Volume 3, Issue 1, 2023

Original Paper

Bioimage Informatics

NRRS: a re-tracing strategy to refine neuron reconstruction

Yiwei Li and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad054, https://doi.org/10.1093/bioadv/vbad054

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Adaptive differentiable grids for cryo-electron tomography reconstruction and denoising

Yuanhao Wang and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad131, https://doi.org/10.1093/bioadv/vbad131

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The impact of similarity metrics on cell-type clustering in highly multiplexed in situ imaging cytometry data

Elijah Willie and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad141, https://doi.org/10.1093/bioadv/vbad141

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mtFRC: depth-dependent resolution quantification of image features in 3D fluorescence microscopy

Neil Wright and Christopher J Rowlands

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad182, https://doi.org/10.1093/bioadv/vbad182

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Cancer

LOCATOR: feature extraction and spatial analysis of the cancer tissue microenvironment using mass cytometry imaging technologies

Rezvan Ehsani and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad146, https://doi.org/10.1093/bioadv/vbad146

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Cheminformatics

MedicaidJS: a FAIR approach to real-time drug analytics

Kunaal Agarwal and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad170, https://doi.org/10.1093/bioadv/vbad170

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Data and Text Mining

Federated learning framework integrating REFINED CNN and Deep Regression Forests

Daniel Nolte and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad036, https://doi.org/10.1093/bioadv/vbad036

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A cloud-based pipeline for analysis of FHIR and long-read data

Tim Dunn and Erdal Cosgun

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbac095, https://doi.org/10.1093/bioadv/vbac095

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Latent disease similarities and therapeutic repurposing possibilities uncovered by multi-modal generative topic modeling of human diseases

Satoshi Kozawa and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad047, https://doi.org/10.1093/bioadv/vbad047

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MonoNet: enhancing interpretability in neural networks via monotonic features

An-Phi Nguyen and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad016, https://doi.org/10.1093/bioadv/vbad016

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Enhancing biomedical search interfaces with images

Juan Trelles Trabucco and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad095, https://doi.org/10.1093/bioadv/vbad095

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A statistical algorithm for outbreak detection in multisite settings: an application to sick leave monitoring

Tom Duchemin and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad079, https://doi.org/10.1093/bioadv/vbad079

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FASTdRNA: a workflow for the analysis of ONT direct RNA sequencing

Xiaofeng Chen and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad099, https://doi.org/10.1093/bioadv/vbad099

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A soft-computation hybrid method for search of the antibiotic-resistant gene in Mycobacterium tuberculosis for promising drug target identification and antimycobacterial lead discovery

Neha Jaiswal and Awanish Kumar

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad090, https://doi.org/10.1093/bioadv/vbad090

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Turtling: a time-aware neural topic model on NIH grant data

Ruiyi Zhang and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad096, https://doi.org/10.1093/bioadv/vbad096

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DPSP: a multimodal deep learning framework for polypharmacy side effects prediction

Raziyeh Masumshah and Changiz Eslahchi

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad110, https://doi.org/10.1093/bioadv/vbad110

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Improving efficiency of fitting Cox proportional hazards models for time-to-event outcomes in genome-wide association studies (GWAS)

Val Gebski and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad148, https://doi.org/10.1093/bioadv/vbad148

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TaxaHFE: a machine learning approach to collapse microbiome datasets using taxonomic structure

Andrew Oliver and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad165, https://doi.org/10.1093/bioadv/vbad165

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Genome Analysis

Identification of a gene expression signature associated with breast cancer survival and risk that improves clinical genomic platforms

Santiago Bueno-Fortes and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad037, https://doi.org/10.1093/bioadv/vbad037

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An immune-suppressing protein in human endogenous retroviruses

Huan Zhang and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad013, https://doi.org/10.1093/bioadv/vbad013

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Deep learning predicts the impact of regulatory variants on cell-type-specific enhancers in the brain

An Zheng and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad002, https://doi.org/10.1093/bioadv/vbad002

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Deep multi-omics integration by learning correlation-maximizing representation identifies prognostically stratified cancer subtypes

Yanrong Ji and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad075, https://doi.org/10.1093/bioadv/vbad075

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Cobind: quantitative analysis of the genomic overlaps

Tao Ma and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad104, https://doi.org/10.1093/bioadv/vbad104

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DANGER analysis: risk-averse on/off-target assessment for CRISPR editing without a reference genome

Kazuki Nakamae and Hidemasa Bono

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad114, https://doi.org/10.1093/bioadv/vbad114

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KAS-Analyzer: a novel computational framework for exploring KAS-seq data

Ruitu Lyu and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad121, https://doi.org/10.1093/bioadv/vbad121

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ProbioMinServer: an integrated platform for assessing the safety and functional properties of potential probiotic strains

Yen-Yi Liu and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad153, https://doi.org/10.1093/bioadv/vbad153

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Guiding the design of well-powered Hi-C experiments to detect differential loops

Sarah M Parker and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad152, https://doi.org/10.1093/bioadv/vbad152

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XHap: haplotype assembly using long-distance read correlations learned by transformers

Shorya Consul and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad169, https://doi.org/10.1093/bioadv/vbad169

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Databases and Ontologies

recountmethylation enables flexible analysis of public blood DNA methylation array data

Sean K Maden and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad020, https://doi.org/10.1093/bioadv/vbad020

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PPIntegrator: semantic integrative system for protein–protein interaction and application for host–pathogen datasets

Yasmmin Côrtes Martins and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad067, https://doi.org/10.1093/bioadv/vbad067

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CroMaSt: a workflow for assessing protein domain classification by cross-mapping of structural instances between domain databases and structural alignment

Hrishikesh Dhondge and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad081, https://doi.org/10.1093/bioadv/vbad081

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Disease Bioinformatics/Translational medicine

Network-augmented compartmental models to track asymptomatic disease spread

Devavrat Vivek Dabke and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad082, https://doi.org/10.1093/bioadv/vbad082

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Gene Regulation

Motif elucidation in ChIP-seq datasets with a knockout control

Danielle Denisko and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad031, https://doi.org/10.1093/bioadv/vbad031

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Learning from small medical data—robust semi-supervised cancer prognosis classifier with Bayesian variational autoencoder

Te-Cheng Hsu and Che Lin

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbac100, https://doi.org/10.1093/bioadv/vbac100

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circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging

Markus Hoffmann and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad093, https://doi.org/10.1093/bioadv/vbad093

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RegCFinder: targeted discovery of genomic subregions with differential read density

Elena Weiß and Caroline C Friedel

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad085, https://doi.org/10.1093/bioadv/vbad085

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scTopoGAN: unsupervised manifold alignment of single-cell data

Akash Singh and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad171, https://doi.org/10.1093/bioadv/vbad171

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A Bayesian approach to differential edges with probabilistic interactions: applications in association and classification

Yu-Jyun Huang and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad172, https://doi.org/10.1093/bioadv/vbad172

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Adversarial training improves model interpretability in single-cell RNA-seq analysis

Mehrshad Sadria and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad166, https://doi.org/10.1093/bioadv/vbad166

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Genetics and Population Analysis

NSPA: characterizing the disease association of multiple genetic interactions at single-subject resolution

Zhendong Sha and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad010, https://doi.org/10.1093/bioadv/vbad010

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A Bayesian model for genomic prediction using metabolic networks

Akio Onogi

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad106, https://doi.org/10.1093/bioadv/vbad106

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An improved framework for detecting discrete epidemiologically meaningful partitions in hierarchically clustered genetic data

David K Jacobson and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad118, https://doi.org/10.1093/bioadv/vbad118

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AdmixPipe v3: facilitating population structure delimitation from SNP data

Steven M Mussmann and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad168, https://doi.org/10.1093/bioadv/vbad168

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Gene Expression

AGRN: accurate gene regulatory network inference using ensemble machine learning methods

Duaa Mohammad Alawad and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad032, https://doi.org/10.1093/bioadv/vbad032

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scAnnotate: an automated cell-type annotation tool for single-cell RNA-sequencing data

Xiangling Ji and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad030, https://doi.org/10.1093/bioadv/vbad030

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Machine learning classifier approaches for predicting response to RTK-type-III inhibitors demonstrate high accuracy using transcriptomic signatures and ex vivo data

Mauricio H Ferrato and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad034, https://doi.org/10.1093/bioadv/vbad034

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Gene prediction

Ab initio gene prediction for protein-coding regions

Lonnie Baker and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad105, https://doi.org/10.1093/bioadv/vbad105

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Data Visualization

OmicsTIDE: interactive exploration of trends in multi-omics data

Theresa A Harbig and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbac093, https://doi.org/10.1093/bioadv/vbac093

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Toward computing attributions for dimensionality reduction techniques

Matthew Scicluna and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad097, https://doi.org/10.1093/bioadv/vbad097

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Metagenomics

Benchmarking of microbiome detection tools on RNA-seq synthetic databases according to diverse conditions

Francisco Jurado-Rueda and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad014, https://doi.org/10.1093/bioadv/vbad014

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Identification of representative species-specific genes for abundance measurements

Trine Zachariasen and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad060, https://doi.org/10.1093/bioadv/vbad060

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A self-knowledge distillation-driven CNN-LSTM model for predicting disease outcomes using longitudinal microbiome data

Daryl L X Fung and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad059, https://doi.org/10.1093/bioadv/vbad059

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Improving taxonomic classification with feature space balancing

Wolfgang Fuhl and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad092, https://doi.org/10.1093/bioadv/vbad092

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Phylogenetics

GPTree Cluster: phylogenetic tree cluster generator in the context of supertree inference

Aleksandr Koshkarov and Nadia Tahiri

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad023, https://doi.org/10.1093/bioadv/vbad023

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SCAMPP+FastTree: improving scalability for likelihood-based phylogenetic placement

Gillian Chu and Tandy Warnow

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad008, https://doi.org/10.1093/bioadv/vbad008

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DISCO+QR: rooting species trees in the presence of GDL and ILS

James Willson and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad015, https://doi.org/10.1093/bioadv/vbad015

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Measuring the relative contribution to predictive power of modern nucleotide substitution modeling approaches

Thomas Bujaki and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad091, https://doi.org/10.1093/bioadv/vbad091

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The Free Lunch is not over yet—systematic exploration of numerical thresholds in maximum likelihood phylogenetic inference

Julia Haag and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad124, https://doi.org/10.1093/bioadv/vbad124

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Sequence Analysis

iEnhancer-ELM: improve enhancer identification by extracting position-related multiscale contextual information based on enhancer language models

Jiahao Li and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad043, https://doi.org/10.1093/bioadv/vbad043

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WITCH-NG: efficient and accurate alignment of datasets with sequence length heterogeneity

Baqiao Liu and Tandy Warnow

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad024, https://doi.org/10.1093/bioadv/vbad024

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baseLess: lightweight detection of sequences in raw MinION data

Ben Noordijk and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad017, https://doi.org/10.1093/bioadv/vbad017

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Prediction of antibody binding to SARS-CoV-2 RBDs

Eric Wang

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbac103, https://doi.org/10.1093/bioadv/vbac103

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Nucleotide augmentation for machine learning-guided protein engineering

Mason Minot and Sai T Reddy

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbac094, https://doi.org/10.1093/bioadv/vbac094

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HMMerge: an ensemble method for multiple sequence alignment

Minhyuk Park and Tandy Warnow

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad052, https://doi.org/10.1093/bioadv/vbad052

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Seedability: optimizing alignment parameters for sensitive sequence comparison

Lorraine A K Ayad and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad108, https://doi.org/10.1093/bioadv/vbad108

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Cell type-specific interaction analysis using doublets in scRNA-seq

Courtney Schiebout and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad120, https://doi.org/10.1093/bioadv/vbad120

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Allele detection using k-mer-based sequencing error profiles

Hufsah Ashraf and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad149, https://doi.org/10.1093/bioadv/vbad149

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EnzymeNet: residual neural networks model for Enzyme Commission number prediction

Naoki Watanabe and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad173, https://doi.org/10.1093/bioadv/vbad173

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PanPA: generation and alignment of panproteome graphs

Fawaz Dabbaghie and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad167, https://doi.org/10.1093/bioadv/vbad167

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Software

EasyCellType: marker-based cell-type annotation by automatically querying multiple databases

Ruoxing Li and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad029, https://doi.org/10.1093/bioadv/vbad029

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Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding

Christine H Chang and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad005, https://doi.org/10.1093/bioadv/vbad005

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LongDat: an R package for covariate-sensitive longitudinal analysis of high-dimensional data

Chia-Yu Chen and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad063, https://doi.org/10.1093/bioadv/vbad063

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A deep-learning-based RNA-seq germline variant caller

Daniel E Cook and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad062, https://doi.org/10.1093/bioadv/vbad062

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SynAI: an AI-driven cancer drugs synergism prediction platform

Kuan Yan and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad160, https://doi.org/10.1093/bioadv/vbad160

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Structural Bioinformatics

SAINT-Angle: self-attention augmented inception-inside-inception network and transfer learning improve protein backbone torsion angle prediction

A K M Mehedi Hasan and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad042, https://doi.org/10.1093/bioadv/vbad042

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Improving classification of correct and incorrect protein–protein docking models by augmenting the training set

Didier Barradas-Bautista and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad012, https://doi.org/10.1093/bioadv/vbad012

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G-RANK: an equivariant graph neural network for the scoring of protein–protein docking models

Ha Young Kim and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad011, https://doi.org/10.1093/bioadv/vbad011

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Computational analyses reveal fundamental properties of the AT structure related to thrombosis

Tiago J S Lopes and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbac098, https://doi.org/10.1093/bioadv/vbac098

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PIQLE: protein–protein interface quality estimation by deep graph learning of multimeric interaction geometries

Md Hossain Shuvo and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad070, https://doi.org/10.1093/bioadv/vbad070

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GDockScore: a graph-based protein–protein docking scoring function

Matthew McFee and Philip M Kim

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad072, https://doi.org/10.1093/bioadv/vbad072

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Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process

Recep Adiyaman and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad078, https://doi.org/10.1093/bioadv/vbad078

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Investigating the conformational landscape of AlphaFold2-predicted protein kinase structures

Carmen Al-Masri and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad129, https://doi.org/10.1093/bioadv/vbad129

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Atomistic simulations suggest dietary flavonoids from Beta vulgaris (beet) as promising inhibitors of human angiotensin-converting enzyme and 2-alpha-adrenergic receptors in hypertension

Joy A Adetunji and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad133, https://doi.org/10.1093/bioadv/vbad133

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Multi-shelled ECIF: improved extended connectivity interaction features for accurate binding affinity prediction

Koji Shiota and Tatsuya Akutsu

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad155, https://doi.org/10.1093/bioadv/vbad155

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Structome: a tool for the rapid assembly of datasets for structural phylogenetics

Ashar J Malik and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad134, https://doi.org/10.1093/bioadv/vbad134

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Systems Biology

Pancancer survival prediction using a deep learning architecture with multimodal representation and integration

Ziling Fan and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad006, https://doi.org/10.1093/bioadv/vbad006

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FLONE: fully Lorentz network embedding for inferring novel drug targets

Yang Yue and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad066, https://doi.org/10.1093/bioadv/vbad066

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SPECK: an unsupervised learning approach for cell surface receptor abundance estimation for single-cell RNA-sequencing data

Azka Javaid and H Robert Frost

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad073, https://doi.org/10.1093/bioadv/vbad073

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BERTwalk for integrating gene networks to predict gene- to pathway-level properties

Rami Nasser and Roded Sharan

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad086, https://doi.org/10.1093/bioadv/vbad086

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Prediction of metabolite–protein interactions based on integration of machine learning and constraint-based modeling

Fayaz Soleymani Babadi and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad098, https://doi.org/10.1093/bioadv/vbad098

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SAGDTI: self-attention and graph neural network with multiple information representations for the prediction of drug–target interactions

Xiaokun Li and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad116, https://doi.org/10.1093/bioadv/vbad116

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Detecting biased validation of predictive models in the positive-unlabeled setting: disease gene prioritization case study

Ivan Molotkov and Mykyta Artomov

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad128, https://doi.org/10.1093/bioadv/vbad128

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QuTIE: quantum optimization for target identification by enzymes

Hoang M Ngo and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad112, https://doi.org/10.1093/bioadv/vbad112

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Immuno-metabolic signaling in leishmaniasis: insights gained from mathematical modeling

Shweta Khandibharad and Shailza Singh

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad125, https://doi.org/10.1093/bioadv/vbad125

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BioNAR: an integrated biological network analysis package in bioconductor

Colin McLean and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad137, https://doi.org/10.1093/bioadv/vbad137

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Identification of disease modules using higher-order network structure

Pramesh Singh and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad140, https://doi.org/10.1093/bioadv/vbad140

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StabJGL: a stability approach to sparsity and similarity selection in multiple-network reconstruction

Camilla Lingjærde and Sylvia Richardson

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad185, https://doi.org/10.1093/bioadv/vbad185

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ISCB-LA Paper

Predicting phenotypes from novel genomic markers using deep learning

Shivani Sehrawat and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad028, https://doi.org/10.1093/bioadv/vbad028

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Review

Bioimage Informatics

Different approaches to Imaging Mass Cytometry data analysis

Vladan Milosevic

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad046, https://doi.org/10.1093/bioadv/vbad046

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Data and Text Mining

Applications of transformer-based language models in bioinformatics: a survey

Shuang Zhang and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad001, https://doi.org/10.1093/bioadv/vbad001

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ProFeatMap: a highly customizable tool for 2D feature representation of protein sets

Goran Bich and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad022, https://doi.org/10.1093/bioadv/vbad022

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Genetics and Population Analysis

Inferring the heritability of bacterial traits in the era of machine learning

T Tien Mai and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad027, https://doi.org/10.1093/bioadv/vbad027

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Immunoinformatics

Enhanced annotation of CD45RA to distinguish T cell subsets in single-cell RNA-seq via machine learning

Ran Ran and Douglas K Brubaker

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad159, https://doi.org/10.1093/bioadv/vbad159

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Application Note

Bioimage Informatics

GlobeCorr: interactive globe-based visualization for correlation datasets

Mariam Arab and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbac099, https://doi.org/10.1093/bioadv/vbac099

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DataCurator.jl: efficient, portable and reproducible validation, curation and transformation of large heterogeneous datasets using human-readable recipes compiled into machine-verifiable templates

Ben Cardoen and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad068, https://doi.org/10.1093/bioadv/vbad068

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SEM3De: image restoration for FIB-SEM

Rayane Hamdane Serir and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad119, https://doi.org/10.1093/bioadv/vbad119

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JEasyTFM: an open-source software package for the analysis of large 2D TFM data within ImageJ

Philippe Carl and Philippe Rondé

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad156, https://doi.org/10.1093/bioadv/vbad156

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Data and Text Mining

Simulation of mass spectrometry-based proteomics data with Synthedia

Michael G Leeming and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbac096, https://doi.org/10.1093/bioadv/vbac096

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CREPE: a Shiny app for transcription factor cataloguing

Diego A Rosado-Tristani and José A Rodríguez-Martínez

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad055, https://doi.org/10.1093/bioadv/vbad055

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StandEnA: a customizable workflow for standardized annotation and generating a presence–absence matrix of proteins

Fatma Chafra and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad069, https://doi.org/10.1093/bioadv/vbad069

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(m, n)-mer—a simple statistical feature for sequence classification

Amanda Araújo Serrão de Andrade and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad088, https://doi.org/10.1093/bioadv/vbad088

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AliGater: a framework for the development of bioinformatic pipelines for large-scale, high-dimensional cytometry data

Ludvig Ekdahl and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad103, https://doi.org/10.1093/bioadv/vbad103

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UniProtExtractR: an app and R package for easily extracting protein-specific UniProtKB information and fine-tuning organelle resolution

Alexandra Panov and J Wade Harper

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad157, https://doi.org/10.1093/bioadv/vbad157

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MBDBMetrics: an online metrics tool to measure the impact of biological data resources

Giuseppe Insana and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad180, https://doi.org/10.1093/bioadv/vbad180

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Data Visualization

Nightingale: web components for protein feature visualization

Gustavo A Salazar and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad064, https://doi.org/10.1093/bioadv/vbad064

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CCPlotR: an R package for the visualization of cell–cell interactions

Sarah Ennis and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad130, https://doi.org/10.1093/bioadv/vbad130

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FORALL: an interactive shiny/R web portal to navigate multi-omics high-throughput data of pediatric acute lymphoblastic leukemia

Luay Aswad and Rozbeh Jafari

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad143, https://doi.org/10.1093/bioadv/vbad143

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escheR: unified multi-dimensional visualizations with Gestalt principles

Boyi Guo and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad179, https://doi.org/10.1093/bioadv/vbad179

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Databases and Ontologies

CoDe: a web-based tool for codon deoptimization

Divya Sharma and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbac102, https://doi.org/10.1093/bioadv/vbac102

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CanIsoNet: a database to study the functional impact of isoform switching events in diseases

Tülay Karakulak and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad050, https://doi.org/10.1093/bioadv/vbad050

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IsoAnalytics: a single-cell proteomics web server

Suzette N Palmer and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad077, https://doi.org/10.1093/bioadv/vbad077

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ZooPathWeb: a comprehensive web resource for zoonotic pathogens

Rui-Si Hu and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad094, https://doi.org/10.1093/bioadv/vbad094

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Genesis-DB: a database for autonomous laboratory systems

Gabriel K Reder and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad102, https://doi.org/10.1093/bioadv/vbad102

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OntoloViz: a GUI for interactive visualization of ranked disease or drug lists using the MeSH and ATC ontologies

Matthias Ley and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad113, https://doi.org/10.1093/bioadv/vbad113

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wTSA-CRAFT: an open-access web server for rapid analysis of thermal shift assay experiments

Victor Reys and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad136, https://doi.org/10.1093/bioadv/vbad136

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PhyloMatcher: a tool for resolving conflicts in taxonomic nomenclature

Jonathan A Rader and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad144, https://doi.org/10.1093/bioadv/vbad144

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D2H2: diabetes data and hypothesis hub

Giacomo B Marino and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad178, https://doi.org/10.1093/bioadv/vbad178

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Genome Analysis

TB-ML—a framework for comparing machine learning approaches to predict drug resistance of Mycobacterium tuberculosis

Julian Libiseller-Egger and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad040, https://doi.org/10.1093/bioadv/vbad040

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cvlr: finding heterogeneously methylated genomic regions using ONT reads

Emanuele Raineri and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbac101, https://doi.org/10.1093/bioadv/vbac101

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snHiC: a complete and simplified snakemake pipeline for grouped Hi-C data analysis

Sebastian Gregoricchio and Wilbert Zwart

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad080, https://doi.org/10.1093/bioadv/vbad080

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KOMPUTE: imputing summary statistics of missing phenotypes in high-throughput model organism data

Coby Warkentin and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad100, https://doi.org/10.1093/bioadv/vbad100

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DOCEST—fast and accurate estimator of human NGS sequencing depth and error rate

Lauris Kaplinski and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad084, https://doi.org/10.1093/bioadv/vbad084

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RibDif2: expanding amplicon analysis to full genomes

Robert Murphy and Mikael Lenz Strube

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad111, https://doi.org/10.1093/bioadv/vbad111

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VCFshiny: an R/Shiny application for interactively analyzing and visualizing genetic variants

Tao Chen and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad107, https://doi.org/10.1093/bioadv/vbad107

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OffRisk: a docker image for annotating CRISPR off-target sites in the human genome

Gil-ad Barkai and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad138, https://doi.org/10.1093/bioadv/vbad138

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PRScalc, a privacy-preserving calculation of raw polygenic risk scores from direct-to-consumer genomics data

Lorena Sandoval and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad145, https://doi.org/10.1093/bioadv/vbad145

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ChromNetMotif: a Python tool to extract chromatin-sate marked motifs in a chromatin interaction network

Benjamin Soibam

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad126, https://doi.org/10.1093/bioadv/vbad126

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Ontologies and Text Mining

The Epilepsy Ontology: a community-based ontology tailored for semantic interoperability and text mining

Astghik Sargsyan and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad033, https://doi.org/10.1093/bioadv/vbad033

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Gene Regulation

nestedcv: an R package for fast implementation of nested cross-validation with embedded feature selection designed for transcriptomics and high-dimensional data

Myles J Lewis and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad048, https://doi.org/10.1093/bioadv/vbad048

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Genetics and Population Analysis

easyPheno: An easy-to-use and easy-to-extend Python framework for phenotype prediction using Bayesian optimization

Florian Haselbeck and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad035, https://doi.org/10.1093/bioadv/vbad035

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HTRX: an R package for learning non-contiguous haplotypes associated with a phenotype

Yaoling Yang and Daniel John Lawson

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad038, https://doi.org/10.1093/bioadv/vbad038

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Exploiting parallelization in positional Burrows–Wheeler transform (PBWT) algorithms for efficient haplotype matching and compression

Rick Wertenbroek and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad021, https://doi.org/10.1093/bioadv/vbad021

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LAVAA: a lightweight association viewer across ailments

Eric B Fauman and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad018, https://doi.org/10.1093/bioadv/vbad018

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1LocusSim a mobile-friendly simulator for teaching population genetics

Antonio Carvajal-Rodríguez

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad087, https://doi.org/10.1093/bioadv/vbad087

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An R package for ensemble learning stacking

Taichi Nukui and Akio Onogi

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad139, https://doi.org/10.1093/bioadv/vbad139

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G2GSnake: a Snakemake workflow for host–pathogen genomic association studies

Zhi Ming Xu and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad142, https://doi.org/10.1093/bioadv/vbad142

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link-ancestors: fast simulation of local ancestry with tree sequence software

Georgia Tsambos and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad163, https://doi.org/10.1093/bioadv/vbad163

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SMapper: visualizing spatial prevalence data of all types, including sparse and incomplete datasets

Lynn Khellaf and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad176, https://doi.org/10.1093/bioadv/vbad176

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Proteomics and Metabolomics

Peak Pair Pruner: a post-processing software to MS-DIAL for peak pair validation and ratio quantification of isotopic labeling LC-MS(/MS) data

Ryan A Smith and Qibin Zhang

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad044, https://doi.org/10.1093/bioadv/vbad044

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Phylogenetics

Phylostems: a new graphical tool to investigate temporal signal of heterochronous sequences datasets

Anna Doizy and others

Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad026, https://doi.org/10.1093/bioadv/vbad026

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