Author

W. E. Johnson

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 5 Biophysics· 2 Immunology· 2 Cancer Biology· 1 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 9 Approach:experimental assay· 6 Approach:statistical model· 6 Research Focus:host-pathogen & immune response· 5 Assay:whole-genome sequencing· 4 Approach:deep learning· 3 Assay:metagenomics· 3 Research Focus:protein folding & dynamics· 3

Frequent Co-Authors

B. Momeni· 2 shared L. Genovese· 2 shared M. Farzan· 2 shared M. Zaccaria· 2 shared T. Nakajima· 2 shared W. Dawson· 2 shared A. A. Gimelbrant· 1 shared A. Byrne· 1 shared

Activity by Year

2018-2024 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 15 mutual co-author links

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2 shared papersBiophysics

B. Momeni

Mutual co-authors in cluster

Author profile →

11 papers

Recent·Most cited

Lipid Peroxidation and Type I Interferon Coupling Fuels Pathogenic Macrophage Activation Causing Tuberculosis Susceptibility

S. M. Yabaji, V. Zhernovkov, P. B. Araveti, S. Lata, O. S. Rukhlenko, S. A. Abdullatif, A. Vanvalkenburg, Y. Alekseev, Q. Ma, G. Dayama, N. C. Lau, W. E. Johnson, W. R. Bishai, N. A. Crossland, J. D. Campbell, , I. Kramnik

This study identifies Myc dysregulation in macrophages as a driver of TB susceptibility by linking lipid peroxidation and IFN-I pathway hyperactivity.

bioRxiv · Mar 5, 2024Immunology

Analysis of nasopharyngeal microbiome patterns in Zambian infants with fatal acute febrile illness

A. R. Odom, J. McClintock, C. J. Gill, R. Pieciak, A. Ismail, W. B. MacLeod, W. E. Johnson, R. Lapidot

The paper analyzes nasopharyngeal microbiome patterns in Zambian infants to identify differences between those who develop fatal acute febrile illness and healthy controls.

bioRxiv · Sep 27, 2023 · PreprintMicrobiology

A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome

P. Chitale, A. D. Lemenze, E. C. Fogarty, A. Shah, C. A. Grady, A. R. Odom-Mabey, W. E. Johnson, J. H. Yang, A. M. Eren, R. Brosch, P. Kumar, D. Alland

The paper updates the M. tuberculosis H37Rv reference genome using Bact-Builder, revealing 6.4 kb of new sequence and ten new regions in widely used strains.

bioRxiv · Jul 15, 2022Microbiology

Recombinant Origin and Interspecies Transmission of a HERV-K(HML-2)-related Primate Retrovirus 1 With a Novel RNA Transport Element

Z. H. Williams, L. Gaucherand, D. C. Lee, S. M. Mostafa, J. Phelan, J. M. Coffin, W. E. Johnson

The paper identifies recent HML-2 provirus activity in rhesus macaques and shows interspecies transmission to gibbons, with a novel RNA transport element replacing the ancestral Rec-RcRE system.

bioRxiv · May 11, 2022Microbiology

Mechanistic investigation of SARS-CoV-2 Omicron variant spike mutants via full quantum mechanical modeling

M. Zaccaria, L. Genovese, B. Lawhorn, W. Dawson, A. S. Joyal, J. Hu, P. Autissier, T. Nakajima, W. E. Johnson, I. Fofana, M. Farzan, B. Momeni

The paper uses quantum mechanical modeling to predict and analyze binding strengths of SARS-CoV-2 spike variants to the human ACE2 receptor, validating predictions experimentally.

bioRxiv · Dec 1, 2021Biophysics

Anticipating future SARS-CoV-2 variants of concern through ab initio quantum mechanical modeling

M. Zaccaria, L. Genovese, M. Farzan, W. Dawson, T. Nakajima, W. E. Johnson, B. Momeni

This paper uses quantum mechanical modeling to predict the impact of SARS-CoV-2 mutations on hACE2 binding and identify potential future variants of concern.

bioRxiv · Nov 25, 2021Biophysics

Novel temporal and spatial patterns of metastatic colonization from rapid-autopsy tumor biopsies

X. Huang, Y. Qiao, S. W. Brady, R. E. Factor, E. Downs-Kelly, A. Farrell, J. A. McQuerry, G. Shrestha, D. F. Jenkins, W. E. Johnson, A. L. Cohen, A. H. Bild, G. T. Marth

This study uses rapid autopsy and whole genome sequencing to analyze metastatic evolution in a patient, identifying subclone incubators and four waves of metastatic expansion.

bioRxiv · Jun 3, 2021Cancer Biology

Species-specific differences in antagonism of APOBEC3 proteins by HIV-2 and SIVsmm Vif proteins

R. Nchioua, D. Kmiec, A. Gaba, C. M. Stürzel, T. Follack, S. Patrick, A. Kirmaier, W. E. Johnson, B. H. Hahn, L. Chelico, F. Kirchhoff

This study compares the ability of HIV-2 and SIVsmm Vif proteins to counteract human APOBEC3 proteins, showing HIV-2 acquired adaptive changes for efficient counteraction in humans.

bioRxiv · Sep 8, 2020 · PreprintImmunology

animalcules: Interactive Microbiome Analytics 1 and Visualization in R

W. E. Johnson, A. Federico, T. Faits, S. Manimaran, S. Monti, Y. Zhao

animalcules provides an interactive R toolkit for analyzing 16S rRNA, shotgun metagenomics, and metatranscriptomics data with visualization and machine learning tools.

bioRxiv · May 29, 2020Microbiology

The ancient fusogen EnvP(b)1 is expressed in human tissues and its structure informs the evolution of gammaretrovirus envelope proteins

K. R. McCarthy, J. L. Timpona, S. Jenni, V. Brusic, W. E. Johnson, S. P. J. WHELAN, L. R. Robinson-McCarthy

The paper identifies EnvP(b)1, an ancient retroviral envelope gene expressed in human tissues, and shows its structural similarity to modern leukemia virus Envs, suggesting a conserved scaffold for receptor binding evolution.

bioRxiv · Apr 22, 2020 · PreprintMicrobiology

Mountain lion genomes provide insights into genetic rescue of inbred populations

N. F. Saremi, M. A. Supple, A. Byrne, J. A. Cahill, L. L. Coutinho, L. Dalen, H. V. Figueiro, W. E. Johnson, H. J. Milne, S. J. O'Brien, B. O'Connell, D. P. Onorato, S. P. Riley, J. A. Sikich, D. R. Stahler, , B. Shapiro

The paper analyzes mountain lion genomes to study genetic rescue effects in inbred populations, finding that translocated individuals quickly lose genetic diversity due to local inbreeding.

bioRxiv · Nov 29, 2018 · PreprintEvolutionary Biology