Volume 40, Issue 12, December 2024

Original Paper

Genome analysis

Tiberius: end-to-end deep learning with an HMM for gene prediction

Lars Gabriel and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae685, https://doi.org/10.1093/bioinformatics/btae685

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• Supplementary data

Micro-DeMix: a mixture beta-multinomial model for investigating the heterogeneity of the stool microbiome compositions

Ruoqian Liu and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae667, https://doi.org/10.1093/bioinformatics/btae667

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Phasing nanopore genome assembly by integrating heterozygous variations and Hi-C data

Jun Zhang and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae712, https://doi.org/10.1093/bioinformatics/btae712

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Identification and annotation of centromeric hypomethylated regions with CDR-Finder

Francesco Kumara Mastrorosa and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae733, https://doi.org/10.1093/bioinformatics/btae733

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Sequence analysis

Predicting the subcellular location of prokaryotic proteins with DeepLocPro

Jaime Moreno and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae677, https://doi.org/10.1093/bioinformatics/btae677

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HAlign 4: a new strategy for rapidly aligning millions of sequences

Tong Zhou and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae718, https://doi.org/10.1093/bioinformatics/btae718

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BWT construction and search at the terabase scale

Heng Li

Bioinformatics, Volume 40, Issue 12, December 2024, btae717, https://doi.org/10.1093/bioinformatics/btae717

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A BLAST from the past: revisiting blastp’s E-value

Yang Young Lu and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae729, https://doi.org/10.1093/bioinformatics/btae729

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Phylogenetics

Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix

Semih Kurt and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae701, https://doi.org/10.1093/bioinformatics/btae701

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spread.gl: visualizing pathogen dispersal in a high-performance browser application

Yimin Li and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae721, https://doi.org/10.1093/bioinformatics/btae721

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Structural bioinformatics

Improved prediction of post-translational modification crosstalk within proteins using DeepPCT

Yu-Xiang Huang and Rong Liu

Bioinformatics, Volume 40, Issue 12, December 2024, btae675, https://doi.org/10.1093/bioinformatics/btae675

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Accurate and transferable drug–target interaction prediction with DrugLAMP

Zhengchao Luo and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae693, https://doi.org/10.1093/bioinformatics/btae693

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Gene expression

Mutual information for detecting multi-class biomarkers when integrating multiple bulk or single-cell transcriptomic studies

Jian Zou and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae696, https://doi.org/10.1093/bioinformatics/btae696

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Virtual tissue expression analysis

Jakob Simeth and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae709, https://doi.org/10.1093/bioinformatics/btae709

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Systems biology

Dynamic modelling of signalling pathways when ordinary differential equations are not feasible

Timo Rachel and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae683, https://doi.org/10.1093/bioinformatics/btae683

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OneSC: a computational platform for recapitulating cell state transitions

Da Peng and Patrick Cahan

Bioinformatics, Volume 40, Issue 12, December 2024, btae703, https://doi.org/10.1093/bioinformatics/btae703

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DrugRepPT: a deep pretraining and fine-tuning framework for drug repositioning based on drug’s expression perturbation and treatment effectiveness

Shuyue Fan and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae692, https://doi.org/10.1093/bioinformatics/btae692

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Ranking antibody binding epitopes and proteins across samples from whole proteome tiled linear peptides

Sean J McIlwain and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae637, https://doi.org/10.1093/bioinformatics/btae637

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Sensitivities in protein allocation models reveal distribution of metabolic capacity and flux control

Samira van den Bogaard and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae691, https://doi.org/10.1093/bioinformatics/btae691

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Fast polypharmacy side effect prediction using tensor factorization

Oliver Lloyd and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae706, https://doi.org/10.1093/bioinformatics/btae706

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DeepRSMA: a cross-fusion-based deep learning method for RNA–small molecule binding affinity prediction

Zhijian Huang and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae678, https://doi.org/10.1093/bioinformatics/btae678

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Data and text mining

FAPM: functional annotation of proteins using multimodal models beyond structural modeling

Wenkai Xiang and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae680, https://doi.org/10.1093/bioinformatics/btae680

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Knowledge mining of brain connectivity in massive literature based on transfer learning

Xiaokang Chai and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae648, https://doi.org/10.1093/bioinformatics/btae648

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HBFormer: a single-stream framework based on hybrid attention mechanism for identification of human-virus protein–protein interactions

Liyuan Zhang and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae724, https://doi.org/10.1093/bioinformatics/btae724

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Bioimage informatics

FEHAT: efficient, large scale and automated heartbeat detection in Medaka fish embryos

Marcio Soares Ferreira and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae664, https://doi.org/10.1093/bioinformatics/btae664

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AltGosling: automatic generation of text descriptions for accessible genomics data visualization

Thomas C Smits and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae670, https://doi.org/10.1093/bioinformatics/btae670

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Applications Note

Genome analysis

Damsel: analysis and visualisation of DamID sequencing in R

Caitlin G Page and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae695, https://doi.org/10.1093/bioinformatics/btae695

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easySCF: a tool for enhancing interoperability between R and Python for efficient single-cell data analysis

Haoyun Zhang and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae710, https://doi.org/10.1093/bioinformatics/btae710

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JARVIS3: an efficient encoder for genomic data

Maria J P Sousa and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae725, https://doi.org/10.1093/bioinformatics/btae725

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Panacus: fast and exact pangenome growth and core size estimation

Luca Parmigiani and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae720, https://doi.org/10.1093/bioinformatics/btae720

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lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R

Asya Khleborodova and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae707, https://doi.org/10.1093/bioinformatics/btae707

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Sequence analysis

Pod5Viewer: a GUI for inspecting raw nanopore sequencing data

Vincent Dietrich and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae665, https://doi.org/10.1093/bioinformatics/btae665

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ViraLM: empowering virus discovery through the genome foundation model

Cheng Peng and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae704, https://doi.org/10.1093/bioinformatics/btae704

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Polyphonia: detecting inter-sample contamination in viral genomic sequencing data

Lydia A Krasilnikova and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae698, https://doi.org/10.1093/bioinformatics/btae698

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Structural bioinformatics

STRPsearch: fast detection of structured tandem repeat proteins

Soroush Mozaffari and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae690, https://doi.org/10.1093/bioinformatics/btae690

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Afpdb: an efficient structure manipulation package for AI protein design

Yingyao Zhou and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae654, https://doi.org/10.1093/bioinformatics/btae654

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Gene expression

Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python

Malte Kuehl and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae700, https://doi.org/10.1093/bioinformatics/btae700

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VSS-Hi-C: variance-stabilized signals for chromatin contacts

Neda Shokraneh Kenari and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae715, https://doi.org/10.1093/bioinformatics/btae715

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GUEST: an R package for handling estimation of graphical structure and multiclassification for error-prone gene expression data

Li-Pang Chen and Hui-Shan Tsao

Bioinformatics, Volume 40, Issue 12, December 2024, btae731, https://doi.org/10.1093/bioinformatics/btae731

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Systems biology

FastTENET: an accelerated TENET algorithm based on manycore computing in Python

Rakbin Sung and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae699, https://doi.org/10.1093/bioinformatics/btae699

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PhosX: data-driven kinase activity inference from phosphoproteomics experiments

Alessandro Lussana and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae697, https://doi.org/10.1093/bioinformatics/btae697

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Data and text mining

Facilitating phenotyping from clinical texts: the medkit library

Antoine Neuraz and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae681, https://doi.org/10.1093/bioinformatics/btae681

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LmRaC: a functionally extensible tool for LLM interrogation of user experimental results

Douglas B Craig and Sorin Drăghici

Bioinformatics, Volume 40, Issue 12, December 2024, btae679, https://doi.org/10.1093/bioinformatics/btae679

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DeepDR: a deep learning library for drug response prediction

Zhengxiang Jiang and Pengyong Li

Bioinformatics, Volume 40, Issue 12, December 2024, btae688, https://doi.org/10.1093/bioinformatics/btae688

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OpenVariant: a toolkit to parse and operate multiple input file formats

David Martínez-Millán and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae714, https://doi.org/10.1093/bioinformatics/btae714

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STRprofiler: efficient comparisons of short tandem repeat profiles for biomedical model authentication

Jared M Andrews and others

Bioinformatics, Volume 40, Issue 12, December 2024, btae713, https://doi.org/10.1093/bioinformatics/btae713

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Bioimage informatics

CVR-BBI: an open-source VR platform for multi-user collaborative brain to brain interfaces

Di Liu and Yina Wei

Bioinformatics, Volume 40, Issue 12, December 2024, btae676, https://doi.org/10.1093/bioinformatics/btae676

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