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Section: Sequence analysis
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Journal Article

NeoDesign: a computational tool for optimal selection of polyvalent neoantigen combinations

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Wenqian Yu and others
Bioinformatics, Volume 40, Issue 10, October 2024, btae585, https://doi.org/10.1093/bioinformatics/btae585
Published: 27 September 2024
Journal Article

Accurate and efficient protein embedding using multi-teacher distillation learning

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Jiayu Shang and others
Bioinformatics, Volume 40, Issue 9, September 2024, btae567, https://doi.org/10.1093/bioinformatics/btae567
Published: 24 September 2024
Journal Article

mgikit: demultiplexing toolkit for MGI fastq files

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Ziad Al Bkhetan and Sen Wang
Bioinformatics, Volume 40, Issue 9, September 2024, btae554, https://doi.org/10.1093/bioinformatics/btae554
Published: 11 September 2024
Journal Article

Pandagma: a tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole-genome duplications

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Steven B Cannon and others
Bioinformatics, Volume 40, Issue 9, September 2024, btae526, https://doi.org/10.1093/bioinformatics/btae526
Published: 24 August 2024
Journal Article

Publication-ready single nucleotide polymorphism visualization with snipit

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Áine O’Toole and others
Bioinformatics, Volume 40, Issue 8, August 2024, btae510, https://doi.org/10.1093/bioinformatics/btae510
Published: 13 August 2024
Journal Article

Interactive visualization of nanopore sequencing signal data with Squigualiser

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Hiruna Samarakoon and others
Bioinformatics, Volume 40, Issue 8, August 2024, btae501, https://doi.org/10.1093/bioinformatics/btae501
Published: 13 August 2024
Journal Article

popDMS infers mutation effects from deep mutational scanning data

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Zhenchen Hong and others
Bioinformatics, Volume 40, Issue 8, August 2024, btae499, https://doi.org/10.1093/bioinformatics/btae499
Published: 08 August 2024
Journal Article

Galaxy Helm chart: a standardized method for deploying production Galaxy servers

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Nuwan Goonasekera and others
Bioinformatics, Volume 40, Issue 8, August 2024, btae486, https://doi.org/10.1093/bioinformatics/btae486
Published: 06 August 2024
Journal Article

RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization

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Can Firtina and others
Bioinformatics, Volume 40, Issue 8, August 2024, btae478, https://doi.org/10.1093/bioinformatics/btae478
Published: 30 July 2024
Journal Article

Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data

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Yichi Zhang and others
Bioinformatics, Volume 40, Issue 7, July 2024, btae417, https://doi.org/10.1093/bioinformatics/btae417
Published: 03 July 2024
Journal Article

GENTANGLE: integrated computational design of gene entanglements

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Jose Manuel Martí and others
Bioinformatics, Volume 40, Issue 7, July 2024, btae380, https://doi.org/10.1093/bioinformatics/btae380
Published: 21 June 2024
Journal Article

BAllC and BAllCools: efficient formatting and operating for single-cell DNA methylation data

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Wei Tian and others
Bioinformatics, Volume 40, Issue 7, July 2024, btae404, https://doi.org/10.1093/bioinformatics/btae404
Published: 21 June 2024
Journal Article

Flexible parsing, interpretation, and editing of technical sequences with splitcode

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Delaney K Sullivan and Lior Pachter
Bioinformatics, Volume 40, Issue 6, June 2024, btae331, https://doi.org/10.1093/bioinformatics/btae331
Published: 14 June 2024
Journal Article

GenoFig: a user-friendly application for the visualization and comparison of genomic regions

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Maxime Branger and Sébastien O Leclercq
Bioinformatics, Volume 40, Issue 6, June 2024, btae372, https://doi.org/10.1093/bioinformatics/btae372
Published: 13 June 2024
Journal Article

SWGTS—a platform for stream-based host DNA depletion

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Philipp Spohr and others
Bioinformatics, Volume 40, Issue 6, June 2024, btae332, https://doi.org/10.1093/bioinformatics/btae332
Published: 24 May 2024
Journal Article

PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping

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Hui Sun and others
Bioinformatics, Volume 40, Issue 5, May 2024, btae323, https://doi.org/10.1093/bioinformatics/btae323
Published: 17 May 2024
Journal Article

PlasCAT: Plasmid Cloud Assembly Tool

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Samuel Peccoud and others
Bioinformatics, Volume 40, Issue 5, May 2024, btae299, https://doi.org/10.1093/bioinformatics/btae299
Published: 02 May 2024
Journal Article

RecGraph: recombination-aware alignment of sequences to variation graphs

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Jorge Avila Cartes and others
Bioinformatics, Volume 40, Issue 5, May 2024, btae292, https://doi.org/10.1093/bioinformatics/btae292
Published: 27 April 2024
Journal Article

For antibody sequence generative modeling, mixture models may be all you need

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Jonathan Parkinson and Wei Wang
Bioinformatics, Volume 40, Issue 5, May 2024, btae278, https://doi.org/10.1093/bioinformatics/btae278
Published: 23 April 2024
Journal Article

Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper

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Charlotte Crauwels and others
Bioinformatics, Volume 40, Issue 5, May 2024, btae276, https://doi.org/10.1093/bioinformatics/btae276
Published: 22 April 2024