Author

N. Youssef

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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Immunology· 4 Evolutionary Biology· 2 Microbiology· 1 Pharmacology & Toxicology· 1 Plant Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 4 Research Focus:host-pathogen & immune response· 3 Assay:proteomics· 3 Approach:statistical model· 3 Research Focus:cell type annotation· 2 Research Focus:chromatin & epigenetic regulation· 2 Approach:deep learning· 2 Research Focus:drug response / drug discovery· 2

Frequent Co-Authors

B. E. Fee· 2 shared D. Marks· 2 shared G. E. Hammer· 2 shared H.-I. Huang· 2 shared J. E. Stajich· 2 shared M. Couger· 2 shared N. N. Thadani· 2 shared P. Notin· 2 shared

Activity by Year

2019-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 12 mutual co-author links

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2 shared papersImmunology

B. E. Fee

Mutual co-authors in cluster

Author profile →

9 papers

Recent·Most cited

Protein design for evaluating vaccines against future viral variation

N. Youssef, S. Gurev, F. Ghantous, K. P. Brock, J. A. Jaimes, N. N. Thadani, A. Dauphin, A. C. Sherman, L. Yurkovetskiy, D. Soto, R. Estanboulieh, B. Kotzen, P. Notin, A. W. Kollasch, A. A. Cohen, , D. Marks

The paper designs SARS-CoV-2 Spike proteins with novel mutations to evaluate vaccine effectiveness against future viral variants using a deep learning model.

bioRxiv · Oct 8, 2023Immunology

GRK specificity and beta gamma dependency determines a GPCR`s potential in biased agonism

E. S. Matthees, J. C. Filor, N. Jaiswal, M. Reichel, N. Youssef, J. Drube, A. Godbole, C. Hoffmann

This paper shows that GRK2/3's interaction with Gβγ is essential for β-arrestin2 recruitment to GPCRs, linking G protein activation to biased agonism potential.

bioRxiv · Jul 14, 2023Pharmacology & Toxicology

Learning from pre-pandemic data to forecast viral escape

N. N. Thadani, S. Gurev, P. Notin, N. Youssef, N. J. Rollins, C. Sander, Y. Gal, D. Marks

This paper develops EVEscape, a framework predicting viral escape mutations using historical data and structural information, showing it can forecast SARS-CoV-2 variants as effectively as experimental methods.

bioRxiv · Jul 21, 2022Immunology

A tomato prolyl-4-hydroxylase causes relocation of abscission zone and alters abscission kinetics

P. Kalaitzis, A. Perrakis, D. Denic, K. N. Blazakis, E. Giannoutsou, D. Kaloudas, C. E. Bita, M. Rizou, A. Krokida, M. Kouhen, A. Lazaridou, K. Mekkaoui, S. Belaidi, Z. E. Zein, M. Khalil, , N. Kalogerakis

This study shows that altering tomato SlP4H3 expression shifts the abscission zone position and modifies ethylene-induced abscission timing depending on the developmental stage.

bioRxiv · Apr 20, 2021 · PreprintPlant Biology

Th17 immunity in the colon is controlled by two novel subsets of colon-specific mononuclear phagocytes

H.-I. Huang, M. L. Jewell, N. Youssef, M.-N. Huang, E. Hauser, B. E. Fee, N. P. Rudemiller, J. Privratsky, J. J. Zhang, E. Reyes, D. Wang, G. A. Taylor, M. D. Gunn, D. C. Ko, D. N. Cook, , G. E. Hammer

This study identifies two novel colon-specific mononuclear phagocyte subsets that are critical for Th17 immunity in the colon.

bioRxiv · Jan 28, 2021Immunology

The ups and downs of amino acid co-evolution: evolutionary Stokes and anti-Stokes shifts

N. Youssef, E. Susko, A. J. Roger, J. P. Bielawski

The paper identifies evolutionary Stokes and anti-Stokes shifts in amino acid propensities, showing that both can arise from epistatic interactions and that stabilizing substitutions are permissive while destabilizing ones are restrictive.

bioRxiv · Aug 31, 2020 · PreprintEvolutionary Biology

Irgm1-deficiency leads to myeloid dysfunction in colon lamina propria and susceptibility to the intestinal pathogen Citrobacter rodentium

G. Taylor, H.-I. Huang, B. E. Fee, N. Youssef, V. Cantillana, A. Schoenborn, A. R. Rogala, A. F. Buckley, B. A. Vallance, A. S. Gulati, G. E. Hammer

This study shows that Irgm1 deficiency causes myeloid cell dysfunction in the colon and increased susceptibility to Citrobacter rodentium infection, independent of intracellular killing.

bioRxiv · Mar 26, 2019Immunology

Molecular dating of the emergence of anaerobic rumen fungi and the impact of laterally acquired genes

Y. Wang, N. Youssef, M. Couger, R. Hanafy, M. Elshahed, J. E. Stajich

This study estimates the divergence time of anaerobic rumen fungi and identifies laterally acquired genes that contribute to their plant biomass degradation capabilities.

bioRxiv · Feb 28, 2019Evolutionary Biology

Horizontal gene transfer as an indispensible driver for Neocallimastigomycota evolution into a distinct gut-dwelling fungal lineage

C. Murphy, N. Youssef, R. A. Hanafy, M. Couger, J. E. Stajich, Y. Wang, K. Baker, S. Dagar, G. Griffith, I. Farag, T. Callaghan, M. S. Elshahed

This paper identifies 283 horizontal gene transfer events in anaerobic gut fungi, showing HGT's role in their adaptation to the herbivorous gut environment.

bioRxiv · Jan 30, 2019Microbiology