Rob Patro

62 papers A* 1B 5C 10Journal 42Unranked 4
YearRankTypeTitle / Venue / Authors
2026 J jnl
Icefish: Practical zk-SNARKs for Verifiable Genomics.
IACR Cryptol. ePrint Arch.
Alexander Frolov, Maurice Shih, Rob Patro, Ian Miers
2025 C ed.
25th International Conference on Algorithms for Bioinformatics, WABI 2025, University of Maryland, College Park, MD, USA, August 20-22, 2025
WABI
Brona Brejová, Rob Patro
2025 J jnl
<tt>Oarfish</tt>: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification.
Bioinform.
Zahra Zare Jousheghani, Noor Pratap Singh, Rob Patro
2025 J jnl
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment.
Bioinform.
Noor Pratap Singh, Jamshed Khan, Rob Patro
2025 C conf
Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs.
WABI
Alessio Campanelli, Giulio Ermanno Pibiri, Rob Patro
2025 B conf
U-Index: A Universal Indexing Framework for Matching Long Patterns.
SEA
Lorraine A. K. Ayad, Gabriele Fici, Ragnar Groot Koerkamp, Grigorios Loukides, Rob Patro, Giulio Ermanno Pibiri, Solon P. Pissis
2025 J jnl
U-index: A Universal Indexing Framework for Matching Long Patterns.
CoRR
Lorraine A. K. Ayad, Gabriele Fici, Ragnar Groot Koerkamp, Grigorios Loukides, Rob Patro, Giulio Ermanno Pibiri, Solon P. Pissis
2024 J jnl
<tt>Forseti</tt>: a mechanistic and predictive model of the splicing status of scRNA-seq reads.
Bioinform.
Dongze He, Yuan Gao, Spencer Skylar Chan, Natalia Quintana-Parrilla, Rob Patro
2024 J jnl
Collapsible tree: interactive web app to present collapsible hierarchies.
Bioinform.
Yuan Gao, Rob Patro, Peng Jiang
2024 J jnl
Designing efficient randstrobes for sequence similarity analyses.
Bioinform.
Moein Karami, Aryan Soltani Mohammadi, Marcel Martin, Baris Ekim, Wei Shen, Lidong Guo, Mengyang Xu, Giulio Ermanno Pibiri, Rob Patro, Kristoffer Sahlin
2024 J jnl
Fast, parallel, and cache-friendly suffix array construction.
Algorithms Mol. Biol.
Jamshed Khan, Tobias Rubel, Erin K. Molloy, Laxman Dhulipala, Rob Patro
2024 J jnl
Fulgor: a fast and compact k-mer index for large-scale matching and color queries.
Algorithms Mol. Biol.
Jason Fan, Jamshed Khan, Noor Pratap Singh, Giulio Ermanno Pibiri, Rob Patro
2024 B conf
Meta-colored Compacted de Bruijn Graphs.
RECOMB
Giulio Ermanno Pibiri, Jason Fan, Rob Patro
2024 J jnl
Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn Graphs
J. Comput. Biol.
Alessio Campanelli, Giulio Ermanno Pibiri, Jason Fan, Rob Patro
2023 C conf
Fast, Parallel, and Cache-Friendly Suffix Array Construction.
WABI
Jamshed Khan, Tobias Rubel, Laxman Dhulipala, Erin K. Molloy, Rob Patro
2023 C conf
Fulgor: A Fast and Compact {k-mer} Index for Large-Scale Matching and Color Queries.
WABI
Jason Fan, Noor Pratap Singh, Jamshed Khan, Giulio Ermanno Pibiri, Rob Patro
2023 B conf
Spectrum Preserving Tilings Enable Sparse and Modular Reference Indexing.
RECOMB
Jason Fan, Jamshed Khan, Giulio Ermanno Pibiri, Rob Patro
2022 J jnl
Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets.
Bioinform.
Wancen Mu, Hirak Sarkar, Avi Srivastava, Kwangbom Choi, Rob Patro, Michael I. Love
2022 J jnl
An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation.
Bioinform.
Fatemeh Almodaresi, Jamshed Khan, Sergey Madaminov, Michael Ferdman, Rob Johnson, Prashant Pandey, Rob Patro
2022 J jnl
Perplexity: evaluating transcript abundance estimation in the absence of ground truth.
Algorithms Mol. Biol.
Jason Fan, Skylar Chan, Rob Patro
2021 J jnl
Compression of quantification uncertainty for scRNA-seq counts.
Bioinform.
Scott Van Buren, Hirak Sarkar, Avi Srivastava, Naim U. Rashid, Rob Patro, Michael I. Love
2021 J jnl
Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections.
Bioinform.
Jamshed Khan, Rob Patro
2021 C conf
Perplexity: Evaluating Transcript Abundance Estimation in the Absence of Ground Truth.
WABI
Jason Fan, Skylar Chan, Rob Patro
2021 J jnl
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data.
PLoS Comput. Biol.
Charlotte Soneson, Avi Srivastava, Rob Patro, Michael B. Stadler
2021 J jnl
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index.
Bioinform.
Fatemeh Almodaresi, Mohsen Zakeri, Rob Patro
2020 J jnl
A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification.
Bioinform.
Avi Srivastava, Laraib Malik, Hirak Sarkar, Rob Patro
2020 J jnl
An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search.
J. Comput. Biol.
Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro
2020 J jnl
Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data.
Bioinform.
Hirak Sarkar, Avi Srivastava, Héctor Corrada Bravo, Michael I. Love, Rob Patro
2020 J jnl
Tximeta: Reference sequence checksums for provenance identification in RNA-seq.
PLoS Comput. Biol.
Michael I. Love, Charlotte Soneson, Peter F. Hickey, Lisa K. Johnson, N. Tessa Pierce, Lori A. Shepherd, Martin Morgan, Rob Patro
2019 B conf
An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search.
RECOMB
Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro
2019 J jnl
Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level.
Bioinform.
Hirak Sarkar, Avi Srivastava, Rob Patro
2019 J jnl
Rich Chromatin Structure Prediction from Hi-C Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Laraib Malik, Rob Patro
2018 J jnl
A space and time-efficient index for the compacted colored de Bruijn graph.
Bioinform.
Fatemeh Almodaresi, Hirak Sarkar, Avi Srivastava, Rob Patro
2018 J jnl
Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis.
Bioinform.
Laraib Malik, Fatemeh Almodaresi, Rob Patro
2018 B conf
Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index.
RECOMB
Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, Michael Ferdman, Rob Johnson, Rob Patro
2018 J jnl
Squeakr: an exact and approximate k-mer counting system.
Bioinform.
Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro
2018 J jnl
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.
F1000Research
Michael I. Love, Charlotte Soneson, Rob Patro
2018 — conf
Towards Selective-Alignment: Bridging the Accuracy Gap between Alignment-Based and Alignment-Free Transcript Quantification.
BCB
Hirak Sarkar, Mohsen Zakeri, Laraib Malik, Rob Patro
2017 — conf
A General-Purpose Counting Filter: Making Every Bit Count.
SIGMOD Conference
Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro
2017 J jnl
Improved data-driven likelihood factorizations for transcript abundance estimation.
Bioinform.
Mohsen Zakeri, Avi Srivastava, Fatemeh Almodaresi, Rob Patro
2017 J jnl
Quark enables semi-reference-based compression of RNA-seq data.
Bioinform.
Hirak Sarkar, Rob Patro
2017 C conf
Rainbowfish: A Succinct Colored de Bruijn Graph Representation.
WABI
Fatemeh Almodaresi, Prashant Pandey, Rob Patro
2017 — conf
Rich Chromatin Structure Prediction from Hi-C Data.
BCB
Laraib Malik, Rob Patro
2017 J jnl
deBGR: an efficient and near-exact representation of the weighted de Bruijn graph.
Bioinform.
Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro
2016 J jnl
A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.
BMC Bioinform.
Rob Patro, Raquel Norel, Robert J. Prill, Julio Saez-Rodriguez, Peter Lorenz, Felix Steinbeck, Bjoern Ziems, Mitja Lustrek, Nicola Barbarini, Alessandra Tiengo, Riccardo Bellazzi, Hans-Jürgen Thiesen, Gustavo Stolovitzky, Carl Kingsford
2016 J jnl
Accurate, Fast and Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes.
CoRR
Avi Srivastava, Hirak Sarkar, Laraib Malik, Rob Patro
2016 J jnl
Efficient Index Maintenance Under Dynamic Genome Modification.
CoRR
Nitish Gupta, Komal Sanjeev, Tim Wall, Carl Kingsford, Rob Patro
2016 J jnl
RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes.
Bioinform.
Avi Srivastava, Hirak Sarkar, Nitish Gupta, Rob Patro
2015 J jnl
Data-dependent bucketing improves reference-free compression of sequencing reads.
Bioinform.
Rob Patro, Carl Kingsford
2015 C conf
Optimizing Read Reversals for Sequence Compression - (Extended Abstract).
WABI
Zhong Sichen, Lu Zhao, Yan Liang, Mohammadzaman Zamani, Rob Patro, Rezaul Chowdhury, Esther M. Arkin, Joseph S. B. Mitchell, Steven Skiena
2015 J jnl
Reference-based compression of short-read sequences using path encoding.
Bioinform.
Carl Kingsford, Rob Patro
2014 J jnl
Identification of alternative topological domains in chromatin.
Algorithms Mol. Biol.
Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford
2013 C conf
Multiscale Identification of Topological Domains in Chromatin.
WABI
Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford
2013 J jnl
Predicting protein interactions via parsimonious network history inference.
Bioinform.
Rob Patro, Carl Kingsford
2013 J jnl
Resolving spatial inconsistencies in chromosome conformation measurements.
Algorithms Mol. Biol.
Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford
2013 J jnl
Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms.
CoRR
Rob Patro, Stephen M. Mount, Carl Kingsford
2013 — conf
Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin.
BCB
Hao Wang, Geet Duggal, Rob Patro, Michelle Girvan, Sridhar Hannenhalli, Carl Kingsford
2012 J jnl
Global network alignment using multiscale spectral signatures.
Bioinform.
Rob Patro, Carl Kingsford
2012 J jnl
Parsimonious reconstruction of network evolution.
Algorithms Mol. Biol.
Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, Carl Kingsford
2012 C conf
Resolving Spatial Inconsistencies in Chromosome Conformation Data.
WABI
Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford
2012 A* conf
The missing models: a data-driven approach for learning how networks grow.
KDD
Rob Patro, Geet Duggal, Emre Sefer, Hao Wang, Darya Filippova, Carl Kingsford
2011 C conf
Parsimonious Reconstruction of Network Evolution.
WABI
Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, Carl Kingsford