Author

Akshay Tambe

California Institute of Technology

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· 2 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Research Focus:clustering· 1 Approach:deep learning· 1 Research Focus:dimensionality reduction· 1 Approach:experimental assay· 1 Approach:graph neural network· 1 Assay:scRNA-seq· 1

Frequent Co-Authors

Adrian L. SanborniD· 1 shared April Schleck· 1 shared Ayah AbdeldayemiD· 1 shared Bo Li· 1 shared Brandon AndersoniD· 1 shared Brent TownshendiD· 1 shared Connor J. StephensiD· 1 shared Gabriel FernsiD· 1 shared

Activity by Year

2017-2023 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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1 shared paperBioinformatics

Adrian L. SanbornORCID

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3 papers

Recent·Most cited

ATOM-1: A Foundation Model for RNA Structure and Function Built on Chemical Mapping Data

Nicholas R. Boyd, Brandon Anderson, Brent Townshend, Ryan Chow, Connor J. Stephens, Ramya Rangan, Matias Kaplan, Meredith Corley, Akshay Tambe, Yuzu Ido, Jake Yukich, Tabitha Tcheau, Ayah Abdeldayem, Gabriel Ferns, Harsh Patel, , Raphael J.L. Townshend

ATOM-1 is an RNA foundation model trained on chemical mapping data, enabling state-of-the-art RNA prediction tasks through small probe neural networks.

bioRxiv · Dec 13, 2023 · PreprintBioinformatics

Barcode identification for single cell genomics

Akshay Tambe, Lior S. Pachter

The paper introduces a method to identify and error-correct DNA barcodes in single-cell sequencing by traversing a de Bruijn graph, improving transcriptome recovery.

BMC Bioinformatics · Jan 17, 2019Peer-reviewedBioinformatics

Prober: A general toolkit for analyzing sequencing-based ‘toeprinting’ assays

Bo Li, Akshay Tambe, Sharon Aviran, Lior Pachter

PROBer is a statistical model that addresses computational challenges in sequencing-based toeprinting assays by learning isoform-specific chemical modification profiles.

Cell Systems · May 1, 2017Peer-reviewedGenomics