Author

B. A. Simmons

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 Ecology· 4 Bioengineering· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 5 Assay:proteomics· 4 Research Focus:ecology & biodiversity· 3 Assay:metagenomics· 3 Approach:statistical model· 3 Organism:bacteria (other)· 2 Research Focus:benchmarking· 2 Approach:experimental assay· 2

Frequent Co-Authors

C. J. Petzold· 4 shared Y. Chen· 4 shared P. D. Adams· 3 shared S. W. Singer· 3 shared A. Eudes· 2 shared A. Mukhopadhyay· 2 shared B. Fong· 2 shared H. Scheller· 2 shared

Activity by Year

2018-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 34 mutual co-author links

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4 shared papersMicrobiology

C. J. Petzold

Mutual co-authors in cluster

Author profile →

10 papers

Recent·Most cited

A murky ruling threatens the fate of millions of US wetlands

B. A. Simmons, M. W. Beck, K. Flaherty-Walia, J. Lewis, E. T. Sherwood

The paper estimates that 22-36% of US wetlands could lose federal protections under the Clean Water Act due to the Sackett v. EPA ruling, with the Midwest and Northeast at highest risk.

bioRxiv · Nov 14, 2023Ecology

Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in Pseudomonas putida M2

S. Shrestha, D. Awasthi, Y. Chen, J. W. Gin, C. J. Petzold, P. D. Adams, B. A. Simmons, S. Singer

This study investigates carbon catabolite repression in Pseudomonas putida M2 during simultaneous sugar and aromatic co-utilization, revealing simultaneous repression by sugars and aromatics and the role of crc and small RNAs.

bioRxiv · May 23, 2023 · PreprintMicrobiology

Revealing Pentose Catabolism in Pseudomonas putida

M.-R. Park, R. Gauttam, B. Fong, Y. Chen, H. G. Lim, A. Feist, A. Mukhopadhyay, C. J. Petzold, B. A. Simmons, S. W. Singer

The paper identifies three Pseudomonas putida isolates with diverse pentose catabolism capabilities and characterizes their genes and pathways for xylose and arabinose oxidation.

bioRxiv · Oct 5, 2022 · PreprintMicrobiology

Mapping the risks of China's global coastal development to marine socio-ecological systems

B. A. Simmons, N. Butt, C. C. O'Hara, R. Ray, Y. Ma, K. P. Gallagher

This study assesses the risks of China's overseas coastal development projects on marine biodiversity and Indigenous communities, identifying high-risk sectors and regions.

bioRxiv · Apr 22, 2022 · PreprintEcology

Assessing Comparative Microbiome Performance in Plant Cell Wall Deconstruction Using Multi-omics-Informed Network Analysis

L. M. Tom, M. Aulitto, Y.-W. Wu, Y. W. Gao, K. Deng, N. Xiao, B. G. Rodriguez, C. Louime, T. R. Northen, A. Eudes, J. Mortimer, P. D. Adams, H. Scheller, B. A. Simmons, J. Ceja-Navarro, S. W. Singer

The paper assesses microbiome performance in plant cell wall deconstruction using network analysis and identifies key microbial populations and enzymes involved.

bioRxiv · Jan 7, 2022 · PreprintMicrobiology

Delivering on Biden's 2030 conservation commitment

B. A. Simmons, C. Nolte, J. McGowan

The paper evaluates different strategies for achieving the 30x30 conservation target in the U.S., highlighting trade-offs in costs, ecosystem representation, and climate mitigation potential across objectives.

bioRxiv · Feb 28, 2021 · PreprintEcology

The status of current and tentative marine natural World Heritage areas

C. Kuempel, B. A. Simmons, M. Davey

The paper assesses human impacts and representation in marine natural World Heritage areas, finding high impacts in tentative sites and gaps in ecoregion and species coverage.

bioRxiv · Feb 28, 2021 · PreprintEcology

Succession of physiological stages hallmarks the transcriptomic response of fungus Aspergillus niger to lignocellulose

J. M. van Munster, P. Daly, M. J. Blythe, R. Ibbett, M. Kokolski, S. Gaddipati, E. Lindquist, V. R. Singan, K. W. Barry, A. M. Lipzen, C. Y. Ngan, C. J. Petzold, L. J. G. Chan, M. Arvas, R. Raulo, , D. B. Archer

This study identifies physiological stages in Aspergillus niger's transcriptomic response to lignocellulose substrates, showing conserved metabolic patterns and substrate-specific adaptations.

bioRxiv · Oct 17, 2019Microbiology

The response of Pseudomonas putida to a complex lignolysate

M.-R. Park, Y. Chen, M. G. Thompson, V. Benites, B. Fong, C. J. Petzold, E. E. K. Baidoo, J. Gladden, P. D. Adams, J. D. Keasling, B. A. Simmons, S. Singer

This paper shows that Pseudomonas putida can grow on lignolysate from sorghum, using aromatic monomers and other unknown factors like amino acids and ionic liquid.

bioRxiv · Sep 10, 2019 · PreprintMicrobiology

Methyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids

J. Dong, Y. Chen, V. T. Benites, E. Baidoo, C. Petzold, H. Beller, A. Eudes, H. Scheller, P. Adams, A. Mukhopadhyay, B. A. Simmons, S. W. Singer

This study enhances methyl ketone production in Pseudomonas putida using plant-derived amino acids from hydrolysates, achieving a 9-fold increase in titer.

bioRxiv · Dec 13, 2018Bioengineering