Content-Type: text/html; Oxford Academic
 
 
 
Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
Bioinformatics  
Volume 40 Issue 10
 
October 2024
 
button-issue.png
 
 
 
 
 
 
Dual-view jointly learning improves personalized drug synergy prediction border=  
 
Xueliang Li, Bihan Shen, Fangyoumin Feng, Kunshi Li, Zhixuan Tang ...
 
 
 
 
 
 
 
MOIRE: a software package for the estimation of allele frequencies and effective multiplicity of infection from polyallelic data border=  
 
Maxwell Murphy, Bryan Greenhouse
 
 
 
Correction
 
 
 
 
Correction to: AgIn: measuring the landscape of CpG methylation of individual repetitive elements border= 
 
 
 
 
Correction to: Teaching bioinformatics through the analysis of SARS-CoV-2: project-based training for computer science students border= 
 
 
 
 
Original Paper
 
 
 
 
Genome analysis
 
 
 
 
Second-order group knockoffs with applications to genome-wide association studies border= 
 
Benjamin B Chu, Jiaqi Gu, Zhaomeng Chen, Tim Morrison, Emmanuel Candès ...
 
 
 
 
Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data border= 
 
Richard Mayne, Shannah Secret, Cyndi Geoghegan, Amy Trebes, Kai Kean ...
 
 
 
Data and text mining
 
 
 
 
HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools border= 
 
Mario Sänger, Samuele Garda, Xing David Wang, Leon Weber-Genzel, Pia Droop ...
 
 
 
Chemical reaction enhanced graph learning for molecule representation border=  
 
Anchen Li, Elena Casiraghi, Juho Rousu
 
 
 
MGRN: toward robust drug recommendation via multi-view gating retrieval network border= 
 
Fanjun Meng, Xiaobo Li, Xiaodi Hou, Mingyu Lu, Yijia Zhang
 
 
 
Structure-inclusive similarity based directed GNN: a method that can control information flow to predict drug'target binding affinity border= 
 
Jipeng Huang, Chang Sun, Minglei Li, Rong Tang, Bin Xie ...
 
 
 
 
Causal enhanced drug'target interaction prediction based on graph generation and multi-source information fusion border= 
 
Guanyu Qiao, Guohua Wang, Yang Li
 
 
 
Learning to explain is a good biomedical few-shot learner border=  
 
Peng Chen, Jian Wang, Ling Luo, Hongfei Lin, Zhihao Yang
 
 
 
Chain-aware graph neural networks for molecular property prediction border=  
 
Honghao Wang, Acong Zhang, Yuan Zhong, Junlei Tang, Kai Zhang ...
 
 
 
PocketDTA: an advanced multimodal architecture for enhanced prediction of drugâˆ'target affinity from 3D structural data of target binding pockets border= 
 
Long Zhao, Hongmei Wang, Shaoping Shi
 
 
 
TarKG: a comprehensive biomedical knowledge graph for target discovery border=  
 
Cong Zhou, Chui-Pu Cai, Xiao-Tian Huang, Song Wu, Jun-Lin Yu ...
 
 
 
A multi-modality and multi-granularity collaborative learning framework for identifying spatial domains and spatially variable genes border= 
 
Xiao Liang, Pei Liu, Li Xue, Baiyun Chen, Wei Liu ...
 
 
 
Gene expression
 
 
 
 
A self-training interpretable cell type annotation framework using specific marker gene border= 
 
Hegang Chen, Yuyin Lu, Yanghui Rao
 
 
 
LineageVAE: reconstructing historical cell states and transcriptomes toward unobserved progenitors border= 
 
Koichiro Majima, Yasuhiro Kojima, Kodai Minoura, Ko Abe, Haruka Hirose ...
 
 
 
Statistical batch-aware embedded integration, dimension reduction, and alignment for spatial transcriptomics border= 
 
Yanfang Li, Shihua Zhang
 
 
 
scDRMAE: integrating masked autoencoder with residual attention networks to leverage omics feature dependencies for accurate cell clustering border= 
 
Tianjiao Zhang, Hongfei Zhang, Jixiang Ren, Zhenao Wu, Zhongqian Zhao ...
 
 
 
Biologically weighted LASSO: enhancing functional interpretability in gene expression data analysis border= 
 
Sofia Mongardi, Silvia Cascianelli, Marco Masseroli
 
 
 
Genetics and population analysis
 
 
 
 
The GenoPred pipeline: a comprehensive and scalable pipeline for polygenic scoring border= 
 
Oliver Pain, Ammar Al-Chalabi, Cathryn M Lewis
 
 
 
BEATRICE: Bayesian fine-mapping from summary data using deep variational inference border= 
 
Sayan Ghosal, Michael C Schatz, Archana Venkataraman
 
 
 
Sequence analysis
 
 
 
 
Prediction of antibiotic resistance mechanisms using a protein language model border= 
 
Kanami Yagimoto, Shion Hosoda, Miwa Sato, Michiaki Hamada
 
 
 
Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network border= 
 
Baixue Qiao, Shuda Wang, Mingjun Hou, Haodi Chen, Zhengwenyang Zhou ...
 
 
 
OligoFormer: an accurate and robust prediction method for siRNA design border=  
 
Yilan Bai, Haochen Zhong, Taiwei Wang, Zhi John Lu
 
 
 
Anti-symmetric framework for balanced learning of protein'protein interactions border= 
 
Tao Tang, Tianyang Li, Weizhuo Li, Xiaofeng Cao, Yuansheng Liu ...
 
 
 
MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification border= 
 
Ruipeng Lu, Tim Dumonceaux, Muhammad Anzar, Athanasios Zovoilis, Kym Antonation ...
 
 
 
Bioimage informatics
 
 
 
 
TAWFN: a deep learning framework for protein function prediction border= 
 
Lu Meng, Xiaoran Wang
 
 
 
Accurate segmentation of intracellular organelle networks using low-level features and topological self-similarity border= 
 
Jiaxing Huang, Yaoru Luo, Yuanhao Guo, Wenjing Li, Zichen Wang ...
 
 
 
Structural Bioinformatics
 
 
 
 
Computational prediction of multiple antigen epitopes border= 
 
Rajalakshmi Viswanathan, Moshe Carroll, Alexandra Roffe, Jorge E Fajardo, Andras Fiser
 
 
 
Towards the accurate modelling of antibodyâˆ'antigen complexes from sequence using machine learning and information-driven docking border= 
 
Marco Giulini, Constantin Schneider, Daniel Cutting, Nikita Desai, Charlotte M Deane ...
 
 
 
Pair-EGRET: enhancing the prediction of protein'protein interaction sites through graph attention networks and protein language models border= 
 
Ramisa Alam, Sazan Mahbub, Md Shamsuzzoha Bayzid
 
 
 
Systems biology
 
 
 
 
GNN4DM: a graph neural network-based method to identify overlapping functional disease modules border= 
 
András Gézsi, Péter Antal
 
 
 
MSDAFL: molecular substructure-based dual attention feature learning framework for predicting drug'drug interactions border= 
 
Chao Hou, Guihua Duan, Cheng Yan
 
 
 
Applications Note
 
 
 
 
Genome analysis
 
 
 
 
MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants border= 
 
Weijia Jin, Yi Xia, Javlon Nizomov, Yunlong Liu, Zhigang Li ...
 
 
 
VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation border= 
 
Yilin Zhu, Guowei Chen, Yanni Sun
 
 
 
PCBS: an R package for fast and accurate analysis of bisulfite sequencing data border= 
 
Kathryn Lande, April E Williams
 
 
 
BioPred: an R package for biomarkers analysis in precision medicine border=  
 
Zihuan Liu, Yan Sun, Xin Huang
 
 
 
Structural bioinformatics
 
 
 
 
DockQ v2: improved automatic quality measure for protein multimers, nucleic acids, and small molecules border= 
 
Claudio Mirabello, Björn Wallner
 
 
 
ABodyBuilder3: improved and scalable antibody structure predictions border=  
 
Henry Kenlay, Frédéric A Dreyer, Daniel Cutting, Daniel Nissley, Charlotte M Deane
 
 
 
Analysis of metadynamics simulations by metadynminer.py border=  
 
Jan Beránek, AleÅ¡ KÅ™enek, VojtÄ›ch Spiwok
 
 
 
Data and text mining
 
 
 
 
GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console border= 
 
Anindita Nath, Savannah Mwesigwa, Yulin Dai, Xiaoqian Jiang, Zhongming Zhao
 
 
 
SurvBal: compositional microbiome balances for survival outcomes border=  
 
Ying Li, Teresa Lee, Kai Marin, Xing Hua, Sujatha Srinivasan ...
 
 
 
Sequence analysis
 
 
 
 
NeoDesign: a computational tool for optimal selection of polyvalent neoantigen combinations border= 
 
Wenqian Yu, Hongwu Yu, Jingjing Zhao, Hena Zhang, Kalam Ke ...
 
 
 
Gene expression
 
 
 
 
vSPACE: exploring virtual spatial representation of articular chondrocytes at the single-cell level border= 
 
Chenyu Zhang, Honglin Wang, Yeonsoo Chung, Seung-Hyun Hong, Merissa Olmer ...
 
 
 
BatchFLEX: feature-level equalization of X-batch border=  
 
Joshua T Davis, Alyssa N Obermayer, Alex C Soupir, Rebecca S Hesterberg, Thac Duong ...
 
 
 
Systems biology
 
 
 
 
Combined LC-MS/MS feature grouping, statistical prioritization, and interactive networking in msFeaST border= 
 
Kevin Mildau, Christoph Büschl, Jürgen Zanghellini, Justin J J van der Hooft
 
 
 
CyCadas: accelerating interactive annotation and analysis of clustered cytometry data border= 
 
Oliver Hunewald, Agnieszka Demczuk, Joseph Longworth, Markus Ollert
 
 
 
RTF: an R package for modelling time course data border=  
 
Eva Brombacher, Clemens Kreutz
 
 
 
DAVID Ortholog: an integrative tool to enhance functional analysis through orthologs 
 
Brad T Sherman, Ganesh Panzade, Tomozumi Imamichi, Weizhong Chang
 
 
 
Phylogenetics
 
 
 
 
Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique border= 
 
Hang Yang, Xiaoxin Lu, Jiaxing Chang, Qing Chang, Wen Zheng ...
 
 
Unsubscribe       Manage email alerts
 
Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK.

Our Privacy Policy sets out how Oxford University Press handles your personal information.

The content of this email is protected by copyright.
 
Oxford University Press
 
 
                                 



This email is intended for bionet@evol.mcmaster.ca. ------=_Part_1758686870.1730656083389--