Robert Patro

发表

Rich chromatin structure prediction from Hi-C data

Laraib Malik, Robert Patro, 2015, bioRxiv.

AtRTD – a comprehensive reference transcript dataset resource for accurate quantification of transcript‐specific expression in Arabidopsis thaliana

E. Eyras, Yamile Marquez, John W. S. Brown, 2015, The New phytologist.

RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis

Katharina M. Hembach, M. Robinson, L. Clement, 2018, Annual Review of Biomedical Data Science.

TransRate: reference-free quality assessment of de novo transcriptome assemblies

S. Kelly, J. Hibberd, Robert Patro, 2015, bioRxiv.

TransRate: reference free quality assessment of de-novo transcriptome assemblies

Richard Smith-Unna, Rob Patro, Julian M. Hibberd, 2015 .

Maximum Likelihood Estimation of Biological Relatedness from Low Coverage Sequencing Data

K. Veeramah, K. Sanjeev, M. Lipatov, 2015, bioRxiv.

Accounting for fragments of unexpected origin improves transcript quantification in RNA-seq simulations focused on increased realism

Mohsen Zakeri, C. Soneson, Carl Kingsford, 2021, bioRxiv.

Alignment and mapping methodology influence transcript abundance estimation

Fatemeh Almodaresi, Mohsen Zakeri, M. Love, 2020, Genome biology.

RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis

Katharina M. Hembach, M. Robinson, L. Clement, 2018, Annual Review of Biomedical Data Science.

ChromoVis : Feature-Rich Layouts of Chromosome Conformation Graphs

Carl Kingsford, Robert Patro, G. Duggal, 2013 .

Detecting isoform-level allelic imbalance accounting for inferential uncertainty

Mohsen Zakeri, M. Love, C. Ackert-Bicknell, 2022, bioRxiv.

TreeTerminus —creating transcript trees using inferential replicate counts

M. Love, Robert Patro, N. P. Singh, 2022, bioRxiv.

Perplexity: evaluating transcript abundance estimation in the absence of ground truth

Rob Patro, Jason Fan, Skylar Chan, 2022, Algorithms for Molecular Biology.

Rich Chromatin Structure Prediction from Hi-C Data

Robert Patro, Laraib Malik, Laraib Malik, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Modeling and Visualization of Human Activities for Multicamera Networks

Rama Chellappa, Aswin C. Sankaranarayanan, Pavan K. Turaga, 2009, EURASIP J. Image Video Process..

Salmon provides fast and bias-aware quantification of transcript expression

Rob Patro, Geet Duggal, Carl Kingsford, 2017, Nature Methods.

A robust and rotationally invariant local surface descriptor with applications to non-local mesh processing

Robert Patro, Amitabh Varshney, André Maximo, 2011, Graph. Model..

Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference

Geet Duggal, Carl Kingsford, Rob Patro, 2017, Nature Methods.

Sketching and Sublinear Data Structures in Genomics

Carl Kingsford, Guillaume Marçais, Rob Patro, 2019, Annual Review of Biomedical Data Science.

deBGR: an efficient and near-exact representation of the weighted de Bruijn graph

Michael A. Bender, Prashant Pandey, Rob Johnson, 2017, Bioinform..

A General-Purpose Counting Filter: Making Every Bit Count

Michael A. Bender, Prashant Pandey, Rob Johnson, 2017, SIGMOD Conference.

Squeakr: An Exact and Approximate k-mer Counting System

Michael A. Bender, Prashant Pandey, Rob Johnson, 2017, bioRxiv.

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

Rob Patro, Carl Kingsford, Stephen M. Mount, 2013, Nature Biotechnology.

Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms pdf

Robert Patro, Carl Kingsford, Stephen M. Mount, 2013, ArXiv.

Global network alignment using multiscale spectral signatures

Robert Patro, Carl Kingsford, Carl Kingsford, 2012, Bioinform..

A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification

Rob Patro, Avi Srivastava, Hirak Sarkar, 2020, bioRxiv.

Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

Avi Srivastava, Laraib Malik, Rob Patro, 2018, Genome Biology.

RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes

Robert Patro, Nitish Gupta, Avi Srivastava, 2015, bioRxiv.

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

Charlotte Soneson, Rob Patro, Michael B. Stadler, 2020, bioRxiv.

Identification of alternative topological domains in chromatin

Robert Patro, Darya Filippova, Geet Duggal, 2014, Algorithms for Molecular Biology.

Resolving spatial inconsistencies in chromosome conformation measurements

Samir Khuller, Robert Patro, Darya Filippova, 2013, Algorithms for Molecular Biology.

Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level

Rob Patro, Avi Srivastava, Hirak Sarkar, 2019, Bioinform..

Graph regularized, semi-supervised learning improves annotation of de novo transcriptomes

Laraib Malik, Rob Patro, Shravya Thatipally, 2016, bioRxiv.

Understanding and evaluating ambiguity in single-cell and single-nucleus RNA-sequencing

C. Soneson, Robert Patro, Dongze He, 2023, bioRxiv.

Alignment and mapping methodology influence transcript abundance estimation

Fatemeh Almodaresi, Charlotte Soneson, Carl Kingsford, 2019, Genome Biology.

A space and time-efficient index for the compacted colored de Bruijn graph

Fatemeh Almodaresi, Robert Patro, Avi Srivastava, 2017, bioRxiv.

Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2

S. Deorowicz, Robert Patro, Marek Kokot, 2021, bioRxiv.

AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite

Fatemeh Almodaresi, Mohsen Zakeri, A. Hatzigeorgiou, 2022, Genome Biology.

Tximeta: Reference sequence checksums for provenance identification in RNA-seq

Charlotte Soneson, Rob Patro, Michael I. Love, 2019, bioRxiv.

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

M. Love, C. Soneson, Robert Patro, 2018, F1000Research.

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

Charlotte Soneson, Rob Patro, Michael I Love, 2018, F1000Research.

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

Charlotte Soneson, Rob Patro, Michael I Love, 2018, F1000Research.

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs

Charlotte Soneson, Rob Patro, Michael I Love, 2018, Life Science Alliance.

Salmon provides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference

Geet Duggal, Carl Kingsford, Michael I. Love, 2015, bioRxiv.

Salmon: Accurate, Versatile and Ultrafast Quantification from RNA-seq Data using Lightweight-Alignment

Geet Duggal, Carl Kingsford, Rob Patro, 2015 .

Alevin: An integrated method for dscRNA-seq quantification

Avi Srivastava, Rob Patro, Ian Sudbery, 2018 .

Accurate, fast, and model-aware transcript expression quantification with Salmon

Geet Duggal, Carl Kingsford, Rob Patro, 2015 .

Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data

Mohsen Zakeri, C. Soneson, Robert Patro, 2021, Nature Methods.

Compression of quantification uncertainty for scRNA-seq counts

Rob Patro, Avi Srivastava, Hirak Sarkar, 2020, bioRxiv.

Computationally Comparing Biological Networks and Reconstructing Their Evolution

Robert Patro, Robert Patro, 2012 .

Parsimonious reconstruction of network evolution

Robert Patro, Carl Kingsford, Emre Sefer, 2011, Algorithms for Molecular Biology.

CSI-Microbes: Identifying cell-type specific intracellular microbes from single-cell RNA-seq data

Mark D. M. Leiserson, A. Schäffer, E. Ruppin, 2021 .

Accurate, Fast and Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes pdf

Robert Patro, Avi Srivastava, Hirak Sarkar, 2016, ArXiv.

Bioconda: sustainable and comprehensive software distribution for the life sciences

Yuri Pirola, Anthony Bretaudeau, Wei Shen, 2017, Nature Methods.

Nonparametric expression analysis using inferential replicate counts

Joseph G Ibrahim, Avi Srivastava, Rob Patro, 2019, bioRxiv.

Multiscale Identification of Topological Domains in Chromatin

Robert Patro, Darya Filippova, Geet Duggal, 2013, WABI.

Salient Frame Detection for Molecular Dynamics Simulations

Dianne P. O'Leary, Robert Patro, Youngmin Kim, 2011, Scientific Visualization: Interactions, Features, Metaphors.

Quark enables semi‐reference‐based compression of RNA‐seq data

Robert Patro, Hirak Sarkar, Robert Patro, 2017, Bioinform..

Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets

M. Love, Kwangbom Choi, Robert Patro, 2021, bioRxiv.

Speeding Up Particle Trajectory Simulations Under Moving Force Fields using Graphic Processing Units

Satyandra K. Gupta, Amitabh Varshney, John P. Dickerson, 2012, J. Comput. Inf. Sci. Eng..

Speeding Up Particle Trajectory Simulations under Moving Force Fields using GPUs

Satyandra K. Gupta, Amitabh Varshney, John P. Dickerson, 2011 .

Social Snapshot: A System for Temporally Coupled Social Photography

Robert Patro, Amitabh Varshney, Cheuk Yiu Ip, 2011, IEEE Computer Graphics and Applications.

Common and differential transcriptional responses to different models of traumatic stress exposure in rats

D. Mckinnon, Moriah L. Jacobson, Robert Patro, 2018, Translational Psychiatry.

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index

M. A. Bender, Fatemeh Almodaresi, M. Ferdman, 2017, bioRxiv.

PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index

Fatemeh Almodaresi, Mohsen Zakeri, Robert Patro, 2021, Bioinform..

MDMap: A system for data-driven layout and exploration of molecular dynamics simulations

Robert Patro, Amitabh Varshney, Cheuk Yiu Ip, 2011, 2011 IEEE Symposium on Biological Data Visualization (BioVis)..

scRNA-seq analysis of colon and esophageal tumors uncovers abundant microbial reads in myeloid cells undergoing proinflammatory transcriptional alterations

Mark D. M. Leiserson, A. Schäffer, E. Ruppin, 2023, bioRxiv.

Predicting protein interactions via parsimonious network history inference

Robert Patro, Carl Kingsford, Carl Kingsford, 2013, Bioinform..

Fulgor: A fast and compact k-mer index for large-scale matching and color queries

Giulio Ermanno Pibiri, Jason Fan, Robert Patro, 2023, bioRxiv.

Spectrum preserving tilings enable sparse and modular reference indexing

Jason Fan, Robert Patro, G. Pibiri, 2023, bioRxiv.

simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry

Robert Patro, Dongze He, 2023, bioRxiv.

Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections

Rob Patro, Jamshed Khan, Robert Patro, 2020, bioRxiv.

An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search

Prashant Pandey, Fatemeh Almodaresi, Michael Ferdman, 2018, bioRxiv.

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin

R. Norel, R. Bellazzi, R. Prill, 2016, BMC Bioinformatics.

Puffaligner: An Efficient and Accurate Aligner Based on the Pufferfish Index

Fatemeh Almodaresi, Rob Patro, Mohsen Zakeri, 2020 .

Algorithms meet sequencing technologies – 10th edition of the RECOMB-Seq workshop

Rob Patro, Leena Salmela, Robert Patro, 2020, iScience.

Meta-colored compacted de Bruijn graphs: overview and challenges

Jason Fan, Robert Patro, G. Pibiri, 2023, bioRxiv.

Rainbowfish: A Succinct Colored de Bruijn Graph Representation

Prashant Pandey, Fatemeh Almodaresi, Robert Patro, 2017, bioRxiv.

Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin

Michelle Girvan, Robert Patro, Geet Duggal, 2013, BCB.

Resolving Spatial Inconsistencies in Chromosome Conformation Data

Samir Khuller, Robert Patro, Darya Filippova, 2012, WABI.

OP-CBIO210312 177..186

Robert Patro, Jamshed Khan, Rob Patro, 2021 .

Towards selective-alignment: Bridging the accuracy gap between alignment-based and alignment-free transcript quantification

Robert Patro, Hirak Sarkar, Laraib Malik, 2017, bioRxiv.

Towards Selective-Alignment: Producing Accurate And Sensitive Alignments Using Quasi-Mapping

Hirak Sarkar, Laraib Malik, Rob Patro, 2017 .

Reference-based compression of short-read sequences using path encoding

Robert Patro, Carl Kingsford, Carl Kingsford, 2015, Bioinform..

Compression of short-read sequences using path encoding

Carl Kingsford, Rob Patro, Carl Kingsford, 2014, bioRxiv.

DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes

Mark D. Robinson, C. Soneson, Robert Patro, 2023, bioRxiv.

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index

M. A. Bender, Fatemeh Almodaresi, M. Ferdman, 2017, bioRxiv.

An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using LSM Trees

Fatemeh Almodaresi, M. Ferdman, P. Pandey, 2021, bioRxiv.

Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets

M. Love, Kwangbom Choi, Robert Patro, 2021, bioRxiv.

Improved data-driven likelihood factorizations for transcript abundance estimation

Fatemeh Almodaresi, Robert Patro, Avi Srivastava, 2017, Bioinform..

Supplementary Methods, Tables, and Figures

M. Love, Kwangbom Choi, Robert Patro, 2022 .

Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data

Rob Patro, Avi Srivastava, Hirak Sarkar, 2020, bioRxiv.

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin

Julio Saez-Rodriguez, Mitja Lustrek, Robert Patro, 2016, BMC Bioinformatics.

Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis

Fatemeh Almodaresi, Robert Patro, Laraib Malik, 2018, Bioinform..

Rich chromatin structure prediction from Hi-C data

Laraib Malik, Robert Patro, 2015, bioRxiv.

scRNA-seq analysis of colon and esophageal tumors uncovers abundant microbial reads in myeloid cells undergoing proinflammatory transcriptional alterations

Mark D. M. Leiserson, A. Schäffer, E. Ruppin, 2020, bioRxiv.

Bioconda: sustainable and comprehensive software distribution for the life sciences

Brent S. Pedersen, James E. Johnson, Alexander S. Rose, 2018, Nature Methods.

Alevin: An integrated method for dscRNA-seq quantiﬁcation

I. Sudbery, Robert Patro, Tom S. Smith, 2018 .

Tree-based differential testing using inferential uncertainty for RNA-Seq

M. Love, Robert Patro, N. P. Singh, 2023, bioRxiv.

SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty

Mohsen Zakeri, M. Love, C. Ackert-Bicknell, 2023, Genome Biology.

Rich Chromatin Structure Prediction from Hi-C Data

Laraib Malik, Robert Patro, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.