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Authors: Lior Pachter
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Journal Article

A machine-readable specification for genomics assays

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Ali Sina Booeshaghi and others
Bioinformatics, Volume 40, Issue 4, April 2024, btae168, https://doi.org/10.1093/bioinformatics/btae168
Published: 05 April 2024
Journal Article

Fast and scalable querying of eukaryotic linear motifs with gget elm

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Laura Luebbert and others
Bioinformatics, Volume 40, Issue 3, March 2024, btae095, https://doi.org/10.1093/bioinformatics/btae095
Published: 20 February 2024
Journal Article

Metadata retrieval from sequence databases with ffq

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Ángel Gálvez-Merchán and others
Bioinformatics, Volume 39, Issue 1, January 2023, btac667, https://doi.org/10.1093/bioinformatics/btac667
Published: 05 January 2023
Journal Article

Efficient querying of genomic reference databases with gget

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Laura Luebbert and Lior Pachter
Bioinformatics, Volume 39, Issue 1, January 2023, btac836, https://doi.org/10.1093/bioinformatics/btac836
Published: 05 January 2023
Journal Article

Normalization of single-cell RNA-seq counts by log(x + 1) or log(1 + x)

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A Sina Booeshaghi and Lior Pachter
Bioinformatics, Volume 37, Issue 15, August 2021, Pages 2223–2224, https://doi.org/10.1093/bioinformatics/btab085
Published: 02 March 2021
Journal Article

Interpretable factor models of single-cell RNA-seq via variational autoencoders

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Valentine Svensson and others
Bioinformatics, Volume 36, Issue 11, June 2020, Pages 3418–3421, https://doi.org/10.1093/bioinformatics/btaa169
Published: 16 March 2020
Journal Article

The barcode, UMI, set format and BUStools

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Páll Melsted and others
Bioinformatics, Volume 35, Issue 21, November 2019, Pages 4472–4473, https://doi.org/10.1093/bioinformatics/btz279
Published: 09 May 2019
Journal Article

Updating RNA-Seq analyses after re-annotation

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Adam Roberts and others
Bioinformatics, Volume 29, Issue 13, July 2013, Pages 1631–1637, https://doi.org/10.1093/bioinformatics/btt197
Published: 14 May 2013
Journal Article

Quantifying uniformity of mapped reads

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Valerie Hower and others
Bioinformatics, Volume 28, Issue 20, October 2012, Pages 2680–2682, https://doi.org/10.1093/bioinformatics/bts451
Published: 18 July 2012
Journal Article

Identification of novel transcripts in annotated genomes using RNA-Seq

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Adam Roberts and others
Bioinformatics, Volume 27, Issue 17, September 2011, Pages 2325–2329, https://doi.org/10.1093/bioinformatics/btr355
Published: 21 June 2011
Journal Article

TopHat: discovering splice junctions with RNA-Seq

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Cole Trapnell and others
Bioinformatics, Volume 25, Issue 9, May 2009, Pages 1105–1111, https://doi.org/10.1093/bioinformatics/btp120
Published: 16 March 2009
Journal Article

Specific alignment of structured RNA: stochastic grammars and sequence annealing

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Robert K. Bradley and others
Bioinformatics, Volume 24, Issue 23, December 2008, Pages 2677–2683, https://doi.org/10.1093/bioinformatics/btn495
Published: 16 September 2008
Journal Article

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements

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Rahul Satija and others
Bioinformatics, Volume 24, Issue 10, May 2008, Pages 1236–1242, https://doi.org/10.1093/bioinformatics/btn104
Published: 18 March 2008
Journal Article

Multiple alignment by sequence annealing

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Ariel S. Schwartz and Lior Pachter
Bioinformatics, Volume 23, Issue 2, January 2007, Pages e24–e29, https://doi.org/10.1093/bioinformatics/btl311
Published: 15 January 2007
Journal Article

Multiple-sequence functional annotation and the generalized hidden Markov phylogeny

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Jon D. McAuliffe and others
Bioinformatics, Volume 20, Issue 12, August 2004, Pages 1850–1860, https://doi.org/10.1093/bioinformatics/bth153
Published: 26 February 2004
Journal Article

HMM sampling and applications to gene finding and alternative splicing

Simon L. Cawley and Lior Pachter
Bioinformatics, Volume 19, Issue suppl_2, September 2003, Pages ii36–ii41, https://doi.org/10.1093/bioinformatics/btg1057
Published: 27 September 2003