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Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
Bioinformatics  
Volume 40 Issue 5
 
May 2024
 
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GradHC: highly reliable gradual hash-based clustering for DNA storage systems border=  
 
Dvir Ben Shabat, Adar Hadad, Avital Boruchovsky, Eitan Yaakobi
 
 
 
 
 
 
 
Revisiting drug'protein interaction prediction: a novel global'local perspective border= 
 
Zhecheng Zhou, Qingquan Liao, Jinhang Wei, Linlin Zhuo, Xiaonan Wu ...
 
 
 
 
 
 
 
CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics border=  
 
Semih Kurt, Mandi Chen, Hosein Toosi, Xinsong Chen, Camilla Engblom ...
 
 
 
Original Paper
 
 
 
 
Genome analysis
 
 
 
 
A data-adaptive methods in detecting exogenous methyltransferase accessible chromatin in human genome using nanopore sequencing border= 
 
Kailing Tu, Xuemei Li, Qilin Zhang, Wei Huang, Dan Xie
 
 
 
wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication border= 
 
Hengchi Chen, Arthur Zwaenepoel, Yves Van de Peer
 
 
 
 
MUSE-XAE: MUtational Signature Extraction with eXplainable AutoEncoder enhances tumour types classification border= 
 
Corrado Pancotti, Cesare Rollo, Francesco Codicè, Giovanni Birolo, Piero Fariselli ...
 
 
 
Sequence Analysis
 
 
 
 
LMCrot: an enhanced protein crotonylation site predictor by leveraging an interpretable window-level embedding from a transformer-based protein language model border= 
 
Pawel Pratyush, Soufia Bahmani, Suresh Pokharel, Hamid D Ismail, Dukka B KC
 
 
 
For antibody sequence generative modeling, mixture models may be all you need border=  
 
Jonathan Parkinson, Wei Wang
 
 
 
RecGraph: recombination-aware alignment of sequences to variation graphs border=  
 
Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti ...
 
 
 
DeepPPAPredMut: deep ensemble method for predicting the binding affinity change in protein'protein complexes upon mutation border= 
 
Rahul Nikam, Sherlyn Jemimah, M Michael Gromiha
 
 
 
 
DeepAVP-TPPred: identification of antiviral peptides using transformed image-based localized descriptors and binary tree growth algorithm border= 
 
Matee Ullah, Shahid Akbar, Ali Raza, Quan Zou
 
 
 
Integrated convolution and self-attention for improving peptide toxicity prediction border= 
 
Shihu Jiao, Xiucai Ye, Tetsuya Sakurai, Quan Zou, Ruijun Liu
 
 
 
Structural bioinformatics
 
 
 
 
AbLEF: antibody language ensemble fusion for thermodynamically empowered property predictions border= 
 
Zachary A Rollins, Talal Widatalla, Andrew Waight, Alan C Cheng, Essam Metwally
 
 
 
MEG-PPIS: a fast protein'protein interaction site prediction method based on multi-scale graph information and equivariant graph neural network border= 
 
Hongzhen Ding, Xue Li, Peifu Han, Xu Tian, Fengrui Jing ...
 
 
 
Chainsaw: protein domain segmentation with fully convolutional neural networks border= 
 
Jude Wells, Alex Hawkins-Hooker, Nicola Bordin, Ian Sillitoe, Brooks Paige ...
 
 
 
Gene expression
 
 
 
 
Peptide set test: a peptide-centric strategy to infer differentially expressed proteins border= 
 
Junmin Wang, Steven Novick
 
 
 
scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism border= 
 
Qun Jiang, Shengquan Chen, Xiaoyang Chen, Rui Jiang
 
 
 
scTPC: a novel semisupervised deep clustering model for scRNA-seq data border=  
 
Yushan Qiu, Lingfei Yang, Hao Jiang, Quan Zou
 
 
 
Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data border= 
 
Marco Stock, Niclas Popp, Jonathan Fiorentino, Antonio Scialdone
 
 
 
Scalable integration of multiomic single-cell data using generative adversarial networks border= 
 
Valentina Giansanti, Francesca Giannese, Oronza A Botrugno, Giorgia Gandolfi, Chiara Balestrieri ...
 
 
 
Inferring gene regulatory networks from single-cell transcriptomics based on graph embedding border= 
 
Yanglan Gan, Jiacheng Yu, Guangwei Xu, Cairong Yan, Guobing Zou
 
 
 
Genetics and population analysis
 
 
 
 
SharePro: an accurate and efficient genetic colocalization method accounting for multiple causal signals border= 
 
Wenmin Zhang, Tianyuan Lu, Robert Sladek, Yue Li, Hamed Najafabadi ...
 
 
 
Genotype sampling for deep-learning assisted experimental mapping of a combinatorially complete fitness landscape border= 
 
Andreas Wagner
 
 
 
Systems biology
 
 
 
 
Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS border= 
 
Remi Trimbour, Ina Maria Deutschmann, Laura Cantini
 
 
 
NeoAgDT: optimization of personal neoantigen vaccine composition by digital twin simulation of a cancer cell population border= 
 
Anja Mösch, Filippo Grazioli, Pierre Machart, Brandon Malone
 
 
 
A supervised Bayesian factor model for the identification of multi-omics signatures border= 
 
Jeremy P Gygi, Anna Konstorum, Shrikant Pawar, Edel Aron, Steven H Kleinstein ...
 
 
 
BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities border= 
 
Telmo Blasco, Francesco Balzerani, Luis V Valcárcel, Pedro Larrañaga, Concha Bielza ...
 
 
 
fastCCLasso: a fast and efficient algorithm for estimating correlation matrix from compositional data border= 
 
Shen Zhang, Huaying Fang, Tao Hu
 
 
 
Bayesian modelling of time series data (BayModTS)'a FAIR workflow to process sparse and highly variable data border= 
 
Sebastian Höpfl, Mohamed Albadry, Uta Dahmen, Karl-Heinz Herrmann, Eva Marie Kindler ...
 
 
 
BindingSiteDTI: differential-scale binding site modelling for drug'target interaction prediction border= 
 
Feng Pan, Chong Yin, Si-Qi Liu, Tao Huang, Zhaoxiang Bian ...
 
 
 
DiSMVC: a multi-view graph collaborative learning framework for measuring disease similarity border= 
 
Hang Wei, Lin Gao, Shuai Wu, Yina Jiang, Bin Liu
 
 
 
GateMeClass: Gate Mining and Classification of cytometry data border=  
 
Simone Caligola, Luca Giacobazzi, Stefania Canè, Antonio Vella, Annalisa Adamo ...
 
 
 
Data and text mining
 
 
 
 
TransGEM: a molecule generation model based on Transformer with gene expression data border= 
 
Yanguang Liu, Hailong Yu, Xinya Duan, Xiaomin Zhang, Ting Cheng ...
 
 
 
From cell lines to cancer patients: personalized drug synergy prediction border=  
 
Halil Ibrahim Kuru, A Ercument Cicek, Oznur Tastan
 
 
 
BTR: a bioinformatics tool recommendation system border=  
 
Ryan Green, Xufeng Qu, Jinze Liu, Tingting Yu
 
 
 
Molecular property prediction based on graph structure learning border=  
 
Bangyi Zhao, Weixia Xu, Jihong Guan, Shuigeng Zhou
 
 
 
Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data border= 
 
Xiaofan Liu, Yuhuan Tao, Zilin Cai, Pengfei Bao, Hongli Ma ...
 
 
 
Databases and ontologies
 
 
 
 
Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning border= 
 
Azza Althagafi, Fernando Zhapa-Camacho, Robert Hoehndorf
 
 
 
Bioimage informatics
 
 
 
 
Automated segmentation and recognition of C. elegans whole-body cells border= 
 
Yuanyuan Li, Chuxiao Lai, Meng Wang, Jun Wu, Yongbin Li ...
 
 
 
Applications Note
 
 
 
 
Genome analysis
 
 
 
 
MammalMethylClock R package: software for DNA methylation-based epigenetic clocks in mammals border= 
 
Joseph Zoller, Steve Horvath
 
 
 
methscore: a comprehensive R function for DNA methylation-based health predictors 
 
Zongli Xu, Liang Niu, Jacob K Kresovich, Jack A Taylor
 
 
 
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets border=  
 
Bryce Kille, Michael G Nute, Victor Huang, Eddie Kim, Adam M Phillippy ...
 
 
 
Sequence analysis
 
 
 
 
SimReadUntil for benchmarking selective sequencing algorithms on ONT devices border= 
 
Maximilian Mordig, Gunnar Rätsch, André Kahles
 
 
 
Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper border= 
 
Charlotte Crauwels, Sophie-Luise Heidig, Adrián Díaz, Wim F Vranken
 
 
 
PlasCAT: Plasmid Cloud Assembly Tool border=  
 
Samuel Peccoud, Casey-Tyler Berezin, Sarah I Hernandez, Jean Peccoud
 
 
 
PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping border= 
 
Hui Sun, Yingfeng Zheng, Haonan Xie, Huidong Ma, Cheng Zhong ...
 
 
 
Phylogenetics
 
 
 
 
pipesnake : generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci border= 
 
Ian G Brennan, Sonal Singhal, Ziad Al Bkhetan
 
 
 
Structural bioinformatics
 
 
 
 
CORDAX web server: an online platform for the prediction and 3D visualization of aggregation motifs in protein sequences border= 
 
Nikolaos Louros, Frederic Rousseau, Joost Schymkowitz
 
 
 
Peptriever: a Bi-Encoder approach for large-scale protein'peptide binding search border= 
 
Roni Gurvich, Gal Markel, Ziaurrehman Tanoli, Tomer Meirson
 
 
 
Gene expression
 
 
 
 
CASCC: a co-expression-assisted single-cell RNA-seq data clustering method border= 
 
Lingyi Cai, Dimitris Anastassiou
 
 
 
greenPipes: an integrated data analysis pipeline for greenCUT&RUN and CUT&RUN genome-localization datasets border= 
 
Sheikh Nizamuddin, H T Marc Timmers
 
 
 
MultiRNAflow: integrated analysis of temporal RNA-seq data with multiple biological conditions border= 
 
Rodolphe Loubaton, Nicolas Champagnat, Pierre Vallois, Laurent Vallat
 
 
 
Genetics and population analysis
 
 
 
 
shinyseg: a web application for flexible cosegregation and sensitivity analysis border= 
 
Christian Carrizosa, Dag E Undlien, Magnus D Vigeland
 
 
 
MPH: fast REML for large-scale genome partitioning of quantitative genetic variation border= 
 
Jicai Jiang
 
 
 
metaGWASmanager: a toolbox for an automated workflow from phenotypes to meta-analysis in GWAS consortia border= 
 
Zulema Rodriguez-Hernandez, Mathias Gorski, Maria Tellez-Plaza, Pascal Schlosser, Matthias Wuttke
 
 
 
Systems biology
 
 
 
 
DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data border= 
 
Johanna Galvis, Joris Guyon, Benjamin Dartigues, Helge Hecht, Björn Grüning ...
 
 
 
Data and text mining
 
 
 
 
NetMe 2.0: a web-based platform for extracting and modeling knowledge from biomedical literature as a labeled graph border= 
 
Antonio Di Maria, Lorenzo Bellomo, Fabrizio Billeci, Alfio Cardillo, Salvatore Alaimo ...
 
 
 
ITree : a user-driven tool for interactive decision-making with classification trees border= 
 
Hubert Sokołowski, Marcin Czajkowski, Anna Czajkowska, Krzysztof Jurczuk, Marek Kretowski
 
 
 
Correction
 
 
 
 
Correction to: kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase border= 
 
 
 
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