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Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
Bioinformatics  
Volume 40 Issue 4
 
April 2024
 
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Original Paper
 
 
 
 
Genome analysis
 
 
 
 
ArCH: improving the performance of clonal hematopoiesis variant calling and interpretation border= 
 
Irenaeus C C Chan, Alex Panchot, Evelyn Schmidt, Samantha McNulty, Brian J Wiley ...
 
 
 
Regional analysis to delineate intrasample heterogeneity with RegionalST border=  
 
Yue Lyu, Chong Wu, Wei Sun, Ziyi Li
 
 
 
Coding genomes with gapped pattern graph convolutional network border=  
 
Ruo Han Wang, Yen Kaow Ng, Xianglilan Zhang, Jianping Wang, Shuai Cheng Li
 
 
 
Prioritization of oligogenic variant combinations in whole exomes border=  
 
Barbara Gravel, Alexandre Renaux, Sofia Papadimitriou, Guillaume Smits, Ann Nowé ...
 
 
 
Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation border= 
 
Andrew G Duncan, Jennifer A Mitchell, Alan M Moses
 
 
 
 
 
Sequence analysis
 
 
 
 
CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing border= 
 
Ali Osman Berk Şapcı, Eleonora Rachtman, Siavash Mirarab
 
 
 
scPathoQuant: a tool for efficient alignment and quantification of pathogen sequence reads from 10× single cell sequencing datasets border= 
 
Leanne S Whitmore, Jennifer Tisoncik-Go, Michael Gale, Jr
 
 
 
Fast peak error correction algorithms for proteoform identification using top-down tandem mass spectra border= 
 
Zhaohui Zhan, Lusheng Wang
 
 
 
MINDG: a drug'target interaction prediction method based on an integrated learning algorithm border= 
 
Hailong Yang, Yue Chen, Yun Zuo, Zhaohong Deng, Xiaoyong Pan ...
 
 
 
TemStaPro: protein thermostability prediction using sequence representations from protein language models border= 
 
Ieva Pudžiuvelyt-, Kliment Olechnovič, Egle Godliauskaite, Kristupas Sermokas, Tomas Urbaitis ...
 
 
 
 
EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery border= 
 
Johanna Elena Schmitz, Nihit Aggarwal, Lukas Laufer, Jörn Walter, Abdulrahman Salhab ...
 
 
 
Designing efficient randstrobes for sequence similarity analyses border=  
 
Moein Karami, Aryan Soltani Mohammadi, Marcel Martin, Barış Ekim, Wei Shen ...
 
 
 
VirusPredictor: XGBoost-based software to predict virus-related sequences in human data border= 
 
Guangchen Liu, Xun Chen, Yihui Luan, Dawei Li
 
 
 
Effect of tokenization on transformers for biological sequences border=  
 
Edo Dotan, Gal Jaschek, Tal Pupko, Yonatan Belinkov
 
 
 
Phylogenetics
 
 
 
 
MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction border= 
 
Fang Wang, Yibin Wang, Xiaofei Zeng, Shengcheng Zhang, Jiaxin Yu ...
 
 
 
phylaGAN: data augmentation through conditional GANs and autoencoders for improving disease prediction accuracy using microbiome data border= 
 
Divya Sharma, Wendy Lou, Wei Xu
 
 
 
Structural bioinformatics
 
 
 
 
Contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction border= 
 
Saisai Sun, Lin Gao
 
 
 
Gene expression
 
 
 
 
HyperTMO: a trusted multi-omics integration framework based on hypergraph convolutional network for patient classification border= 
 
Haohua Wang, Kai Lin, Qiang Zhang, Jinlong Shi, Xinyu Song ...
 
 
 
scDAC: deep adaptive clustering of single-cell transcriptomic data with coupled autoencoder and Dirichlet process mixture model border= 
 
Sijing An, Jinhui Shi, Runyan Liu, Yaowen Chen, Jing Wang ...
 
 
 
Hi-GeoMVP: a hierarchical geometry-enhanced deep learning model for drug response prediction border= 
 
Yurui Chen, Louxin Zhang
 
 
 
Systems biology
 
 
 
 
GraphPath: a graph attention model for molecular stratification with interpretability based on the pathway'pathway interaction network border= 
 
Teng Ma, Jianxin Wang
 
 
 
DrugMGR: a deep bioactive molecule binding method to identify compounds targeting proteins border= 
 
Xiaokun Li, Qiang Yang, Long Xu, Weihe Dong, Gongning Luo ...
 
 
 
Clustering single-cell multi-omics data via graph regularized multi-view ensemble learning border= 
 
Fuqun Chen, Guanhua Zou, Yongxian Wu, Le Ou-Yang
 
 
 
Data and text mining
 
 
 
 
MolFeSCue: enhancing molecular property prediction in data-limited and imbalanced contexts using few-shot and contrastive learning border= 
 
Ruochi Zhang, Chao Wu, Qian Yang, Chang Liu, Yan Wang ...
 
 
 
CTEC: a cross-tabulation ensemble clustering approach for single-cell RNA sequencing data analysis border= 
 
Liang Wang, Chenyang Hong, Jiangning Song, Jianhua Yao
 
 
 
MoleMCL: a multi-level contrastive learning framework for molecular pre-training border= 
 
Xinyi Zhang, Yanni Xu, Changzhi Jiang, Lian Shen, Xiangrong Liu
 
 
 
Advancing entity recognition in biomedicine via instruction tuning of large language models border= 
 
Vipina K Keloth, Yan Hu, Qianqian Xie, Xueqing Peng, Yan Wang ...
 
 
 
Causal-ARG: a causality-guided framework for annotating properties of antibiotic resistance genes border= 
 
Weizhong Zhao, Junze Wu, Xingpeng Jiang, Tingting He, Xiaohua Hu
 
 
 
Literature mining discerns latent disease'gene relationships border=  
 
Priyadarshini Rai, Atishay Jain, Shivani Kumar, Divya Sharma, Neha Jha ...
 
 
 
Bioimage informatics
 
 
 
 
A model-based hierarchical Bayesian approach to Sholl analysis border= 
 
Erik VonKaenel, Alexis Feidler, Rebecca Lowery, Katherine Andersh, Tanzy Love ...
 
 
 
NIEND: neuronal image enhancement through noise disentanglement border=  
 
Zuo-Han Zhao, Lijuan Liu, Yufeng Liu
 
 
 
MotGen: a closed-loop bacterial motility control framework using generative adversarial networks 
 
BoGeum Seo, DoHee Lee, Heungjin Jeon, Junhyoung Ha, SeungBeum Suh
 
 
 
FPLS-DC: functional partial least squares through distance covariance for imaging genetics border= 
 
Wenliang Pan, Yue Shan, Chuang Li, Shuai Huang, Tengfei Li ...
 
 
 
Applications Note
 
 
 
 
Genome analysis
 
 
 
 
POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy border= 
 
Martin Hölzer
 
 
 
EpiCarousel: memory- and time-efficient identification of metacells for atlas-level single-cell chromatin accessibility data border= 
 
Sijie Li, Yuxi Li, Yu Sun, Yaru Li, Xiaoyang Chen ...
 
 
 
Integrative annotation scores of variants for impact on RNA binding protein activities border= 
 
Jingqi Duan, Audrey P Gasch, Sündüz Keleş
 
 
 
GAUSS: a summary-statistics-based R package for accurate estimation of linkage disequilibrium for variants, Gaussian imputation, and TWAS analysis of cosmopolitan cohorts border= 
 
Donghyung Lee, Silviu-Alin Bacanu
 
 
 
Sequence analysis
 
 
 
 
Icarust, a real-time simulator for Oxford Nanopore adaptive sampling border= 
 
Rory Munro, Satrio Wibowo, Alexander Payne, Matthew Loose
 
 
 
Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries border= 
 
Jochen Weile, Gabrielle Ferra, Gabriel Boyle, Sriram Pendyala, Clara Amorosi ...
 
 
 
Rapid multiple protein sequence search by parallel and heterogeneous computation border= 
 
Jiefu Li, Ziyuan Wang, Xuwei Fan, Ruijie Yao, Guoqing Zhang ...
 
 
 
Phylogenetics
 
 
 
 
AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss border= 
 
Benoit Morel, Tom A Williams, Alexandros Stamatakis, Gergely J Szöll'si
 
 
 
Structural bioinformatics
 
 
 
 
CLAUDIO: automated structural analysis of cross-linking data border= 
 
Alexander Röhl, Eugen Netz, Oliver Kohlbacher, Hadeer Elhabashy
 
 
 
Integrating physics in deep learning algorithms: a force field as a PyTorch module border= 
 
Gabriele Orlando, Luis Serrano, Joost Schymkowitz, Frederic Rousseau
 
 
 
3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures border= 
 
Victoria Ruiz-Serra, Samuel Valentini, Sergi Madroñero, Alfonso Valencia, Eduard Porta-Pardo
 
 
 
rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments border= 
 
Jonathan L Price, Omer Ziv, Malte L Pinckert, Andrew Lim, Eric A Miska
 
 
 
Gene expression
 
 
 
 
ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells border= 
 
Andrew Jiang, Russell G Snell, Klaus Lehnert
 
 
 
shinyExprPortal: a configurable shiny' portal for sharing analysis of molecular expression data border= 
 
Rafael Henkin, Katriona Goldmann, Myles Lewis, Michael R Barnes
 
 
 
Efficient cytometry analysis with FlowSOM in Python boosts interoperability with other single-cell tools border= 
 
Artuur Couckuyt, Benjamin Rombaut, Yvan Saeys, Sofie Van Gassen
 
 
 
Genetics and population analysis
 
 
 
 
Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations border= 
 
Kangcheng Hou, Stephanie Gogarten, Joohyun Kim, Xing Hua, Julie-Alexia Dias ...
 
 
 
Systems biology
 
 
 
 
PyCoMo: a python package for community metabolic model creation and analysis border= 
 
Michael Predl, Marianne Mießkes, Thomas Rattei, Jürgen Zanghellini
 
 
 
pyaging : a Python-based compendium of GPU-optimized aging clocks border= 
 
Lucas Paulo de Lima Camillo
 
 
 
Data and text mining
 
 
 
 
GINSA: an accumulator for paired locality and next-generation small ribosomal subunit sequence data border= 
 
Eric Odle, Samuel Kahng, Siratee Riewluang, Kyoko Kurihara, Kevin C Wakeman
 
 
 
longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types border= 
 
Jonas Hagenberg, Monika Budde, Teodora Pandeva, Ivan Kondofersky, Sabrina K Schaupp ...
 
 
 
VarChat: the generative AI assistant for the interpretation of human genomic variations border= 
 
Federica De Paoli, Silvia Berardelli, Ivan Limongelli, Ettore Rizzo, Susanna Zucca
 
 
 
DrivR-Base: a feature extraction toolkit for variant effect prediction model construction border= 
 
Amy Francis, Colin Campbell, Tom R Gaunt
 
 
 
Databases and ontologies
 
 
 
 
PyCoM: a python library for large-scale analysis of residue'residue coevolution data border= 
 
Philipp Bibik, Sabriyeh Alibai, Alessandro Pandini, Sarath Chandra Dantu
 
 
 
A machine-readable specification for genomics assays border=  
 
Ali Sina Booeshaghi, Xi Chen, Lior Pachter
 
 
 
The IDSM mass spectrometry extension: searching mass spectra using SPARQL border=  
 
Jakub Galgonek, Jiří Vondrášek
 
 
 
Bioimage informatics
 
 
 
 
ViNe-Seg: deep-learning-assisted segmentation of visible neurons and subsequent analysis embedded in a graphical user interface border= 
 
Nicolas Ruffini, Saleh Altahini, Stephan Weißbach, Nico Weber, Jonas Milkovits ...
 
 
 
Correction
 
 
 
 
Correction to: Rapid generation of high-quality structure figures for publication with PyMOL-PUB border= 
 
 
 
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