Subject: New issue: Bioinformatics, Volume 41, Issue 2, February 2025

Volume 41, Issue 2, February 2025

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Review

Sequence analysis

Functional profiling of the sequence stockpile: a protein pair-based assessment of in silico prediction tools

R Prabakaran,Yana Bromberg and others

Original Paper

Genome analysis

HiCForecast: dynamic network optical flow estimation algorithm for spatiotemporal Hi-C data forecasting

Dmitry Pinchuk,H M A Mohit Chowdhury and others

Multidimensional scaling improves distance-based clustering for microbiome data

Guanhua Chen,Xinyue Wang and others

CRAmed: a conditional randomization test for high-dimensional mediation analysis in sparse microbiome data

Tiantian Liu,Xiangnan Xu and others

Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations

Lin Du,Hammad Farooq and others

GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions

Zhenmiao Zhang,Ishaan Gupta and others

PhyloMix: enhancing microbiome-trait association prediction through phylogeny-mixing augmentation

Yifan Jiang,Disen Liao and others

SCEMENT: scalable and memory efficient integration of large-scale single-cell RNA-sequencing data

Sriram P Chockalingam,Maneesha Aluru and others

Sequence analysis

ELLIPSIS: robust quantification of splicing in scRNA-seq

Marie Van Hecke,Niko Beerenwinkel and others

Structural bioinformatics

MEGA-GO: functions prediction of diverse protein sequence length using Multi-scalE Graph Adaptive neural network

Yujian Lee,Peng Gao and others

Enhanced O-glycosylation site prediction using explainable machine learning technique with spatial local environment

Seokyoung Hong,Krishna Gopal Chattaraj and others

Robustly interrogating machine learning-based scoring functions: what are they learning?

Guy Durant,Fergus Boyles and others

ParaSurf: a surface-based deep learning approach for paratope'antigen interaction prediction

Angelos-Michael Papadopoulos,Apostolos Axenopoulos and others

FoldX force field revisited, an improved version

Javier Delgado,Raul Reche and others

Gene expression

A comprehensive graph neural network method for predicting triplet motifs in disease'drug'gene interactions

Chuanze Kang,Zonghuan Liu and others

Prediction of gene expression using histone modification patterns extracted by Particle Swarm Optimization

Niels Benjamin Paul,Jonas Chanrithy Wolber and others

SSL-VQ: vector-quantized variational autoencoders for semi-supervised prediction of therapeutic targets across diverse diseases

Satoko Namba,Chen Li and others

scHNTL: single-cell RNA-seq data clustering augmented by high-order neighbors and triplet loss

Hua Meng,Chuan Qin and others

Systems biology

NMFProfiler: a multi-omics integration method for samples stratified in groups

AurÃ©lie MercadiÃ©,Ã‰lÃ©onore Gravier and others

MolFCL: predicting molecular properties through chemistry-guided contrastive and prompt learning

Xiang Tang,Qichang Zhao and others

ESPClust: unsupervised identification of modifiers for the effect size profile in omics association studies

Francisco J PÃ©rez-Reche,Nathan J Cheetham and others

Data and text mining

Vistla: identifying influence paths with information theory

Miron B Kursa,Jonathan Wren

Trajectory Inference with Cell'Cell Interactions (TICCI): intercellular communication improves the accuracy of trajectory inference methods

Yifeng Fu,Hong Qu and others

A conditional denoising VAE-based framework for antimicrobial peptides generation with preserving desirable properties

Weizhong Zhao,Kaijieyi Hou and others

Bioimage informatics

CAMIL: channel attention-based multiple instance learning for whole slide image classification

Jinyang Mao,Junlin Xu and others

Prediction of molecular subtypes for endometrial cancer based on hierarchical foundation model

Haoyu Cui,Qinhao Guo and others

Applications Note

Genome analysis

doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications

Fabricio Almeida-Silva,Yves Van de Peer and others

DNAdesign: feature-aware in silico design of synthetic DNA through mutation

Yingfei Wang,Jinsen Li and others

mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies

Tatiana A Gurbich,Martin Beracochea and others

Sequence analysis

VirDetector: a bioinformatic pipeline for virus surveillance using nanopore sequencing

Nick Laurenz Kaiser,Martin H Groschup and others

tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets

Max R Brown,Pablo Manuel Gonzalez de La Rosa and others

Gene expression

tagtango: an application to compare single-cell annotations

Bernat Bramon Mora,Helen Lindsay and others

scatterbar: an R package for visualizing proportional data across spatially resolved coordinates

Dee Velazquez,Jean Fan and others

Genetics and population analysis

PNL: a software to build polygenic risk scores using a super learner approach based on PairNet, a Convolutional Neural Network

Ting-Huei Chen,Chia-Jung Lee and others

Systems biology

COBREXA 2: tidy and scalable construction of complex metabolic models

Miroslav KratochvÃl,St Elmo Wilken and others

NetworkCommons: bridging data, knowledge, and methods to build and evaluate context-specific biological networks

Victor Paton,Denes TÃ¼rei and others

Data and text mining

ipd: an R package for conducting inference on predicted data

Stephen Salerno,Jiacheng Miao and others

Databases and ontologies

ESCARGOT: an AI agent leveraging large language models, dynamic graph of thoughts, and biomedical knowledge graphs for enhanced reasoning

Nicholas Matsumoto,Hyunjun Choi and others

Bioimage informatics

tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling

Thomas-Otavio Peulen,Katherina Hemmen and others

International Society for Computational Biology

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