Author

Jonathan T. Smith

Broad InstituteORCID 0000-0002-4279-8220Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Genetics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 2 Organism:human· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Research Focus:clustering· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1 Assay:long-read sequencing· 1

Frequent Co-Authors

Aziz M. Al’KhafajiiD· 2 shared Kiran V. GarimellaiD· 2 shared Michael GatzeniD· 2 shared Allyson Day· 1 shared Anthony PhilippakisiD· 1 shared Asa ShiniD· 1 shared Aviv RegeviD· 1 shared Beri Shifaw· 1 shared

Activity by Year

2022-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 28 mutual co-author links

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2 shared papersGenomics

Aziz M. Al’KhafajiORCID

Mutual co-authors in cluster

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3 papers

Recent·Most cited

GenomicsGenome biologyPeer-reviewedApr 11, 2026

Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data

Sean Simmons, Xian Adiconis, Nathan Haywood…·Joshua Z. Levin

This paper develops computational tools for allelic imbalance analysis using single-nucleus RNA-seq and demonstrates their application in a Parkinson's disease cohort.

1 citation

humansnRNA-seq

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GeneticsNature BiotechnologyPeer-reviewedJun 8, 2023

High-throughput RNA isoform sequencing using programmable cDNA concatenation

Aziz M. Al’Khafaji, Jonathan T. Smith, Kiran V. Garimella…·Nir Hacohen

This paper introduces MAS-ISO-seq, a method to boost throughput of long-read RNA sequencing for isoform discovery, showing improved detection of differentially spliced genes and cell clustering in T cells.

200 citationstop 1%

humanlong-read sequencing

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BioinformaticsbioRxivPreprintApr 5, 2022

Deploying genomics workflows on high performance computing (HPC) platforms: storage, memory, and compute considerations

Marissa E. Powers, Keith Mannthey, Priyanka Sebastian…·Paolo Narvaez

This paper provides infrastructure recommendations for optimizing genomics workflows on HPC platforms through benchmarking and profiling.

1 citation

whole-genome sequencingbenchmark study

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