Rob Patro

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Carl KingsfordProfessor, Computational Biology Department, School of Computer Science, CarnegieVerified email at cs.cmu.edu
Michael I. LoveAssociate Professor, Biostatistics & Genetics, UNC-Chapel HillVerified email at email.unc.edu
Geet DuggalPh.D. Student, School of Computer Science, Carnegie Mellon UniversityVerified email at cs.cmu.edu
Avi SrivastavaAssistant Professor, The Wistar InstituteVerified email at wistar.org
Hirak SarkarLudwig Scholar at Princeton UniversityVerified email at hms.harvard.edu
Rafael A IrizarryProfessor, Biostatistics and Computational Biology, Dana-Farber and HarvardVerified email at ds.dfci.harvard.edu
Charlotte SonesonResearch Associate, FMI, BaselVerified email at fmi.ch
Fatemeh AlmodaresiPostdoctoral Fellow, Ontario Institute for Cancer ResearchVerified email at oicr.on.ca
Mohsen ZakeriJohns Hopkins UniversityVerified email at jhu.edu
Prashant PandeyKhoury College of Computer Sciences, Northeastern UniversityVerified email at northeastern.edu
Laraib Iqbal MalikAbbVieVerified email at abbvie.com
Rob JohnsonVMware ResearchVerified email at vmware.com
Jamshed KhanUniversity of MarylandVerified email at cs.umd.edu
Darya FilippovaHippocraticAIVerified email at hippocraticai.com
Richard Smith-UnnaLabDAO. Formerly @ Resurgo Genetics, Department of Plant Sciences, University of CambridgeVerified email at labdao.com
Chris BoursnellUniversity of CambridgeVerified email at cam.ac.uk
Michael A. BenderStony Brook UniversityVerified email at cs.stonybrook.edu
Amitabh VarshneyDean, College of Computer, Mathematical, and Natural Sciences,Professor of Computer ScienceVerified email at cs.umd.edu
Steve KellyUniversity of OxfordVerified email at plants.ox.ac.uk
Julian M HibberdDepartment of Plant Sciences, University of CambridgeVerified email at cam.ac.uk

Rob Patro

Associate Professor, Department of Computer Science, University of Maryland

Verified email at cs.umd.edu - Homepage

computational biology bioinformatics algorithms cs theory parallel computing


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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	10012	2017
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	1227	2018
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	808	2016
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	799	2014
Best practices for single-cell analysis across modalities L Heumos, AC Schaar, C Lance, A Litinetskaya, F Drost, L Zappia, ... Nature Reviews Genetics 24 (8), 550-572, 2023	550	2023
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	265	2020
Global network alignment using multiscale spectral signatures R Patro, C Kingsford Bioinformatics 28 (23), 3105-3114, 2012	255	2012
Identification of alternative topological domains in chromatin D Filippova, R Patro, G Duggal, C Kingsford Algorithms for Molecular Biology 9, 1-11, 2014	251	2014
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	222	2019
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	205	2017
Alignment and mapping methodology influence transcript abundance estimation A Srivastava, L Malik, H Sarkar, M Zakeri, F Almodaresi, C Soneson, ... Genome biology 21, 1-29, 2020	179	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 (1), 139-173, 2019	165	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	142	2016
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification MI Love, C Soneson, R Patro F1000Research 7, 2018	141	2018
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	125	2018
Squeakr: an exact and approximate k-mer counting system P Pandey, MA Bender, R Johnson, R Patro Bioinformatics 34 (4), 568-575, 2018	115	2018
Nonparametric expression analysis using inferential replicate counts A Zhu, A Srivastava, JG Ibrahim, R Patro, MI Love Nucleic Acids Research 47 (18), e105-e105, 2019	105	2019
Maximum likelihood estimation of biological relatedness from low coverage sequencing data M Lipatov, K Sanjeev, R Patro, KR Veeramah BioRxiv, 023374, 2015	102	2015
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	97	2018
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	80	2015

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