Author

Kseniia Kholina

Duke 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 Synthetic Biology· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Organism:bacteria (other)· 1 Research Focus:benchmarking· 1 Assay:metagenomics· 1 Assay:protein sequence· 1 Research Focus:protein structure prediction· 1 Approach:statistical model· 1

Frequent Co-Authors

Pranam ChatterjeeiD· 2 shared Alexandra L. Hoffman· 1 shared Allison J. LopatkiniD· 1 shared Ashwini R. Shende· 1 shared César A. Villalobos· 1 shared Daniel Mark ShapiroiD· 1 shared Dongheon LeeiD· 1 shared Emma J. ChoryiD· 1 shared

Activity by Year

2024-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersSynthetic Biology

Pranam ChatterjeeORCID

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2 papers

Recent·Most cited

A foundation model for microbial growth dynamics

Zachary A. Holmes, Irida Shyti, Alexandra L. Hoffman, Katherine E. Duncker, Helena R. Ma, Zhengqing Zhou, Dongheon Lee, Rohan Maddamsetti, Kyeri Kim, Emrah Şimşek, Grayson S. Hamrick, Hye-In Son, César A. Villalobos, Jia Grace Lu, Yuanchi Ha, , Lingchong You

This paper develops a foundation model for microbial growth dynamics using self-supervised learning on diverse datasets, enabling accurate reconstruction and prediction of growth patterns and antibiotic responses.

bioRxiv · Dec 3, 2025 · PreprintSynthetic Biology

FusOn-pLM: A Fusion Oncoprotein-Specific Language Model via Focused Probabilistic Masking

Sophia Vincoff, Shrey Goel, Kseniia Kholina, Rishab Pulugurta, Pranay Vure, Pranam Chatterjee

This paper introduces FusOn-pLM, a protein language model fine-tuned on fusion oncoprotein sequences using a novel masked language modeling strategy, improving performance on specific benchmarks and disorder prediction tasks.

bioRxiv · Jun 3, 2024 · PreprintBioinformatics