Rob Patro
Rob Patro
Associate Professor, Department of Computer Science, University of Maryland
Verified email at - Homepage
Cited by
Cited by
Salmon provides fast and bias-aware quantification of transcript expression
R Patro, G Duggal, MI Love, RA Irizarry, C Kingsford
Nature methods 14 (4), 417-419, 2017
Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
R Patro, SM Mount, C Kingsford
Nature biotechnology 32 (5), 462-464, 2014
TransRate: reference-free quality assessment of de novo transcriptome assemblies
R Smith-Unna, C Boursnell, R Patro, JM Hibberd, S Kelly
Genome research 26 (8), 1134-1144, 2016
Bioconda: sustainable and comprehensive software distribution for the life sciences
B Grüning, R Dale, A Sjödin, BA Chapman, J Rowe, CH Tomkins-Tinch, ...
Nature methods 15 (7), 475-476, 2018
Global network alignment using multiscale spectral signatures
R Patro, C Kingsford
Bioinformatics 28 (23), 3105-3114, 2012
Identification of alternative topological domains in chromatin
D Filippova, R Patro, G Duggal, C Kingsford
Algorithms for Molecular Biology 9, 1-11, 2014
A general-purpose counting filter: Making every bit count
P Pandey, MA Bender, R Johnson, R Patro
Proceedings of the 2017 ACM international conference on Management of Data …, 2017
Alevin efficiently estimates accurate gene abundances from dscRNA-seq data
A Srivastava, L Malik, T Smith, I Sudbery, R Patro
Genome biology 20, 1-16, 2019
RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes
A Srivastava, H Sarkar, N Gupta, R Patro
Bioinformatics 32 (12), i192-i200, 2016
Tximeta: Reference sequence checksums for provenance identification in RNA-seq
MI Love, C Soneson, PF Hickey, LK Johnson, NT Pierce, L Shepherd, ...
PLoS computational biology 16 (2), e1007664, 2020
RNA sequencing data: hitchhiker's guide to expression analysis
K Van den Berge, KM Hembach, C Soneson, S Tiberi, L Clement, MI Love, ...
Annual Review of Biomedical Data Science 2, 139-173, 2019
Alignment and mapping methodology influence transcript abundance estimation
A Srivastava, L Malik, H Sarkar, M Zakeri, F Almodaresi, C Soneson, ...
Genome biology 21 (1), 1-29, 2020
Mantis: a fast, small, and exact large-scale sequence-search index
P Pandey, F Almodaresi, MA Bender, M Ferdman, R Johnson, R Patro
Cell systems 7 (2), 201-207. e4, 2018
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
MI Love, C Soneson, R Patro
F1000Research 7, 952, 2018
Squeakr: an exact and approximate k-mer counting system
P Pandey, MA Bender, R Johnson, R Patro
Bioinformatics 34 (4), 568-575, 2018
Maximum likelihood estimation of biological relatedness from low coverage sequencing data
M Lipatov, K Sanjeev, R Patro, KR Veeramah
BioRxiv, 023374, 2015
Salmon provides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference
R Patro, G Duggal, MI Love, RA Irizarry, C Kingsford
BioRxiv, 021592, 2015
Rainbowfish: a succinct colored de Bruijn graph representation
F Almodaresi, P Pandey, R Patro
bioRxiv, 138016, 2017
A space and time-efficient index for the compacted colored de Bruijn graph
F Almodaresi, H Sarkar, A Srivastava, R Patro
Bioinformatics 34 (13), i169-i177, 2018
Reference-based compression of short-read sequences using path encoding
C Kingsford, R Patro
Bioinformatics 31 (12), 1920-1928, 2015
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