According to our database1, Robert Patro
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Squeakr: an exact and approximate k-mer counting system.
A space and time-efficient index for the compacted colored de Bruijn graph.
Improved data-driven likelihood factorizations for transcript abundance estimation.
Quark enables semi-reference-based compression of RNA-seq data.
deBGR: an efficient and near-exact representation of the weighted de Bruijn graph.
Rainbowfish: A Succinct Colored de Bruijn Graph Representation.
Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017
A General-Purpose Counting Filter: Making Every Bit Count.
Proceedings of the 2017 ACM International Conference on Management of Data, 2017
Rich Chromatin Structure Prediction from Hi-C Data.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017
Accurate, Fast and Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes.
Efficient Index Maintenance Under Dynamic Genome Modification.
A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.
BMC Bioinformatics, 2016
RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes.
Data-dependent bucketing improves reference-free compression of sequencing reads.
Reference-based compression of short-read sequences using path encoding.
Optimizing Read Reversals for Sequence Compression - (Extended Abstract).
Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015
Identification of alternative topological domains in chromatin.
Algorithms for Molecular Biology, 2014
Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms.
Predicting protein interactions via parsimonious network history inference.
Resolving spatial inconsistencies in chromosome conformation measurements.
Algorithms for Molecular Biology, 2013
Multiscale Identification of Topological Domains in Chromatin.
Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013
Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin.
Proceedings of the ACM Conference on Bioinformatics, 2013
Computationally Comparing Biological Networks and Reconstructing Their Evolution.
PhD thesis, 2012
Global network alignment using multiscale spectral signatures.
Parsimonious reconstruction of network evolution.
Algorithms for Molecular Biology, 2012
Resolving Spatial Inconsistencies in Chromosome Conformation Data.
Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012
The missing models: a data-driven approach for learning how networks grow.
Proceedings of the 18th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2012
A robust and rotationally invariant local surface descriptor with applications to non-local mesh processing.
Graphical Models, 2011
Social Snapshot: A System for Temporally Coupled Social Photography.
IEEE Computer Graphics and Applications, 2011
Parsimonious Reconstruction of Network Evolution.
Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011
Salient Frame Detection for Molecular Dynamics Simulations.
Proceedings of the Scientific Visualization: Interactions, Features, Metaphors, 2011
MDMap: A system for data-driven layout and exploration of molecular dynamics simulations.
Proceedings of the 2011 IEEE Symposium on Biological Data Visualization, 2011
Saliency Guided Summarization of Molecular Dynamics Simulations.
Proceedings of the Scientific Visualization: Advanced Concepts, 2010
Modeling and Visualization of Human Activities for Multicamera Networks.
EURASIP J. Image and Video Processing, 2009