Volume 39, Issue 11, November 2023

Original Paper

Genome analysis

EVRC: reconstruction of chromosome 3D structure models using error-vector resultant algorithm with clustering coefficient

Xiao Wang and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad638, https://doi.org/10.1093/bioinformatics/btad638

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A safety framework for flow decomposition problems via integer linear programming

Fernando H C Dias and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad640, https://doi.org/10.1093/bioinformatics/btad640

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Hidden Markov random field models for cell-type assignment of spatially resolved transcriptomics

Cheng Zhong and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad641, https://doi.org/10.1093/bioinformatics/btad641

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CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction

Trisevgeni Rapakoulia and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad687, https://doi.org/10.1093/bioinformatics/btad687

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Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads

Dmitry N Konanov and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad702, https://doi.org/10.1093/bioinformatics/btad702

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Sequence analysis

LexicHash: sequence similarity estimation via lexicographic comparison of hashes

Grant Greenberg and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad652, https://doi.org/10.1093/bioinformatics/btad652

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Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites

Shihu Jiao and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad627, https://doi.org/10.1093/bioinformatics/btad627

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Multiple sequence alignment based on deep reinforcement learning with self-attention and positional encoding

Yuhang Liu and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad636, https://doi.org/10.1093/bioinformatics/btad636

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EMNGly: predicting N-linked glycosylation sites using the language models for feature extraction

Xiaoyang Hou and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad650, https://doi.org/10.1093/bioinformatics/btad650

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Determining epitope specificity of T-cell receptors with transformers

Abdul Rehman Khan and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad632, https://doi.org/10.1093/bioinformatics/btad632

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ORI-Explorer: a unified cell-specific tool for origin of replication sites prediction by feature fusion

Zeeshan Abbas and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad664, https://doi.org/10.1093/bioinformatics/btad664

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CoreDetector: a flexible and efficient program for core-genome alignment of evolutionary diverse genomes

Mario Fruzangohar and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad628, https://doi.org/10.1093/bioinformatics/btad628

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PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model

Jun Wu and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad690, https://doi.org/10.1093/bioinformatics/btad690

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Phylogenetics

An evolution strategy approach for the balanced minimum evolution problem

Andrea Gasparin and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad660, https://doi.org/10.1093/bioinformatics/btad660

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Structural bioinformatics

THPLM: a sequence-based deep learning framework for protein stability changes prediction upon point variations using pretrained protein language model

Jianting Gong and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad646, https://doi.org/10.1093/bioinformatics/btad646

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PC_ali: a tool for improved multiple alignments and evolutionary inference based on a hybrid protein sequence and structure similarity score

Ugo Bastolla and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad630, https://doi.org/10.1093/bioinformatics/btad630

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Hunting down zinc(II)-binding sites in proteins with distance matrices

Vincenzo Laveglia and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad653, https://doi.org/10.1093/bioinformatics/btad653

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PROSTATA: a framework for protein stability assessment using transformers

Dmitriy Umerenkov and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad671, https://doi.org/10.1093/bioinformatics/btad671

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Modified RNAs and predictions with the ViennaRNA Package

Yuliia Varenyk and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad696, https://doi.org/10.1093/bioinformatics/btad696

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Molecular generation strategy and optimization based on A2C reinforcement learning in de novo drug design

Qian Wang and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad693, https://doi.org/10.1093/bioinformatics/btad693

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Gene expression

Automated calibration of consensus weighted distance-based clustering approaches using sharp

Barbara Bodinier and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad635, https://doi.org/10.1093/bioinformatics/btad635

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dsRID: in silico identification of dsRNA regions using long-read RNA-seq data

Ryo Yamamoto and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad649, https://doi.org/10.1093/bioinformatics/btad649

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An integrative pipeline for circular RNA quantitative trait locus discovery with application in human T cells

Dat Thanh Nguyen

Bioinformatics, Volume 39, Issue 11, November 2023, btad667, https://doi.org/10.1093/bioinformatics/btad667

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DOSE-L1000: unveiling the intricate landscape of compound-induced transcriptional changes

Junmin Wang and Steven Novick

Bioinformatics, Volume 39, Issue 11, November 2023, btad683, https://doi.org/10.1093/bioinformatics/btad683

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ReGeNNe: genetic pathway-based deep neural network using canonical correlation regularizer for disease prediction

Divya Sharma and Wei Xu

Bioinformatics, Volume 39, Issue 11, November 2023, btad679, https://doi.org/10.1093/bioinformatics/btad679

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BELMM: Bayesian model selection and random walk smoothing in time-series clustering

Olli Sarala and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad686, https://doi.org/10.1093/bioinformatics/btad686

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Genetics and population analysis

Bayesian linear mixed model with multiple random effects for prediction analysis on high-dimensional multi-omics data

Yang Hai and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad647, https://doi.org/10.1093/bioinformatics/btad647

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Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNA-seq data with SCANet

Mhaned Oubounyt and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad644, https://doi.org/10.1093/bioinformatics/btad644

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Systems biology

An automated model annotation system (AMAS) for SBML models

Woosub Shin and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad658, https://doi.org/10.1093/bioinformatics/btad658

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Optimization of drug–target affinity prediction methods through feature processing schemes

Xiaoqing Ru and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad615, https://doi.org/10.1093/bioinformatics/btad615

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Explainable Multilayer Graph Neural Network for cancer gene prediction

Michail Chatzianastasis and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad643, https://doi.org/10.1093/bioinformatics/btad643

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Program for Integration and Rapid Analysis of Mass Isotopomer Distributions (PIRAMID)

Javier D Gomez and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad661, https://doi.org/10.1093/bioinformatics/btad661

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Open MoA: revealing the mechanism of action (MoA) based on network topology and hierarchy

Xinmeng Liao and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad666, https://doi.org/10.1093/bioinformatics/btad666

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Exploiting the structure of biochemical pathways to investigate dynamical properties with neural networks for graphs

Michele Fontanesi and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad678, https://doi.org/10.1093/bioinformatics/btad678

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PiDeeL: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas

Gun Kaynar and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad684, https://doi.org/10.1093/bioinformatics/btad684

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SSLpheno: a self-supervised learning approach for gene–phenotype association prediction using protein–protein interactions and gene ontology data

Xuehua Bi and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad662, https://doi.org/10.1093/bioinformatics/btad662

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FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes

Emad Alamoudi and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad674, https://doi.org/10.1093/bioinformatics/btad674

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gmcoda: Graphical model for multiple compositional vectors in microbiome studies

Huaying Fang

Bioinformatics, Volume 39, Issue 11, November 2023, btad700, https://doi.org/10.1093/bioinformatics/btad700

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Data and text mining

DELFOS—drug efficacy leveraging forked and specialized networks—benchmarking scRNA-seq data in multi-omics-based prediction of cancer sensitivity

Luiz Felipe Piochi and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad645, https://doi.org/10.1093/bioinformatics/btad645

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MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval

Qiao Jin and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad651, https://doi.org/10.1093/bioinformatics/btad651

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Automated exploitation of deep learning for cancer patient stratification across multiple types

Pingping Sun and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad654, https://doi.org/10.1093/bioinformatics/btad654

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Integration of multiple terminology bases: a multi-view alignment method using the hierarchical structure

Peihong Hu and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad689, https://doi.org/10.1093/bioinformatics/btad689

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BELB: a biomedical entity linking benchmark

Samuele Garda and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad698, https://doi.org/10.1093/bioinformatics/btad698

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Database and ontologies

AFRbase: a database of protein mutations responsible for antifungal resistance

Aakriti Jain and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad677, https://doi.org/10.1093/bioinformatics/btad677

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Applications Note

Genome analysis

MosaiCatcher v2: a single-cell structural variations detection and analysis reference framework based on Strand-seq

Thomas Weber and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad633, https://doi.org/10.1093/bioinformatics/btad633

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ScanNeo2: a comprehensive workflow for neoantigen detection and immunogenicity prediction from diverse genomic and transcriptomic alterations

Richard A Schäfer and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad659, https://doi.org/10.1093/bioinformatics/btad659

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Compositional analysis of microbiome data using the linear decomposition model (LDM)

Yi-Juan Hu and Glen A Satten

Bioinformatics, Volume 39, Issue 11, November 2023, btad668, https://doi.org/10.1093/bioinformatics/btad668

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regioneReloaded: evaluating the association of multiple genomic region sets

Roberto Malinverni and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad704, https://doi.org/10.1093/bioinformatics/btad704

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Sequence analysis

fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing

Romain Derelle and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad648, https://doi.org/10.1093/bioinformatics/btad648

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RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures

Xiaoming Xu and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad695, https://doi.org/10.1093/bioinformatics/btad695

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Structural bioinformatics

PICKLUSTER: a protein-interface clustering and analysis plug-in for UCSF ChimeraX

Luca R Genz and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad629, https://doi.org/10.1093/bioinformatics/btad629

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TT3D: Leveraging precomputed protein 3D sequence models to predict protein–protein interactions

Samuel Sledzieski and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad663, https://doi.org/10.1093/bioinformatics/btad663

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Cyclone: open-source package for simulation and analysis of finite dynamical systems

Elena S Dimitrova and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad634, https://doi.org/10.1093/bioinformatics/btad634

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PyPCN: protein contact networks in PyMOL

Serena Rosignoli and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad675, https://doi.org/10.1093/bioinformatics/btad675

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Examining DNA breathing with pyDNA-EPBD

Anowarul Kabir and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad699, https://doi.org/10.1093/bioinformatics/btad699

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Gene expression

aPEAR: an R package for autonomous visualization of pathway enrichment networks

Ieva Kerseviciute and Juozas Gordevicius

Bioinformatics, Volume 39, Issue 11, November 2023, btad672, https://doi.org/10.1093/bioinformatics/btad672

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oggmap: a Python package to extract gene ages per orthogroup and link them with single-cell RNA data

Kristian K Ullrich and Nikoleta E Glytnasi

Bioinformatics, Volume 39, Issue 11, November 2023, btad657, https://doi.org/10.1093/bioinformatics/btad657

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Genetics and population analysis

Expanded utility of the R package, qgg, with applications within genomic medicine

Palle Duun Rohde and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad656, https://doi.org/10.1093/bioinformatics/btad656

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Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics

Megan M Shuey and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad655, https://doi.org/10.1093/bioinformatics/btad655

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Systems biology

IDESS: a toolbox for identification and automated design of stochastic gene circuits

Carlos Sequeiros and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad682, https://doi.org/10.1093/bioinformatics/btad682

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Ensemble-GNN: federated ensemble learning with graph neural networks for disease module discovery and classification

Bastian Pfeifer and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad703, https://doi.org/10.1093/bioinformatics/btad703

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pyPESTO: a modular and scalable tool for parameter estimation for dynamic models

Yannik Schälte and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad711, https://doi.org/10.1093/bioinformatics/btad711

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Data and text mining

RNA interaction format: a general data format for RNA interactions

Richard A Schäfer and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad665, https://doi.org/10.1093/bioinformatics/btad665

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PhasiHunter: a robust phased siRNA regulatory cascade mining tool based on multiple reference sequences

Zerong Feng and others

Bioinformatics, Volume 39, Issue 11, November 2023, btad676, https://doi.org/10.1093/bioinformatics/btad676

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Correction

Correction to: CITEdb: a manually curated database of cell–cell interactions in human

Bioinformatics, Volume 39, Issue 11, November 2023, btad669, https://doi.org/10.1093/bioinformatics/btad669

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Correction to: Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads

Bioinformatics, Volume 39, Issue 11, November 2023, btad697, https://doi.org/10.1093/bioinformatics/btad697

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Correction to: HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition

Bioinformatics, Volume 39, Issue 11, November 2023, btad705, https://doi.org/10.1093/bioinformatics/btad705

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