Author

T. Hughes

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

Biology Disciplines

Click to filter author papers

Microbiology· 3 Biochemistry· 1 Bioengineering· 1 Cancer Biology· 1 Plant Biology· 1 Scientific Communication & Education· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Organism:human· 5 Research Focus:cell type annotation· 4 Approach:experimental assay· 4 Research Focus:differential expression· 3 Research Focus:gene regulatory network inference· 3 Research Focus:chromatin & epigenetic regulation· 2 Research Focus:clustering· 2 Research Focus:benchmarking· 1

Frequent Co-Authors

A. A. Webb· 1 shared A. Cano· 1 shared A. Gomez· 1 shared A. Greenland· 1 shared A. K. Shalek· 1 shared A. Nava· 1 shared A. Niemann· 1 shared A. Rohde· 1 shared

Activity by Year

2018-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 5 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

1 shared paperPlant Biology

A. A. Webb

Mutual co-authors in cluster

Author profile →

8 papers

Recent·Most cited

Single-strain behavior predicts responses to environmental pH and osmolality in the gut microbiota.

K. M. Ng, S. Pannu, S. Liu, J. C. Burckhardt, T. Hughes, W. Van Treuren, J. Nguyen, K. Naqvi, B. Nguyen, C. A. Clayton, D. M. Pepin, S. R. Collins, C. Tropini

This study predicts microbiota responses to environmental pH and osmolality by analyzing bacterial growth under controlled conditions and identifying predictive genes and pathways.

bioRxiv · Aug 31, 2022Microbiology

Overexpression of the WAPO-A1 gene increases the number of spikelets per spike in bread wheat

L. M. Wittern, J. M. Barrero, W. D. Bovill, K. L. Verbyla, T. Hughes, S. M. Swain, G. Steed, A. A. Webb, K. Gardner, A. Greenland, J. Jacobs, C. Frohberg, R.-C. Schmidt, C. Cavanagh, A. Rohde, , M. A. Hannah

This study identifies and functionally validates the WAPO1 gene's role in increasing spikelets per spike in wheat, showing its positive correlation with yield potential.

bioRxiv · Apr 1, 2022Plant Biology

Taxonomic classification methods reveal a new subgenus in the paramyxovirus subfamily Orthoparamyxovirinae

H. L. Wells, E. Loh, A. Nava, M. H. Lee, J. Lee, J. R. A. Sukor, I. Navarrete-Macias, E. Liang, C. Firth, J. Epstein, M. Rostal, C. Zambrana-Torrelio, K. A. Murray, P. Daszak, T. Goldstein, , S. J. Anthony

The paper uses taxonomic classification methods to identify a new subgenus in the Orthoparamyxovirinae subfamily based on viral genome sequences from bats.

bioRxiv · Oct 12, 2021Microbiology

Single-cell analysis reveals mechanisms of plasticity of leukemia initiating cells

V. Morris, W. Marion, T. Hughes, P. Sousa, P. Sensharma, Y. Pikman, M. Harris, A. K. Shalek, T. North, G. Q. Daley, E. Lummertz da Rocha, G. Rowe

The paper uses single-cell transcriptomics to show that leukemia initiating cells can convert between states, with MYC-driven oxidative phosphorylation controlling this plasticity.

bioRxiv · Apr 29, 2020 · PreprintCancer Biology

Optically Activated, Customizable, Excitable Cells- A Kuhl Platform for Evolving Next Gen Biosensors

M. A. Thomas, T. Hughes

The paper develops a high-throughput live cell system using optogenetics to screen voltage and Ca2+ sensors by modulating ion channels and cAMP levels.

bioRxiv · Feb 3, 2020 · PreprintBioengineering

Transparent and Reproducible Research Practices in the Surgical Literature

T. Hughes, A. Niemann, D. Tritz, K. Boyer, H. Robbins, M. Vassar

This study assesses transparency and reproducibility in surgical literature, finding low availability of materials, protocols, data, and analysis scripts, and minimal pre-registration and citations.

bioRxiv · Oct 7, 2019Scientific Communication & Education

Supragingival plaque microbiome ecology and functional potential in the context of health and disease

J. Espinoza, D. Harkins, M. Torralba, A. Gomez, S. Highlander, M. Jones, P. Leong, R. Saffery, M. Bockmann, C. Kuelbs, J. Inman, T. Hughes, J. M. Craig, K. E. Nelson, C. Dupont

This study examines the supragingival plaque microbiome in children to link microbial diversity and function to caries, identifying key metabolic pathways and novel microbes associated with disease.

bioRxiv · May 21, 2018Microbiology

A structural mechanism for directing inverse agonism of PPARγ

R. Brust, J. Shang, J. Fuhrmann, J. Bass, A. Cano, Z. Heidari, I. Chrisman, A.-L. Blayo, P. Griffin, T. Kamenecka, T. Hughes, D. Kojetin

The paper shows how a phenyl-to-pyridyl substitution in PPARγ ligands converts an antagonist to an inverse agonist through a water-mediated hydrogen bond network involving Arg288.

bioRxiv · Jan 17, 2018Biochemistry