Author

Navid Naderializadeh

Duke UniversityORCID 0000-0002-4891-6726Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 4

Signature Assays, Organisms & Methods

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Approach:optimal transport· 3 Assay:protein sequence· 3 Research Focus:deconvolution· 1 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Research Focus:perturbation response prediction· 1 Research Focus:protein structure prediction· 1 Assay:proteomics· 1

Frequent Co-Authors

Rohit SinghiD· 2 shared Christian DallagoiD· 1 shared Erik J. SoderblomiD· 1 shared Sahil S Patel· 1 shared Scott H. SoderlingiD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

5 top collaborators · 3 mutual co-author links

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2 shared papersBioinformatics

Rohit SinghORCID

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4 papers

Recent·Most cited

EvoPool: Evolution-Guided Pooling of Protein Language Model Embeddings

Navid Naderializadeh, Rohit Singh

EvoPool improves variant effect prediction by integrating evolutionary information into protein language model embeddings using optimal transport.

bioRxiv · Feb 4, 2026 · PreprintBioinformatics

Context-Aware Protein Representations Using Protein Language Models and Optimal Transport

Sahil S Patel, Navid Naderializadeh

COPTER improves protein representation by incorporating context using optimal transport, achieving better performance in drug target and perturbation response predictions.

bioRxiv · Jan 26, 2026 · PreprintBioinformatics

Protein Language Model-Aligned Spectra Embeddings for De Novo Peptide Sequencing

Navid Naderializadeh, Christian Dallago, Erik J. Soderblom, Scott H. Soderling

PLMNovo improves de novo peptide sequencing by aligning spectrum and peptide embeddings using pre-trained protein language models.

bioRxiv · Oct 1, 2025 · PreprintBioinformatics

Aggregating Residue-Level Protein Language Model Embeddings with Optimal Transport

Navid Naderializadeh, Rohit Singh

This paper introduces an optimal transport-based method to aggregate residue-level protein language model embeddings into fixed-length representations, showing improved performance over average pooling for downstream tasks.

Bioinformatics Advances · Dec 26, 2024Peer-reviewedBioinformatics