Author

A. J. Hockenberry

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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Evolutionary Biology· 3 Biophysics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:gene regulatory network inference· 2 Research Focus:protein folding & dynamics· 2 Assay:protein sequence· 2 Organism:bacteria (other)· 1 Assay:bulk RNA-seq· 1 Research Focus:chromatin & epigenetic regulation· 1 Approach:comparative / phylogenetic analysis· 1

Frequent Co-Authors

C. O. Wilke· 4 shared L. A. Amaral· 1 shared L. C. Vieira· 1 shared M. C. Jewett· 1 shared M. J. McGuffie· 1 shared M. M. Johnson· 1 shared

Activity by Year

2018-2023 · peak 2/yr

Co-Author Collaboration Network

6 top collaborators · 9 mutual co-author links

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4 shared papersEvolutionary Biology

C. O. Wilke

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4 papers

Recent·Most cited

Growth-dependent gene expression variation influences the strength of codon usage biases

M. M. Johnson, A. J. Hockenberry, M. J. McGuffie, L. C. Vieira, C. O. Wilke

The paper shows that growth rate-dependent gene expression variation significantly influences codon usage biases in microbial genomes.

bioRxiv · Mar 14, 2023Evolutionary Biology

Phylogenetic weighting does little to improve the accuracy of evolutionary coupling analyses

A. J. Hockenberry, C. O. Wilke

This study evaluates various weighting methods for evolutionary coupling analysis and finds that current best practices outperform alternatives, with minor benefits from sequence weighting compared to post-hoc scaling.

bioRxiv · Aug 15, 2019Evolutionary Biology

Evolutionary couplings detect side-chain interactions

A. J. Hockenberry, C. O. Wilke

This paper shows evolutionary coupling algorithms better detect side-chain interactions than backbone interactions, highlighting the importance of considering interaction types in contact prediction.

bioRxiv · Dec 20, 2018Biophysics

Selection removes Shine-Dalgarno-like sequences from within protein coding genes

A. J. Hockenberry, L. A. Amaral, M. C. Jewett, C. O. Wilke

The paper shows that Shine-Dalgarno sequences within bacterial genes are less conserved and likely deleterious, leading to reduced ATG start codons downstream.

bioRxiv · Mar 8, 2018Evolutionary Biology