Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses.

Autor: Lubow J; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America., Levoir LM; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America., Ralph DK; Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America., Belmont L; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America.; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America., Contreras M; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America., Cartwright-Acar CH; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America., Kikawa C; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America.; Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.; Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America., Kannan S; Integral Molecular, Inc., Philadelphia, Pennsylvania, United States of America., Davidson E; Integral Molecular, Inc., Philadelphia, Pennsylvania, United States of America., Duran V; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America.; Chan Zuckerberg Biohub, San Francisco, California, United States of America., Rebellon-Sanchez DE; Clinical Research Center, Fundación Valle del Lili, Cali, Colombia., Sanz AM; Clinical Research Center, Fundación Valle del Lili, Cali, Colombia., Rosso F; Clinical Research Center, Fundación Valle del Lili, Cali, Colombia.; Department of Internal Medicine, Division of Infectious Diseases, Fundación Valle del Lili, Cali, Colombia., Doranz BJ; Integral Molecular, Inc., Philadelphia, Pennsylvania, United States of America., Einav S; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America.; Chan Zuckerberg Biohub, San Francisco, California, United States of America.; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America., Matsen Iv FA; Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America.; Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.; Department of Statistics, University of Washington, Seattle, Washington, United States of America.; Howard Hughes Medical Institute, Seattle, Washington, United States of America., Goo L; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America.

Publikováno v: PLoS pathogens [PLoS Pathog] 2023 Oct 09; Vol. 19 (10), pp. e1011722. Date of Electronic Publication: 2023 Oct 09 (Print Publication: 2023).

Inference of B cell clonal families using heavy/light chain pairing information.

Autor: Ralph DK; Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America., Matsen FA 4th; Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.; Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.; Department of Statistics, University of Washington, Seattle, Washington, United States of America.; Howard Hughes Medical Institute, Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.

Publikováno v: PLoS computational biology [PLoS Comput Biol] 2022 Nov 28; Vol. 18 (11), pp. e1010723. Date of Electronic Publication: 2022 Nov 28 (Print Publication: 2022).

Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies.

Autor: Doepker LE; Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States., Danon S; Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States., Harkins E; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States., Ralph DK; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States., Yaffe Z; Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States.; Medical Scientist Training Program, University of Washington School of Medicine, Seattle, United States., Garrett ME; Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States.; Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, United States., Dhar A; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.; Department of Statistics, University of Washington, Seattle, United States., Wagner C; Medical Scientist Training Program, University of Washington School of Medicine, Seattle, United States., Stumpf MM; Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States., Arenz D; Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States., Williams JA; Department of Medicinal Chemistry, University of Washington, Seattle, United States., Jaoko W; Department of Medicinal Microbiology, University of Nairobi, Nairobi, Kenya., Mandaliya K; Coast Provincial General Hospital, Women's Health Project, Mombasa, Kenya., Lee KK; Department of Medicinal Chemistry, University of Washington, Seattle, United States., Matsen FA 4th; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States., Overbaugh JM; Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States.; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.

Publikováno v: ELife [Elife] 2021 Jan 11; Vol. 10. Date of Electronic Publication: 2021 Jan 11.

A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis.

Autor: Dhar A; Department of Statistics, University of Washington, Seattle, Washington, United States of America.; Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America., Ralph DK; Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America., Minin VN; Department of Statistics, University of California, Irvine, California, United States of America., Matsen FA 4th; Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.

Publikováno v: PLoS computational biology [PLoS Comput Biol] 2020 Aug 17; Vol. 16 (8), pp. e1008030. Date of Electronic Publication: 2020 Aug 17 (Print Publication: 2020).

AIRR Community Standardized Representations for Annotated Immune Repertoires.

Autor: Vander Heiden JA; Department of Neurology, Yale School of Medicine, New Haven, CT, United States., Marquez S; Department of Pathology, Yale School of Medicine, New Haven, CT, United States., Marthandan N; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada., Bukhari SAC; Department of Pathology, Yale School of Medicine, New Haven, CT, United States., Busse CE; Division of B Cell Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany., Corrie B; Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada., Hershberg U; School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States.; Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, United States.; Department of Human Biology, Faculty of Sciences, University of Haifa, Haifa, Israel., Kleinstein SH; Department of Pathology, Yale School of Medicine, New Haven, CT, United States.; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States., Matsen Iv FA; Fred Hutchinson Cancer Research Center, Seattle, WA, United States., Ralph DK; Fred Hutchinson Cancer Research Center, Seattle, WA, United States., Rosenfeld AM; School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States., Schramm CA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States., Christley S; Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, United States., Laserson U; Department of Genetics and Genomic Sciences and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.

Publikováno v: Frontiers in immunology [Front Immunol] 2018 Sep 28; Vol. 9, pp. 2206. Date of Electronic Publication: 2018 Sep 28 (Print Publication: 2018).