Publications

2024

Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment

Noor Singh, Jamshed Khan, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2024

Collapsible tree: interactive web app to present collapsible hierarchies

Yuan Gao, Rob Patro, Jiang Peng

Bioinformatics paper

2024

Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn Graphs ^*

Alessio Campanelli, Giulio Ermanno Pibiri, Jason Fan, Rob Patro

Journal of Computational Biology paper

2024

A renewed call for open artificial intelligence in biomedicine

Anthony Gitter, James S. Fraser, Tamir Gonen, Rob Patro, Hannah K. Wayment-Steele, Alicia Williams, Benjamin Haibe‐Kains, Roland L. Dunbrack, Cameron Cook, Anshul Kundaje, Michael M. Hoffman, Anne E. Carpenter, Stephanie A. Wankowicz, Kresten Lindorff‐Larsen

paper

2024

A replicable and modular benchmark for long-read transcript quantification methods

Zahra Zare Jousheghani, Noor Singh, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2024

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

Rob Patro, Charlotte Soneson, Michael I. Love

UNC Libraries paper

2024

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

Michael I. Love, Mark D. Robinson, Shobbir Hussain, Rob Patro, Charlotte Soneson, Dheeraj Malhotra

UNC Libraries paper

2024

Where the patterns are: repetition-aware compression for colored de Bruijn graphs ^⋆

Alessio Campanelli, Giulio Ermanno Pibiri, Jason Fan, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2024

Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes

Welles Robinson, Joshua K. Stone, Fiorella Schischlik, Billel Gasmi, Michael C. Kelly, Charlie Seibert, Kimia Dadkhah, E. Michael Gertz, Joo Sang Lee, Kaiyuan Zhu, Lichun Ma, Xin Wei Wang, S. Cenk Şahinalp, Rob Patro, Mark D.M. Leiserson, Curtis C. Harris, Alejandro A. Schäffer, Eytan Ruppin

Science Advances paper

2024

DifferentialRegulation : a Bayesian hierarchical approach to identify differentially regulated genes

Simone Tiberi, Joël Meili, Peiying Cai, Charlotte Soneson, Dongze He, Hirak Sarkar, Alejandra Avalos‐Pacheco, Rob Patro, Mark D. Robinson

Biostatistics paper

2024

Fast, parallel, and cache-friendly suffix array construction

Jamshed Khan, Tobias Rubel, Erin K. Molloy, Laxman Dhulipala, Rob Patro

Algorithms for Molecular Biology paper

2024

`Forseti` : a mechanistic and predictive model of the splicing status of scRNA-seq reads

Dongze He, Yuan Gao, Spencer Skylar Chan, Natalia Quintana-Parrilla, Rob Patro

Bioinformatics paper

2024

Designing efficient randstrobes for sequence similarity analyses

Moein Karami, Aryan Soltani Mohammadi, Marcel Martin, Barış Ekim, Wei Shen, Lidong Guo, Mengyang Xu, Giulio Ermanno Pibiri, Rob Patro, Kristoffer Sahlin

Bioinformatics paper

2024

Oarfish: Enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification

Zahra Zare Jousheghani, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2024

Forseti: A mechanistic and predictive model of the splicing status of scRNA-seq reads

Dongze He, Yuan Gao, Spencer Skylar Chan, Natalia Quintana-Parrilla, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2024

scCensus: Off-target scRNA-seq reads reveal meaningful biology

Dongze He, Stephen M. Mount, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2024

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

Jason Fan, Jamshed Khan, Noor Singh, Giulio Ermanno Pibiri, Rob Patro

Algorithms for Molecular Biology paper

2024

Meta-colored Compacted de Bruijn Graphs

Giulio Ermanno Pibiri, Jason Fan, Rob Patro

Lecture notes in computer science paper

2023

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

Noor Singh, Euphy Wu, Jason Fan, Michael I. Love, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2023

Designing efficient randstrobes for sequence similarity analyses

Moein Karami, Aryan Soltani Mohammadi, Marcel Martin, Barış Ekim, Wei Shen, Lidong Guo, Mengyang Xu, Giulio Ermanno Pibiri, Rob Patro, Kristoffer Sahlin

bioRxiv (Cold Spring Harbor Laboratory) paper

2023

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

Dongze He, Rob Patro

Bioinformatics paper

2023

DifferentialRegulation : a Bayesian hierarchical approach to identify differentially regulated genes

Simone Tiberi, Joël Meili, Peiying Cai, Charlotte Soneson, Dongze He, Hirak Sarkar, Alejandra Avalos‐Pacheco, Rob Patro, Mark D. Robinson

bioRxiv (Cold Spring Harbor Laboratory) paper

2023

Meta-colored compacted de Bruijn graphs

Giulio Ermanno Pibiri, Jason Fan, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2023

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

Euphy Wu, Noor Singh, Kwangbom Choi, Mohsen Zakeri, Matthew Vincent, Gary A. Churchill, Cheryl L. Ackert‐Bicknell, Rob Patro, Michael I. Love

Genome biology paper

2023

TreeTerminus —creating transcript trees using inferential replicate counts

Noor Singh, Michael I. Love, Rob Patro

iScience paper

2023

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

Jason Fan, Noor Singh, Jamshed Khan, Giulio Ermanno Pibiri, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2023

R Packages used in TreeTerminus paper

Noor Singh, Michael I. Love, Rob Patro

Zenodo (CERN European Organization for Nuclear Research) paper

2023

Abstract 1400: Novel expression biomarkers via prediction of response to FOLFIRINOX (FFX) treatment for PDAC

Hossein Asghari, Ehsan Haghshenas, Roby Thomas, Eric T. Schultz, Rob Patro, Stan Skrzypczak, Carl Kingsford

Cancer Research paper

2023

Best practices for single-cell analysis across modalities

Lukas Heumos, Anna C. Schaar, Christopher Lance, Anastasia Litinetskaya, Felix Drost, Luke Zappia, Malte Lücken, Daniel Strobl, Juan Henao, Fabiola Curion, Hananeh Aliee, Meshal Ansari, Pau Badia-i-Mompel, Maren Büttner, Emma Dann, Daniel Dimitrov, Leander Dony, Amit Frishberg, Dongze He, Soroor Hediyeh-zadeh, Leon Hetzel, Ignacio L. Ibarra, Matthew G. Jones, Mohammad Lotfollahi, Laura D. Martens, Christian L. Müller, Mor Nitzan, Johannes Ostner, Giovanni Palla, Rob Patro, Zoe Piran, Ciro Ramírez-Suástegui, Julio Sáez-Rodríguez, Hirak Sarkar, Benjamin Schubert, Lisa Sikkema, Avi Srivastava, Jovan Tanevski, Isaac Virshup, Philipp Weiler, Herbert B. Schiller, Fabian J. Theis

Nature Reviews Genetics paper

2023

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

Dongze He, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2023

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

Dongze He, Charlotte Soneson, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2023

Spectrum Preserving Tilings Enable Sparse and Modular Reference Indexing

Jason Fan, Jamshed Khan, Giulio Ermanno Pibiri, Rob Patro

Lecture notes in computer science paper

2022

TreeTerminus - Creating transcript trees using inferential replicate counts

Noor Singh, Michael I. Love, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2022

Spectrum preserving tilings enable sparse and modular reference indexing

Jason Fan, Jamshed Khan, Giulio Ermanno Pibiri, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2022

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

Jamshed Khan, Marek Kokot, Sebastian Deorowicz, Rob Patro

Genome biology paper

2022

Detecting isoform-level allelic imbalance accounting for inferential uncertainty

Euphy Wu, Noor Singh, Kwangbom Choi, Mohsen Zakeri, Matthew Vincent, Gary A. Churchill, Cheryl L. Ackert‐Bicknell, Rob Patro, Michael I. Love

bioRxiv (Cold Spring Harbor Laboratory) paper

2022

Abstract 3048: CSI-Microbes: Identifying cell-type specific intracellular microbes from single-cell RNA-seq data

Welles Robinson, Fiorella Schischlik, E. Michael Gertz, Joo Sang Lee, Kaiyuan Zhu, S. Cenk Şahinalp, Rob Patro, Mark D.M. Leiserson, Alejandro A. Schäffer, Eytan Ruppin

Cancer Research paper

2022

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

Wancen Mu, Hirak Sarkar, Avi Srivastava, Kwangbom Choi, Rob Patro, Michael I. Love

Bioinformatics paper

2022

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

Jason Fan, Spencer Skylar Chan, Rob Patro

Algorithms for Molecular Biology paper

2022

An incrementally updatable and scalable system for large-scale sequence search using the Bentley–Saxe transformation

Fatemeh Almodaresi, Jamshed Khan, Sergey Madaminov, Michael Ferdman, Rob Johnson, Prashant Pandey, Rob Patro

Bioinformatics paper

2022

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

Dongze He, Mohsen Zakeri, Hirak Sarkar, Charlotte Soneson, Avi Srivastava, Rob Patro

Nature Methods paper

2022

AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite

Giorgos Skoufos, Fatemeh Almodaresi, Mohsen Zakeri, Joseph N. Paulson, Rob Patro, Artemis G. Hatzigeorgiou, Ioannis S. Vlachos

Genome biology paper

2021

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

Jamshed Khan, Marek Kokot, Sebastian Deorowicz, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2021

Salmon sci-RNA-seq3 tutorial

Gaurav Sharma, Rob Patro

Zenodo (CERN European Organization for Nuclear Research) paper

2021

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

Wancen Mu, Hirak Sarkar, Avi Srivastava, Kwangbom Choi, Rob Patro, Michael I. Love

bioRxiv (Cold Spring Harbor Laboratory) paper

2021

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

Dongze He, Mohsen Zakeri, Hirak Sarkar, Charlotte Soneson, Avi Srivastava, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2021

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

Fatemeh Almodaresi, Mohsen Zakeri, Rob Patro

Bioinformatics paper

2021

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

Fatemeh Almodaresi, Mohsen Zakeri, Rob Patro

Zenodo (CERN European Organization for Nuclear Research) paper

2021

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

Jamshed Khan, Rob Patro

Bioinformatics paper

2021

A like-for-like comparison of lightweight-mapping pipelines for single-cell RNA-seq data pre-processing

Mohsen Zakeri, Avi Srivastava, Hirak Sarkar, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2021

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

Fatemeh Almodaresi, Jamshed Khan, Sergey Madaminov, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2021

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

Avi Srivastava, Mohsen Zakeri, Hirak Sarkar, Charlotte Soneson, Carl Kingsford, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2021

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

Charlotte Soneson, Avi Srivastava, Rob Patro, Michael Stadler

PLoS Computational Biology paper

2021

Compression of quantification uncertainty for scRNA-seq counts

Scott Van Buren, Hirak Sarkar, Avi Srivastava, Naim U. Rashid, Rob Patro, Michael I. Love

Bioinformatics paper

2021

Perplexity: Evaluating Transcript Abundance Estimation in the Absence of Ground Truth

Jason Fan, Spencer Skylar Chan, Rob Patro

DROPS (Schloss Dagstuhl – Leibniz Center for Informatics) paper

2020

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

Rob Patro, Leena Salmela

iScience paper

2020

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

Jamshed Khan, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2020

Alignment and mapping methodology influence transcript abundance estimation

Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro

Genome biology paper

2020

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

Fatemeh Almodaresi, Mohsen Zakeri, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2020

Compression of quantification uncertainty for scRNA-seq counts

Scott Van Buren, Hirak Sarkar, Avi Srivastava, Naim U. Rashid, Rob Patro, Michael I. Love

bioRxiv (Cold Spring Harbor Laboratory) paper

2020

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

Avi Srivastava, Laraib Malik, Hirak Sarkar, Rob Patro

Bioinformatics paper

2020

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

Hirak Sarkar, Avi Srivastava, Héctor Corrada Bravo, Michael I. Love, Rob Patro

Bioinformatics paper

2020

Novel target discovery in pembrolizumab-resistant gastric cancer using a comprehensive RNA-seq analysis pipeline.

Jeeyun Lee, Seung Tae Kim, Kyoung‐Mee Kim, Eric Schultz, Stan Skrzypczak, Rob Patro, Carl Kingsford

Journal of Clinical Oncology paper

2020

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

Welles Robinson, Joshua K. Stone, Fiorella Schischlik, Billel Gasmi, Michael C. Kelly, Charlie Seibert, Kimia Dadkhah, E. Michael Gertz, Joo Sang Lee, Kaiyuan Zhu, Lichun Ma, Xin Wei Wang, S. Cenk Şahinalp, Rob Patro, Mark D.M. Leiserson, Curtis C. Harris, Alejandro A. Schäffer, Eytan Ruppin

bioRxiv (Cold Spring Harbor Laboratory) paper

2020

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

Avi Srivastava, Laraib Malik, Hirak Sarkar, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2020

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

Hirak Sarkar, Avi Srivastava, Héctor Corrada Bravo, Michael I. Love, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2020

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

Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro

Journal of Computational Biology paper

2020

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

Charlotte Soneson, Avi Srivastava, Rob Patro, Michael Stadler

bioRxiv (Cold Spring Harbor Laboratory) paper

2020

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

Michael I. Love, Charlotte Soneson, Peter F. Hickey, Lisa K. Johnson, N. Tessa Pierce‐Ward, Lori Shepherd, Martin Morgan, Rob Patro

PLoS Computational Biology paper

2020

Accurate, efficient, and uncertainty-aware expression quantification of single-cell RNA-seq data

Hirak Sarkar, Avi Srivastava, Mohsen Zakeri, Scott Van Buren, Naim U. Rashid, Michael I. Love, Rob Patro

Figshare paper

2020

Interpretable deep learning algorithms for prokaryotic genome annotation

Hirak Sarkar, Rob Patro, Mohammad Ruhul Amin

Faculty of 1000 Research Ltd paper

2020

Referee report. For: GFF Utilities: GffRead and GffCompare [version 1; peer review: 3 approved]

Rob Patro

Faculty of 1000 Research Ltd paper

2019

Estimation of Indoor Air Pollution Levels in the Upper Himalaya

Anita Chaturvedi, Paurav Mehta, E Abba, Priya Ranjan, A. K. Verma, Rob Patro

Environmental Epidemiology paper

2019

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

Michael I. Love, Charlotte Soneson, Peter F. Hickey, Lisa K. Johnson, N. Tessa Pierce‐Ward, Lori Shepherd, Martin Morgan, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2019

Nonparametric expression analysis using inferential replicate counts

Anqi Zhu, Avi Srivastava, Joseph G. Ibrahim, Rob Patro, Michael I. Love

Nucleic Acids Research paper

2019

Alignment and mapping methodology influence transcript abundance estimation

Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2019

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

Hirak Sarkar, Avi Srivastava, Rob Patro

Bioinformatics paper

2019

RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis

Koen Van den Berge, Katharina Hembach, Charlotte Soneson, Simone Tiberi, Lieven Clement, Michael I. Love, Rob Patro, Mark D. Robinson

Annual Review of Biomedical Data Science paper

2019

Sketching and Sublinear Data Structures in Genomics

Guillaume Marçais, Brad Solomon, Rob Patro, Carl Kingsford

Annual Review of Biomedical Data Science paper

2019

Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

Avi Srivastava, Laraib Malik, Tom Smith, Ian Sudbery, Rob Patro

Genome biology paper

2019

Nonparametric expression analysis using inferential replicate counts

Anqi Zhu, Avi Srivastava, Joseph G. Ibrahim, Rob Patro, Michael I. Love

bioRxiv (Cold Spring Harbor Laboratory) paper

2019

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

Charlotte Soneson, Michael I. Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, Mark D. Robinson

Life Science Alliance paper

2019

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

Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro

Lecture notes in computer science paper

2018

RNA sequencing data: hitchhiker's guide to expression analysis

Koen Van den Berge, Katharina Hembach, Charlotte Soneson, Simone Tiberi, Lieven Clement, Michael I. Love, Rob Patro, Mark D. Robinson

paper

2018

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

Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2018

RNA sequencing data: hitchhiker's guide to expression analysis

Koen Van den Berge, Katharina Hembach, Charlotte Soneson, Simone Tiberi, Lieven Clement, Michael I. Love, Rob Patro, Mark D. Robinson

paper

2018

RNA sequencing data: hitchhiker's guide to expression analysis

Koen Van den Berge, Katharina Hembach, Charlotte Soneson, Simone Tiberi, Lieven Clement, Michael I. Love, Rob Patro, Mark D. Robinson

paper

2018

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

Michael I. Love, Charlotte Soneson, Rob Patro

F1000Research paper

2018

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

Michael I. Love, Charlotte Soneson, Rob Patro

F1000Research paper

2018

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

Moriah L. Jacobson, Lydia A. Kim, Robert Patro, Barbara Rosati, David McKinnon

Translational Psychiatry paper

2018

Towards Selective-Alignment

Hirak Sarkar, Mohsen Zakeri, Laraib Malik, Rob Patro

paper

2018

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

Charlotte Soneson, Michael I. Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, Mark D. Robinson

bioRxiv (Cold Spring Harbor Laboratory) paper

2018

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

Rob Patro, Geet Duggal, Carl Kingsford

Research Showcase @ Carnegie Mellon University (Carnegie Mellon University) paper

2018

Rich Chromatin Structure Prediction from Hi-C Data

Laraib Malik, Rob Patro

IEEE/ACM Transactions on Computational Biology and Bioinformatics paper

2018

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

Michael I. Love, Charlotte Soneson, Rob Patro

F1000Research paper

2018

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

Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, Michael Ferdman, Rob Johnson, Rob Patro

Cell Systems paper

2018

Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

Avi Srivastava, Laraib Malik, Tom Smith, Ian Sudbery, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2018

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

Laraib Malik, Fatemeh Almodaresi, Rob Patro

Bioinformatics paper

2018

Crow: Fast and accurate expression estimation from long reads

Laraib Malik, Avi Srivastava, Rob Patro

Research in Computational Molecular Biology paper

2018

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

Fatemeh Almodaresi, Hirak Sarkar, Avi Srivastava, Rob Patro

Bioinformatics paper

2018

Mantis: A Fast, Small, And Exact Large-Scale Sequence-Search Index - Experiment List

Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, Michael Ferdman, Rob Johnson, Rob Patro

Figshare paper

2018

Referee report. For: False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors [version 1; referees: 2 approved]

Rob Patro

Faculty of 1000 Research Ltd paper

2017

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

Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, Michael Ferdman, Rob Johnson, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2017

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Björn Grüning, Ryan Dale, Andreas Sjödin, Brad Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Adam Caprez, Bérénice Batut, Mathias Haudgaard, Thomas Cokelaer, Kyle A. Beauchamp, Brent S. Pedersen, Youri Hoogstrate, Anthony Bretaudeau, Devon Ryan, Gildas Le Corguillé, Dilmurat Yusuf, Sebastián Luna-Valero, Rory Kirchner, Karel Břinda, Thomas Wollmann, Martin Raden, Simon J. van Heeringen, Nicola Soranzo, Lorena Pantano, Zachary Charlop–Powers, Per Unneberg, Matthias De Smet, Marcel Martin, Greg Von Kuster, Tiago Antão, Milad Miladi, Kevin Thornton, Christian Brueffer, Marius van den Beek, Daniel Maticzka, Clemens Blank, Sebastian Will, Kévin Gravouil, Joachim Wolff, Manuel Holtgrewe, Jörg Fallmann, Vitor C. Piro, Ilya Shlyakhter, Ayman Yousif, Philip Mabon, Xiao‐Ou Zhang, Wei Shen, Jennifer Cabral, Cristel G. Thomas, Eric Enns, Joseph Brown, Jorrit Boekel, Mattias de Hollander, Jerome Kelleher, Nitesh Turaga, Julian R. de Ruiter, Dave Bouvier, Simon Gladman, Saket Choudhary, Nicholas Harding, Florian Eggenhofer, Arne Kratz, Zhuoqing Fang, Robert Kleinkauf, Henning Timm, Peter Cock, Enrico Seiler, Colin Brislawn, Thi Hong Hai Nguyen, Endre Bakken Stovner, Philip Ewels, Matt Chambers, James E. Johnson, Emil Hägglund, Simon Ye, Roman Valls Guimerà, Elmar Pruesse, Walter Dunn, Lance Parsons, Rob Patro, David Koppstein, Elena Grassi, Inken Wohlers, Alex Reynolds, MacIntosh Cornwell, Nicholas Stoler, Daniel Blankenberg, Guowei He, Marcel Bargull, Alexander Junge, Rick Farouni, Mallory Freeberg, Sourav Singh, Daniel R. Bogema, Fabio Cumbo, Liang-Bo Wang, David E. Larson, Matthew L. Workentine

bioRxiv (Cold Spring Harbor Laboratory) paper

2017

Squeakr: an exact and approximate k -mer counting system

Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro

Bioinformatics paper

2017

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

Fatemeh Almodaresi, Hirak Sarkar, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2017

Rich Chromatin Structure Prediction from Hi-C Data

Laraib Malik, Rob Patro

paper

2017

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

Hirak Sarkar, Rob Patro

Bioinformatics paper

2017

Rainbowfish: A Succinct Colored de Bruijn Graph Representation

Fatemeh Almodaresi, Prashant Pandey, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2017

A General-Purpose Counting Filter

Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro

paper

2017

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

Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro

Bioinformatics paper

2017

Improved data-driven likelihood factorizations for transcript abundance estimation

Mohsen Zakeri, Avi Srivastava, Fatemeh Almodaresi, Rob Patro

Bioinformatics paper

2017

Squeakr: An Exact and Approximate k -mer Counting System

Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2017

Salmon provides fast and bias-aware quantification of transcript expression

Rob Patro, Geet Duggal, Michael I. Love, Rafael A. Irizarry, Carl Kingsford

Nature Methods paper

2017

Rainbowfish: A Succinct Colored de Bruijn Graph Representation

Fatemeh Almodaresi, Prashant Pandey, Rob Patro

DROPS (Schloss Dagstuhl – Leibniz Center for Informatics) paper

2017

deBGR: An efficient and exact representation of the weighted de Bruijn graph

Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro

Faculty of 1000 Research Ltd paper

2016

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

Laraib Malik, Shravya Thatipally, Nikhil Junneti, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2016

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

Hirak Sarkar, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2016

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

Avi Srivastava, Hirak Sarkar, Nitish Gupta, Rob Patro

Bioinformatics paper

2016

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

Richard Smith-Unna, Chris Boursnell, Rob Patro, Julian M. Hibberd, Steven Kelly

Genome Research paper

2016

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

Avi Srivastava, Hirak Sarkar, Laraib Malik, Robert Patro

arXiv (Cornell University) paper

2016

Efficient Index Maintenance Under Dynamic Genome Modification

Nitish Gupta, Komal Sanjeev, Tim Wall, Carl Kingsford, Robert Patro

arXiv (Cornell University) paper

2016

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

Rob Patro, Raquel Norel, Robert J. Prill, Julio Sáez-Rodríguez, Peter Lorenz, Felix Steinbeck, Bjoern Ziems, Mitja Luštrek, Nicola Barbarini, Alessandra Tiengo, Riccardo Bellazzi, Hans‐Jürgen Thiesen, Gustavo Stolovitzky, Carl Kingsford

BMC Bioinformatics paper

2016

piquant: piquant version 1.1.2

Owen Dando, Rob Patro

Zenodo (CERN European Organization for Nuclear Research) paper

2016

Referee report. For: Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences [version 1; referees: 2 approved]

Rob Patro

Faculty of 1000 Research Ltd paper

2016

Additional file 5 of A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin

Rob Patro, Raquel Norel, Robert J. Prill, Julio Sáez-Rodríguez, Peter Lorenz, Felix Steinbeck, Bjoern Ziems, Mitja LuĹĄtrek, Nicola Barbarini, Alessandra Tiengo, Riccardo Bellazzi, Hans-JĂźrgen Thiesen, Gustavo Stolovitzky, Carl Kingsford

Figshare paper

2016

Additional file 5 of A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin

Rob Patro, Raquel Norel, Robert J. Prill, Julio Sáez-Rodríguez, Peter Lorenz, Felix Steinbeck, Bjoern Ziems, Mitja LuĹĄtrek, Nicola Barbarini, Alessandra Tiengo, Riccardo Bellazzi, Hans-JĂźrgen Thiesen, Gustavo Stolovitzky, Carl Kingsford

Figshare paper

2015

Rich chromatin structure prediction from Hi-C data

Laraib Malik, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2015

RapMap: A Rapid, Sensitive and Accurate Tool for Mapping RNA-seq Reads to Transcriptomes

Avi Srivastava, Hirak Sarkar, Nitish Gupta, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2015

Maximum Likelihood Estimation of Biological Relatedness from Low Coverage Sequencing Data

Mikhail Lipatov, Komal Sanjeev, Rob Patro, Krishna R. Veeramah

bioRxiv (Cold Spring Harbor Laboratory) paper

2015

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

Rob Patro, Geet Duggal, Michael I. Love, Rafael A. Irizarry, Carl Kingsford

bioRxiv (Cold Spring Harbor Laboratory) paper

2015

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

Richard Smith-Unna, Chris Boursnell, Rob Patro, Julian M. Hibberd, Steven Kelly

bioRxiv (Cold Spring Harbor Laboratory) paper

2015

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

Runxuan Zhang, Cristiane P. G. Calixto, Nikoleta A. Τzioutziou, Allan B. James, Craig G. Simpson, Wenbin Guo, Yamile Márquez, Maria Kalyna, Rob Patro, Eduardo Eyras, Andrea Barta, Hugh G. Nimmo, John W. Brown

New Phytologist paper

2015

piquant: piquant version 1.1.1

Owen Dando, Rob Patro

Zenodo (CERN European Organization for Nuclear Research) paper

2015

Not-quite alignments: Salmon, Kallisto and Efficient Quantification of RNA-Seq data

Robert Patro

The Winnower paper

Link Open access PDF

2015

Data-dependent bucketing improves reference-free compression of sequencing reads

Rob Patro, Carl Kingsford

Bioinformatics paper

2015

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

Carl Kingsford, Rob Patro

Bioinformatics paper

2015

Optimizing Read Reversals for Sequence Compression

Zhong Sichen, Lu Zhao, Yan Liang, Mohammadzaman Zamani, Rob Patro, Rezaul Chowdhury, Esther M. Arkin, Joseph S. B. Mitchell, Steven Skiena

Lecture notes in computer science paper

2015

Referee report. For: The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]

Rob Patro

Faculty of 1000 Research Ltd paper

2015

Optimizing Read Reversals for Sequence Compression - (Extended Abstract).

Zhong Sichen, Lu Zhao, Yan Liang, Mohammadzaman Zamani, Robert Patro, Rezaul Chowdhury, Esther M. Arkin, Joseph S. B. Mitchell, Steven Skiena

Workshop on Algorithms in Bioinformatics paper

2014

Compression of short-read sequences using path encoding

Carl Kingsford, Rob Patro

bioRxiv (Cold Spring Harbor Laboratory) paper

2014

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

Rob Patro, Stephen M. Mount, Carl Kingsford

Nature Biotechnology paper

2014

Health and cinema. Healthy leisure profile

J. Corbalán, V. García-Peñas, R. Limiñana, Ramón Martín-Brufau, Rob Patro

Personality and Individual Differences paper

2014

Identification of alternative topological domains in chromatin

Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford

Algorithms for Molecular Biology paper

2013

Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin

Hao Wang, Geet Duggal, Rob Patro, Michelle Girvan, Sridhar Hannenhalli, Carl Kingsford

paper

2013

Multiscale Identification of Topological Domains in Chromatin

Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford

arXiv (Cornell University) paper

2013

Predicting protein interactions via parsimonious network history inference

Rob Patro, Carl Kingsford

Bioinformatics paper

2013

Resolving spatial inconsistencies in chromosome conformation measurements

Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford

Algorithms for Molecular Biology paper

2013

Multiscale Identification of Topological Domains in Chromatin

Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford

Lecture notes in computer science paper

2012

Global network alignment using multiscale spectral signatures

Rob Patro, Carl Kingsford

Bioinformatics paper

2012

Parsimonious reconstruction of network evolution

Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, Carl Kingsford

Algorithms for Molecular Biology paper

2012

The missing models

Robert Patro, Geet Duggal, Emre Sefer, Hao Wang, Darya Filippova, Carl Kingsford

paper

2012

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

Robert Patro, John P. Dickerson, Sujal Bista, Satyandra K. Gupta, Amitabh Varshney

Journal of Computing and Information Science in Engineering paper

2012

Resolving Spatial Inconsistencies in Chromosome Conformation Data

Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford

Lecture notes in computer science paper

2012

Title of dissertation: COMPUTATIONALLY COMPARING BIOLOGICAL NETWORKS AND RECONSTRUCTING THEIR EVOLUTION

Robert Patro, Carl Kingsford

paper

2011

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

Robert Patro, Cheuk Yiu Ip, Sujal Bista, D. Thirumalai, Samuel S. Cho, Amitabh Varshney

paper

2011

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

André Maximo, Rob Patro, Amitabh Varshney, Ricardo Farias

Graphical Models paper

2011

Parsimonious Reconstruction of Network Evolution

Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, Carl Kingsford

Lecture notes in computer science paper

2011

Speeding Up Particle Trajectory Simulations under Moving Force Fields using GPUs

Robert Patro, John P. Dickerson, Sujal Bista, Satyandra K. Gupta, Amitabh Varshney

paper

2011

Salient Frame Detection for Molecular Dynamics Simulations

Youngmin Kim, Robert Patro, Cheuk Yiu Ip, Dianne P. O’Leary, Andriy Anishkin

DROPS (Schloss Dagstuhl – Leibniz Center for Informatics) paper

2010

Social Snapshot: A System for Temporally Coupled Social Photography

Rob Patro, Cheuk Yiu Ip, Sujal Bista, Amitabh Varshney

IEEE Computer Graphics and Applications paper

2010

Saliency Guided Summarization of Molecular Dynamics Simulations

Robert Patro, Cheuk Yiu Ip, Amitabh Varshney

Leibniz-Zentrum für Informatik (Schloss Dagstuhl) paper

2009

Modeling and Visualization of Human Activities for Multicamera Networks

Aswin C. Sankaranarayanan, Robert Patro, Pavan Turaga, Amitabh Varshney, Rama Chellappa

EURASIP Journal on Image and Video Processing paper

2008

HPV and Cervical Cancer: Screening of Young Women for the Presence of Human Papillomavirus Infection

Palika Datta, Rob Patro, Neerja Bhatla, Nilanchali Singh

International Journal of Infectious Diseases paper

2006

A Survey of Some Recent Results in Comptuer Graphics

Robert Patro

paper