Rob Patro

Biochemistry, Genetics and Molecular BiologyComputer Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

1in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 1 indexed paper attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

Papers

Driven by 44 papers. Top paper: “Best practices for single-cell analysis across modalities”.

Best practices for single-cell analysis across modalities

Nature Reviews Genetics(2023)10.1038/s41576-023-00586-w

N/A

1.0DataRank · unranked

1013 citations

Anna Christina Schaar, Christopher Lance, Anastasia Litinetskaya, Felix Drost, Luke Zappia +34 more

deBGR: an efficient and near-exact representation of the weighted de Bruijn graph

Bioinformatics(2017)10.1093/bioinformatics/btx261

N/A

0.564DataRank · unranked

42 citations

Michael A Bender, Rob Johnson, Rob Patro, Prashant Pandey

AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite

Genome biology(2022)10.1186/s13059-022-02610-4

N/A

0.464DataRank · unranked

21 citations

Fatemeh Almodaresi, Mohsen Zakeri, Joseph N. Paulson, Rob Patro, Artemis G. Hatzigeorgiou +2 more

Cuttlefish: Fast, parallel, and low-memory compaction of de Bruijn graphs from large-scale genome collections

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.21.349605

N/A

0DataRank · unranked

6 citations

Rob Patro, Jamshed Khan

scRNA-seq analysis of colon and esophageal tumors uncovers abundant microbial reads in myeloid cells undergoing proinflammatory transcriptional alterations

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.14.096230

N/A

0DataRank · unranked

5 citations

Joshua K. Stone, Fiorella Schischlik, Billel Gasmi, Michael C. Kelly, Charlie Seibert +13 more

Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.07.029967

N/A

0DataRank · unranked

3 citations

Avi Srivastava, Héctor Corrada Bravo, Michael I. Love, Rob Patro, Hirak Sarkar

A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.10.035899

N/A

0DataRank · unranked

2 citations

Laraib Malik, Hirak Sarkar, Rob Patro, Avi Srivastava

Compression of quantification uncertainty for scRNA-seq counts

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.06.189639

N/A

0DataRank · unranked

2 citations

Hirak Sarkar, Avi Srivastava, Naim U. Rashid, Rob Patro, Michael I. Love +1 more

Algorithms meet sequencing technologies – 10th edition of the RECOMB-Seq workshop

iScience(2020)10.1016/j.isci.2020.101956

N/A

0DataRank · unranked

0 citations

Leena Salmela, Rob Patro

Referee report. For: GFF Utilities: GffRead and GffCompare [version 1; peer review: 3 approved]

Faculty of 1000 Research Ltd(2020)10.5256/f1000research.25718.r62867

N/A

0DataRank · unranked

0 citations

Rob Patro

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

PLoS Computational Biology(2021)10.1371/journal.pcbi.1008585

N/A

0DataRank · unranked

76 citations

Avi Srivastava, Rob Patro, Michael Stadler, Charlotte Soneson

Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections

Bioinformatics(2021)10.1093/bioinformatics/btab309

N/A

0DataRank · unranked

40 citations

Rob Patro, Jamshed Khan

Compression of quantification uncertainty for scRNA-seq counts

Bioinformatics(2021)10.1093/bioinformatics/btab001

N/A

0DataRank · unranked

7 citations

Hirak Sarkar, Avi Srivastava, Naim U. Rashid, Rob Patro, Michael I. Love +1 more

Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.29.450377

N/A

0DataRank · unranked

13 citations

Mohsen Zakeri, Hirak Sarkar, Charlotte Soneson, Avi Srivastava, Rob Patro +1 more

Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.14.472718

N/A

0DataRank · unranked

7 citations

Marek Kokot, Sebastian Deorowicz, Rob Patro, Jamshed Khan

Airpart : Interpretable statistical models for analyzing allelic imbalance in single-cell datasets

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.15.464546

N/A

0DataRank · unranked

1 citations

Hirak Sarkar, Avi Srivastava, Kwangbom Choi, Rob Patro, Michael I. Love +1 more

Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2

Genome biology(2022)10.1186/s13059-022-02743-6

N/A

0DataRank · unranked

54 citations

Marek Kokot, Sebastian Deorowicz, Rob Patro, Jamshed Khan

Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets

Bioinformatics(2022)10.1093/bioinformatics/btac212

N/A

0DataRank · unranked

24 citations

Hirak Sarkar, Avi Srivastava, Kwangbom Choi, Rob Patro, Michael I. Love +1 more

An incrementally updatable and scalable system for large-scale sequence search using the Bentley–Saxe transformation

Bioinformatics(2022)10.1093/bioinformatics/btac142

N/A

0DataRank · unranked

11 citations

Jamshed Khan, Sergey Madaminov, Michael Ferdman, Rob Johnson, Prashant Pandey +2 more

Perplexity: evaluating transcript abundance estimation in the absence of ground truth

Algorithms for Molecular Biology(2022)10.1186/s13015-022-00214-y

N/A

0DataRank · unranked

0 citations

Spencer Skylar Chan, Rob Patro, Jason Fan

simpleaf : a simple, flexible, and scalable framework for single-cell data processing using alevin-fry

Bioinformatics(2023)10.1093/bioinformatics/btad614

N/A

0DataRank · unranked

23 citations

Rob Patro, Dongze He

TreeTerminus —creating transcript trees using inferential replicate counts

iScience(2023)10.1016/j.isci.2023.106961

N/A

0DataRank · unranked

2 citations

Michael I. Love, Rob Patro, Noor Singh

Spectrum Preserving Tilings Enable Sparse and Modular Reference Indexing

Lecture notes in computer science(2023)10.1007/978-3-031-29119-7_2

N/A

0DataRank · unranked

16 citations

Jamshed Khan, Giulio Ermanno Pibiri, Rob Patro, Jason Fan

Understanding and evaluating ambiguity in single-cell and single-nucleus RNA-sequencing

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.04.522742

N/A

0DataRank · unranked

13 citations

Charlotte Soneson, Rob Patro, Dongze He

Fulgor: A fast and compact k -mer index for large-scale matching and color queries

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.09.539895

N/A

0DataRank · unranked

9 citations

Noor Singh, Jamshed Khan, Giulio Ermanno Pibiri, Rob Patro, Jason Fan

Meta-colored compacted de Bruijn graphs

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.21.550101

N/A

0DataRank · unranked

2 citations

Jason Fan, Rob Patro, Giulio Ermanno Pibiri

DifferentialRegulation : a Bayesian hierarchical approach to identify differentially regulated genes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.17.553679

N/A

0DataRank · unranked

0 citations

Joël Meili, Peiying Cai, Charlotte Soneson, Dongze He, Hirak Sarkar +4 more

Fulgor: a fast and compact k-mer index for large-scale matching and color queries

Algorithms for Molecular Biology(2024)10.1186/s13015-024-00251-9

N/A

0DataRank · unranked

39 citations

Jamshed Khan, Noor Singh, Giulio Ermanno Pibiri, Rob Patro, Jason Fan

Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn Graphs *

Journal of Computational Biology(2024)10.1089/cmb.2024.0714

N/A

0DataRank · unranked

12 citations

Giulio Ermanno Pibiri, Jason Fan, Rob Patro, Alessio Campanelli

Forseti : a mechanistic and predictive model of the splicing status of scRNA-seq reads

Bioinformatics(2024)10.1093/bioinformatics/btae207

N/A

0DataRank · unranked

4 citations

Yuan Gao, Spencer Skylar Chan, Natalia Quintana-Parrilla, Rob Patro, Dongze He

Collapsible tree: interactive web app to present collapsible hierarchies

Bioinformatics(2024)10.1093/bioinformatics/btae645

N/A

0DataRank · unranked

2 citations

Rob Patro, Jiang Peng, Yuan Gao

DifferentialRegulation : a Bayesian hierarchical approach to identify differentially regulated genes

Biostatistics(2024)10.1093/biostatistics/kxae017

N/A

0DataRank · unranked

1 citations

Joël Meili, Peiying Cai, Charlotte Soneson, Dongze He, Hirak Sarkar +4 more

Fast, parallel, and cache-friendly suffix array construction

Algorithms for Molecular Biology(2024)10.1186/s13015-024-00263-5

N/A

0DataRank · unranked

1 citations

Tobias Rubel, Erin K. Molloy, Laxman Dhulipala, Rob Patro, Jamshed Khan

Oarfish: Enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.28.582591

N/A

0DataRank · unranked

18 citations

Rob Patro, Zahra Zare Jousheghani

Meta-colored Compacted de Bruijn Graphs

Lecture notes in computer science(2024)10.1007/978-1-0716-3989-4_9

N/A

0DataRank · unranked

7 citations

Jason Fan, Rob Patro, Giulio Ermanno Pibiri

Forseti: A mechanistic and predictive model of the splicing status of scRNA-seq reads

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.01.577813

N/A

0DataRank · unranked

1 citations

Yuan Gao, Spencer Skylar Chan, Natalia Quintana-Parrilla, Rob Patro, Dongze He

Where the patterns are: repetition-aware compression for colored de Bruijn graphs ⋆

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.09.602727

N/A

0DataRank · unranked

0 citations

Giulio Ermanno Pibiri, Jason Fan, Rob Patro, Alessio Campanelli

Faster and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.02.636161

N/A

0DataRank · unranked

2 citations

Laxman Dhulipala, Prashant Pandey, Rob Patro, Jamshed Khan

Tree-based differential testing using inferential uncertainty for RNA-seq

Genome Research(2025)10.1101/gr.279981.124

N/A

0DataRank · unranked

1 citations

Euphy Wu, Jason Fan, Michael I. Love, Rob Patro, Noor Singh

Faster Run-Length Compressed Suffix Arrays

Research Portal (King's College London)(2025)10.4230/lipics.sea.2025.4

N/A

0DataRank · unranked

0 citations

Fici, Gabriele, Groot Koerkamp, Ragnar, Loukides, Grigorios, Rob Patro, Giulio Ermanno Pibiri +2 more

mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.24.690271

N/A

0DataRank · unranked

0 citations

Siddhant Bharti, Prajwal Singhania, Rakrish Dhakal, Thomas J. Dahlstrom, Groot Koerkamp, Ragnar +1 more

Oarfish: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification

Bioinformatics(2025)10.1093/bioinformatics/btaf240

N/A

0DataRank · unranked

22 citations

Noor Singh, Rob Patro, Zahra Zare Jousheghani

Tximeta: Reference sequence checksums for provenance identification in RNA-seq

PLoS Computational Biology(2020)10.1371/journal.pcbi.1007664

N/A

0DataRank · unranked

384 citations

Charlotte Soneson, Peter F. Hickey, Lisa K. Johnson, N. Tessa Pierce‐Ward, Lori Shepherd +3 more

A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification

Bioinformatics(2020)10.1093/bioinformatics/btaa450

N/A

0DataRank · unranked

27 citations

Laraib Malik, Hirak Sarkar, Rob Patro, Avi Srivastava