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PMC Full-Text Search Results

Items: 1 to 20 of 8808

1.
Predicting circRNA–disease associations with shared units and multi-channel attention mechanisms
Xue Zhang, Quan Zou, Mengting Niu, Chunyu Wang
Bioinformatics. 2025 Mar; 41(3): btaf088. Published online 2025 Mar 5. doi: 10.1093/bioinformatics/btaf088
PMCID:
PMC11919450
ArticlePDF–2.1M
2.
Sul-BertGRU: an ensemble deep learning method integrating information entropy-enhanced BERT and directional multi-GRU for S-sulfhydration sites prediction
Xirun Wei, Qiao Ning, Kuiyang Che, Zhaowei Liu, Hui Li, Shikai Guo
Bioinformatics. 2025 Mar; 41(3): btaf078. Published online 2025 Feb 20. doi: 10.1093/bioinformatics/btaf078
PMCID:
PMC11908646
ArticlePDF–3.0M
3.
CryoTEN: efficiently enhancing cryo-EM density maps using transformers
Joel Selvaraj, Liguo Wang, Jianlin Cheng
Bioinformatics. 2025 Mar; 41(3): btaf092. Published online 2025 Feb 27. doi: 10.1093/bioinformatics/btaf092
PMCID:
PMC11906401
ArticlePDF–3.8M
4.
Significance in scale space for Hi-C data
Rui Liu, Zhengwu Zhang, Hyejung Won, J S Marron
Bioinformatics. 2025 Mar; 41(3): btaf026. Published online 2025 Feb 27. doi: 10.1093/bioinformatics/btaf026
PMCID:
PMC11879645
ArticlePDF–4.7M
5.
AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow
Ali Hamraoui, Laurent Jourdren, Morgane Thomas-Chollier
Bioinformatics. 2025 Mar; 41(3): btaf087. Published online 2025 Feb 22. doi: 10.1093/bioinformatics/btaf087
PMCID:
PMC11897429
ArticlePDF–2.5M
6.
AskBeacon—performing genomic data exchange and analytics with natural language
Anuradha Wickramarachchi, Shakila Tonni, Sonali Majumdar, Sarvnaz Karimi, Sulev Kõks, Brendan Hosking, Jordi Rambla, Natalie A Twine, Yatish Jain, Denis C Bauer
Bioinformatics. 2025 Mar; 41(3): btaf079. Published online 2025 Feb 22. doi: 10.1093/bioinformatics/btaf079
PMCID:
PMC11889448
ArticlePDF–1.9M
7.
GCLink: a graph contrastive link prediction framework for gene regulatory network inference
Weiming Yu, Zerun Lin, Miaofang Lan, Le Ou-Yang
Bioinformatics. 2025 Mar; 41(3): btaf074. Published online 2025 Feb 17. doi: 10.1093/bioinformatics/btaf074
PMCID:
PMC11881698
ArticlePDF–4.5M
8.
TiltRec: an ultra-fast and open-source toolkit for cryo-electron tomographic reconstruction
Yanxin Jiao, Hongjia Li, Yang Xue, Guoliang Yang, Lei Qi, Fa Zhang, Dawei Zang, Renmin Han
Bioinformatics. 2025 Mar; 41(3): btaf068. Published online 2025 Feb 14. doi: 10.1093/bioinformatics/btaf068
PMCID:
PMC11886794
ArticlePDF–834K
9.
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, Syue-Pu Chen, Shang-Jung Wu, Cathy S J Fann
Bioinformatics. 2025 Feb; 41(2): btaf071. Published online 2025 Feb 14. doi: 10.1093/bioinformatics/btaf071
PMCID:
PMC11879176
ArticlePDF–1.8M
10.
Single-cell copy number calling and event history reconstruction
Jack Kuipers, Mustafa Anıl Tuncel, Pedro F Ferreira, Katharina Jahn, Niko Beerenwinkel
Bioinformatics. 2025 Mar; 41(3): btaf072. Published online 2025 Feb 13. doi: 10.1093/bioinformatics/btaf072
PMCID:
PMC11897432
ArticlePDF–8.6M
11.
ELLIPSIS: robust quantification of splicing in scRNA-seq
Marie Van Hecke, Niko Beerenwinkel, Thibault Lootens, Jan Fostier, Robrecht Raedt, Kathleen Marchal
Bioinformatics. 2025 Feb; 41(2): btaf028. Published online 2025 Feb 12. doi: 10.1093/bioinformatics/btaf028
PMCID:
PMC11878791
ArticlePDF–3.1M
12.
Prediction of molecular subtypes for endometrial cancer based on hierarchical foundation model
Haoyu Cui, Qinhao Guo, Jun Xu, Xiaohua Wu, Chengfei Cai, Yiping Jiao, Wenlong Ming, Hao Wen, Xiangxue Wang
Bioinformatics. 2025 Feb; 41(2): btaf059. Published online 2025 Feb 11. doi: 10.1093/bioinformatics/btaf059
PMCID:
PMC11878776
ArticlePDF–5.1M
13.
MolFCL: predicting molecular properties through chemistry-guided contrastive and prompt learning
Xiang Tang, Qichang Zhao, Jianxin Wang, Guihua Duan
Bioinformatics. 2025 Feb; 41(2): btaf061. Published online 2025 Feb 8. doi: 10.1093/bioinformatics/btaf061
PMCID:
PMC11878793
ArticlePDF–2.7M
14.
NMFProfiler: a multi-omics integration method for samples stratified in groups
Aurélie Mercadié, Éléonore Gravier, Gwendal Josse, Isabelle Fournier, Cécile Viodé, Nathalie Vialaneix, Céline Brouard
Bioinformatics. 2025 Feb; 41(2): btaf066. Published online 2025 Feb 8. doi: 10.1093/bioinformatics/btaf066
PMCID:
PMC11855281
ArticlePDF–4.4M
15.
COBREXA 2: tidy and scalable construction of complex metabolic models
Miroslav Kratochvíl, St Elmo Wilken, Oliver Ebenhöh, Reinhard Schneider, Venkata P Satagopam
Bioinformatics. 2025 Feb; 41(2): btaf056. Published online 2025 Feb 8. doi: 10.1093/bioinformatics/btaf056
PMCID:
PMC11842047
ArticlePDF–1.5M
16.
FoldX force field revisited, an improved version
Javier Delgado, Raul Reche, Damiano Cianferoni, Gabriele Orlando, Rob van der Kant, Frederic Rousseau, Joost Schymkowitz, Luis Serrano
Bioinformatics. 2025 Feb; 41(2): btaf064. Published online 2025 Feb 6. doi: 10.1093/bioinformatics/btaf064
PMCID:
PMC11879241
ArticlePDF–3.5M
17.
ESPClust: unsupervised identification of modifiers for the effect size profile in omics association studies
Francisco J Pérez-Reche, Nathan J Cheetham, Ruth C E Bowyer, Ellen J Thompson, Francesca Tettamanzi, Cristina Menni, Claire J Steves
Bioinformatics. 2025 Feb; 41(2): btaf065. Published online 2025 Feb 6. doi: 10.1093/bioinformatics/btaf065
PMCID:
PMC11879214
ArticlePDF–4.0M
18.
MUSET: set of utilities for constructing abundance unitig matrices from sequencing data
Riccardo Vicedomini, Francesco Andreace, Yoann Dufresne, Rayan Chikhi, Camila Duitama González
Bioinformatics. 2025 Mar; 41(3): btaf054. Published online 2025 Feb 3. doi: 10.1093/bioinformatics/btaf054
PMCID:
PMC11897428
ArticlePDF–1.1M
19.
Trajectory Inference with Cell–Cell Interactions (TICCI): intercellular communication improves the accuracy of trajectory inference methods
Yifeng Fu, Hong Qu, Dacheng Qu, Min Zhao
Bioinformatics. 2025 Feb; 41(2): btaf027. Published online 2025 Feb 3. doi: 10.1093/bioinformatics/btaf027
PMCID:
PMC11829803
ArticlePDF–3.2M
20.
Privacy-preserving framework for genomic computations via multi-key homomorphic encryption
Mina Namazi, Mohammadali Farahpoor, Erman Ayday, Fernando Pérez-González
Bioinformatics. 2025 Mar; 41(3): btae754. Published online 2025 Jan 31. doi: 10.1093/bioinformatics/btae754
PMCID:
PMC11890293
ArticlePDF–1.7M

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