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ArticlesPeer ReviewedFull Text
Alevin efficiently estimates accurate gene abundances from dscRNA-seq data
Author / Creator:Srivastava, Avi ; Malik, Laraib ; Smith, Tom ; Sudbery, Ian ; Patro, Rob
Publisher:England: BioMed Central
Journal title:Genome Biology, 2019-03, Vol.20 (1), p.65-65, Article 65
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ArticlesPeer ReviewedFull Text
Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
Author / Creator:Khan, Jamshed ; Kokot, Marek ; Deorowicz, Sebastian ; Patro, Rob
Publisher:London: BioMed Central Ltd
Journal title:Genome Biology, 2022-09, Vol.23 (1), p.190-190, Article 190
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ArticlesPeer ReviewedFull Text
Alignment and mapping methodology influence transcript abundance estimation
Author / Creator:Srivastava, Avi ; Malik, Laraib ; Sarkar, Hirak ; Zakeri, Mohsen ; Almodaresi, Fatemeh ; Soneson, Charlotte ; Love, Michael I. ; Kingsford, Carl ; Patro, Rob
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2020-09, Vol.21 (1), p.239-239, Article 239
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ArticlesPeer ReviewedFull Text
Tximeta: Reference sequence checksums for provenance identification in RNA-seq
Author / Creator:Love, Michael I. ; Soneson, Charlotte ; Hickey, Peter F. ; Johnson, Lisa K. ; Pierce, N. Tessa ; Shepherd, Lori ; Morgan, Martin ; Patro, Rob
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2020-02, Vol.16 (2), p.e1007664
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ArticlesPeer ReviewedFull Text
Identification of alternative topological domains in chromatin
Author / Creator:Filippova, Darya ; Patro, Rob ; Duggal, Geet ; Kingsford, Carl
Publisher:England: BioMed Central Ltd
Journal title:Algorithms for molecular biology, 2014-05, Vol.9 (1), p.14-14, Article 14
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ArticlesPeer ReviewedFull Text
Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data
Author / Creator:He, Dongze ; Zakeri, Mohsen ; Sarkar, Hirak ; Soneson, Charlotte ; Srivastava, Avi ; Patro, Rob
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2022-03, Vol.19 (3), p.316-322
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ArticlesPeer ReviewedFull Text
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data
Author / Creator:Soneson, Charlotte ; Srivastava, Avi ; Patro, Rob ; Stadler, Michael B.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2021-01, Vol.17 (1), p.e1008585-e1008585
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ArticlesPeer ReviewedFull Text
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
Author / Creator:Love, Michael I ; Soneson, Charlotte ; Patro, Rob
Publisher:England: Faculty of 1000 Ltd
Journal title:F1000 research, 2018, Vol.7, p.952
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ArticlesPeer ReviewedFull Text
Fulgor: a fast and compact k-mer index for large-scale matching and color queries
Author / Creator:Fan, Jason ; Khan, Jamshed ; Singh, Noor Pratap ; Pibiri, Giulio Ermanno ; Patro, Rob
Publisher:England: BioMed Central
Journal title:Algorithms for molecular biology, 2024-01, Vol.19 (1), p.3-21, Article 3
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ArticlesPeer ReviewedFull Text
Fast, parallel, and cache-friendly suffix array construction
Author / Creator:Khan, Jamshed ; Rubel, Tobias ; Molloy, Erin ; Dhulipala, Laxman ; Patro, Rob
Publisher:England: BioMed Central Ltd
Journal title:Algorithms for molecular biology, 2024-04, Vol.19 (1), p.16-16, Article 16
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ArticlesPeer ReviewedFull Text
Perplexity: evaluating transcript abundance estimation in the absence of ground truth
Author / Creator:Fan, Jason ; Chan, Skylar ; Patro, Rob
Publisher:England: BioMed Central
Journal title:Algorithms for molecular biology, 2022-03, Vol.17 (1), p.6-6, Article 6
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ArticlesPeer ReviewedFull Text
AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite
Author / Creator:Skoufos, Giorgos ; Almodaresi, Fatemeh ; Zakeri, Mohsen ; Paulson, Joseph N. ; Patro, Rob ; Hatzigeorgiou, Artemis G. ; Vlachos, Ioannis S.
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2022-01, Vol.23 (1), p.39-39, Article 39
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ArticlesPeer ReviewedFull Text
SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty
Author / Creator:Wu, Euphy Y. ; Singh, Noor P. ; Choi, Kwangbom ; Zakeri, Mohsen ; Vincent, Matthew ; Churchill, Gary A. ; Ackert-Bicknell, Cheryl L. ; Patro, Rob ; Love, Michael I.
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2023-07, Vol.24 (1), p.165-165, Article 165
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ArticlesPeer ReviewedFull Text
AtRTD – a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana
Author / Creator:Zhang, Runxuan ; Calixto, Cristiane P. G. ; Tzioutziou, Nikoleta A. ; James, Allan B. ; Simpson, Craig G. ; Guo, Wenbin ; Marquez, Yamile ; Kalyna, Maria ; Patro, Rob ; Eyras, Eduardo ; Barta, Andrea ; Nimmo, Hugh G. ; Brown, John W. S.
Publisher:England: New Phytologist Trust
Journal title:The New phytologist, 2015-10, Vol.208 (1), p.96-101
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ArticlesPeer ReviewedFull Text
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
Author / Creator:Love, Michael I. ; Soneson, Charlotte ; Patro, Rob
Journal title:F1000 research, 2018, Vol.7, p.952
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ArticlesPeer ReviewedFull Text
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification [version 2; peer review: 1 approved, 2 approved with reservations]
Author / Creator:Love, Michael I ; Soneson, Charlotte ; Patro, Rob
Publisher:F1000 Research Ltd
Journal title:F1000 research, 2018-01, Vol.7, p.952-952
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Parsimonious reconstruction of network evolution
Author / Creator:Patro, Rob ; Sefer, Emre ; Malin, Justin ; Marçais, Guillaume ; Navlakha, Saket ; Kingsford, Carl
Publisher:England: BioMed Central Ltd
Journal title:Algorithms for molecular biology, 2012-09, Vol.7 (1), p.25-25, Article 25
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ArticlesPeer ReviewedFull Text
Salmon provides fast and bias-aware quantification of transcript expression
Author / Creator:Patro, Rob ; Duggal, Geet ; Love, Michael I ; Irizarry, Rafael A ; Kingsford, Carl
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2017-04, Vol.14 (4), p.417-419
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ArticlesPeer ReviewedFull Text
Best practices for single-cell analysis across modalities
Author / Creator:Heumos, Lukas ; Schaar, Anna C. ; Lance, Christopher ; Litinetskaya, Anastasia ; Drost, Felix ; Zappia, Luke ; Lücken, Malte D. ; Strobl, Daniel C. ; Henao, Juan ; Curion, Fabiola ; Schiller, Herbert B. ; Theis, Fabian J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature reviews. Genetics, 2023-08, Vol.24 (8), p.550-572
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Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
Author / Creator:Patro, Rob ; Mount, Stephen M ; Kingsford, Carl
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2014-05, Vol.32 (5), p.462-464
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Showing 1 to 20 of 69 results

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Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

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

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Alignment and mapping methodology influence transcript abundance estimation

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

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Identification of alternative topological domains in chromatin

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

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

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

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

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Fast, parallel, and cache-friendly suffix array construction

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

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AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite

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

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

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

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Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification [version 2; peer review: 1 approved, 2 approved with reservations]

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Parsimonious reconstruction of network evolution

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Salmon provides fast and bias-aware quantification of transcript expression

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Best practices for single-cell analysis across modalities

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

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