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  1. Article

    Open Access

    Distinguishing features of long COVID identified through immune profiling

    Post-acute infection syndromes may develop after acute viral disease1. Infection with SARS-CoV-2 can result in the development of a post-acute infection syndrome known as long COVID. Individuals with long COVID f...

    Jon Klein, Jamie Wood, Jillian R. Jaycox, Rahul M. Dhodapkar, Peiwen Lu in Nature (2023)

  2. Article

    Open Access

    Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection

    Identification of host determinants of coronavirus infection informs mechanisms of viral pathogenesis and can provide new drug targets. Here we demonstrate that mammalian SWItch/Sucrose Non-Fermentable (mSWI/S...

    ** Wei, A**kya Patil, Clayton K. Collings, Mia Madel Alfajaro in Nature Genetics (2023)

  3. Article

    Open Access

    Plasmodium infection is associated with cross-reactive antibodies to carbohydrate epitopes on the SARS-CoV-2 Spike protein

    Sero-surveillance can monitor and project disease burden and risk. However, SARS-CoV-2 antibody test results can produce false positive results, limiting their efficacy as a sero-surveillance tool. False posit...

    Sarah Lapidus, Feimei Liu, Arnau Casanovas-Massana, Yile Dai in Scientific Reports (2022)

  4. Article

    Open Access

    Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia

    Although microbial populations in the gut microbiome are associated with COVID-19 severity, a causal impact on patient health has not been established. Here we provide evidence that gut microbiome dysbiosis is...

    Lucie Bernard-Raichon, Mericien Venzon, Jon Klein in Nature Communications (2022)

  5. Article

    Multiscale PHATE identifies multimodal signatures of COVID-19

    As the biomedical community produces datasets that are increasingly complex and high dimensional, there is a need for more sophisticated computational tools to extract biological insights. We present Multiscal...

    Manik Kuchroo, Jessie Huang, Patrick Wong, Jean-Christophe Grenier in Nature Biotechnology (2022)

  6. Article

    Open Access

    High-resolution epitope map** and characterization of SARS-CoV-2 antibodies in large cohorts of subjects with COVID-19

    As Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to spread, characterization of its antibody epitopes, emerging strains, related coronaviruses, and even the human proteome in naturally...

    Winston A. Haynes, Kathy Kamath, Joel Bozekowski in Communications Biology (2021)

  7. Article

    Open Access

    Serological assessment of SARS-CoV-2 infection during the first wave of the pandemic in Louisville Kentucky

    Serological assays intended for diagnosis, sero-epidemiologic assessment, and measurement of protective antibody titers upon infection or vaccination are essential for managing the SARS-CoV-2 pandemic. Serolog...

    Krystal T. Hamorsky, Adrienne M. Bushau-Sprinkle, Kathleen Kitterman in Scientific Reports (2021)

  8. Article

    Reply to: A finding of sex similarities rather than differences in COVID-19 outcomes

    Takehiro Takahashi, Mallory K. Ellingson, Patrick Wong, Benjamin Israelow in Nature (2021)

  9. Article

    Author Correction: Delayed production of neutralizing antibodies correlates with fatal COVID-19

    Carolina Lucas, Jon Klein, Maria E. Sundaram, Feimei Liu, Patrick Wong in Nature Medicine (2021)

  10. Article

    Delayed production of neutralizing antibodies correlates with fatal COVID-19

    Recent studies have provided insights into innate and adaptive immune dynamics in coronavirus disease 2019 (COVID-19). However, the exact features of antibody responses that govern COVID-19 disease outcomes re...

    Carolina Lucas, Jon Klein, Maria E. Sundaram, Feimei Liu, Patrick Wong in Nature Medicine (2021)

  11. Article

    Diverse functional autoantibodies in patients with COVID-19

    COVID-19 manifests with a wide spectrum of clinical phenotypes that are characterized by exaggerated and misdirected host immune responses16. Although pathological innate immune activation is well-documented in ...

    Eric Y. Wang, Tianyang Mao, Jon Klein, Yile Dai, John D. Huck, Jillian R. Jaycox in Nature (2021)

  12. Article

    Sex differences in immune responses that underlie COVID-19 disease outcomes

    There is increasing evidence that coronavirus disease 2019 (COVID-19) produces more severe symptoms and higher mortality among men than among women15. However, whether immune responses against severe acute respi...

    Takehiro Takahashi, Mallory K. Ellingson, Patrick Wong, Benjamin Israelow in Nature (2020)

  13. Article

    Longitudinal analyses reveal immunological misfiring in severe COVID-19

    Recent studies have provided insights into the pathogenesis of coronavirus disease 2019 (COVID-19)14. However, the longitudinal immunological correlates of disease outcome remain unclear. Here we serially analys...

    Carolina Lucas, Patrick Wong, Jon Klein, Tiago B. R. Castro, Julio Silva in Nature (2020)

  14. No Access

    Chapter

    Genetic Programming with Historically Assessed Hardness

    Jon Klein, Lee Spector in Genetic Programming Theory and Practice VI (2009)

  15. No Access

    Chapter

    3D Multi-Agent Simulations in the breve Simulation Environment

    Jon Klein, Lee Spector in Artificial Life Models in Software (2009)

  16. No Access

    Chapter

    Multidimensional Tags, Cooperative Populations, and Genetic Programming

    We present new results on the evolution of tag-mediated cooperation, demonstrating that the use of multidimensional tags can enhance the emergence of high levels of cooperation. We discuss these results in the...

    Lee Spector, Jon Klein in Genetic Programming Theory and Practice IV (2007)

  17. No Access

    Chapter

    Trivial Geography in Genetic Programming

    Geographical distribution is widely held to be a major determinant of evolutionary dynamics. Correspondingly, genetic programming theorists and practitioners have long developed, used, and studied systems in w...

    Lee Spector, Jon Klein in Genetic Programming Theory and Practice III (2006)

  18. No Access

    Article

    Emergence of Collective Behavior in Evolving Populations of Flying Agents

    We demonstrate the emergence of collective behavior in two evolutionary computation systems, one an evolutionary extension of a classic (highly constrained) flocking algorithm and the other a relatively un-con...

    Lee Spector, Jon Klein, Chris Perry in Genetic Programming and Evolvable Machines (2005)

  19. No Access

    Chapter and Conference Paper

    Emergence of Collective Behavior in Evolving Populations of Flying Agents

    We demonstrate the emergence of collective behavior in two evolutionary computation systems, one an evolutionary extension of a classic (highly constrained) flocking algorithm and the other a relatively un-con...

    Lee Spector, Jon Klein, Chris Perry in Genetic and Evolutionary Computation — GEC… (2003)