American Naturalist
Frank T. Wen, Anup Malani and Sarah Cobey
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Of variants and vaccines, Cell
Nathan D. Grubaugh and Sarah Cobey
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Improvements in Severe Acute Respiratory Syndrome Coronavirus 2 testing cascade in the United States: data from serial cross-sectional assessments, Clinical Infectious Diseases
Steven J. Clipman, Amy Wesolowski, Shruti H. Mehta, Sarah Cobey, Derek A. T. Cummings and Sunil S. Solomon
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Fractionation of COVID-19 vaccine doses could extend limited supplies and reduce mortality, Nature Medicine
Benjamin J. Cowling, Wey Wen Lim and Sarah Cobey
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Influenza immune escape under heterogeneous host immune histories, Trends in Microbiology
Rachel J. Oidtman, Philip Arevalo, Qifang Bi, Lauren McGough, Christopher Joel Russo, Diana Vera Cruz, Marcos Costa Vieira and Katelyn M. Gostic
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Lineage-specific protection and immune imprinting shape the age distributions of influenza B cases, Nature Communications
Marcos C. Vieira, Celeste M. Donato, Philip Arevalo, Guus F. Rimmelzwaan, Timothy Wood, Liza Lopez, Q. Sue Huang, Vijaykrishna Dhanasekaran, Katia Koelle and Sarah Cobey
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Geographic and demographic heterogeneity of SARS-CoV-2 diagnostic testing in Illinois, USA, March to December 2020, BMC Public Health
Tobias M. Holden, Reese A. K. Richardson, Philip Arevalo, Wayne A. Duffus, Manuela Runge, Elena Whitney, Leslie Wise, Ngozi O. Ezike, Sarah Patrick, Sarah Cobey and Jaline Gerardin
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Investigate the origins of COVID-19, Science
Jesse D. Bloom, Yujia Alina Chan, Ralph S. Baric, Pamela J. Bjorkman, Sarah Cobey, Benjamin E. Deverman, David N. Fisman, Ravindra Gupta, Akiko Iwasaki, Marc Lipsitch, Ruslan Medzhitov, Richard A. Neher, Rasmus Nielsen, Nick Patterson, Tim Stearns, Erik van Nimwegen, Michael Worobey and David A. Relman
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Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination, Nature Reviews Immunology
Sarah Cobey, Daniel B. Larremore, Yonatan H. Grad and Marc Lipsitch
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COVID-19 infection, reinfection, and vaccine effectiveness in Arizona frontline and essential workers: Protocol for a longitudinal cohort study, JMIR Research Protocols
Karen Lutrick, Katherine D. Ellingson, Zoe Baccam, Patrick Rivers, Shawn Beitel, Joel Parker, James Hollister, Xiaoxiao Sun, Joe K. Gerald, Kenneth Komatsu, Elizabeth Kim, Bonnie LaFleur, Lauren Grant, Young M. Yoo, Archana Kumar, Julie Mayo Lamberte, Benjamin J. Cowling, Sarah Cobey, Natalie J. Thornburg, Jennifer K. Meece, Preeta Kutty, Janko Nikolich-Zugich, Mark G. Thompson and Jefferey L. Burgess
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pdf
An egg-derived sulfated N-Acetyllactosamine glycan is an antigenic decoy of influenza virus vaccines, mBio
Jenna J. Guthmiller, Henry A. Utset, Carole Henry, Lei Li, Nai-Ying Zheng, Weina Sun, Marcos C. Vieira, Seth Zost, Min Huang, Scott E. Hensley, Sarah Cobey, Peter Palese and Patrick C. Wilson
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Model-informed COVID-19 vaccine prioritization strategies by age and serostatus, Science
Kate M. Bubar, Kyle Reinholt, Stephen M. Kissler, Marc Lipsitch, Sarah Cobey, Yonatan Grad and Daniel B. Larremore
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Preexisting immunity shapes distinct antibody landscapes after influenza virus infection and vaccination in humans, Science Translational Medicine
Haley L. Dugan, Jenna J. Guthmiller, Philip Arevalo, Min Huang, Yao-Qing Chen, Karlynn E. Neu, Carole Henry, Nai-Ying Zheng, Linda Yu-Ling Lan, Micah E. Tepora, Olivia Stovicek, Dalia Bitar, Anna-Karin E. Palm, Christopher T. Stamper, Siriruk Changrob, Henry A. Utset, Lynda Coughlan, Florian Krammer, Sarah Cobey and Patrick C. Wilson
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Practical considerations for measuring the effective reproductive number, Rt, PLOS Computational Biology
Katelyn M. Gostic, Lauren McGough, Edward Baskerville, Sam Abbott, Keya Joshi, Christine Tedijanto, Rebecca Kahn, Rene Niehus, James A. Hay, Pablo M. De Salazar, Joel Hellewell, Sophie Meakin, James Munday, Nikos Bosse, Katharine Sherratt, Robin M. Thompson, Laura F. White, Jana Huisman, Jérémie Scire, Sebastian Bonhoeffer, Tanja Stadler, Jacco Wallinga, Sebastian Funk, Marc Lipsitch and Sarah Cobey
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pdf
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github
Middle-aged individuals may be in a perpetual state of H3N2 influenza virus susceptibility, Nature Communications
Sigrid Gouma, Kangchon Kim, Madison E. Weirick, Megan E. Gumina, Angela Branche, David J. Topham, Emily T. Martin, Arnold S. Monto, Sarah Cobey and Scott E. Hensley
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github
Earliest infections predict the age distribution of seasonal influenza A cases, eLife
Philip Arevalo, Huong Q. McLean, Edward A. Belongia and Sarah Cobey
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pdf
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github
Modeling infectious disease dynamics, Science
Sarah Cobey
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Comparison of human H3N2 antibody responses elicited by egg-based, cell-based, and recombinant protein-based influenza vaccines during the 2017-2018 season, Clinical Infectious Diseases
Sigrid Gouma, Seth J. Zost, Kaela Parkhouse, Angela Branche, David J. Topham, Sarah Cobey and Scott E. Hensley
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pdf
Age-specific differences in the dynamics of protective immunity to influenza, Nature Communications
Sylvia Ranjeva, Rahul Subramanian, Vicky J. Fang, Gabriel M. Leung, Dennis K. M. Ip, Ranawaka A.P.M. Perera, J. S. Malik Peiris, Benjamin J. Cowling* and Sarah Cobey*
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github
Influenza virus vaccination elicits poorly adapted B cell responses in elderly individuals, Cell Host & Microbe
Carole Henry, Nai-Ying Zheng, Min Huang, Alexandra Cabanov, Karla Thatcher Rojas, Kaval Kaur, Sarah F. Andrews, Anna-Karin E. Palm, Yao-Qing Chen, Yang Li, Katerina Hoskova, Henry A. Utset, Marcos C. Vieira, Jens Wrammert, Rafi Ahmed, Jeanne Holden-Wiltse, David J. Topham, John J. Treanor, Hildegund C. Ertl, Kenneth E. Schmader, Sarah Cobey, Florian Krammer, Scott E. Hensley, Harry Greenberg, Xiao-Song He and Patrick C.Wilson
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pdf
Spec-seq unveils transcriptional subpopulations of antibody-secreting cells following influenza vaccination, The Journal of Clinical Investigation
Karlynn E. Neu, Jenna J. Guthmiller, Min Huang, Jennifer La, Marcos C. Vieira, Kangchon Kim, Nai-Ying Zheng, Mario Cortese, Micah E. Tepora, Natalie J. Hamel, Karla Thatcher Rojas, Carole Henry, Dustin Shaw, Charles L. Dulberger, Bali Pulendran, Sarah Cobey, Aly A. Khan and Patrick C. Wilson
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Repeated vaccination may protect children from influenza infection, JAMA Network Open
Sarah Cobey
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pdf
Estimating vaccine-driven selection in seasonal influenza, Viruses
Frank T. Wen, Sidney M. Bell, Trevor Bedford and Sarah Cobey
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pdf
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github
Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a vaccine, PLOS Computational Biology
Francisco Y. Cai, Thomas Fussell, Sarah Cobey and Marc Lipsitch
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pdf
Characterization of the immunologic repertoire: A quick start guide, Immunological Reviews
Patrick C. Wilson and Sarah Cobey
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pdf
Immune history and influenza vaccine effectiveness, Vaccines
Joseph A. Lewnard and Sarah Cobey
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pdf
Selection and neutral mutations drive pervasive mutability losses in long-lived B cell lineages, Molecular Biology and Evolution
Marcos C. Vieira, Daniel Zinder and Sarah Cobey
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Poor immunogenicity, not vaccine strain egg adaptation, may explain the low H3N2 influenza vaccine effectiveness in 2012-2013, Clinical Infectious Diseases
Sarah Cobey, Sigrid Gouma, Kaela Parkhouse, Benjamin S. Chambers, Hildegund C. Ertl, Kenneth E. Schmader, Rebecca A. Halpin, Xudong Lin, Timothy B. Stockwell, Suman R. Das, Emily Landon, Vera Tesic, Ilan Youngster, Benjamin A. Pinsky, David E. Wentworth, Scott E. Hensley and Yonatan H. Grad
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pdf
Contemporary H3N2 influenza viruses have a glycosylation site that alters binding of antibodies to egg-adapted vaccine strains, Proceedings of the National Academy of Sciences
Seth J. Zost, Kaela Parkhouse, Megan E. Gumina, Kangchon Kim, Sebastian Diaz Perez, Patrick C. Wilson, John J. Treanor, Andrea J. Sant, Sarah Cobey and Scott E. Hensley
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pdf
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github
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press release
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F1000 recommendation
Recurring infection with ecologically distinct human papillomavirus (HPV) types can explain high prevalence and diversity, Proceedings of the National Academy of Sciences
Sylvia Ranjeva, Edward B. Baskerville, Vanja Dukic, Luisa L. Villa, Eduardo Lazcano-Ponce, Anna R. Giuliano, Greg Dwyer and Sarah Cobey
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github
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press release
Host population structure and treatment frequency maintain balancing selection on drug resistance, Journal of the Royal Society Interface
Sarah Cobey, Edward B. Baskerville, Caroline Colijn, William Hanage, Christophe Fraser and Marc Lipsitch
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pdf
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github
Immune history and influenza virus susceptibility, Current Opinion in Virology
Sarah Cobey and Scott E. Hensley
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local file
Sick if you do, sick if you don’t, Nature Ecology & Evolution
Sarah Cobey
url
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pdf
Does influenza drive absolute humidity?, Proceedings of the National Academy of Sciences
Edward B. Baskerville and Sarah Cobey
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pdf
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github
Limits to causal inference with state-space reconstruction for infectious disease, PLOS One
Sarah Cobey and Edward B. Baskerville
url
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pdf
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github
Viral factors in influenza pandemic risk assessment, eLife
Marc Lipsitch, Wendy Barclay, Rahul Raman, Charles J. Russell, Jessica A. Belser, Sarah Cobey, Peter M. Kasson, James O. Lloyd-Smith, Sebastian Maurer-Stroh, Steven Riley, Catherine A. A. Beauchemin, Trevor Bedford, Thomas C. Friedrich, Andreas Handel, Sander Herfst, Pablo R. Murcia, Benjamin Roche, Claus O. Wilke and Colin A. Russell
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pdf
Explaining the geographical origins of seasonal influenza A (H3N2), Proceedings of the Royal Society B
Frank Wen, Trevor Bedford and Sarah Cobey
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pdf
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github
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press release
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local file
K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets, Microbial Genomics
Alberto Pessia, Yonatan Grad, Sarah Cobey, Juha Santeri Puranen and Jukka Corander
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pdf
The evolution within us, Philosophical Transactions of the Royal Society B
Sarah Cobey, Patrick Wilson and Frederick A. Matsen IV
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pdf
Tradeoffs in antibody repertoires to complex antigens, Philosophical Transactions of the Royal Society B
Lauren M. Childs, Edward B. Baskerville and Sarah Cobey
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pdf
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github
Fighting microbial drug resistance: a primer on the role of evolutionary biology in public health, Evolutionary Applications
Gabriel G. Perron, R. Fredrik Inglis, Pleuni S. Pennings and Sarah Cobey
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pdf
Pathogen evolution and the immunological niche, Annals of the New York Academy of Sciences
Sarah Cobey
url
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pdf
Improving influenza vaccine virus selection: Report of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14-16 June 2010 (2013), Influenza and Other Respiratory Diseases
WHO Writing Group, William K. Ampofo, Norman Baylor, Sarah Cobey, Nancy J. Cox, Sharon Daves, Steven Edwards, Neil Ferguson, Gary Grohmann, Alan Hay, Jacqueline Katz, Kornnika Kullabutr, Linda Lambert, Roland Levandowski, A. C. Mishra, Arnold Monto, Marilda Siqueira, Masato Tashiro, Anthony L. Waddell, Niteen Wairagkar, John Wood, Maria Zambon and Wenqing Zhang
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pdf
The Hospital Microbiome Project: Meeting report for the 2nd Hospital Microbiome Project, Chicago, USA, January 15th, 2013 (2013), Standards in Genomic Sciences
Benjamin D. Shogan, Daniel P. Smith, Aaron I. Packman, Scott T. Kelley, Emily M Landon, Seema Bhangar, Gary J. Vora, Rachael M. Jones, Kevin Keegan, Brent Stephens, Tiffanie Ramos, Benjamin C. Kirkup, Jr., Hal Levin, Mariana Rosenthal, Betsy Foxman, Eugene B. Chang, Jeffrey Siegel, Sarah Cobey, Gary An, John C. Alverdy, Paula J. Olsiewski, Mark O. Martin, Rachel Marrs, Mark Hernandez, Scott Christley, Michael Morowitz, Stephen Weber and Jack Gilbert
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pdf
Pathogen coexistence through hidden regimes of apparent competition (2013), American Naturalist
Sarah Cobey and Marc Lipsitch
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pdf
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github
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local file
Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes (2012), Science
Sarah Cobey and Marc Lipsitch
url
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github
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F1000 recommendation
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local file
Anticipating the species jump: Surveillance for emerging viral threats (2011), Zoonoses and Public Health
M. L. Flanagan, C. Parrish, S. Cobey, G. E. Glass, R. M. Bush and T. J. Leighton
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local file
Predicting the epidemic sizes of influenza A/H1N1, A/H3N2, and B: a statistical method (2011), PLOS Medicine
Edward Goldstein, Sarah Cobey, Saki Takahashi, Joel C. Miller and Marc Lipsitch
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pdf
Strength and tempo of selection revealed in viral gene genealogies (2011), BMC Evolutionary Biology
Trevor Bedford, Sarah Cobey and Mercedes Pascual
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pdf
Consequences of host heterogeneity, epitope immunodominance, and immune breadth for strain competition (2011), Journal of Theoretical Biology
Sarah Cobey and Mercedes Pascual
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local file
Ecological factors driving the long-term evolution of influenza’s host range (2010), Proceedings of the Royal Society B
Sarah Cobey, Mercedes Pascual and Ulf Dieckmann
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pdf
Global migration dynamics underlie evolution and persistence of human influenza A (H3N2) (2010), PLOS Pathogens
Trevor Bedford, Sarah Cobey, Peter Beerli and Mercedes Pascual
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pdf
Capturing escape in infectious disease dynamics (2008), Trends in Ecology and Evolution
Sarah Cobey and Katia Koelle
url
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local file
Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans (2006), Science
Katia Koelle*, Sarah Cobey*, Bryan Grenfell and Mercedes Pascual
url
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local file
Sea lampreys in the Great Lakes (2005), Ecological Networks
Sarah Cobey
url