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Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
Bioinformatics  
Volume 40 Issue 7
 
July 2024
 
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Review
 
 
 
 
Sequence analysis
 
 
 
 
A survey of BWT variants for string collections border= 
 
Davide Cenzato, Zsuzsanna Lipták
 
 
 
Original Paper
 
 
 
 
Genome analysis
 
 
 
 
Pangenome graph layout by Path-Guided Stochastic Gradient Descent border= 
 
Simon Heumos, Andrea Guarracino, Jan-Niklas M Schmelzle, Jiajie Li, Zhiru Zhang ...
 
 
 
Unravelling reference bias in ancient DNA datasets border=  
 
Stephanie Dolenz, Tom van der Valk, Chenyu Jin, Jonas Oppenheimer, Muhammad Bilal Sharif ...
 
 
 
ALLSTAR : inference of reliAble causaL ruLes between Somatic muTAtions and canceR phenotypes border= 
 
Dario Simionato, Antonio Collesei, Federica Miglietta, Fabio Vandin
 
 
 
SCCNAInfer: a robust and accurate tool to infer the absolute copy number on scDNA-seq data 
 
Liting Zhang, Xin Maizie Zhou, Xian Mallory
 
 
 
 
Exploring gene content with pangene graphs border= 
 
Heng Li, Maximillian Marin, Maha R Farhat
 
 
 
Sequence analysis
 
 
 
 
A deep learning method to predict bacterial ADP-ribosyltransferase toxins border= 
 
Dandan Zheng, Siyu Zhou, Lihong Chen, Guansong Pang, Jian Yang
 
 
 
GraphADT: empowering interpretable predictions of acute dermal toxicity with multi-view graph pooling and structure remapping border= 
 
Xinqian Ma, Xiangzheng Fu, Tao Wang, Linlin Zhuo, Quan Zou
 
 
 
isolateR: an R package for generating microbial libraries from Sanger sequencing data border= 
 
Brendan Daisley, Sarah J Vancuren, Dylan J L Brettingham, Jacob Wilde, Simone Renwick ...
 
 
 
Efficient construction and utilization of k -ordered FM-indexes with kISS for ultra-fast read mapping in large genomes border= 
 
Zheng-Dao Yang, Hsuan-Yu Kuo, Po-Wei Hsieh, Jui-Hung Hung
 
 
 
 
HyperGen: compact and efficient genome sketching using hyperdimensional vectors border= 
 
Weihong Xu, Po-Kai Hsu, Niema Moshiri, Shimeng Yu, Tajana Rosing
 
 
 
Phylogenetics
 
 
 
 
Weighted centroid trees: a general approach to summarize phylogenies in single-labeled tumor mutation tree inference border= 
 
Hamed Vasei, Mohammad-Hadi Foroughmand-Araabi, Amir Daneshgar
 
 
 
Structural bioinformatics
 
 
 
 
Surface-based multimodal protein'ligand binding affinity prediction border= 
 
Shiyu Xu, Lian Shen, Menglong Zhang, Changzhi Jiang, Xinyi Zhang ...
 
 
 
Representations of lipid nanoparticles using large language models for transfection efficiency prediction border= 
 
Saeed Moayedpour, Jonathan Broadbent, Saleh Riahi, Michael Bailey, Hoa V. Thu ...
 
 
 
Efficient protein structure archiving using ProteStAr border=  
 
Sebastian Deorowicz, Adam GudyÅ›
 
 
 
Geometric epitope and paratope prediction border=  
 
Marco Pegoraro, Clémentine Dominé, Emanuele Rodolà, Petar VeliÄković, Andreea Deac
 
 
 
A curated rotamer library for common post-translational modifications of proteins 
 
Oufan Zhang, Shubhankar A Naik, Zi Hao Liu, Julie Forman-Kay, Teresa Head-Gordon
 
 
 
Enhancing predictions of protein stability changes induced by single mutations using MSA-based language models border= 
 
Francesca Cuturello, Marco Celoria, Alessio Ansuini, Alberto Cazzaniga
 
 
 
Gene expression
 
 
 
 
SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis border= 
 
Gohta Aihara, Kalen Clifton, Mayling Chen, Zhuoyan Li, Lyla Atta ...
 
 
 
PredGCN: a Pruning-enabled Gene-Cell Net for automatic cell annotation of single cell transcriptome data border= 
 
Qi Qi, Yunhe Wang, Yujian Huang, Yi Fan, Xiangtao Li
 
 
 
D'or: deep orienter of protein'protein interaction networks border=  
 
Daniel Pirak, Roded Sharan
 
 
 
scMaSigPro: differential expression analysis along single-cell trajectories border=  
 
Priyansh Srivastava, Marta Benegas Coll, Stefan Götz, María José Nueda, Ana Conesa
 
 
 
Unraveling spatial domain characterization in spatially resolved transcriptomics with robust graph contrastive clustering border= 
 
Yingxi Zhang, Zhuohan Yu, Ka-Chun Wong, Xiangtao Li
 
 
 
Controlled noise: evidence of epigenetic regulation of single-cell expression variability border= 
 
Yan Zhong, Siwei Cui, Yongjian Yang, James J Cai
 
 
 
Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro border= 
 
Zhanhe Chang, Yunfan Xu, Xin Dong, Yawei Gao, Chenfei Wang
 
 
 
Genetics and population analysis
 
 
 
 
A multi-bin rarefying method for evaluating alpha diversities in TCR sequencing data border= 
 
Mo Li, Xing Hua, Shuai Li, Michael C Wu, Ni Zhao
 
 
 
Detecting gene'environment interactions from multiple continuous traits border=  
 
Wan-Yu Lin
 
 
 
Systems biology
 
 
 
 
Optimizing data integration improves gene regulatory network inference in Arabidopsis thaliana border= 
 
Océane Cassan, Charles-Henri Lecellier, Antoine Martin, Laurent Bréhélin, Sophie Lèbre
 
 
 
Reverse network diffusion to remove indirect noise for better inference of gene regulatory networks border= 
 
Jiating Yu, Jiacheng Leng, Fan Yuan, Duanchen Sun, Ling-Yun Wu
 
 
 
SFINN: inferring gene regulatory network from single-cell and spatial transcriptomic data with shared factor neighborhood and integrated neural network border= 
 
Yongjie Wang, Fengfan Zhou, Jinting Guan
 
 
 
DualNetGO: a dual network model for protein function prediction via effective feature selection border= 
 
Zhuoyang Chen, Qiong Luo
 
 
 
Adaptive space search-based molecular evolution optimization algorithm border=  
 
Fei Wang, Xianglong Cheng, Xin Xia, Chunhou Zheng, Yansen Su
 
 
 
Data and text mining
 
 
 
 
HGTDR: Advancing drug repurposing with heterogeneous graph transformers border= 
 
Ali Gharizadeh, Karim Abbasi, Amin Ghareyazi, Mohammad R K Mofrad, Hamid R Rabiee
 
 
 
FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology border= 
 
Tudor Groza, Dylan Gration, Gareth Baynam, Peter N Robinson
 
 
 
Document-level biomedical relation extraction via hierarchical tree graph and relation segmentation module border= 
 
Jianyuan Yuan, Fengyu Zhang, Yimeng Qiu, Hongfei Lin, Yijia Zhang
 
 
 
Assessing citation integrity in biomedical publications: corpus annotation and NLP models border= 
 
Maria Janina Sarol, Shufan Ming, Shruthan Radhakrishna, Jodi Schneider, Halil Kilicoglu
 
 
 
MiPRIME: an integrated and intelligent platform for mining primer and probe sequences of microbial species border= 
 
Zhiming Zhang, Jing Ren, Lili Ren, Lanying Zhang, Qubo Ai ...
 
 
 
DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data border= 
 
Guangzhi Xiong, Nathan J LeRoy, Stefan Bekiranov, Nathan C Sheffield, Aidong Zhang
 
 
 
A deep learning architecture for metabolic pathway prediction border=  
 
Mayank Baranwal, Abram Magner, Paolo Elvati, Jacob Saldinger, Angela Violi ...
 
 
 
MetaHD: a multivariate meta-analysis model for metabolomics data border=  
 
Jayamini C Liyanage, Luke Prendergast, Robert Staudte, Alysha M De Livera
 
 
 
Bioimage informatics
 
 
 
 
A Spatial Omnibus Test (SPOT) for Spatial Proteomic Data border= 
 
Sarah Samorodnitsky, Katie Campbell, Antoni Ribas, Michael C Wu
 
 
 
LarvaTagger: manual and automatic tagging of Drosophila larval behaviour border= 
 
François Laurent, Alexandre Blanc, Lilly May, Lautaro Gándara, Benjamin T Cocanougher ...
 
 
 
Knowledge transfer from macro-world to micro-world: enhancing 3D Cryo-ET classification through fine-tuning video-based deep models border= 
 
Sabhay Jain, Xingjian Li, Min Xu
 
 
 
Time-efficient filtering of imaging polarimetric data by checking physical realizability of experimental Mueller matrices border= 
 
Tatiana Novikova, Alexey Ovchinnikov, Gleb Pogudin, Jessica C Ramella-Roman
 
 
 
Applications Note
 
 
 
 
Genome analysis
 
 
 
 
hictk: blazing fast toolkit to work with .hic and .cool files border= 
 
Roberto Rossini, Jonas Paulsen
 
 
 
mLiftOver: harmonizing data across Infinium DNA methylation platforms border=  
 
Brian H Chen, Wanding Zhou
 
 
 
GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes border= 
 
Vadim A Pisarenco, Joel Vizueta, Julio Rozas
 
 
 
Sequence analysis
 
 
 
 
BAllC and BAllCools: efficient formatting and operating for single-cell DNA methylation data border= 
 
Wei Tian, Wubin Ding, Jiawei Shen, Daofeng Li, Ting Wang ...
 
 
 
Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data border= 
 
Yichi Zhang, Chenghui Hu, Xiaohui Wu, Jian Song
 
 
 
GENTANGLE: integrated computational design of gene entanglements 
 
Jose Manuel Martí, Chloe Hsu, Charlotte Rochereau, Chenling Xu, Tomasz Blazejewski ...
 
 
 
Phylogenetics
 
 
 
 
Drawing mitochondrial genomes with circularMT border= 
 
Simon J Goodman, Ian M Carr
 
 
 
Structural bioinformatics
 
 
 
 
Protein interaction explorer (PIE): a comprehensive platform for navigating protein'protein interactions and ligand binding pockets border= 
 
Fabien Mareuil, Alexandra Moine-Franel, Anuradha Kar, Michael Nilges, Constantin Bogdan Ciambur ...
 
 
 
ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries border= 
 
Kyle Swanson, Parker Walther, Jeremy Leitz, Souhrid Mukherjee, Joseph C Wu ...
 
 
 
Melodia: a Python library for protein structure analysis border=  
 
Rinaldo W Montalvão, William R Pitt, Vitor B Pinheiro, Tom L Blundell
 
 
 
Gene expression
 
 
 
 
CodonBERT: a BERT-based architecture tailored for codon optimization using the cross-attention mechanism border= 
 
Zilin Ren, Lili Jiang, Yaxin Di, Dufei Zhang, Jianli Gong ...
 
 
 
ScType enables fast and accurate cell type identification from spatial transcriptomics data border= 
 
Kristen Nader, Misra Tasci, Aleksandr Ianevski, Andrew Erickson, Emmy W Verschuren ...
 
 
 
msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease border= 
 
Thang V Pham, Alex A Henneman, Nam X Truong, Connie R Jimenez
 
 
 
InstaPrism: an R package for fast implementation of BayesPrism border=  
 
Mengying Hu, Maria Chikina
 
 
 
Compound-SNE: comparative alignment of t-SNEs for multiple single-cell omics data visualization border= 
 
Colin G Cess, Laleh Haghverdi
 
 
 
Systems biology
 
 
 
 
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets border= 
 
Cedric Landerer, Maxim Scheremetjew, HongKee Moon, Lena Hersemann, Agnes Toth-Petroczy
 
 
 
hopsy ' a methods marketplace for convex polytope sampling in Python border=  
 
Richard D Paul, Johann F Jadebeck, Anton Stratmann, Wolfgang Wiechert, Katharina Nöh
 
 
 
MetaboLink: a web application for streamlined processing and analysis of large-scale untargeted metabolomics data border= 
 
Ana Mendes, Jesper Foged Havelund, Jonas Lemvig, Veit Schwämmle, Nils J Færgeman
 
 
 
Genetics and population analysis
 
 
 
 
MethParquet: an R package for rapid and efficient DNA methylation association analysis adopting Apache Parquet border= 
 
Ziqing Wang, Michael Cassidy, Danielle A Wallace, Tamar Sofer
 
 
 
DODGE: automated point source bacterial outbreak detection using cumulative long term genomic surveillance border= 
 
Michael Payne, Dalong Hu, Qinning Wang, Geraldine Sullivan, Rikki M Graham ...
 
 
 
Bioimage informatics
 
 
 
 
Automated, image-based quantification of peroxisome characteristics with perox-per-cell border= 
 
Maxwell L Neal, Nandini Shukla, Fred D Mast, Jean-Claude Farré, Therese M Pacio ...
 
 
 
Correction
 
 
 
 
Correction to: The 2024 ISCB Innovator Award'Dr Su-In Lee border= 
 
 
 
 
Retraction
 
 
 
 
Retraction and replacement of: A deep learning architecture for metabolic pathway prediction border= 
 
 
 
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