Author

B. C. Thomas

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· 12 Cancer Biology· 2 Immunology· 2 Paleontology· 1

Signature Assays, Organisms & Methods

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Assay:metagenomics· 11 Approach:experimental assay· 8 Organism:human· 8 Approach:statistical model· 8 Research Focus:cell type annotation· 6 Research Focus:clustering· 5 Research Focus:differential expression· 4 Research Focus:ecology & biodiversity· 4

Frequent Co-Authors

J. F. Banfield· 11 shared K. Anantharaman· 4 shared M. R. Olm· 3 shared A. J. Armstrong· 2 shared A. Lavy· 2 shared A.-M. Cepika· 2 shared C. Waichler· 2 shared D. Burstein· 2 shared

Activity by Year

2017-2024 · peak 7/yr

Co-Author Collaboration Network

10 top collaborators · 10 mutual co-author links

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11 shared papersMicrobiology

J. F. Banfield

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Author profile →

17 papers

Recent·Most cited

Epigenetic signature and key transcriptional regulators of human antigen-specific type 1 regulatory T cells

A.-M. Cepika, L. Amaya, C. Waichler, M. Narula, M. M. Mantilla, B. C. Thomas, P. P. Chen, R. A. Freeborn, M. Pavel-Dinu, J. Nideffer, M. Porteus, R. Bacchetta, F. Mueller, W. J. Greenleaf, H. Y. Chang, M. G. Roncarolo

This study identifies the epigenetic signature and key transcription factors regulating human antigen-specific Tr1 cells, revealing their unique biology and potential for therapeutic applications.

bioRxiv · Mar 7, 2024 · PreprintImmunology

AML/T cell interactomics uncover correlates of patient outcomes and the key role of ICAM1 in T cell killing of AML

E. C. Sayitoglu, B. A. Luca, A. P. Boss, B. C. Thomas, R. A. Freeborn, M. J. Uyeda, P. P. Chen, Y. Nakauchi, C. Waichler, N. J. Lacayo, R. Bacchetta, R. Majeti, A. J. Gentles, A.-M. Cepika, M. G. Roncarolo

The paper identifies ICAM1 as a key factor in T cell killing of AML by analyzing transcriptional programs in AML and T cell interactions.

bioRxiv · Sep 21, 2023Immunology

A synthetic lethal screen for Snail-induced enzalutamide resistance identifies JAK/STAT signaling as a therapeutic vulnerability in prostate cancer

K. E. Ware, B. C. Thomas, P. Olawuni, M. U. Sheth, N. Hawkey, Y. M, B. C. Miller, K. Vietor, M. K. Jolly, S. Y. Kim, A. J. Armstrong, J. A. Somarelli

The paper identifies JAK/STAT signaling as a therapeutic target for Snail-induced enzalutamide-resistant prostate cancer through synthetic lethal screens and validation in a resistant cell model.

bioRxiv · Nov 15, 2022Cancer Biology

Subsurface carbon monoxide oxidation capacity revealed through genome-resolved metagenomics of a carboxydotroph

A. Mu, B. C. Thomas, J. Banfield, J. W. Moreau

The paper uses genome-resolved metagenomics to show a shift in CO-oxidation potential by Carboxydocella in a deep aquifer after CO2 injection.

bioRxiv · Jun 25, 2020Microbiology

Convergent evolution of p38/MAPK activation in hormone resistant prostate cancer mediates pro-survival, immune evasive, and metastatic phenotypes

K. E. Ware, S. Gupta, J. Eng, G. Kemeny, B. J. Puviindran, W.-C. Foo, L. A. Crawford, R. G. Almquist, D. Runyambo, B. C. Thomas, M. U. Sheth, A. Agarwal, M. Pierobon, E. F. Petricoin, D. L. Corcoran, , J. Somarelli

This study identifies p38/MAPK pathway activation as a convergent mechanism driving survival, immune evasion, and metastasis in hormone-resistant prostate cancer.

bioRxiv · Apr 22, 2020 · PreprintCancer Biology

Genome-resolved metagenomics and detailed geochemical speciation analyses yield new insights into microbial mercury cycling in geothermal springs

C. Gionfriddo, M. Stott, J. F. Power, J. M. Ogorek, D. P. Krabbenhoft, R. R. Wick, K. E. Holt, L.-X. Chen, B. C. Thomas, J. F. Banfield, J. W. Moreau

This paper identifies microorganisms involved in mercury cycling in geothermal springs using metagenomics and geochemical analysis, revealing new insights into microbial mercury speciation and biogeochemical processes.

bioRxiv · Feb 3, 2020Microbiology

Differential gene expression and the importance of regulatory ncRNAs in acidophilic microorganisms

D. S. Aliaga Goltsman, L. Hauser, M. Dasari, B. C. Thomas, J. F. BANFIELD

The paper analyzes gene expression in acidophilic microorganisms, showing how environmental conditions shape transcriptional profiles and highlighting the role of non-coding RNAs in gene regulation.

bioRxiv · Feb 2, 2019 · PreprintMicrobiology

Processing of grassland soil C-N compounds into soluble and volatile molecules is depth stratified and mediated by genomically novel bacteria and archaea

S. Diamond, P. Andeer, Z. Li, A. Crits-Christoph, D. Burstein, K. Anantharaman, K. R. Lane, B. C. Thomas, C. Pan, T. Northen, J. F. Banfield

The paper links genomically novel soil microbes to depth-stratified carbon and nitrogen cycling by analyzing metagenomic and proteomic data from grassland soils.

bioRxiv · Oct 17, 2018 · PreprintMicrobiology

Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock

A. Lavy, D. Geller McGrath, P. B. Matheus Carnevali, J. Wan, W. Dong, T. Tokunaga, B. C. Thomas, K. H. Williams, S. Hubbard, J. F. Banfield

The paper examines microbial community structure and function across a hillslope-riparian transect, finding that proximity to the stream, groundwater, and weathered bedrock significantly influences microbial composition and metabolic potential.

bioRxiv · Sep 21, 2018Microbiology

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome

D. S. A. Goltsman, C. L. Sun, D. M. Proctor, D. B. DiGiulio, A. Robaczewska, B. C. Thomas, G. M. Shaw, D. K. Stevenson, S. P. Holmes, J. F. Banfield, D. A. Relman

This study uses metagenomic analysis with strain-level resolution to examine the human pregnancy microbiome, revealing gestational age and health complications influence microbial community composition and function.

bioRxiv · Aug 21, 2018Microbiology

Megaphage infect Prevotella and variants are widespread in gut microbiomes

A. E. Devoto, J. M. Santini, M. R. Olm, K. Anantharaman, P. Munk, J. Tung, E. A. Archie, P. J. Turnbaugh, K. D. Seed, R. Blekhman, F. M. Aarestrup, B. C. Thomas, J. F. Banfield

The paper identifies large phage (Lak phage) in gut microbiomes that infect Prevotella and are widespread, especially in developing-world individuals.

bioRxiv · Jun 27, 2018Microbiology

Hydrogen-based metabolism - An ancestral trait in lineages sibling to the Cyanobacteria

P. B. Matheus Carnevali, F. Schulz, C. J. Castelle, R. Kantor, P. Shih, I. Sharon, J. Santini, M. Olm, Y. Amano, B. C. Thomas, K. Anantharaman, D. Burstein, E. D. Becraft, R. Stepanauskas, T. Woyke, J. F. Banfield

This paper predicts the metabolisms of Margulisbacteria and Saganbacteria using genomic data and compares them to their phylogenetic neighbors, supporting the hypothesis that their ancestor used hydrogen metabolism and fermentation.

bioRxiv · May 25, 2018Microbiology

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms

B. Brooks, M. R. Olm, B. A. Firek, R. Baker, D. Geller-McGrath, S. R. Reimer, K. R. Soenjoyo, J. S. Yip, D. Dahan, B. C. Thomas, M. J. Morowitz, J. F. Banfield

The paper investigates how the gut microbiome of premature infants shapes the microbial composition of NICU rooms over time.

bioRxiv · May 7, 2018Microbiology

Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles

C. T. Brown, W. Xiong, M. R. Olm, B. C. Thomas, R. Baker, B. Firek, M. J. Morowitz, R. L. Hettich, J. F. Banfield

This study examines microbial colonization in premature infants, finding distinct proteomic profiles among related bacterial strains and correlations with NEC development.

bioRxiv · Mar 6, 2018Microbiology

Terrestrial effects of moderately nearby supernovae

A. L. Melott, B. C. Thomas

The paper examines the terrestrial effects of moderately nearby supernovae, finding increased cancer and mutation rates in large organisms and heightened lightning and wildfire activity due to cosmic rays.

bioRxiv · Dec 8, 2017Paleontology

Dramatic expansion of microbial groups that shape the global sulfur cycle

K. Anantharaman, S. P. Jungbluth, R. S. Kantor, A. Lavy, L. A. Warren, M. S. Rappe, B. C. Thomas, J. F. Banfield

This study identifies sulfate reduction capacity in twelve bacterial and archaeal phyla, doubling the known diversity of microbes involved in the sulfur cycle.

bioRxiv · Jul 21, 2017Microbiology

Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy

C. M. K. Sieber, A. J. Probst, A. Sharrar, B. C. Thomas, M. Hess, S. G. Tringe, J. F. Banfield

This paper introduces DAS Tool, a metagenomic binning method that improves genome recovery accuracy and completeness across diverse samples.

bioRxiv · Feb 11, 2017Microbiology