Publications

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122 publications

1. 2026

   Gravlax: an annotation-independent molecular evidence archive for single-cell RNA-seq

   Rob Patro

   bioRxiv (Cold Spring Harbor Laboratory) paper

   DOI Open access PDF

2. 2026

   Compression of quantification uncertainty for scRNA-seq counts

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

   UNC Libraries paper

   DOI Open access PDF

3. 2026

   Bramble: projection of spliced genomic alignments into transcriptomic space for improved transcript quantification

   Zoe Rudnick, Ales Varabyou, Rob Patro, Mihaela Pertea

   bioRxiv (Cold Spring Harbor Laboratory) paper

   DOI Open access PDF

4. 2026

   A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes

   Elbay Aliyev, Akshay Avvaru, Wouter De Coster, Garrison M. Arner, Denis M. Nyaga, Sophia B Gibson, Ben Weisburd, Bida Gu, Claudia Gonzaga-Jauregui, Jonas A. Gustafson, Joy Goffena, Wayne E. Clarke, Evan E. Eichler, Theodore M. Nelson, Anthony A. Snead, Xinxia Peng, Marcelo Ayllon, Nikhita Damaraju, Miranda Zalusky, Kendra Hoekzema, David Twesigomwe, Lei Yang, Phillip A. Richmond, Nathan D. Olson, Andrea Guarracino, Qiuhui Li, Angela L Miller, Zachary B. Anderson, Sophie H. R. Storz, Anna Okula Basile, André Corvelo, Catherine E. Reeves, Adrienne Helland, Rajeeva Musunuri, Mahler Revsine, Karynne E. Patterson, Cate Randall Paschal, Christina Zakarian, Sara Goodwin, Tanner D. Jensen, Esther Robb, W. Richard McCombie, Fritz Joachim Sedlazeck, Justin M. Zook, Stephen B. Montgomery, Erik P. Garrison, Mikhail Kolmogorov, Michael C. Schatz, Richard N. McLaughlin, Michael C. Zody, Prof Matthew Loose, Miten Jain, Rob Patro, Caitlin N. Jacques, Mark Chaisson, Danny E. Miller, Elizabeth Ostrowski, Harriet Dashnow

   Genome biology paper

   DOI Open access PDF

5. 2026

   Scientific computing in the age of agentic AI: an exploratory field report

   Jeremy Zheng Li, Alex Rubinsteyn, Sergey Feldman, Timothy J. O’Donnell, James M. Ferguson, Rob Patro, Ian Driver, Philip Ewels, Felix Krueger, Philipp Angerer, Ilan Gold, Jonathan Manning, Lukas Heumos, Mamad Ahangari, Varun Goyal, Hassan Masoudi, Brent S. Pedersen, Andrew Bai, Heng Li, Suyash Shringarpure, Gene Myers, Andrew Ho

   bioRxiv (Cold Spring Harbor Laboratory) paper

   DOI Open access PDF

6. 2026

   SEQPROC: an efficient, flexible, and concise tool for sequence geometry description and transformation

   Noah Cape, Elan Fisher, Daniel Liu, Rob Patro

   bioRxiv (Cold Spring Harbor Laboratory) paper

   DOI Open access PDF

7. 2026

   Optimizing sparse and skew hashing: faster k -mer dictionaries

   Giulio Ermanno Pibiri, Rob Patro

   Bioinformatics paper

   DOI Open access PDF

8. 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 C. Casellas, Rob Patro, Carson C. Chow, Daniel R. Larson

   bioRxiv (Cold Spring Harbor Laboratory) paper

   DOI Open access PDF

9. 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

10. 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

11. 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

12. 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

13. 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

14. 2025

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

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

    Genome Research paper

    DOI Open access PDF

15. 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

16. 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

17. 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

18. 2025

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

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

    arXiv (Cornell University) paper

    DOI Open access PDF

19. 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

20. 2024

    Collapsible tree: interactive web app to present collapsible hierarchies

    Yuan Gao, Rob Patro, Peng Jiang

    Bioinformatics paper

    DOI Open access PDF

21. 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

22. 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 Bharat Kundaje, Michael M. Hoffman, Anne E. Carpenter, Stephanie A. M. Wankowicz, Kresten Lindorff‐Larsen

    paper

    DOI Open access PDF

23. 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

24. 2024

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

    Rob Patro, Charlotte Soneson, Michael I. Love

    Carolina Digital Repository (University of North Carolina at Chapel Hill) paper

    DOI Open access PDF

25. 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

    Carolina Digital Repository (University of North Carolina at Chapel Hill) paper

    DOI Open access PDF

26. 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, Edward Michael Gertz, Joo Sang Lee, Kaiyuan Zhu, Lichun Ma, Xin Wei Wang, Cenk Sahinalp, Rob Patro, Mark D.M. Leiserson, Curtis C. Harris, Alejandro A. Schäffer, Eytan Ruppin

    Science Advances paper

    DOI Open access PDF

27. 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

28. 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

29. 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

30. 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

31. 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

32. 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

33. 2024

    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

    Algorithms for Molecular Biology paper

    DOI Open access PDF

34. 2023

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

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

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

35. 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

36. 2023

    Meta-colored compacted de Bruijn graphs

    Giulio Ermanno Pibiri, Jason Fan, Rob Patro

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

37. 2023

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

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

    Genome biology paper

    DOI Open access PDF

38. 2023

    TreeTerminus —creating transcript trees using inferential replicate counts

    Noor Singh, Michael I. Love, Rob Patro

    iScience paper

    DOI Open access PDF

39. 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

40. 2023

    Best practices for single-cell analysis across modalities

    Lukas Heumos, Anna Christina Schaar, Christopher Lance, Anastasia Litinetskaya, Felix Drost, Luke Zappia, Malte D. Luecken, Daniel C. 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 Joachim Theis

    Nature Reviews Genetics 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

    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

43. 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

44. 2022

    Detecting isoform-level allelic imbalance accounting for inferential uncertainty

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

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

45. 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

46. 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

47. 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

48. 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

49. 2022

    AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite

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

    Genome biology paper

    DOI Open access PDF

50. 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

51. 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

52. 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

53. 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

54. 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

55. 2021

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

    Charlotte Soneson, Avi Srivastava, Rob Patro, Michael Beda Stadler

    PLoS Computational Biology paper

    DOI Open access PDF

56. 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

57. 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

58. 2020

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

    Rob Patro, Leena Salmela

    iScience paper

    DOI Open access PDF

59. 2020

    Alignment and mapping methodology influence transcript abundance estimation

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

    Genome biology paper

    DOI Open access PDF

60. 2020

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

    Avi Srivastava, Laraib Iqbal Malik, Hirak Sarkar, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

61. 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

62. 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, Edward Michael Gertz, Joo Sang Lee, Kaiyuan Zhu, Lichun Ma, Xin Wei Wang, Cenk Sahinalp, Rob Patro, Mark D.M. Leiserson, Curtis C. Harris, Alejandro A. Schäffer, Eytan Ruppin

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

63. 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

64. 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 A. Shepherd, Martin T. Morgan, Rob Patro

    PLoS Computational Biology paper

    DOI Open access PDF

65. 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

66. 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

67. 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 Open access PDF

68. 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

69. 2019

    Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

    Avi Srivastava, Laraib Iqbal Malik, Tom S. Smith, Ian M. Sudbery, Rob Patro

    Genome biology paper

    DOI Open access PDF

70. 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

71. 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

72. 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

73. 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

74. 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

75. 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

76. 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 H. McKinnon

    Translational Psychiatry paper

    DOI Open access PDF

77. 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

78. 2018

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

    Rob Patro, Geet Duggal, Carl Kingsford

    KiltHub Repository paper

    DOI Open access PDF

79. 2018

    Rich Chromatin Structure Prediction from Hi-C Data

    Laraib Iqbal Malik, Rob Patro

    IEEE Transactions on Computational Biology and Bioinformatics paper

    DOI Open access PDF

80. 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

81. 2018

    Bioconda: 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 Brinda, 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 Antao, Milad Miladi, Kevin Thornton, Christian Brueffer, Marius Van Beek, Daniel Maticzka, Clemens Blank, Sebastian Will, K´evin Gravouil, Joachim Wolff, Manuel Holtgrewe, Jörg Fallmann, Vitor C. Piro, Ilya Shlyakhter, Ayman Yousif, Philip Mabon, Xiao‐Ou Zhang, Wei Shen, Jennifer Cabral, Cristel 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, Hai Nguyen, Endre Bakken Stovner, Philip Ewels, Matt Chambers, James E. Johnson, Emil Hägglund, Simon Ye, Roman Valls Guimera, Elmar Pruesse, W. Augustine Dunn, Lance Parsons, Rob Patro, David Koppstein, Elena Grassi, Inken Wohlers, Alex Reynolds, Macintosh Cornwell (7913225), Nicholas Stoler, Daniel Blankenberg, Guowei He, Marcel Bargull, Alexander Junge, Rick Farouni, Mallory Freeberg, Sourav Singh, Daniel Ross Bogema, Fabio Cumbo, Liang-Bo Wang, David E. Larson, Matthew L. Workentine

    Nature Methods paper

    DOI Open access PDF

82. 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

83. 2018

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

    Laraib Iqbal Malik, Fatemeh Almodaresi, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

84. 2018

    Crow: Fast and accurate expression estimation from long reads

    Laraib Iqbal Malik, Avi Srivastava, Rob Patro

    Research in Computational Molecular Biology paper

    Link

85. 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

86. 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

87. 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

88. 2017

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

    Hirak Sarkar, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

89. 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

90. 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

91. 2017

    Improved data-driven likelihood factorizations for transcript abundance estimation

    Mohsen Zakeri, Avi Srivastava, Fatemeh Almodaresi, Rob Patro

    Bioinformatics paper

    DOI Open access PDF

92. 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

93. 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

94. 2016

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

    Laraib Iqbal Malik, Shravya Thatipally, Nikhil Junneti, Rob Patro

    bioRxiv (Cold Spring Harbor Laboratory) paper

    DOI Open access PDF

95. 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

96. 2016

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

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

    Genome Research paper

    DOI Open access PDF

97. 2016

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

    Avi Srivastava, Hirak Sarkar, Laraib Iqbal Malik, Robert Patro

    arXiv (Cornell University) paper

    DOI Open access PDF

98. 2016

    Efficient Index Maintenance Under Dynamic Genome Modification

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

    arXiv (Cornell University) paper

    DOI Open access PDF

99. 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 A. Stolovitzky, Carl Kingsford

    BMC Bioinformatics paper

    DOI Open access PDF

100. 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 A. Stolovitzky, Carl Kingsford

     Figshare paper

     DOI Open access PDF

101. 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

102. 2015

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

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

     bioRxiv (Cold Spring Harbor Laboratory) paper

     DOI Open access PDF

103. 2015

     At RTD – 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

104. 2015

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

     Robert Patro

     The Winnower paper

     Link Open access PDF

105. 2015

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

     Rob Patro, Carl Kingsford

     Bioinformatics paper

     DOI Open access PDF

106. 2015

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

     Carl Kingsford, Rob Patro

     Bioinformatics paper

     DOI Open access PDF

107. 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

108. 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

109. 2013

     Multiscale Identification of Topological Domains in Chromatin

     Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford

     arXiv (Cornell University) paper

     DOI Open access PDF

110. 2013

     Predicting protein interactions via parsimonious network history inference

     Rob Patro, Carl Kingsford

     Bioinformatics paper

     DOI Open access PDF

111. 2013

     Resolving spatial inconsistencies in chromosome conformation measurements

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

     Algorithms for Molecular Biology paper

     DOI Open access PDF

112. 2012

     Global network alignment using multiscale spectral signatures

     Rob Patro, Carl Kingsford

     Bioinformatics paper

     DOI Open access PDF

113. 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

114. 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

115. 2012

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

     Robert Patro, Carl Kingsford

     paper

     Link

116. 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

117. 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

118. 2011

     Salient Frame Detection for Molecular Dynamics Simulations

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

     DROPS (Schloss Dagstuhl – Leibniz Center for Informatics) paper

     DOI Open access PDF

119. 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

120. 2010

     Saliency Guided Summarization of Molecular Dynamics Simulations

     Robert Patro, Cheuk Yiu Ip, Amitabh Varshney

     DROPS (Schloss Dagstuhl – Leibniz Center for Informatics) paper

     DOI Open access PDF

121. 2009

     Modeling and Visualization of Human Activities for Multicamera Networks

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

     EURASIP Journal on Image and Video Processing paper

     DOI Open access PDF

122. 2006

     A Survey of Some Recent Results in Comptuer Graphics

     Robert Patro

     paper

     Link

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