Rob Patro

ScholarGPS® ID: 36193074416369

Affiliation

University of Maryland, College Park, United States

Affiliation History

Field

Engineering and Computer Science

Discipline

Computer Science

Top Specialties

Metrics Summary

Publication Count

Predicted Citations

10,969

Predicted h-index

Ranking

Publications and Citation History

Publications based on Top Specialties

Types of Publication

Publications
Books
Patents
NIH/NSF

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Forseti : a mechanistic and predictive model of the splicing status of scRNA-seq reads (journal article) He, Dongze \| Gao, Yuan \| Chan, Spencer Skylar \| Quintana-Parrilla, Natalia \| Patro, Rob Bioinformatics, volume 40, issue Supplement_1, pages i297-i306 (2024). 10.1093/bioinformatics/btae207 Cite \| Source
DifferentialRegulation : a Bayesian hierarchical approach to identify differentially regulated genes (journal article) Tiberi, Simone \| Meili, Joël \| Cai, Peiying \| Soneson, Charlotte \| He, Dongze \| Sarkar, Hirak \| Avalos-Pacheco, Alejandra \| Patro, Rob \| Robinson, Mark D Biostatistics (2024). 10.1093/biostatistics/kxae017 Cite \| Source
Fast, parallel, and cache-friendly suffix array construction (journal article) Khan, Jamshed \| Rubel, Tobias \| Molloy, Erin \| Dhulipala, Laxman \| Patro, Rob Algorithms for Molecular Biology, volume 19, issue 1 (2024). 10.1186/s13015-024-00263-5 Cite \| Source
Designing efficient randstrobes for sequence similarity analyses (journal article) Karami, Moein \| Soltani Mohammadi, Aryan \| Martin, Marcel \| Ekim, Barış \| Shen, Wei \| Guo, Lidong \| Xu, Mengyang \| Pibiri, Giulio Ermanno \| Patro, Rob \| Sahlin, Kristoffer Bioinformatics, volume 40, issue 4 (2024). 10.1093/bioinformatics/btae187 Cite \| Source
Fulgor: a fast and compact k-mer index for large-scale matching and color queries (journal article) Fan, Jason \| Khan, Jamshed \| Singh, Noor Pratap \| Pibiri, Giulio Ermanno \| Patro, Rob Algorithms for Molecular Biology, volume 19, issue 1 (2024). 10.1186/s13015-024-00251-9 Cited by (4) \| Cite \| Source
Meta-colored Compacted de Bruijn Graphs (book chapter) In Research in Computational Molecular Biology Pibiri, Giulio Ermanno \| Fan, Jason \| Patro, Rob Springer Nature Switzerland (2024) 10.1007/978-1-0716-3989-4_9 Cite \| Source
simpleaf : a simple, flexible, and scalable framework for single-cell data processing using alevin-fry (journal article) He, Dongze \| Patro, Rob Bioinformatics, volume 39, issue 10 (2023). 10.1093/bioinformatics/btad614 Cited by (1) \| Cite \| Source
SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty (journal article) Wu, Euphy Y. \| Singh, Noor P. \| Choi, Kwangbom \| Zakeri, Mohsen \| Vincent, Matthew \| Churchill, Gary A. \| Ackert-Bicknell, Cheryl L. \| Patro, Rob \| Love, Michael I. Genome Biology, volume 24, issue 1 (2023). 10.1186/s13059-023-03003-x Cited by (1) \| Cite \| Source
TreeTerminus —creating transcript trees using inferential replicate counts (journal article) Singh, Noor Pratap \| Love, Michael I. \| Patro, Rob iScience, volume 26, issue 6, pages 106961- (2023). 10.1016/j.isci.2023.106961 Cite \| Source
Spectrum Preserving Tilings Enable Sparse and Modular Reference Indexing (book chapter) In Research in Computational Molecular Biology Fan, Jason \| Khan, Jamshed \| Pibiri, Giulio Ermanno \| Patro, Rob Springer Nature Switzerland (2023) 10.1007/978-3-031-29119-7_2 Cited by (3) \| Cite \| Source
Perplexity: evaluating transcript abundance estimation in the absence of ground truth (journal article) Fan, Jason \| Chan, Skylar \| Patro, Rob Algorithms for Molecular Biology, volume 17, issue 1 (2022). 10.1186/s13015-022-00214-y Cite \| Source
AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite (journal article) Skoufos, Giorgos \| Almodaresi, Fatemeh \| Zakeri, Mohsen \| Paulson, Joseph N. \| Patro, Rob \| Hatzigeorgiou, Artemis G. \| Vlachos, Ioannis S. Genome Biology, volume 23, issue 1 (2022). 10.1186/s13059-022-02610-4 Cited by (5) \| Cite \| Source
Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2 (journal article) Khan, Jamshed \| Kokot, Marek \| Deorowicz, Sebastian \| Patro, Rob Genome Biology, volume 23, issue 1 (2022). 10.1186/s13059-022-02743-6 Cited by (10) \| Cite \| Source
An incrementally updatable and scalable system for large-scale sequence search using the Bentley–Saxe transformation (journal article) Almodaresi, Fatemeh \| Khan, Jamshed \| Madaminov, Sergey \| Ferdman, Michael \| Johnson, Rob \| Pandey, Prashant \| Patro, Rob Bioinformatics, volume 38, issue 12, pages 3155-3163 (2022). 10.1093/bioinformatics/btac142 Cited by (2) \| Cite \| Source
Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets (journal article) Mu, Wancen \| Sarkar, Hirak \| Srivastava, Avi \| Choi, Kwangbom \| Patro, Rob \| Love, Michael I Bioinformatics, volume 38, issue 10, pages 2773-2780 (2022). 10.1093/bioinformatics/btac212 Cited by (6) \| Cite \| Source
Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data (journal article) He, Dongze \| Zakeri, Mohsen \| Sarkar, Hirak \| Soneson, Charlotte \| Srivastava, Avi \| Patro, Rob Nature Methods, volume 19, issue 3, pages 316-322 (2022). 10.1038/s41592-022-01408-3 Cited by (22) \| Cite \| Source
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index (journal article) Almodaresi, Fatemeh \| Zakeri, Mohsen \| Patro, Rob Bioinformatics, volume 37, issue 22, pages 4048-4055 (2021). 10.1093/bioinformatics/btab408 Cited by (13) \| Cite \| Source
Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections (journal article) Khan, Jamshed \| Patro, Rob Bioinformatics, volume 37, issue Supplement_1, pages i177-i186 (2021). 10.1093/bioinformatics/btab309 Cited by (9) \| Cite \| Source
Compression of quantification uncertainty for scRNA-seq counts (journal article) Van Buren, Scott \| Sarkar, Hirak \| Srivastava, Avi \| Rashid, Naim U \| Patro, Rob \| Love, Michael I Bioinformatics, volume 37, issue 12, pages 1699-1707 (2021). 10.1093/bioinformatics/btab001 Cited by (3) \| Cite \| Source
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data (journal article) Soneson, Charlotte \| Srivastava, Avi \| Patro, Rob \| Stadler, Michael B. PLOS Computational Biology, volume 17, issue 1, pages e1008585- (2021). 10.1371/journal.pcbi.1008585 Cited by (24) \| Cite \| Source

Title	Investigators	Year	Expiration	Amount
CAREER: A Comprehensive and Lightweight Framework for Transcriptome Analysis	Patro, Robert	04-13-2020	01-31-2023	$523,529
CSR: Medium: Approximate Membership Query Data Structures in Computational Biology and Storage	Patro, Robert \| Bender, Michael \| Ferdman, Michael	08-15-2018	07-31-2022	$889,876
CAREER: A Comprehensive and Lightweight Framework for Transcriptome Analysis	Patro, Robert	02-01-2018	06-30-2020	$444,170
Bilateral BBSRC-NSF/BIO: ABI Innovation: Data-driven hierarchical analysis of de novo transcriptomes	Hibberd, Julian \| Patro, Robert	07-01-2016	06-30-2018	$310,627

Title	Investigators	Year	Cost	Agency
A Modular Framework for Accurate, Efficient, and Reproducible Analysis of RNA-Seq Data	Love, Michael Isaiah \| Patro, Robert	2020	$293,841	NATIONAL HUMAN GENOME RESEARCH INSTITUTE
A Modular Framework for Accurate, Efficient, and Reproducible Analysis of RNA-Seq Data	Love, Michael Isaiah \| Patro, Robert	2019	$1	NATIONAL HUMAN GENOME RESEARCH INSTITUTE
A Modular Framework for Accurate, Efficient, and Reproducible Analysis of RNA-Seq Data	Love, Michael Isaiah \| Patro, Robert	2019	$304,592	NATIONAL HUMAN GENOME RESEARCH INSTITUTE
A Modular Framework for Accurate, Efficient, and Reproducible Analysis of RNA-Seq Data	Love, Michael Isaiah \| Patro, Robert	2018	$320,128	NATIONAL HUMAN GENOME RESEARCH INSTITUTE