Author

Shaked Afik

University of California, BerkeleyORCID 0000-0002-0287-1550Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 2 Assay:scRNA-seq· 2 Approach:statistical model· 2 Research Focus:cell-cell communication· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Organism:mouse· 1

Frequent Co-Authors

Nir YosefiD· 2 shared Arlene H Sharpe· 1 shared Daniel C Douek· 1 shared Eleanor J Barnes· 1 shared Gabriel Raulet· 1 shared Jernej Godec· 1 shared Kathleen B Yates· 1 shared Kevin Bi· 1 shared

Activity by Year

2017-2019 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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2 shared papersBioinformatics

Nir YosefORCID

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2 papers

Recent·Most cited

BioinformaticsLife Science AlliancePeer-reviewedAug 1, 2019

Reconstructing B cell receptor sequences from short-read single cell RNA-sequencing with BRAPeS

Shaked Afik, Gabriel Raulet, Nir Yosef

BRAPeS reconstructs B cell receptor sequences from short-read single cell RNA-sequencing with high accuracy and success rate.

9 citations

scRNA-seqstatistical model

𝕏 PostBluesky

BioinformaticsNucleic Acids ResearchPeer-reviewedJul 17, 2017

Targeted reconstruction of T cell receptor sequence from single cell RNA-sequencing links CDR3 length to T cell differentiation state

Shaked Afik, Kathleen B Yates, Kevin Bi…·Nir Yosef

This study develops TRAPeS, a tool to reconstruct TCR sequences from scRNA-seq data, and shows that CDR3 length correlates with T cell differentiation state in YFV-specific CD8+ T cells.

DOI 10.1093/nar/gkx615

𝕏 PostBluesky