Author

Benjamin Krummenacher

Carnegie Mellon University

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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Bioinformatics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:gene regulatory network inference· 2 Research Focus:cell-cell communication· 1 Research Focus:database / resource· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1 Organism:human· 1 Approach:machine learning (classical)· 1 Assay:protein sequence· 1

Frequent Co-Authors

David Ryan KoesiD· 2 shared A Hyun KimiD· 1 shared Abhinav AdduriiD· 1 shared Andrew T. McNuttiD· 1 shared Bahar Behsaz· 1 shared Caleb N. EllingtoniD· 1 shared Camilla Bodden· 1 shared Donghui YaniD· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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2 shared papersSystems Biology

David Ryan KoesORCID

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2 papers

Recent·Most cited

NEMO recruitment at single cytokine-receptor complexes shows quantized dynamics independent of ligand affinity

A Hyun Kim, Benjamin Krummenacher, Jason Yeung, David Ryan Koes, Robin Lee

The paper investigates how IL-1 receptor signaling dynamics are quantized and independent of ligand affinity using experimental and modeling approaches.

Cell Reports · Dec 1, 2025Peer-reviewedSystems Biology

Interpretable adenylation domain specificity prediction using protein language models

Abhinav Adduri, Andrew T. McNutt, Caleb N. Ellington, Krish Suraparaju, Nan Fang, Donghui Yan, Benjamin Krummenacher, Sitong Li, Camilla Bodden, Eric P. Xing, Bahar Behsaz, David Ryan Koes, Hosein Mohimani

The paper introduces MASPR, a machine learning method using protein language models to predict adenylation domain substrate specificities, enabling the prediction of hybrid NRP-PK natural products.

bioRxiv · Jan 13, 2025 · PreprintBioinformatics