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ORCIDRob Patro
Person information
- affiliation (PhD 2012): University of Maryland, Center for Bioinformatics and Computational Biology, College Park, MD, USA
- affiliation (2014-2019): Stony Brook University, Department of Computer Science, NY, USA
- affiliation (2012-2014): Carnegie Mellon University, Lane Center for Computational Biology, Pittsburgh, PA, USA
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2020 – today
- 2024
[j35]Jason Fan, Jamshed Khan, Noor Pratap Singh
, Giulio Ermanno Pibiri, Rob Patro:
Fulgor: a fast and compact k-mer index for large-scale matching and color queries. Algorithms Mol. Biol. 19(1): 3 (2024)- [j34]Jamshed Khan, Tobias Rubel, Erin K. Molloy, Laxman Dhulipala, Rob Patro:
Fast, parallel, and cache-friendly suffix array construction. Algorithms Mol. Biol. 19(1): 16 (2024) - [c18]Giulio Ermanno Pibiri, Jason Fan, Rob Patro:
Meta-colored Compacted de Bruijn Graphs. RECOMB 2024: 131-146 - 2023
- [j33]Dongze He, Rob Patro:
simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry. Bioinform. 39(10) (2023) - [c17]Jason Fan, Jamshed Khan, Giulio Ermanno Pibiri, Rob Patro:
Spectrum Preserving Tilings Enable Sparse and Modular Reference Indexing. RECOMB 2023: 21-40 - [c16]Jamshed Khan, Tobias Rubel, Laxman Dhulipala, Erin K. Molloy, Rob Patro:
Fast, Parallel, and Cache-Friendly Suffix Array Construction. WABI 2023: 16:1-16:21 - [c15]Jason Fan, Noor Pratap Singh, Jamshed Khan, Giulio Ermanno Pibiri, Rob Patro:
Fulgor: A Fast and Compact {k-mer} Index for Large-Scale Matching and Color Queries. WABI 2023: 18:1-18:21 - 2022
- [j32]Jason Fan, Skylar Chan, Rob Patro:
Perplexity: evaluating transcript abundance estimation in the absence of ground truth. Algorithms Mol. Biol. 17(1): 6 (2022) - [j31]Wancen Mu, Hirak Sarkar, Avi Srivastava, Kwangbom Choi, Rob Patro, Michael I. Love:
Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets. Bioinform. 38(10): 2773-2780 (2022) - [j30]Fatemeh Almodaresi, Jamshed Khan, Sergey Madaminov, Michael Ferdman, Rob Johnson, Prashant Pandey, Rob Patro:
An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation. Bioinform. 38(12): 3155-3163 (2022) - 2021
- [j29]Scott Van Buren, Hirak Sarkar, Avi Srivastava, Naim U. Rashid, Rob Patro, Michael I. Love:
Compression of quantification uncertainty for scRNA-seq counts. Bioinform. 37(12): 1699-1707 (2021) - [j28]Fatemeh Almodaresi, Mohsen Zakeri, Rob Patro:
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index. Bioinform. 37(22): 4048-4055 (2021) - [j27]Jamshed Khan, Rob Patro:
Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections. Bioinform. 37(Supplement): 177-186 (2021) - [j26]Charlotte Soneson, Avi Srivastava, Rob Patro, Michael B. Stadler:
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data. PLoS Comput. Biol. 17(1) (2021) - [c14]Jason Fan, Skylar Chan, Rob Patro:
Perplexity: Evaluating Transcript Abundance Estimation in the Absence of Ground Truth. WABI 2021: 4:1-4:22 - 2020
- [j25]Hirak Sarkar, Avi Srivastava, Héctor Corrada Bravo, Michael I. Love, Rob Patro:
Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data. Bioinform. 36(Supplement-1): i102-i110 (2020) - [j24]Avi Srivastava, Laraib Malik, Hirak Sarkar, Rob Patro:
A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification. Bioinform. 36(Supplement-1): i292-i299 (2020) - [j23]Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro:
An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search. J. Comput. Biol. 27(4): 485-499 (2020) - [j22]Michael I. Love, Charlotte Soneson, Peter F. Hickey, Lisa K. Johnson, N. Tessa Pierce, Lori A. Shepherd, Martin Morgan, Rob Patro:
Tximeta: Reference sequence checksums for provenance identification in RNA-seq. PLoS Comput. Biol. 16(2) (2020)
2010 – 2019
- 2019
- [j21]Hirak Sarkar, Avi Srivastava, Rob Patro:
Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level. Bioinform. 35(14): i136-i144 (2019) - [j20]Laraib Malik, Rob Patro:
Rich Chromatin Structure Prediction from Hi-C Data. IEEE ACM Trans. Comput. Biol. Bioinform. 16(5): 1448-1458 (2019) - [c13]Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro:
An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search. RECOMB 2019: 1-18 - 2018
- [j19]Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro:
Squeakr: an exact and approximate k-mer counting system. Bioinform. 34(4): 568-575 (2018) - [j18]Fatemeh Almodaresi, Hirak Sarkar, Avi Srivastava, Rob Patro:
A space and time-efficient index for the compacted colored de Bruijn graph. Bioinform. 34(13): i169-i177 (2018) - [j17]Laraib Malik, Fatemeh Almodaresi, Rob Patro:
Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis. Bioinform. 34(19): 3265-3272 (2018) - [c12]Hirak Sarkar, Mohsen Zakeri, Laraib Malik, Rob Patro:
Towards Selective-Alignment: Bridging the Accuracy Gap between Alignment-Based and Alignment-Free Transcript Quantification. BCB 2018: 27-36 - [c11]Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, Michael Ferdman, Rob Johnson, Rob Patro:
Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index. RECOMB 2018: 271-273 - [i4]Michael I. Love, Charlotte Soneson, Rob Patro:
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification. F1000Research 7: 952 (2018) - 2017
- [j16]Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro:
deBGR: an efficient and near-exact representation of the weighted de Bruijn graph. Bioinform. 33(14): i133-i141 (2017) - [j15]Mohsen Zakeri, Avi Srivastava, Fatemeh Almodaresi, Rob Patro:
Improved data-driven likelihood factorizations for transcript abundance estimation. Bioinform. 33(14): i142-i151 (2017) - [j14]Hirak Sarkar, Rob Patro:
Quark enables semi-reference-based compression of RNA-seq data. Bioinform. 33(21): 3380-3386 (2017) - [c10]Laraib Malik, Rob Patro:
Rich Chromatin Structure Prediction from Hi-C Data. BCB 2017: 184-193 - [c9]Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro:
A General-Purpose Counting Filter: Making Every Bit Count. SIGMOD Conference 2017: 775-787 - [c8]Fatemeh Almodaresi, Prashant Pandey, Rob Patro:
Rainbowfish: A Succinct Colored de Bruijn Graph Representation. WABI 2017: 18:1-18:15 - 2016
- [j13]Avi Srivastava, Hirak Sarkar, Nitish Gupta, Rob Patro:
RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes. Bioinform. 32(12): 192-200 (2016) - [j12]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:
A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. BMC Bioinform. 17: 155 (2016) - [i3]Nitish Gupta, Komal Sanjeev, Tim Wall, Carl Kingsford, Rob Patro:
Efficient Index Maintenance Under Dynamic Genome Modification. CoRR abs/1604.03132 (2016) - [i2]Avi Srivastava, Hirak Sarkar, Laraib Malik, Rob Patro:
Accurate, Fast and Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes. CoRR abs/1604.03250 (2016) - 2015
- [j11]Carl Kingsford, Rob Patro:
Reference-based compression of short-read sequences using path encoding. Bioinform. 31(12): 1920-1928 (2015) - [j10]Rob Patro, Carl Kingsford:
Data-dependent bucketing improves reference-free compression of sequencing reads. Bioinform. 31(17): 2770-2777 (2015) - [c7]Zhong Sichen, Lu Zhao, Yan Liang, Mohammadzaman Zamani, Rob Patro, Rezaul Chowdhury, Esther M. Arkin, Joseph S. B. Mitchell, Steven Skiena:
Optimizing Read Reversals for Sequence Compression - (Extended Abstract). WABI 2015: 189-202 - 2014
- [j9]Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford:
Identification of alternative topological domains in chromatin. Algorithms Mol. Biol. 9: 14 (2014) - 2013
- [j8]Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford:
Resolving spatial inconsistencies in chromosome conformation measurements. Algorithms Mol. Biol. 8: 8 (2013) - [j7]Rob Patro, Carl Kingsford:
Predicting protein interactions via parsimonious network history inference. Bioinform. 29(13): 237-246 (2013) - [c6]Hao Wang, Geet Duggal, Rob Patro, Michelle Girvan, Sridhar Hannenhalli, Carl Kingsford:
Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin. BCB 2013: 306 - [c5]Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford:
Multiscale Identification of Topological Domains in Chromatin. WABI 2013: 300-312 - [i1]Rob Patro, Stephen M. Mount, Carl Kingsford:
Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms. CoRR abs/1308.3700 (2013) - 2012
- [b1]Robert Patro:
Computationally Comparing Biological Networks and Reconstructing Their Evolution. University of Maryland, College Park, MD, USA, 2012 - [j6]Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, Carl Kingsford:
Parsimonious reconstruction of network evolution. Algorithms Mol. Biol. 7: 25 (2012) - [j5]Rob Patro, Carl Kingsford:
Global network alignment using multiscale spectral signatures. Bioinform. 28(23): 3105-3114 (2012) - [j4]Robert Patro, John P. Dickerson, Sujal Bista, Satyandra K. Gupta, Amitabh Varshney:
Speeding Up Particle Trajectory Simulations Under Moving Force Fields using Graphic Processing Units. J. Comput. Inf. Sci. Eng. 12(2) (2012) - [c4]Rob Patro, Geet Duggal, Emre Sefer, Hao Wang, Darya Filippova, Carl Kingsford:
The missing models: a data-driven approach for learning how networks grow. KDD 2012: 42-50 - [c3]Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford:
Resolving Spatial Inconsistencies in Chromosome Conformation Data. WABI 2012: 288-300 - 2011
- [j3]Robert Patro, Cheuk Yiu Ip, Sujal Bista, Amitabh Varshney:
Social Snapshot: A System for Temporally Coupled Social Photography. IEEE Computer Graphics and Applications 31(1): 74-84 (2011) - [j2]André Maximo, Robert Patro, Amitabh Varshney, Ricardo C. Farias:
A robust and rotationally invariant local surface descriptor with applications to non-local mesh processing. Graph. Model. 73(5): 231-242 (2011) - [c2]Robert Patro, Cheuk Yiu Ip, Sujal Bista, D. Thirumalai, Samuel S. Cho, Amitabh Varshney:
MDMap: A system for data-driven layout and exploration of molecular dynamics simulations. BioVis 2011: 111-118 - [c1]Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, Carl Kingsford:
Parsimonious Reconstruction of Network Evolution. WABI 2011: 237-249 - [p2]Youngmin Kim, Robert Patro, Cheuk Yiu Ip, Dianne P. O'Leary, Andriy Anishkin:
Salient Frame Detection for Molecular Dynamics Simulations. Scientific Visualization: Interactions, Features, Metaphors 2011: 160-175 - 2010
- [p1]Robert Patro, Cheuk Yiu Ip, Amitabh Varshney:
Saliency Guided Summarization of Molecular Dynamics Simulations. Scientific Visualization: Advanced Concepts 2010: 321-335
2000 – 2009
- 2009
- [j1]Aswin C. Sankaranarayanan, Robert Patro, Pavan K. Turaga, Amitabh Varshney, Rama Chellappa:
Modeling and Visualization of Human Activities for Multicamera Networks. EURASIP J. Image Video Process. 2009 (2009)
Coauthor Index
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last updated on 2024-10-24 20:32 CEST by the dblp team
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