Rob Patro

Latest

• Accounting for fragments of unexpected origin improves transcript quantification in RNA-seq simulations focused on increased realism
• Alignment and mapping methodology influence transcript abundance estimation
• Sketching and Sublinear Data Structures in Genomics
• Salmon provides fast and bias-aware quantification of transcript expression
• A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin
• Efficient index maintenance under dynamic genome modification
• Data-dependent bucketing improves reference-free compression of sequencing reads
• Reference-based compression of short-read sequences using path encoding
• Identification of alternative topological domains in chromatin
• Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
• Multiscale identification of topological domains in chromatin
• Predicting protein interactions via parsimonious network history inference
• Resolving spatial inconsistencies in chromosome conformation measurements
• Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin
• Global network alignment using multiscale spectral signatures
• Parsimonious reconstruction of network evolution
• Resolving spatial inconsistencies in chromosome conformation data