Author

B. D. Topcuoglu

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 Immunology· 1

Signature Assays, Organisms & Methods

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Assay:metagenomics· 5 Organism:human· 4 Approach:machine learning (classical)· 3 Research Focus:benchmarking· 2 Research Focus:clustering· 2 Approach:experimental assay· 2 Assay:bulk RNA-seq· 1 Approach:deep learning· 1

Frequent Co-Authors

P. D. Schloss· 4 shared C. R. Armour· 2 shared J. Wiens· 2 shared M. T. Ruffin· 2 shared N. A. Lesniak· 2 shared A. Garretto· 1 shared A. L. Reens· 1 shared B. Larson· 1 shared

Activity by Year

2019-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 12 mutual co-author links

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4 shared papersMicrobiology

P. D. Schloss

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Author profile →

6 papers

Recent·Most cited

Machine learning classification by fitting amplicon sequences to existing OTUs

C. R. Armour, K. L. Sovacool, W. L. Close, B. D. Topcuoglu, J. Wiens, P. D. Schloss

The paper evaluates OptiFit, a method to fit new sequences to existing OTUs, finding it performs as well or better than de novo and database-reference-based clustering in classifying colonic screen relevant neoplasia.

bioRxiv · Sep 1, 2022Microbiology

A Goldilocks Principle for the Gut Microbiome: Taxonomic Resolution Matters for Microbiome-Based Classification of Colorectal Cancer

C. R. Armour, B. D. Topcuoglu, A. Garretto, P. D. Schloss

This study finds that optimal taxonomic resolution for microbiome-based colorectal cancer classification is at the family level, with performance decreasing at finer resolutions like ASVs.

bioRxiv · Oct 22, 2021Microbiology

Vaccine Hyporesponse Induced By Individual Antibiotic Treatment In Mice And Non-Human Primates Is Diminished Upon Recovery Of The Gut Microbiome

G. Swaminathan, M. Citron, J. Xiao, J. E. Norton, A. L. Reens, B. D. Topcuoglu, J. M. Maritz, K.-J. Lee, D. Freed, T. M. Weber, C. H. White, M. Kadam, E. Spofford, E. Bryant-Hall, G. Salituro, , G. D. Hannigan

This study shows that antibiotic-induced gut microbiome disruption reduces vaccine response in mice and non-human primates, but recovery of microbiome diversity restores immune responses.

bioRxiv · Apr 2, 2021Immunology

Seafloor incubation experiment with deep-sea hydrothermal vent fluid reveals effect of pressureand lag time on autotrophic microbial communities

C. S. Fortunato, D. A. Butterfield, B. Larson, N. Lawrence-Slavas, C. Algar, L. Z. Allen, J. F. Holden, G. Proskurowski, E. Reddington, L. C. Stewart, B. D. Topcuoglu, J. J. Vallino, J. A. Huber

The paper compares in situ and shipboard microbial incubations of deep-sea hydrothermal vent fluids, finding that pressure and lag time affect microbial community activity and gene expression.

bioRxiv · Nov 11, 2020Microbiology

A framework for effective application of machine learning to microbiome-based classification problems

B. D. Topcuoglu, N. A. Lesniak, M. T. Ruffin, J. Wiens, P. D. Schloss

This paper evaluates ML models for predicting colonic neoplasias using 16S rRNA data, finding that L2-regularized logistic regression offers a balance of performance, speed, and interpretability.

mBio · Jun 30, 2020Peer-reviewedMicrobiology

Fecal short-chain fatty acids are not predictive of colonic tumor status and cannot be predicted based on bacterial community structure

M. A. Sze, B. D. Topcuoglu, N. A. Lesniak, M. T. Ruffin, P. D. Schloss

This study finds that fecal SCFA concentrations are not associated with colonic tumor status and cannot be predicted from bacterial community structure.

mBio · Aug 27, 2019Peer-reviewedMicrobiology