Author

M. Thompson

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· 6 Bioengineering· 3 Animal Behavior & Cognition· 1 Biochemistry· 1 Biophysics· 1 Ecology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:experimental assay· 7 Approach:statistical model· 5 Approach:deep learning· 4 Research Focus:drug response / drug discovery· 3 Organism:human· 3 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Assay:DNA methylation· 2

Frequent Co-Authors

J. D. Keasling· 4 shared A. Mukhopadhyay· 3 shared C. J. Petzold· 2 shared J. S. Fraser· 2 shared M. J. S. Kelly· 2 shared P. Cruz-Morales· 2 shared P. M. Shih· 2 shared T. Kortemme· 2 shared

Activity by Year

2018-2023 · peak 6/yr

Co-Author Collaboration Network

10 top collaborators · 22 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

4 shared papersMicrobiology

J. D. Keasling

Mutual co-authors in cluster

Author profile →

13 papers

Recent·Most cited

Genetically refactored Agrobacterium-mediated transformation

M. Thompson, L. D. Kirkpatrick, G. M. Geiselman, L. M. Waldburger, A. N. Pearson, M. Szarzanowicz, K. M. Vuu, K. Markel, N. F. Hummel, D. D. Suazo, C. Tahmin, R. Cui, S. Liu, J. Cevallos, H. Pannu, , P. M. Shih

This paper refactors the Agrobacterium tumor-inducing plasmid into a minimal set of genes for plant and fungal transformation, demonstrating a bottom-up engineering approach.

bioRxiv · Oct 13, 2023 · PreprintMicrobiology

Honeybee cognition as a tool for scientific engagement

J. A. Denton, I. Koludarov, M. Thompson, J. Bryk, M. Velasque

The paper demonstrates how honeybee cognition can be used to engage high-school students in scientific research, showing caffeine improves learning while dopamine does not.

bioRxiv · May 8, 2021Animal Behavior & Cognition

Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study

A. E. Kim, E. Brandstetter, N. Wilcox, J. Heimonen, C. Graham, P. D. Han, L. M. Starita, D. J. McCulloch, A. M. Casto, D. A. Nickerson, M. M. Van de Loo, J. Mooney, M. Ilcisin, K. A. Fay, J. Lee, , H. Chu

The paper evaluates the quality of specimens and results from a home-based respiratory surveillance study to assess its feasibility for community-level monitoring of respiratory pathogens.

bioRxiv · Dec 7, 2020Microbiology

Functional analysis of the fatty acid and alcohol metabolism of Pseudomonas putida using RB-TnSeq

M. Thompson, M. Incha, A. Pearson, M. Schmidt, W. Sharpless, C. Eiben, P. Cruz-Morales, J. Blake-Hedges, Y. Liu, C. Adams, R. Haushalter, R. Krishna, P. Lichtner, L. M. Blank, A. Mukhopadhyay, , J. D. Keasling

This study uses RB-TnSeq to functionally analyze fatty acid and alcohol metabolism in Pseudomonas putida, identifying gene roles and catabolic pathways for isoprenol and isopentanol.

Applied and Environmental Microbiology · Oct 15, 2020Peer-reviewedMicrobiology

Chemoinformatic-guided engineering of polyketide synthases

A. Zargar, R. Lal, L. Valencia, J. Wang, T. Backman, P. Cruz-Morales, A. Kothari, M. Werts, A. Wong, C. B. Bailey, A. Loubat, Y. Liu, Y. Chen, V. Benites, S. Chang, , J. D. Keasling

This study uses chemoinformatics to engineer polyketide synthases for producing saturated β-carbon compounds, finding a correlation between chemical similarity and product titers.

bioRxiv · May 10, 2020Biochemistry

Low Intensity Vibration Restores Nuclear YAP Levels and Acute YAP Nuclear Shuttling in Mesenchymal Stem Cells Subjected to Simulated Microgravity

M. Thompson, K. Woods, J. K. Newberg, J. T. Oxford, G. Uzer

This study shows that low intensity vibration (LIV) restores YAP nuclear levels and enhances YAP nuclear entry in mesenchymal stem cells under simulated microgravity.

bioRxiv · May 4, 2020Bioengineering

Population dynamics analysis of Saccharomyces cerevisiae deletion library during fed-batch cultivation using Bar-seq

M. Wehrs, M. Thompson, D. Banerjee, J.-P. Prahl, C. A. Barcelos, J. Moon, N. M. Morella, Z. Costello, J. D. Keasling, P. M. Shih, D. Tanjore, A. Mukhopadhyay

The paper uses Bar-seq to analyze population dynamics of a yeast deletion library during fed-batch cultivation, identifying genes associated with stress responses in industrial fermentation.

bioRxiv · Apr 27, 2020Microbiology

Expanding the space of protein geometries by computational design of de novo fold families

X. Pan, M. Thompson, Y. Zhang, L. Lin, J. S. Fraser, M. J. S. Kelly, T. Kortemme

A computational method expands the structure space of designer proteins by systematically sampling loop-helix-loop geometries.

bioRxiv · Apr 14, 2020Bioengineering

Winner(s)-take-all: nonlinear amplification of DNA-encoded library

M. Cui, F. Reddavide, S. Heiden, M. Thompson, L. Mannocci, Y. Zhang

This paper develops a winner(s)-take-all method for nonlinear amplification of DNA-encoded libraries, demonstrating its application in decoding DNA-encoded chemical libraries.

bioRxiv · Aug 24, 2019 · PreprintBioengineering

Growth behavior and glyphosate resistance level in 10 biotypes of Echinochloa colona in Australia

G. Mahajan, V. Kaur, M. Thompson, B. S. Chauhan

This study examines growth behavior and glyphosate resistance in 10 biotypes of Echinochloa colona in Australia, finding significant variation in growth traits and resistance levels, with some biotypes being highly resistant and productive.

bioRxiv · Aug 7, 2019Ecology

Computational design of a modular protein sense/response system

A. A. Glasgow, Y.-M. Huang, D. J. Mandell, M. Thompson, R. Ritterson, A. L. Loshbaugh, J. Pellegrino, C. Krivacic, R. A. Pache, K. A. Barlow, N. Ollikainen, D. Jeon, M. J. S. Kelly, J. S. Fraser, T. Kortemme

This paper designs modular protein sensors that respond to specific small molecule inputs using a computational strategy.

bioRxiv · May 24, 2019Biophysics

Large-scale chemical-genetics yields new Mycobacterium tuberculosis inhibitor classes

E. O. Johnson, E. LaVerriere, M. Stanley, E. Office, E. Meyer, T. Kawate, J. Gomez, R. E. Audette, N. Bandyopadhyay, N. Betancourt, K. Delano, I. Da Silva, J. Davis, C. Gallo, M. Gardner, , Schnappinge

This study uses a novel chemical-genetics screening strategy to identify new inhibitors of Mycobacterium tuberculosis, revealing novel compound classes targeting previously unexplored bacterial targets.

bioRxiv · Jan 16, 2019Microbiology

Modeling the temporal dynamics of the gut microbial community in adults and infants

L. Shenhav, O. Furman, L. Briscoe, M. Thompson, I. Mizrahi, E. Halperin

The paper introduces MTV-LMM, a model for predicting gut microbiome temporal dynamics, and shows it outperforms existing methods by revealing significant time-dependent microbial patterns in both infants and adults.

bioRxiv · Apr 5, 2018Microbiology