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Section: SEQUENCE ANALYSIS
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Journal Article

De novo clustering of large long-read transcriptome datasets with isONclust3

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Alexander J Petri and Kristoffer Sahlin
Bioinformatics, Volume 41, Issue 5, May 2025, btaf207, https://doi.org/10.1093/bioinformatics/btaf207
Published: 23 April 2025
Journal Article

ProtNote: a multimodal method for protein–function annotation

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Samir Char and others
Bioinformatics, Volume 41, Issue 5, May 2025, btaf170, https://doi.org/10.1093/bioinformatics/btaf170
Published: 15 April 2025
Journal Article

OLTA: Optimizing bait seLection for TArgeted sequencing

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Mete Orhun Minbay and others
Bioinformatics, Volume 41, Issue 4, April 2025, btaf146, https://doi.org/10.1093/bioinformatics/btaf146
Published: 02 April 2025
Journal Article

Negative dataset selection impacts machine learning-based predictors for multiple bacterial species promoters

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Marcelo González and others
Bioinformatics, Volume 41, Issue 4, April 2025, btaf135, https://doi.org/10.1093/bioinformatics/btaf135
Published: 27 March 2025
Journal Article

AVPpred-BWR: antiviral peptides prediction via biological words representation

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Zhuoyu Wei and others
Bioinformatics, Volume 41, Issue 4, April 2025, btaf126, https://doi.org/10.1093/bioinformatics/btaf126
Published: 27 March 2025
Journal Article

scMUSCL: multi-source transfer learning for clustering scRNA-seq data

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Arash Khoeini and others
Bioinformatics, Volume 41, Issue 5, May 2025, btaf137, https://doi.org/10.1093/bioinformatics/btaf137
Published: 27 March 2025
Journal Article

RNALoc-LM: RNA subcellular localization prediction using pre-trained RNA language model

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Min Zeng and others
Bioinformatics, Volume 41, Issue 4, April 2025, btaf127, https://doi.org/10.1093/bioinformatics/btaf127
Published: 22 March 2025
Journal Article

CaLMPhosKAN: prediction of general phosphorylation sites in proteins via fusion of codon aware embeddings with amino acid aware embeddings and wavelet-based Kolmogorov–Arnold network

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Pawel Pratyush and others
Bioinformatics, Volume 41, Issue 4, April 2025, btaf124, https://doi.org/10.1093/bioinformatics/btaf124
Published: 21 March 2025
Journal Article

Generating multiple alignments on a pangenomic scale

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Jannik Olbrich and others
Bioinformatics, Volume 41, Issue 3, March 2025, btaf104, https://doi.org/10.1093/bioinformatics/btaf104
Published: 17 March 2025
Journal Article

Leveraging basecaller’s move table to generate a lightweight k-mer model for nanopore sequencing analysis

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Hiruna Samarakoon and others
Bioinformatics, Volume 41, Issue 4, April 2025, btaf111, https://doi.org/10.1093/bioinformatics/btaf111
Published: 14 March 2025
Journal Article

QuickEd: high-performance exact sequence alignment based on bound-and-align

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Max Doblas and others
Bioinformatics, Volume 41, Issue 3, March 2025, btaf112, https://doi.org/10.1093/bioinformatics/btaf112
Published: 13 March 2025
Journal Article

EPIPDLF: a pretrained deep learning framework for predicting enhancer–promoter interactions

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Zhichao Xiao and others
Bioinformatics, Volume 41, Issue 5, May 2025, btae716, https://doi.org/10.1093/bioinformatics/btae716
Published: 01 March 2025
Journal Article

PharaCon: a new framework for identifying bacteriophages via conditional representation learning

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Zeheng Bai and others
Bioinformatics, Volume 41, Issue 3, March 2025, btaf085, https://doi.org/10.1093/bioinformatics/btaf085
Published: 24 February 2025
Journal Article

EpicPred: predicting phenotypes driven by epitope-binding TCRs using attention-based multiple instance learning

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Jaemin Jeon and others
Bioinformatics, Volume 41, Issue 3, March 2025, btaf080, https://doi.org/10.1093/bioinformatics/btaf080
Published: 21 February 2025
Journal Article

MOSTPLAS: a self-correction multi-label learning model for plasmid host range prediction

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Wei Zou and others
Bioinformatics, Volume 41, Issue 3, March 2025, btaf075, https://doi.org/10.1093/bioinformatics/btaf075
Published: 17 February 2025
Journal Article

ELLIPSIS: robust quantification of splicing in scRNA-seq

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Marie Van Hecke and others
Bioinformatics, Volume 41, Issue 2, February 2025, btaf028, https://doi.org/10.1093/bioinformatics/btaf028
Published: 12 February 2025
Journal Article

DeepES: deep learning-based enzyme screening to identify orphan enzyme genes

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Keisuke Hirota and others
Bioinformatics, Volume 41, Issue 3, March 2025, btaf053, https://doi.org/10.1093/bioinformatics/btaf053
Published: 06 February 2025
Journal Article

Embed-Search-Align: DNA sequence alignment using Transformer models

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Pavan Holur and others
Bioinformatics, Volume 41, Issue 3, March 2025, btaf041, https://doi.org/10.1093/bioinformatics/btaf041
Published: 06 February 2025
Journal Article

TPepRet: a deep learning model for characterizing T-cell receptors–antigen binding patterns

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Meng Wang and others
Bioinformatics, Volume 41, Issue 1, January 2025, btaf022, https://doi.org/10.1093/bioinformatics/btaf022
Published: 28 January 2025
Journal Article

Functional profiling of the sequence stockpile: a protein pair-based assessment of in silico prediction tools

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R Prabakaran and Yana Bromberg
Bioinformatics, Volume 41, Issue 2, February 2025, btaf035, https://doi.org/10.1093/bioinformatics/btaf035
Published: 24 January 2025