Modeling and Visualization of Human Activities for Multicamera Networks. - Aswin C. Sankaranarayanan; Robert Patro; Pavan K. Turaga; Amitabh Varshney; Rama Chellappa (EURASIP J. Image Video Process., 2009)

Saliency Guided Summarization of Molecular Dynamics Simulations. - Robert Patro; Cheuk Yiu Ip; Amitabh Varshney (Scientific Visualization: Advanced Concepts, 2010)

MDMap: A system for data-driven layout and exploration of molecular dynamics simulations. - Robert Patro; Cheuk Yiu Ip; Sujal Bista; D. Thirumalai; Samuel S. Cho; Amitabh Varshney (BioVis, 2011)

Salient Frame Detection for Molecular Dynamics Simulations. - Youngmin Kim; Robert Patro; Cheuk Yiu Ip; Dianne P. O'Leary; Andriy Anishkin (Scientific Visualization: Interactions, Features, Metaphors, 2011)

Social Snapshot: A System for Temporally Coupled Social Photography. - Robert Patro; Cheuk Yiu Ip; Sujal Bista; Amitabh Varshney (IEEE Computer Graphics and Applications, 2011)

A robust and rotationally invariant local surface descriptor with applications to non-local mesh processing. - André Maximo; Robert Patro; Amitabh Varshney; Ricardo C. Farias (Graph. Model., 2011)

The missing models: a data-driven approach for learning how networks grow. - Rob Patro; Geet Duggal; Emre Sefer; Hao Wang 024; Darya Filippova; Carl Kingsford (KDD, 2012)

Resolving Spatial Inconsistencies in Chromosome Conformation Data. - Geet Duggal; Rob Patro; Emre Sefer; Hao Wang 024; Darya Filippova; Samir Khuller; Carl Kingsford (WABI, 2012)

Parsimonious reconstruction of network evolution. - Rob Patro; Emre Sefer; Justin Malin; Guillaume Marçais; Saket Navlakha; Carl Kingsford (Algorithms Mol. Biol., 2012)

Global network alignment using multiscale spectral signatures. - Rob Patro; Carl Kingsford (Bioinform., 2012)

Speeding Up Particle Trajectory Simulations Under Moving Force Fields using Graphic Processing Units. - Robert Patro; John P. Dickerson; Sujal Bista; Satyandra K. Gupta; Amitabh Varshney (J. Comput. Inf. Sci. Eng., 2012)

Computationally Comparing Biological Networks and Reconstructing Their Evolution. - Robert Patro (2012)

Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin. - Hao Wang 024; Geet Duggal; Rob Patro; Michelle Girvan; Sridhar Hannenhalli; Carl Kingsford (BCB, 2013)

Multiscale Identification of Topological Domains in Chromatin. - Darya Filippova; Rob Patro; Geet Duggal; Carl Kingsford (WABI, 2013)

Resolving spatial inconsistencies in chromosome conformation measurements. - Geet Duggal; Rob Patro; Emre Sefer; Hao Wang 024; Darya Filippova; Samir Khuller; Carl Kingsford (Algorithms Mol. Biol., 2013)

Predicting protein interactions via parsimonious network history inference. - Rob Patro; Carl Kingsford (Bioinform., 2013)

Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms. - Rob Patro; Stephen M. Mount; Carl Kingsford (CoRR, 2013)

Identification of alternative topological domains in chromatin. - Darya Filippova; Rob Patro; Geet Duggal; Carl Kingsford (Algorithms Mol. Biol., 2014)

Optimizing Read Reversals for Sequence Compression - (Extended Abstract). - Zhong Sichen; Lu Zhao; Yan Liang; Mohammadzaman Zamani; Rob Patro; Rezaul Chowdhury; Esther M. Arkin; Joseph S. B. Mitchell; Steven Skiena (WABI, 2015)

Reference-based compression of short-read sequences using path encoding. - Carl Kingsford; Rob Patro (Bioinform., 2015)

Data-dependent bucketing improves reference-free compression of sequencing reads. - Rob Patro; Carl Kingsford (Bioinform., 2015)

RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes. - Avi Srivastava; Hirak Sarkar; Nitish Gupta; Rob Patro (Bioinform., 2016)

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. - 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; et al. (BMC Bioinform., 2016)

Efficient Index Maintenance Under Dynamic Genome Modification. - Nitish Gupta; Komal Sanjeev; Tim Wall; Carl Kingsford; Rob Patro (CoRR, 2016)

Accurate, Fast and Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes. - Avi Srivastava; Hirak Sarkar; Laraib Malik; Rob Patro (CoRR, 2016)

A General-Purpose Counting Filter: Making Every Bit Count. - Prashant Pandey 001; Michael A. Bender; Rob Johnson 001; Rob Patro (SIGMOD Conference, 2017)

Rainbowfish: A Succinct Colored de Bruijn Graph Representation. - Fatemeh Almodaresi; Prashant Pandey 001; Rob Patro (WABI, 2017)

deBGR: an efficient and near-exact representation of the weighted de Bruijn graph. - Prashant Pandey 001; Michael A. Bender; Rob Johnson 001; Rob Patro (Bioinform., 2017)

Quark enables semi-reference-based compression of RNA-seq data. - Hirak Sarkar; Rob Patro (Bioinform., 2017)

Improved data-driven likelihood factorizations for transcript abundance estimation. - Mohsen Zakeri; Avi Srivastava; Fatemeh Almodaresi; Rob Patro (Bioinform., 2017)

Towards Selective-Alignment: Bridging the Accuracy Gap between Alignment-Based and Alignment-Free Transcript Quantification. - Hirak Sarkar; Mohsen Zakeri; Laraib Malik; Rob Patro (BCB, 2018)

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index. - Prashant Pandey 001; Fatemeh Almodaresi; Michael A. Bender; Michael Ferdman; Rob Johnson 001; Rob Patro (RECOMB, 2018)

A space and time-efficient index for the compacted colored de Bruijn graph. - Fatemeh Almodaresi; Hirak Sarkar; Avi Srivastava; Rob Patro (Bioinform., 2018)

Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis. - Laraib Malik; Fatemeh Almodaresi; Rob Patro (Bioinform., 2018)

Squeakr: an exact and approximate k-mer counting system. - Prashant Pandey 001; Michael A. Bender; Rob Johnson 001; Rob Patro (Bioinform., 2018)

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification. - Michael I. Love; Charlotte Soneson; Rob Patro (F1000Research, 2018)

An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search. - Fatemeh Almodaresi; Prashant Pandey 001; Michael Ferdman; Rob Johnson 001; Rob Patro (RECOMB, 2019)

Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level. - Hirak Sarkar; Avi Srivastava; Rob Patro (Bioinform., 2019)

Rich Chromatin Structure Prediction from Hi-C Data. - Laraib Malik; Rob Patro (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data. - Hirak Sarkar; Avi Srivastava; Héctor Corrada Bravo; Michael I. Love; Rob Patro (Bioinform., 2020)

A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification. - Avi Srivastava; Laraib Malik; Hirak Sarkar; Rob Patro (Bioinform., 2020)

An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search. - Fatemeh Almodaresi; Prashant Pandey 001; Michael Ferdman; Rob Johnson 001; Rob Patro (J. Comput. Biol., 2020)

Tximeta: Reference sequence checksums for provenance identification in RNA-seq. - Michael I. Love; Charlotte Soneson; Peter F. Hickey; Lisa K. Johnson; N. Tessa Pierce; Lori A. Shepherd; Martin Morgan; Rob Patro (PLoS Comput. Biol., 2020)

Compression of quantification uncertainty for scRNA-seq counts. - Scott Van Buren; Hirak Sarkar; Avi Srivastava; Naim U. Rashid; Rob Patro; Michael I. Love (Bioinform., 2021)

Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections. - Jamshed Khan; Rob Patro (Bioinform., 2021)

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data. - Charlotte Soneson; Avi Srivastava; Rob Patro; Michael B. Stadler (PLoS Comput. Biol., 2021)

PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index. - Fatemeh Almodaresi; Mohsen Zakeri; Rob Patro (Bioinform., 2021)

Perplexity: evaluating transcript abundance estimation in the absence of ground truth. - Jason Fan; Skylar Chan; Rob Patro (Algorithms Mol. Biol., 2022)

An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation. - Fatemeh Almodaresi; Jamshed Khan; Sergey Madaminov; Michael Ferdman; Rob Johnson 001; Prashant Pandey 001; Rob Patro (Bioinform., 2022)

Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets. - Wancen Mu; Hirak Sarkar; Avi Srivastava; Kwangbom Choi; Rob Patro; Michael I. Love (Bioinform., 2022)

Spectrum Preserving Tilings Enable Sparse and Modular Reference Indexing. - Jason Fan; Jamshed Khan; Giulio Ermanno Pibiri; Rob Patro (RECOMB, 2023)

simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry. - Dongze He; Rob Patro (Bioinform., 2023)

Meta-colored Compacted de Bruijn Graphs. - Giulio Ermanno Pibiri; Jason Fan; Rob Patro (RECOMB, 2024)

Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads. - Dongze He; Yuan Gao; Spencer Skylar Chan; Natalia Quintana-Parrilla; Rob Patro (Bioinform., 2024)

Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn Graphs*. - Alessio Campanelli; Giulio Ermanno Pibiri; Jason Fan; Rob Patro (J. Comput. Biol., 2024)

Fulgor: a fast and compact k-mer index for large-scale matching and color queries. - Jason Fan; Jamshed Khan; Noor Pratap Singh; Giulio Ermanno Pibiri; Rob Patro (Algorithms Mol. Biol., 2024)

Fast, parallel, and cache-friendly suffix array construction. - Jamshed Khan; Tobias Rubel; Erin K. Molloy; Laxman Dhulipala; Rob Patro (Algorithms Mol. Biol., 2024)

Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs. - Alessio Campanelli; Giulio Ermanno Pibiri; Rob Patro (WABI, 2025)

U-Index: A Universal Indexing Framework for Matching Long Patterns. - Lorraine A. K. Ayad; Gabriele Fici; Ragnar Groot Koerkamp; Grigorios Loukides; Rob Patro; Giulio Ermanno Pibiri; Solon P. Pissis (SEA, 2025)