Author

Nirali Somia

Cold Spring Harbor Laboratory

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

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Bioinformatics· 1 Genetics· 1 Genomics· 1

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Research Focus:benchmarking· 2 Assay:DNA methylation· 2 Research Focus:gene regulatory network inference· 2 Assay:bulk RNA-seq· 1 Organism:C. elegans· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Approach:diffusion model· 1

Frequent Co-Authors

Peter K. KooiD· 2 shared Yiyang YuiD· 2 shared Ziqi TangiD· 2 shared Alejandra DurániD· 1 shared Anirban SarkariD· 1 shared Caroline AragóniD· 1 shared Da-Wei LiniD· 1 shared Divya Alley· 1 shared

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2024-2025 · peak 2/yr

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10 top collaborators · 29 mutual co-author links

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2 shared papersBioinformatics

Peter K. KooORCID

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3 papers

Recent·Most cited

Evaluating the representational power of pre-trained DNA language models for regulatory genomics

Ziqi Tang, Nirali Somia, Yiyang Yu, Peter K. Koo

This study evaluates pre-trained DNA language models' ability to predict and interpret cell-type-specific functional genomics data, finding they do not outperform conventional machine learning approaches.

Genome biology · Jul 14, 2025Peer-reviewedBioinformatics

The L1CAM SAX-7 is an antagonistic modulator of Erk signaling

Melinda Moseley-Alldredge, Caroline Aragón, Marcus Vargus, Divya Alley, Nirali Somia, Lihsia Chen

The paper shows SAX-7/L1CAM antagonizes ERK signaling in both neuronal and non-neuronal processes in C. elegans.

bioRxiv · Sep 14, 2024 · PreprintGenetics

Designing DNA With Tunable Regulatory Activity Using Discrete Diffusion

Anirban Sarkar, Alejandra Durán, Yiyang Yu, Da-Wei Lin, Yijie Kang, Nirali Somia, Pablo Mantilla, Jessica Zhou, Masayuki Nagai, Ziqi Tang, Kaarina Hanington, Kenneth Chang, Peter K. Koo

This paper introduces D3, a generative model for designing regulatory DNA with tunable activity, showing improved performance over baselines in sequence generation and activity prediction.

bioRxiv · May 23, 2024 · PreprintGenomics