Author

Shreya Basnet

University of Missouri

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· 3

Signature Assays, Organisms & Methods

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Assay:ChIP-seq· 3 Research Focus:differential expression· 3 Approach:deep learning· 2 Organism:human· 2 Approach:transformer / foundation model· 2 Research Focus:benchmarking· 1 Approach:contrastive learning· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Jianlin Jack ChengiD· 3 shared Lyuwei WangiD· 1 shared Ping Liu· 1 shared

Activity by Year

2026-2026 · peak 3/yr

Co-Author Collaboration Network

3 top collaborators · 3 mutual co-author links

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3 shared papersBioinformatics

Jianlin Jack ChengORCID

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3 papers

Recent·Most cited

TransBind2: Improving Transcription Factor-DNA Binding Prediction with Multimodal Data and Bidirectional Cross Attention

Shreya Basnet, Jianlin Jack Cheng

TransBind2 improves TF-DNA binding prediction by integrating TF structure, chromatin context, and bidirectional cross-attention, achieving high accuracy across human ChIP-seq data and cross-species predictions.

bioRxiv · Sep 14, 2026 · PreprintBioinformatics

TFBindFormer: A Cross-Attention Transformer for Transcription Factor-DNA Binding Prediction

Ping Liu, Lyuwei Wang, Shreya Basnet, Jianlin Jack Cheng

TFBindFormer improves TF-DNA binding prediction by integrating DNA and TF protein features using cross-attention, outperforming DNA-only models.

bioRxiv · Apr 15, 2026 · PreprintBioinformatics

Integrating Protein and DNA Embeddings for Improving Genome-Wide Transcription Factor Binding Site Prediction

Shreya Basnet, Jianlin Jack Cheng

TransBind improves TF binding site prediction by integrating DNA sequences with protein embeddings, achieving higher accuracy and generalizability for new TFs.

NAR Genomics and Bioinformatics · Mar 27, 2026Peer-reviewedBioinformatics