COMBINE-lab

Publications

A searchable list of the lab's publications, updated automatically each week from OpenAlex. For an alternative view with citation graphs, see Rob Patro's Google Scholar profile.

This list is generated automatically from OpenAlex and may not be perfectly complete or up to date. If you notice a missing or incorrect entry, please let us know.

153 publications

  1. 2026

    Optimizing sparse and skew hashing: faster k -mer dictionaries

    Giulio Ermanno Pibiri, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

  2. 2026

    Highly Constrained Kinetic Models for Single-Cell Gene Expression Analysis

    Hyeon Jin Cho, Christopher H. Bohrer, Paweł Trzaskoma, Jee Min Kim, Aleksandra Pękowska, Rafael Casellas, Rob Patro, Carson C. Chow, Daniel R Larson

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

  3. 2026

    QCatch: a framework for quality control assessment and analysis of single-cell sequencing data

    Yuan Gao, Dongze He, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

  4. 2026

    k ache-hash: A dynamic, concurrent, and cache-efficient hash table for streaming k -mer operations

    Jamshed Khan, Rob Patro, Prashant Pandey

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

  5. 2026

    Optimizing sparse and skew hashing: faster k -mer dictionaries

    Giulio Ermanno Pibiri, Rob Patro

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

  6. 2026

    Kaminari: a frugal colored index for approximate k -mer queries

    Victor Levallois, Yoshihiro Shibuya, Bertrand Le Gal, Yoann Dufresne, Rob Patro, Pierre Peterlongo, Giulio Ermanno Pibiri

    Bioinformatics Advances paper

    DOI Open access PDF

  7. 2025

    mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing

    Rob Patro, Siddhant Bharti, Prajwal Singhania, Rakrish Dhakal, Thomas J. Dahlstrom, Ragnar Groot Koerkamp

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

  8. 2025

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

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

    Genome Research paper

    DOI Open access PDF

  9. 2025

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

    Zahra Zare Jousheghani, Noor Singh, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

  10. 2025

    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

    Bioinformatics paper

    DOI Open access PDF

  11. 2025

    Kaminari: a resource-frugal index for approximate colored k -mer queries

    Victor Levallois, Yoshihiro Shibuya, Bertrand Le Gal, Rob Patro, Pierre Peterlongo, Giulio Ermanno Pibiri

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

  12. 2025

    Contributions of the Petabyte Scale Sequence Search Codeathon toward efforts to scale sequence-based searches on SRA

    Priyanka Ghosh, Kjiersten Fagnan, Ryan Connor, Ravinder Pannu, Travis J. Wheeler, Mihai Pop, C. Titus Brown, Tessa Pierce-Ward, Rob Patro, Jacquelyn S. Michaelis, Thomas Madden, Christiam Camacho, Olaitan I. Awe, Arianna I. Krinos, René K. M. Xavier, R Polo, Jack W Roddy, Adelaide Rhodes, Alexander P. Sweeten, Adrian Viehweger, Barış Ekim, Harihara Subrahmaniam Muralidharan, Amatur Rahman, Vinícius W. Salazar, Andrew Tritt, Thomas Colligan, Katrina Kalantar, Krause, Genevieve R., Taylor Reiter, George T. Lesica, Artem Babaian, Victor S.‐Y. Lin, Sergey Madaminov, Vadim Zalunin, David M. Kristensen, Alexa M. Salsbury, Daniel P. Rice, J. Rodney Brister

    arXiv (Cornell University) paper

    DOI Open access PDF

  13. 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

    DOI Open access PDF

  14. 2024

    Collapsible tree: interactive web app to present collapsible hierarchies

    Yuan Gao, Rob Patro, Jiang Peng

    Bioinformatics paper

    DOI Open access PDF

  15. 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

    DOI Open access PDF

  16. 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

    DOI Open access PDF

  17. 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

    DOI Open access PDF

  18. 2024

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

    Rob Patro, Charlotte Soneson, Michael I. Love

    UNC Libraries paper

    DOI Open access PDF

  19. 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

    DOI Open access PDF

  20. 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

    DOI Open access PDF

  21. 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

    DOI Open access PDF

  22. 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

    DOI Open access PDF

  23. 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

    DOI Open access PDF

  24. 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

    DOI Open access PDF

  25. 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

    DOI Open access PDF

  26. 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

    DOI Open access PDF

  27. 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

    DOI Open access PDF

  28. 2024

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

    Dongze He, Stephen M. Mount, Rob Patro

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

  29. 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

    DOI Open access PDF

  30. 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

    DOI Open access PDF

  31. 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

    DOI Open access PDF

  32. 2023

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

    Dongze He, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

  33. 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

    DOI Open access PDF

  34. 2023

    Meta-colored compacted de Bruijn graphs

    Giulio Ermanno Pibiri, Jason Fan, Rob Patro

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

  35. 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

    DOI Open access PDF

  36. 2023

    TreeTerminus —creating transcript trees using inferential replicate counts

    Noor Singh, Michael I. Love, Rob Patro

    iScience paper

    DOI Open access PDF

  37. 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

    DOI Open access PDF

  38. 2023

    R Packages used in TreeTerminus paper

    Noor Singh, Michael I. Love, Rob Patro

    Zenodo (CERN European Organization for Nuclear Research) paper

    DOI Open access PDF

  39. 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

    DOI Open access PDF

  40. 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

    DOI Open access PDF

  41. 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

    DOI Open access PDF

  42. 2022

    TreeTerminus - Creating transcript trees using inferential replicate counts

    Noor Singh, Michael I. Love, Rob Patro

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

  43. 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

    DOI Open access PDF

  44. 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

    DOI Open access PDF

  45. 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

    DOI Open access PDF

  46. 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

    DOI Open access PDF

  47. 2022

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

    Jason Fan, Spencer Skylar Chan, Rob Patro

    Algorithms for Molecular Biology paper

    DOI Open access PDF

  48. 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

    DOI Open access PDF

  49. 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

    DOI Open access PDF

  50. 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

    DOI Open access PDF

  51. 2022

    Additional file 4 of 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

    Open MIND paper

    DOI

  52. 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

    DOI Open access PDF

  53. 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

    DOI Open access PDF

  54. 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

    DOI Open access PDF

  55. 2021

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

    Fatemeh Almodaresi, Mohsen Zakeri, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

  56. 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

    DOI Open access PDF

  57. 2021

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

    Jamshed Khan, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

  58. 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

    DOI Open access PDF

  59. 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

    DOI Open access PDF

  60. 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

    DOI Open access PDF

  61. 2021

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

    Charlotte Soneson, Avi Srivastava, Rob Patro, Michael Stadler

    PLoS Computational Biology paper

    DOI Open access PDF

  62. 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

    DOI Open access PDF

  63. 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

    DOI Open access PDF

  64. 2020

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

    Rob Patro, Leena Salmela

    iScience paper

    DOI Open access PDF

  65. 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

    DOI Open access PDF

  66. 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

    DOI Open access PDF

  67. 2020

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

    Fatemeh Almodaresi, Mohsen Zakeri, Rob Patro

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

  68. 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

    DOI Open access PDF

  69. 2020

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

    Avi Srivastava, Laraib Malik, Hirak Sarkar, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

  70. 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

    DOI Open access PDF

  71. 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

    DOI Open access PDF

  72. 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

    DOI Open access PDF

  73. 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

    DOI Open access PDF

  74. 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

    DOI Open access PDF

  75. 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

    DOI Open access PDF

  76. 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

    DOI Open access PDF

  77. 2020

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

    Rob Patro

    Faculty of 1000 Research Ltd paper

    DOI Open access PDF

  78. 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

    DOI Open access PDF

  79. 2019

    Nonparametric expression analysis using inferential replicate counts

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

    Nucleic Acids Research paper

    DOI Open access PDF

  80. 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

    DOI Open access PDF

  81. 2019

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

    Hirak Sarkar, Avi Srivastava, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

  82. 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

    DOI

  83. 2019

    Sketching and Sublinear Data Structures in Genomics

    Guillaume Marçais, Brad Solomon, Rob Patro, Carl Kingsford

    Annual Review of Biomedical Data Science paper

    DOI Open access PDF

  84. 2019

    Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

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

    Genome biology paper

    DOI Open access PDF

  85. 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

    DOI Open access PDF

  86. 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

    DOI Open access PDF

  87. 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

    DOI Open access PDF

  88. 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

    DOI Open access PDF

  89. 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

    DOI Open access PDF

  90. 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

    DOI Open access PDF

  91. 2018

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

    Michael I. Love, Charlotte Soneson, Rob Patro

    F1000Research paper

    DOI Open access PDF

  92. 2018

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

    Michael I. Love, Charlotte Soneson, Rob Patro

    F1000Research paper

    DOI Open access PDF

  93. 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

    DOI Open access PDF

  94. 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

    DOI Open access PDF

  95. 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

    DOI

  96. 2018

    Rich Chromatin Structure Prediction from Hi-C Data

    Laraib Malik, Rob Patro

    IEEE/ACM Transactions on Computational Biology and Bioinformatics paper

    DOI

  97. 2018

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

    Michael I. Love, Charlotte Soneson, Rob Patro

    F1000Research paper

    DOI Open access PDF

  98. 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

    DOI Open access PDF

  99. 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

    DOI Open access PDF

  100. 2018

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

    Laraib Malik, Fatemeh Almodaresi, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

  101. 2018

    Crow: Fast and accurate expression estimation from long reads

    Laraib Malik, Avi Srivastava, Rob Patro

    Research in Computational Molecular Biology paper

    Link

  102. 2018

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

    Fatemeh Almodaresi, Hirak Sarkar, Avi Srivastava, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

  103. 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

    DOI Open access PDF

  104. 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

    DOI Open access PDF

  105. 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

    DOI Open access PDF

  106. 2017

    Squeakr: an exact and approximate k -mer counting system

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

    Bioinformatics paper

    DOI Open access PDF

  107. 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

    DOI Open access PDF

  108. 2017

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

    Hirak Sarkar, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

  109. 2017

    Rainbowfish: A Succinct Colored de Bruijn Graph Representation

    Fatemeh Almodaresi, Prashant Pandey, Rob Patro

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

  110. 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

    DOI Open access PDF

  111. 2017

    Improved data-driven likelihood factorizations for transcript abundance estimation

    Mohsen Zakeri, Avi Srivastava, Fatemeh Almodaresi, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

  112. 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

    DOI Open access PDF

  113. 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

    DOI Open access PDF

  114. 2017

    Rainbowfish: A Succinct Colored de Bruijn Graph Representation

    Fatemeh Almodaresi, Prashant Pandey, Rob Patro

    DROPS (Schloss Dagstuhl – Leibniz Center for Informatics) paper

    DOI Open access PDF

  115. 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

    DOI Open access PDF

  116. 2016

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

    Hirak Sarkar, Rob Patro

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

  117. 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

    DOI Open access PDF

  118. 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

    DOI Open access PDF

  119. 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

    DOI Open access PDF

  120. 2016

    Efficient Index Maintenance Under Dynamic Genome Modification

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

    arXiv (Cornell University) paper

    DOI Open access PDF

  121. 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

    DOI Open access PDF

  122. 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

    DOI Open access PDF

  123. 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

    DOI Open access PDF

  124. 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

    DOI Open access PDF

  125. 2015

    Rich chromatin structure prediction from Hi-C data

    Laraib Malik, Rob Patro

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

  126. 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

    DOI Open access PDF

  127. 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

    DOI Open access PDF

  128. 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

    DOI Open access PDF

  129. 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

    DOI Open access PDF

  130. 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

    DOI Open access PDF

  131. 2015

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

    Robert Patro

    The Winnower paper

    Link Open access PDF

  132. 2015

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

    Rob Patro, Carl Kingsford

    Bioinformatics paper

    DOI Open access PDF

  133. 2015

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

    Carl Kingsford, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

  134. 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

    DOI Open access PDF

  135. 2014

    Compression of short-read sequences using path encoding

    Carl Kingsford, Rob Patro

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

  136. 2014

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

    Rob Patro, Stephen M. Mount, Carl Kingsford

    Nature Biotechnology paper

    DOI Open access PDF

  137. 2014

    Health and cinema. Healthy leisure profile

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

    Personality and Individual Differences paper

    DOI

  138. 2014

    Identification of alternative topological domains in chromatin

    Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford

    Algorithms for Molecular Biology paper

    DOI Open access PDF

  139. 2013

    Multiscale Identification of Topological Domains in Chromatin

    Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford

    arXiv (Cornell University) paper

    DOI Open access PDF

  140. 2013

    Predicting protein interactions via parsimonious network history inference

    Rob Patro, Carl Kingsford

    Bioinformatics paper

    DOI Open access PDF

  141. 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

    DOI Open access PDF

  142. 2012

    Global network alignment using multiscale spectral signatures

    Rob Patro, Carl Kingsford

    Bioinformatics paper

    DOI Open access PDF

  143. 2012

    Parsimonious reconstruction of network evolution

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

    Algorithms for Molecular Biology paper

    DOI Open access PDF

  144. 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

    DOI

  145. 2012

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

    Robert Patro, Carl Kingsford

    paper

    Link

  146. 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

    DOI

  147. 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

    Link

  148. 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

    DOI Open access PDF

  149. 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

    DOI

  150. 2010

    Saliency Guided Summarization of Molecular Dynamics Simulations

    Robert Patro, Cheuk Yiu Ip, Amitabh Varshney

    Leibniz-Zentrum für Informatik (Schloss Dagstuhl) paper

    DOI Open access PDF

  151. 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

    DOI Open access PDF

  152. 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

    DOI Open access PDF

  153. 2006

    A Survey of Some Recent Results in Comptuer Graphics

    Robert Patro

    paper

    Link