Author

A. K. Aditham

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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Biophysics· 3 Microbiology· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 3 Assay:DNA methylation· 3 Research Focus:cell type annotation· 2 Assay:ChIP-seq· 2 Research Focus:chromatin & epigenetic regulation· 2 Research Focus:gene regulatory network inference· 2 Organism:yeast· 2 Research Focus:drug response / drug discovery· 1

Frequent Co-Authors

P. M. Fordyce· 2 shared A. A. Shrikumar· 1 shared A. Afek· 1 shared A. Chavez· 1 shared A. F. Kratz· 1 shared A. Kundaje· 1 shared A. M. Alexandari· 1 shared A. M. Keys· 1 shared

Activity by Year

2017-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 18 mutual co-author links

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2 shared papersBiophysics

P. M. Fordyce

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Author profile →

4 papers

Recent·Most cited

The Functional Landscape of SARS-CoV-2 3CL Protease

S. Iketani, S. J. Hong, J. Sheng, F. Bahari, B. Culbertson, F. F. Atanaki, A. K. Aditham, A. F. Kratz, M. I. Luck, R. Tian, S. P. Goff, H. Montazeri, Y. Sabo, D. D. Ho, A. Chavez

This study maps the functional landscape of SARS-CoV-2 3CL protease by profiling all single mutants and identifies resistance mutations to nirmatrelvir.

bioRxiv · Jun 23, 2022 · PreprintMicrobiology

Short tandem repeats bind transcription factors to tune eukaryotic gene expression

C. A. Horton, A. M. Alexandari, M. G. B. Hayes, E. Marklund, J. M. Schaepe, A. K. Aditham, N. Shah, A. A. Shrikumar, A. Afek, W. J. Greenleaf, R. Gordan, J. Zeitlinger, A. Kundaje, P. M. Fordyce

This study shows STRs modulate TF-DNA interactions by altering binding affinities and on rates, impacting gene expression through increased TF density near target sites.

bioRxiv · May 24, 2022Biophysics

High-throughput binding affinity measurements for mutations spanning a transcription factor-DNA interface reveal affinity and specificity determinants

A. K. Aditham, C. J. Markin, D. A. Mokhtari, N. V. DelRosso, P. M. Fordyce

The paper measures binding affinities of TF mutants and DNA variants to identify affinity and specificity determinants in the TF-DNA interface.

bioRxiv · Jun 22, 2020Biophysics

Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding

D. D. Le, T. C. Shimko, A. K. Aditham, A. M. Keys, Y. Orenstein, P. Fordyce

The paper measures TF-DNA binding energies for yeast TFs using a novel sequencing assay and finds that flanking mutations significantly affect binding energy, challenging current site definitions.

bioRxiv · Sep 26, 2017Biophysics