Sotabase

Career

· Associate Professor, University of Maryland2020–
· Postdoctoral Researcher, Carnegie Mellon University2014–
· Co-founder and CTO, Ocean Genomics Inc.

Publications (62)

Bioconda: sustainable and comprehensive software distribution for the life sciences
Nature Methods · 2018
1,368
cited
Tximeta: Reference sequence checksums for provenance identification in RNA-seq
bioRxiv · 2019
274
cited
Alevin efficiently estimates accurate gene abundances from dscRNA-seq data
Genome Biology · 2018
216
cited
Alignment and mapping methodology influence transcript abundance estimation
Genome Biology · 2019
132
cited
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
F1000Research · 2018
126
cited
RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis
Annual Review of Biomedical Data Science · 2018
115
cited
Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data
Nature Methods · 2021
87
cited
Nonparametric expression analysis using inferential replicate counts
bioRxiv · 2019
86
cited
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data
bioRxiv · 2020
45
cited
Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
Genome Biology · 2021
43
cited
Sketching and Sublinear Data Structures in Genomics
Annual Review of Biomedical Data Science · 2019
42
cited
Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections
bioRxiv · 2020
30
cited
A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
Life Science Alliance · 2018
21
cited
Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level
Bioinform. · 2019
20
cited
A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification
bioRxiv · 2020
19
cited
Oarfish: Enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification
bioRxiv · 2024
19
cited
An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search
bioRxiv · 2018
17
cited
Spectrum preserving tilings enable sparse and modular reference indexing
bioRxiv · 2023
16
cited
Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets
bioRxiv · 2021
15
cited
Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes
Science Advances · 2024
14
cited
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Rob Patro | Researcher Profile | Sotabase | Sotabase