Subject: Bioinformatics Table of Contents for January 2025 Oxford Academic
 
 
 
Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
Bioinformatics  
Volume 41 Issue 1
 
January 2025
 
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Original Paper
 
 
 
 
Genome analysis
 
 
 
 
SCARAP: scalable cross-species comparative genomics of prokaryotes 
 
Stijn Wittouck, Tom Eilers, Vera van Noort, Sarah Lebeer
 
 
 
CrossIsoFun: predicting isoform functions using the integration of multi-omics data 
 
Yiwei Liu, Hong-Dong Li, Jianxin Wang
 
 
 
End-to-end simulation of nanopore sequencing signals with feed-forward transformers 
 
Denis Beslic, Martin Kucklick, Susanne Engelmann, Stephan Fuchs, Bernhard Y Renard ...
 
 
 
Integrating single-cell multimodal epigenomic data using 1D convolutional neural networks 
 
Chao Gao, Joshua D Welch
 
 
 
Fast and exact gap-affine partial order alignment with POASTA  
 
Lucas R van Dijk, Abigail L Manson, Ashlee M Earl, Kiran V Garimella, Thomas Abeel
 
 
 
 
 
Sequence analysis
 
 
 
 
DiffPaSS'high-performance differentiable pairing of protein sequences using soft scores 
 
Umberto Lupo, Damiano Sgarbossa, Martina Milighetti, Anne-Florence Bitbol
 
 
 
A near-tight lower bound on the density of forward sampling schemes  
 
Bryce Kille, Ragnar Groot Koerkamp, Drake McAdams, Alan Liu, Todd J Treangen
 
 
 
m5c-iEnsem: 5-methylcytosine sites identification through ensemble models  
 
Anas Bilal, Fawaz Khaled Alarfaj, Rafaqat Alam Khan, Muhammad Taseer Suleman, Haixia Long
 
 
 
Nanopore decoding with speed and versatility for data storage  
 
Kevin D Volkel, Paul W Hook, Albert Keung, Winston Timp, James M Tuck
 
 
 
PHIStruct: improving phage'host interaction prediction at low sequence similarity settings using structure-aware protein embeddings 
 
Mark Edward M Gonzales, Jennifer C Ureta, Anish M S Shrestha
 
 
 
 
EnrichRBP: an automated and interpretable computational platform for predicting and analysing RNA-binding protein events 
 
Yubo Wang, Haoran Zhu, Yansong Wang, Yuning Yang, Yujian Huang ...
 
 
 
DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning 
 
Castrense Savojardo, Matteo Manfredi, Pier Luigi Martelli, Rita Casadio
 
 
 
TPepRet: a deep learning model for characterizing T-cell receptors'antigen binding patterns 
 
Meng Wang, Wei Fan, Tianrui Wu, Min Li
 
 
 
Phylogenetics
 
 
 
 
BetaAlign: a deep learning approach for multiple sequence alignment 
 
Edo Dotan, Elya Wygoda, Noa Ecker, Michael Alburquerque, Oren Avram ...
 
 
 
Structural Bioinformatics
 
 
 
 
TargetSA: adaptive simulated annealing for target-specific drug design 
 
Zhe Xue, Chenwei Sun, Wenhao Zheng, Jiancheng Lv, Xianggen Liu
 
 
 
TPepPro: a deep learning model for predicting peptide'protein interactions  
 
Xiaohong Jin, Zimeng Chen, Dan Yu, Qianhui Jiang, Zhuobin Chen ...
 
 
 
Ligand identification in CryoEM and X-ray maps using deep learning  
 
Jacek Karolczak, Anna Przybyłowska, Konrad Szewczyk, Witold Taisner, John M Heumann ...
 
 
 
CParty: hierarchically constrained partition function of RNA pseudoknots  
 
Mateo Gray, Luke Trinity, Ulrike Stege, Yann Ponty, Sebastian Will ...
 
 
 
DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence 
 
Jesse Durham, Jing Zhang, Richard D Schaeffer, Qian Cong
 
 
 
CryptoBench: cryptic protein'ligand binding sites dataset and benchmark  
 
Vít Å krhák, Marian Novotný, Christos P Feidakis, Radoslav Krivák, David Hoksza
 
 
 
RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction 
 
Clément Bernard, Guillaume Postic, Sahar Ghannay, Fariza Tahi
 
 
 
Transcription factor prediction using protein 3D secondary structures  
 
Jeanine Liebold, Fabian Neuhaus, Janina Geiser, Stefan Kurtz, Jan Baumbach ...
 
 
 
Gene expression
 
 
 
 
VarNMF: non-negative probabilistic factorization with source variation 
 
Ela Fallik, Nir Friedman
 
 
 
Bayesian gene set benchmark dose estimation for "omic" responses 
 
Daniel Zilber, Kyle P Messier, John House, Fred Parham, Scott S Auerbach ...
 
 
 
Genetics and population analysis
 
 
 
 
The scalable variant call representation: enabling genetic analysis beyond one million genomes 
 
Timothy Poterba, Christopher Vittal, Daniel King, Daniel Goldstein, Jacqueline I Goldstein ...
 
 
 
Funmap: integrating high-dimensional functional annotations to improve fine-mapping 
 
Yuekai Li, Jiashun Xiao, Jingsi Ming, Yicheng Zeng, Mingxuan Cai
 
 
 
Systems biology
 
 
 
 
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits 
 
Daniel Mechtersheimer, Wenze Ding, Xiangnan Xu, Sanghyun Kim, Carolyn Sue ...
 
 
 
Accelerated enumeration of extreme rays through a positive-definite elementarity test 
 
Wannes Mores, Satyajeet S Bhonsale, Filip Logist, Jan F M Van Impe
 
 
 
QuICSeedR: an R package for analyzing fluorophore-assisted seed amplification assay data 
 
Manci Li, Damani N Bryant, Sarah Gresch, Marissa S Milstein, Peter R Christenson ...
 
 
 
PCA-based spatial domain identification with state-of-the-art performance  
 
Darius P Schaub, Behnam Yousefi, Nico Kaiser, Robin Khatri, Victor G Puelles ...
 
 
 
PredCMB: predicting changes in microbial metabolites based on the gene'metabolite network analysis of shotgun metagenome data 
 
Jungyong Ji, Sungwon Jung
 
 
 
Data and text mining
 
 
 
 
MMOSurv: meta-learning for few-shot survival analysis with multi-omics data 
 
Gang Wen, Limin Li
 
 
 
FuncFetch: an LLM-assisted workflow enables mining thousands of enzyme'substrate interactions from published manuscripts 
 
Nathaniel Smith, Xinyu Yuan, Chesney Melissinos, Gaurav Moghe
 
 
 
Heterogeneous entity representation for medicinal synergy prediction  
 
Jiawei Wu, Jun Wen, Mingyuan Yan, Anqi Dong, Shuai Gao ...
 
 
 
Improving generalizability of drug'target binding prediction by pre-trained multi-view molecular representations 
 
Xike Ouyang, Yannuo Feng, Chen Cui, Yunhe Li, Li Zhang ...
 
 
 
Bioimage informatics
 
 
 
 
Quantitative analysis of the dexamethasone side effect on human-derived young and aged skeletal muscle by myotube and nuclei segmentation using deep learning 
 
Seonghwan Park, Min Young Kim, Jaewon Jeong, Sohae Yang, Minseok S Kim ...
 
 
 
Modeling multi-stage disease progression and identifying genetic risk factors via a novel collaborative learning method 
 
Duo Xi, Minjianan Zhang, Muheng Shang, Lei Du, Junwei Han
 
 
 
Autoencoder-based phenotyping of ophthalmic images highlights genetic loci influencing retinal morphology and provides informative biomarkers 
 
Panagiotis I Sergouniotis, Adam Diakite, Kumar Gaurav, Naomi Allen, Tariq Aslam ...
 
 
 
A semi-supervised fracture-attention model for segmenting tubular objects with improved topological connectivity 
 
Yanfeng Zhou, Liqun Zhong, Zichen Wang, Yang Ge
 
 
 
Applications Note
 
 
 
 
Genome analysis
 
 
 
 
Gretl'variation GRaph Evaluation TooLkit 
 
Sebastian Vorbrugg, Ilja Bezrukov, Zhigui Bao, Detlef Weigel
 
 
 
Rnalib: a Python library for custom transcriptomics analyses  
 
Niko Popitsch, Stefan L Ameres
 
 
 
Crypt4GH-JS : securely storing sensitive data online with client-side encryption 
 
Fabienne Thelen, Jannis Hochmuth, Sven Griep, Benedikt Schwab, Alexander Goesmann ...
 
 
 
Sequence analysis
 
 
 
 
The Naïve Bayes classifier++ for metagenomic taxonomic classification'query evaluation 
 
Haozhe (Neil) Duan, Gavin Hearne, Robi Polikar, Gail L Rosen
 
 
 
Semblans: automated assembly and processing of RNA-seq data  
 
Miles D Woodcock-Girard, Eric C Bretz, Holly M Robertson, Karolis Ramanauskas, Jarrad T Hampton-Marcell ...
 
 
 
MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation 
 
Farid Chaabane, Trestan Pillonel, Claire Bertelli
 
 
 
Proteoform identification and quantification based on alignment graphs  
 
Zhaohui Zhan, Lusheng Wang
 
 
 
Structural bioinformatics
 
 
 
 
MapTurns: mapping the structure, H-bonding, and contexts of beta turns in proteins 
 
Nicholas E Newell
 
 
 
MOLGENIS Armadillo: a lightweight server for federated analysis using DataSHIELD 
 
Tim Cadman, Mariska K Slofstra, Marije A van der Geest, Demetris Avraam, Tom R P Bishop ...
 
 
 
Gene expression
 
 
 
 
NLSDeconv: an efficient cell-type deconvolution method for spatial transcriptomics data 
 
Yunlu Chen, Feng Ruan, Ji-Ping Wang
 
 
 
SuperSpot: coarse graining spatial transcriptomics data into metaspots  
 
Matei Teleman, Aurélie A G Gabriel, Léonard Hérault, David Gfeller
 
 
 
Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels 
 
Danqing Yin, Yue Cao, Junyi Chen, Candice L Y Mak, Ken H O Yu ...
 
 
 
Genetics and population analysis
 
 
 
 
A hypercubic Mk model framework for capturing reversibility in disease, cancer, and evolutionary accumulation modelling 
 
Iain G Johnston, Ramon Diaz-Uriarte
 
 
 
PheWAS analysis on large-scale biobank data with PheTK 
 
Tam C Tran, David J Schlueter, Chenjie Zeng, Huan Mo, Robert J Carroll ...
 
 
 
FlexLMM: a Nextflow linear mixed model framework for GWAS  
 
Saul Pierotti, Tomas Fitzgerald, Ewan Birney
 
 
 
Systems biology
 
 
 
 
The FunCoup Cytoscape App: multi-species network analysis and visualization 
 
Davide Buzzao, Lukas Steininger, Dimitri Guala, Erik L L Sonnhammer
 
 
 
Data and text mining
 
 
 
 
SampleExplorer: using language models to discover relevant transcriptome data 
 
Wee Loong Chin, Timo Lassmann
 
 
 
nipalsMCIA : flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares 
 
Max Mattessich, Joaquin Reyna, Edel Aron, Ferhat Ay, Misha Kilmer ...
 
 
 
Bioimage informatics
 
 
 
 
Open Chrono-Morph Viewer: visualize big bioimage time series containing heterogeneous volumes 
 
Andre C Faubert, Shang Wang
 
 
 
Correction
 
 
 
 
Correction to: Damsel: analysis and visualisation of DamID sequencing in R 
 
 
 
 
Expression of Concern
 
 
 
 
Expression of Concern: Cleavage-Stage Embryo Segmentation Using SAM-Based Dual Branch Pipeline: Development and Evaluation with the CleavageEmbryo Dataset 
 
 
 
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