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Authors: Benedict Paten
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Journal Article

Optimal gap-affine alignment in O(s) space

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Santiago Marco-Sola and others
Bioinformatics, Volume 39, Issue 2, February 2023, btad074, https://doi.org/10.1093/bioinformatics/btad074
Published: 07 February 2023
Journal Article

GBZ file format for pangenome graphs

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Jouni Sirén and Benedict Paten
Bioinformatics, Volume 38, Issue 22, 15 November 2022, Pages 5012–5018, https://doi.org/10.1093/bioinformatics/btac656
Published: 30 September 2022
Journal Article

Efficient dynamic variation graphs

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Jordan M Eizenga and others
Bioinformatics, Volume 36, Issue 21, November 2020, Pages 5139–5144, https://doi.org/10.1093/bioinformatics/btaa640
Published: 16 July 2020
Journal Article

Distance indexing and seed clustering in sequence graphs

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Xian Chang and others
Bioinformatics, Volume 36, Issue Supplement_1, July 2020, Pages i146–i153, https://doi.org/10.1093/bioinformatics/btaa446
Published: 13 July 2020
Journal Article

Gaussian mixture model-based unsupervised nucleotide modification number detection using nanopore-sequencing readouts

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Hongxu Ding and others
Bioinformatics, Volume 36, Issue 19, October 2020, Pages 4928–4934, https://doi.org/10.1093/bioinformatics/btaa601
Published: 29 June 2020
Journal Article

Sequence tube maps: making graph genomes intuitive to commuters

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Wolfgang Beyer and others
Bioinformatics, Volume 35, Issue 24, December 2019, Pages 5318–5320, https://doi.org/10.1093/bioinformatics/btz597
Published: 01 August 2019
Journal Article

Haplotype-aware graph indexes

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Jouni Sirén and others
Bioinformatics, Volume 36, Issue 2, January 2020, Pages 400–407, https://doi.org/10.1093/bioinformatics/btz575
Published: 26 July 2019
Journal Article

Modelling haplotypes with respect to reference cohort variation graphs

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Yohei Rosen and others
Bioinformatics, Volume 33, Issue 14, July 2017, Pages i118–i123, https://doi.org/10.1093/bioinformatics/btx236
Published: 12 July 2017
Journal Article

Canonical, stable, general mapping using context schemes

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Adam M. Novak and others
Bioinformatics, Volume 31, Issue 22, November 2015, Pages 3569–3576, https://doi.org/10.1093/bioinformatics/btv435
Published: 27 July 2015
Journal Article

Comparative assembly hubs: Web-accessible browsers for comparative genomics

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Ngan Nguyen and others
Bioinformatics, Volume 30, Issue 23, December 2014, Pages 3293–3301, https://doi.org/10.1093/bioinformatics/btu534
Published: 18 August 2014
Journal Article

Ragout—a reference-assisted assembly tool for bacterial genomes

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Mikhail Kolmogorov and others
Bioinformatics, Volume 30, Issue 12, June 2014, Pages i302–i309, https://doi.org/10.1093/bioinformatics/btu280
Published: 11 June 2014
Journal Article

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

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Brian J. Raney and others
Bioinformatics, Volume 30, Issue 7, April 2014, Pages 1003–1005, https://doi.org/10.1093/bioinformatics/btt637
Published: 13 November 2013
Journal Article

HAL: a hierarchical format for storing and analyzing multiple genome alignments

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Glenn Hickey and others
Bioinformatics, Volume 29, Issue 10, May 2013, Pages 1341–1342, https://doi.org/10.1093/bioinformatics/btt128
Published: 16 March 2013
Journal Article

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment

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Benedict Paten and others
Bioinformatics, Volume 25, Issue 3, February 2009, Pages 295–301, https://doi.org/10.1093/bioinformatics/btn630
Published: 04 December 2008