News

2024

November 1
Welcome to Graham Northrup, who is joining the lab for his postdoc. Welcome Graham!
September 25
We welcome new graduate student, Rita Wang to Cobey Lab this week. Welcome Rita!
August 13
Lauren McGough discusses her research goals around understanding dynamical patterns of pathogen evolution at the National Institute for Theory and Mathematics in Biology, Research-in-Progress series.
August 1
Congratulations to Daniel (Sang Woo) on being awarded a highly competitive LSRF fellowship!
July 23
We publish our first paper on the DRIVE Study, a randomized clinical trial to examine the effects of repeated influenza vaccination in adults. (Only some warm-up results in this one.)
July 22
Welcome to Sang Woo (Daniel) Park, who is joining the lab for his postdoc. He will work with us on the community ecology of pathogens.
June 11
Lauren's paper on the interaction of immune memory and viral evolution is published in PNAS.
January 5
We find that strong immune memory biases may make influenza, SARS-CoV-2, and other pathogens more likely to diversify, in contrast to prevailing theory that ignores these biases.

2023

October 27
We find that measuring neutralizing antibodies at the population level can help predict which clade of influenza will dominate and which age groups will be infected.
October 24
We are pleased to welcome Mennatallah Gouda as a new Research Analyst to the Cobey Lab team. Welcome!
October 2
Alexander Pillai begins his PhD in the lab!
March 18
Sarah weighs in on the new evidence for market origins in the New York Times.
March 17
In collaboration with the US Flu Vaccine Effectiveness Network and researchers at the CDC and Harvard School of Public Health, we report that repeat vaccination effects cannot be fully explained by clinical infection history or differences in the timing of vaccination between people---but influenza infections that are not medically attended might explain this puzzling phenomenon.
February 1
Using simulations and experiments, Marcos Vieira and colleagues find that B cell evolution has many paths to high affinity and is not constrained by fitness differences hardcoded in germline immunoglobulin genes.
January 30
Welcome to Jessie Schmidt, our new grants specialist and program manager!

2022

September 21
Congratulations to Phil, who has started as new faculty at Wesleyan University; to Katie, who is leading a new group at CDC's Center for Forecasting and Outbreak Analytics; to Diana, who has transitioned to a bioinformatics position at U. Chicago's Center for Research Informatics; and to Qifang, who has turned to the "dark side" (her words) of consulting! Unsurprisingly, the lab is hiring again!
August 13
Welcome to Manon Ragonnet, a new research scientist who brings her phylogenetics expertise to bear on our efforts to integrate evo-epidemiological models.
July 1
Sarah has been promoted to full professor.
May 1
Welcome to Alex Byrnes, our new senior research programmer, to Alonzo Finch, a undergraduate statistics major at U. Chicago and research assistant, and to Patrick McChesney, incoming senior research scientist!
March 28
Sarah, Jesse Bloom, and Tyler Starr describe past and future SARS-2 evolution in a recent New York Times opinion.
February 1
Katie is interviewed by the Atlantic on COVID-19 vaccines and the fate of Delta. In the past few months, the lab has contributed to other stories in STAT, Scientific American, the Atlantic, the Chicago Tribune, the New York Times, and other media.

2021

December 12
Sarah publishes "A Scientist's Guide to Understanding Omicron" with Jesse Bloom in the New York Times.
October 20
Our lab needs to grow! We are searching for several postdocs or senior research scientists and a software engineer/developer. More here.
July 14
Our new paper finds the strange age distribution of flu B cases might be explained by the order in which individuals are infected with different strains, with extra protection against B/Yamagata in people first infected with it.
July 6
Sarah, Ben Cowling, and Wey Wen Lim write in Nature Medicine that to extend vaccine supply, fractional dosing of mRNA vaccines should be considered. This was covered in STAT News, Nature, and the Financial Times.
June 10
Phil, Elena, and Sarah worked with Jaline Gerardin's group at Northwestern, along with epidemiologists from the CDC and Illinois Department of Public Health, to document severe COVID-19 testing disparities and low case ascertainment in Illinois.
May 28
Since spring 2020, our group has provided weekly and then biweekly reports and briefings to the Illinois governor's office, Illinois Department of Public Health, and city and county public health departments. This week marks potentially our last report, although we continue to maintain local transmission estimates and historical analyses at illinoiscovid.org.
May 16
CNN interviews Katie about temperature checkpoints.
May 13
Sarah is a signatory to a letter published today in Science calling for more transparent and rigorous investigation of SARS-CoV-2 origins. She was also interviewed in the New York Times.
April 13
We argue in Nature Reviews Immunology that concerns about evolution should not hold back efforts to expand vaccination coverage, including through delayed second dosing. Sarah presented this case in an invited talk at the WHO Global Consultation on SARS-CoV-2 variants on March 29, and the paper was noted in the New York Times, Roll Call, and Stat.
April 1
We are excited to be part of a new seven-year NIAID-funded CEIRR center to do basic research on the dynamics of influenza and SARS-CoV-2. We'll be working closely with collaborators at the University of Pennsylvania, University of Michigan, Fred Hutchinson Cancer Research Center, University of Hong Kong, University of Arizona, and other sites.
March 23
Katie and Sarah discuss epidemic metrics with Quanta Magazine, which had also interviewed Katie in January. We have also recently talked with the New York Times, Al Jazeera, Washington Post, Science, Nature, The Atlantic, Vox (twice), Stat, MIT Technology Review, Scientific American, ABC News, Science News, and BBC Future. Vaccine misallocation at U. Chicago was covered in the Chicago Tribune.

2020

November 30
Welcome to Qifang Bi, who recently completed her PhD in epidemiology at Johns Hopkins SPH. Qifang will be investigating immune responses to SARS-CoV-2 for the PARIS-SPARTA studies and variation in the effectiveness of the seasonal flu vaccine. She will be co-advised by Marc Lipsitch.
October 19
Our NIH-funded DRIVE Study, which investigates the effect of seasonal influenza vaccination and infection on immune responses, starts enrollment in Hong Kong!
September 11
Sarah discusses university reopenings with Chris Hayes on MSNBC and the New York Times.
September 1
Welcome to Rachel Oidtman, PhD, a new postdoc in the lab! She'll work on modeling longitudinally the development of immune protection to flu.
July 15
Now out in eLife: We show individuals' early influenza infections shape flu epidemiology and vaccine effectiveness decades later.
July 3
Interviews with Scientific American, The Atlantic, Vox, Chicago Tribune, and WBEZ about recent epidemic dynamics and surveillance.
June 23
Our preprint reviews some common pitfalls and opportunities in Rt estimation.
June 15
Diana Vera Cruz, PhD, joins the lab as a research scientist. She'll be analyzing immune responses to a universal influenza vaccine candidate. Welcome, Diana!
May 28
Undergraduate students Elena Whitney and Dannie Griggs join us for the summer! Interviews with the Washington Post, Seattle Times, Chicago Tribune, and the Chicago Maroon. Phil is featured in the Hyde Park Herald.
April 30
Congratulations to Dr. Marcos Vieira on his impressive PhD defense!
April 24
Some simple theory and flu-driven observations applied to SARS-CoV-2, now published in Science. Interviews this week with WGN TV, Scientific American, Vox, Science Friday, and Dagens Nyheter.
April 23
Our COVID-19 team is profiled in the Chicago Tribune. We've also been on BBC World Service, WGN Radio, CNN Tonight with Don Lemon, Fox News Radio Rundown, Chicago's Morning Answer, and Nature news.
March 23
Most of the lab is now working full-time, and then some, on the COVID-19 response. We are so happy to be joined by alumni Frank Wen, Sylvia Ranjeva, and Ed Baskerville!
March 10
Welcome to Lauren McGough! With her NIH Kirschstein (F32) fellowship, Lauren will investigate the foundations of adaptive immune evolution.
March 6
Katie discusses her recent paper on the ineffectiveness of travel screening for SARS-CoV-2 and general pandemic matters with the Chicago Tribune, Science News, Yahoo News Canada, Outbreak News, and other outlets. Sarah talks with CBS-2 Chicago.
January 2
Welcome to Spencer Carran! He'll be studying influenza vaccine immunogenicity and effectiveness.

2019

September 1
Welcome to Katie Gostic, who starts her James S. McDonnell Foundation Postdoctoral Fellowship!
August 29
We are delighted to have been awarded funding through the Gates Grand Challenge for Universal Influenza Vaccine Development (as part of a team with Patrick Wilson, Florian Krammer, Jesse Bloom, Ian Wilson, and Andrew Ward) and separately from the NIH NIAID as part of a seven-year Collaborative Influenza Vaccine Innovation Center (CIVIC), headed by Florian Krammer and Rafi Ahmed.
July 26
Congratulations to Phil on being awarded an F32!
July 14
First flu infections determine susceptibility throughout life, and potentially vaccine effectiveness. New preprint by Phil (and a parallel study by Katie Gostic, who joins the lab this fall).
July 1
Our R01 to model the longitudinal development of immunity to influenza (with collaborator Aubree Gordon at U. Michigan) begins!
June 20
We say good-bye to Ed, who is heading off to found his own startup to save us from Facebook and all the rest. His statistical and programming advice will live on in our models forever.
April 10
Our paper in Nature Communications shows how immune memory shapes protection to influenza in adults and children. Bonuses: Estimation of imprinting effects, epidemic sizes, household transmission, & more!
March 8
Angsty germophobia and germophilia on display in this Nerdette podcast.

2018

September 18
We find evidence of some vaccine-induced evolution in flu.
June 29
Sarah eventually checks her text messages and discovers she has been awarded tenure!
June 26
Our special issue of Immunological Reviews, "Characterization of the Immunological Repertoire", hits the stands.
June 1
Ed returns to the fold to model the development of immunity to flu. True to form, he immediately proposes provocatively simple models. It's good to have him back!
May 25
Sylvia, Sarah, and collaborators statistically model serological data and find differences in the dynamics of influenza immunity between children and adults.
May 21
Sarah and Joe Lewnard describe the challenges of understanding how the influenza vaccine's effectiveness varies with individuals' histories of exposure to flu.
May 17
Congratulations to Frank on his successful PhD defense! We are happy to have him around another few months before he returns to medical school.
May 10
Marcos has been awarded a William Rainey Harper Fellowship, one of the University of Chicago's highest honors. Congratulations, Marcos!
April 27
Congratulations to Sylvia for successfully defending her PhD thesis!
February 16
Marcos, Sarah, and collaborators had a paper accepted for publication in Molecular Biology and Evolution showing that mutability losses in long-lived B cell lineages are intrinsic to the neutral and adaptive evolution of B cell populations.
February 5
Sarah and collaborators had a paper accepted for publication in Clinical Infectious Diseases showing that low H3N2 vaccine efficacy in 2012-2013 may have been due to the emergence of antigenically novel influenza strains, and not due to a failure of the egg-adapted strain to induce an immune response to the intended vaccine strain.

2017

December 5
Sylvia, Sarah, Greg Dwyer, and collaborators published a paper in PNAS showing that the high prevalence of HPV in men can be explained by repeated or sustained infections with ecologically distinct HPV types.
November 11
Kangchon, Sarah, and collaborators published a paper in PNAS showing that a glycosylation site in contemporary H3N2 viruses alters antibody binding by egg-adapted vaccine strains.
October 6
Phil Arevalo joins the lab as a postdoctoral researcher. Welcome, Phil!
July 17
Marcos and Sarah find loss of mutability in long-lived B cell receptor sequences.
July 14
Frank and Sarah, in collaboration with Anup Malani (University of Chicago Law School), examine the impact of vaccines on the evolution of seasonal influenza and the associated implications for public health policy.
July 11
Sarah and collaborators find evidence that low seasonal influenza vaccine effectiveness in 2012-13 was not caused by egg-adaptative mutations.
July 8
Sarah and Ed's paper on the coexistence of drug-sensitive and drug-resistant pneumococcus strains is in preprint at the Journal of the Royal Society Interface.
June 1
Rohan Dandavati and Graham Northrup join the Cobey lab. Welcome!
April 20
Sarah and Ed examine the coexistence of drug-sensitive and drug-resistant pneumococcus strains.
April 17
Kangchon Kim joins the lab as a postdoc! Welcome, Kangchon!
January 23
Scott Hensley and Sarah propose that many patterns in influenza immunology make sense in light of original sin.
January 12
Rahul is interviewed on Chicago's public radio station about his recent PLOS Computational Biology paper!

2016

December 28
Sarah and Ed's paper on the challenges of causal inference with CCM has been published.
December 15
Sylvia was awarded an NIH F30 grant. Congratulations, Sylvia!
September 14
Frank and Sarah's paper on the phylogeography of influenza (in collaboration with Trevor Bedford) was published in Proceedings B and featured in a Science Life article.
May 12
Frank and Marcos both successfully defended their dissertation proposals this week and are now PhD candidates. Congratulations!
April 18
Sarah gives a seminar in the NYU Department of Biology.
January 6
Sarah and Ed's new paper shows that causal inference using state-space reconstruction is unreliable in natural systems.

2015

December 10
Daniel Zinder joins the lab as a postdoc! Welcome, Daniel!
December 1
Colin Kyle joins the lab as a research programmer. Welcome, Colin!
November 27
Sarah was interviewed on NPR about influenza's phylogeography and its coevolution with the immune system.
September 14
Rahul Subramanian begins his PhD in the lab!
July 20
Publication of theme issue, "The dynamics of antibody repertoires" of the Philosophical Transactions of the Royal Society B
July 20
Sarah teaches a 2.5-day course on "Pathogen evolution, selection, and immunity" with Trevor Bedford at the Statistics and Modeling in Infectious Diseases (SISMID) summer school in Seattle.
July 8
Sarah talks at the Forecasting Evolution? conference in Lisbon.
June 22
Frank Wen begins his PhD in the lab!
June 15
Lev Tsypin, a third year undergraduate, begins his summer rotation in the lab! He'll be working with Igor on fitting nonlinear dynamics.
May 14
Igor Vasiljevic joins the lab to investigate methods to fit stochastic, nonlinear dynamical models.
March 23
Our special issue on microbial resistance is published in Evolutionary Applications.
March 22
Sarah co-chairs a special session on systems immunology at the Keystone Symposium on the Golden Anniversary of B Cell Discovery.
March 19
Sarah presents at the RAPIDD workshop "Modeling and predicting influenza phenotypes" at Cambridge University.

2014

December 1
Congratulations to Sylvia for successfully defending her thesis proposal!
November 29
Congratulations to Marcos, whose paper has just been published in Ecology Letters!
November 24
Sarah and Fred Wulczyn receive a seed grant from the University of Chicago's BIG Ideas Generator to test methods of state-space reconstruction.
November 18
Sarah talks at the Center of the Study of Biodiversity in Amazonia's thematic school, "Advanced methods and applications in ecology, evolution, and control of infectious diseases".
October 6
Sarah receives the NIH New Innovator Award, which provides five years of support for the project "Modeling the Evolutionary Dynamics of Immunity to Influenza for Vaccine Development"
September 15
Welcome to Marcos Vieira, who begins his PhD studies in our lab!
July 17
Our new paper argues that pathogens evolve in a more complex immune environment than most models assume, and the differences matter.
June 26
Sarah and Patrick Wilson (co-PI) receive the McDonnell Foundation's Studying Complex System Scholar Award for "Measuring the predictability of evolution through adaptive immunity."
May 5
The third meeting of our NESCent working group takes place in Durham, NC.
May 1
Congratulations to Frank, who'll be starting at the University of Chicago's MD/PhD program this summer!
April 2
Sarah gives a talk at the Jacques Monod conference on viral evolution in Roscoff, France.
January 27
The second meeting of our NESCent working group takes places in Durham, NC.

2013

December 11
Sarah gives a talk at the J. Craig Venter Institute.
November 4
The first meeting of our NESCent working group takes place in Durham, NC.
October 14
Collaborator Lauren Childs visits from HSPH.
October 14
Sarah and Jack Gilbert receive a $75,000 seed grant from the DoE to develop methods to infer pathogen interactions.
October 4
Sarah gives a talk at Swarthmore.
August 20
Sarah co-chairs a symposium on the evolution and genetics of drug resistance at the European Society of Evolutionary Biology conference in Lisbon, Portugal.
August 12
Sylvia Ranjeva begins her rotation in the lab! She'll be working on a HPV project she started with Greg Dwyer.
July 17
Frank Wen joins the lab to work on the phylogeography of influenza!

 

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