Qi Wu, Yinbo Liu, Feng Yang, Weihong Huang, Xiaolei Zhu, Juan Liu
{"title":"Decoupling topological and molecular features for interpretable biomolecular interaction prediction.","authors":"Qi Wu, Yinbo Liu, Feng Yang, Weihong Huang, Xiaolei Zhu, Juan Liu","doi":"10.1093/bib/bbag471","DOIUrl":"10.1093/bib/bbag471","url":null,"abstract":"<p><p>Predicting biomolecular interactions is fundamental to understanding cellular mechanisms and advancing drug discovery. However, biomolecular interactions exhibit immense diversity across multiple dimensions. Most existing computational methods are designed to handle one specific task or data modality, which limits their applicability and generalization capability in broader scenarios. To address this methodological rigidity, we propose a flexible framework for multi-modal feature fusion in biomolecular interaction prediction (FlexBIP). The core of FlexBIP lies in its modular architecture, which decouples intrinsic molecular features from complex graph topologies, enabling the adaptive integration of node attributes, edge properties, and auxiliary graph information. The flexible fusion methodology breaks through the limitations of task-specific models. This design enables FlexBIP to adaptively process and integrate biological data of different types and from various sources, including homogeneous interactions between molecules of the same type, heterogeneous interactions between different molecular classes, as well as qualitative binary, multi-class, and quantitative regression prediction tasks. Our research has yielded exciting results. In extensive testing across 15 benchmark datasets, covering 8 major categories of biomolecular associations, FlexBIP's performance comprehensively surpasses that of 25 state-of-the-art specialized models. Crucially, in data-scarce \"cold-start\" scenarios that simulate the discovery of new molecules, FlexBIP continues to demonstrate remarkable robustness and predictive accuracy. Furthermore, FlexBIP provides robust and reliable interpretability for various downstream analysis tasks.</p>","PeriodicalId":9209,"journal":{"name":"Briefings in bioinformatics","volume":"27 5","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13544631/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"OmniExtract: an automatic data extraction tool based on large language model and prompt engineering.","authors":"Yibo Wang, Bixia Tang, Sicheng Wu, Shaoqi Bei, Xiaojing Gao, Yueyue Wu, Shuying Liu, Huangxia Hu, Yuyan Meng, Demian Kong, Wenming Zhao","doi":"10.1093/bib/bbag502","DOIUrl":"10.1093/bib/bbag502","url":null,"abstract":"<p><p>Extracting structured information from documents or scientific papers is crucial for data sharing and retrieval. Recent advances in large language models (LLMs) have demonstrated strong capabilities in language understanding, and a number of LLM-based tools have been developed for extraction-oriented tasks. However, it's still difficult to find a universal and user-friendly tool for various practical extraction tasks. To address this challenge, we propose OmniExtract, an automatic data extraction tool with user-friendly configuration files that can adapt to various data extraction tasks. OmniExtract employs a prompt optimization method to refine task-specific prompts and achieve high extraction performance. It also supports comprehensive data extraction from both documents and tables, making it applicable to a broad range of data sources. Evaluation results show that OmniExtract obtains a high accuracy ~90% for three datasets. Furthermore, two additional data extraction applications of OmniExtract in real-world scenarios have been presented, achieving an accuracy of 92.21% and ~90% precision and recall, respectively. Specifically, OmniExtract can handle tabular files of various sizes and formats, and achieve over 99% precision and recall on table information extraction tasks. The data reliability performance shows that OmniExtract is a valuable tool for database updating. An online testing service is available at https://ngdc.cncb.ac.cn/omniextract/. The service can be deployed locally with the code in https://github.com/wyb39/OmniExtract.</p>","PeriodicalId":9209,"journal":{"name":"Briefings in bioinformatics","volume":"27 5","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13577667/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148975823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"DPAS-Graph: adaptive spatial-feature relation learning for spatial RNA-to-protein prediction and virtual protein profiling.","authors":"Mingyuan Xu, Zhixin Dong, Bisheng Xia","doi":"10.1093/bib/bbag480","DOIUrl":"10.1093/bib/bbag480","url":null,"abstract":"<p><p>Paired spatial multi-omics provides a supervised basis for learning RNA-protein correspondence in situ, but predicting protein abundance from spatial transcriptomic data alone remains challenging across tissue contexts and protein panels. Here, we present DPAS-Graph, an adaptive relation-learning framework for spatial RNA-to-protein prediction. Rather than directly merging spatial proximity and transcriptomic similarity as fixed graph priors, DPAS-Graph represents them as two relation channels on a shared edge support and updates their contributions during representation learning for protein prediction. Its Niche-Coupled Field Encoder combines layer-wise edge-relation modeling, intra-branch relation refinement, and cross-branch residual correction to learn spot representations for protein abundance prediction. In a leave-one-dataset-out benchmark across seven paired spatial multi-omics datasets, DPAS-Graph achieved lower aggregate prediction errors and improved spot-level agreement of protein expression profiles, with gains mainly reflected in error-based metrics and PCC-Spot. Spatial autocorrelation and protein-derived domain agreement analyses were further used to characterize the spatial behavior of the predicted protein maps. When applied to external RNA-only spatial sections, DPAS-Graph generated qualitatively interpretable marker-level virtual protein maps, illustrating its use as a complementary tool for protein-level interpretation of transcriptomics-only spatial data.</p>","PeriodicalId":9209,"journal":{"name":"Briefings in bioinformatics","volume":"27 5","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13552503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148910736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"TL-HDMR: a transfer learning framework for advancing equitable causal inference reveals metabolic signatures of stroke across multiple ancestries.","authors":"Lei Hou, Xiao-Hua Zhou, Fuzhong Xue, Hao Chen","doi":"10.1093/bib/bbag473","DOIUrl":"10.1093/bib/bbag473","url":null,"abstract":"<p><p>The limited genetic diversity in genome-wide association studies (GWAS) poses a significant challenge to the generalizability and equity of biomedical discoveries. Most causal inferences, particularly from high-dimensional phenomes (e.g. metabolomics), are primarily based on European populations, and their applicability to other ancestries remains uncertain. Traditional multivariable Mendelian randomization (MVMR) methods further struggle in high-dimensional and correlated settings due to collinearity and model instability. To bridge this gap, we present a two-step transfer learning framework for high-dimensional MR (TL-HDMR), designed to enhance causal exposure detection in understudied populations. Our approach leverages the Minimax Concave Penalty for asymptotically unbiased estimation amidst exposure correlations. Crucially, we introduce two novel pre-transfer procedures-HDMR.TSD for sourcing beneficial data and HDMR.PRESSO for filtering pleiotropic instruments-to ensure robust knowledge transfer. Extensive simulations demonstrated TL-HDMR's superior performance in ROC curves and mean absolute error over alternative methods. When applied to identify causal metabolites for stroke across multi-ancestry cohorts (European, East Asian, South Asian, and African), TL-HDMR successfully pinpointed both shared and ethnic-specific causal biomarkers, showcasing its unique capability for equitable causal inference. This work provides a powerful statistical tool that not only addresses critical methodological challenges but also promotes inclusivity and fairness in human health research.</p>","PeriodicalId":9209,"journal":{"name":"Briefings in bioinformatics","volume":"27 5","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13548331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148900086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"PMPIHGLL: predicting metabolite-protein interactions using dual hypergraph convolutional networks and large language models.","authors":"Lei Chen, Zhitong Jin, Ying Shao, Bo Zhou","doi":"10.1093/bib/bbag489","DOIUrl":"10.1093/bib/bbag489","url":null,"abstract":"<p><p>Metabolite-protein interactions (MPIs) play pivotal roles in regulating cellular processes and metabolic pathways and have important implications for systems biology and drug discovery. Although several computational models have been proposed, alternative approaches are needed to broaden the methodological toolkit for MPI prediction. In this study, we developed a new deep-learning model for predicting MPIs. Chemical and protein large language models were used to generate informative representations of metabolites and proteins. For each entity type, we constructed two K-nearest-neighbor hypergraphs using different values of K, thereby capturing higher-order relationships at different scales and expanding the feature-learning space. A dual hypergraph convolutional network (HGCN) learned from these relationships. The resulting high-level features were further processed using a channel-wise attention mechanism and a one-dimensional convolutional neural network (1D-CNN) to obtain integrated metabolite and protein representations. Finally, a fully connected layer generated the predictions. The model was evaluated on four MPI datasets using global five-fold cross-validation; AUC and AUPR exceeded 0.9 on most datasets. Local five-fold cross-validation and an independent test further indicated that the model could predict MPIs involving previously unobserved metabolites or proteins. The model outperformed several existing MPI prediction models and related models adapted to this task. Ablation studies supported the rationale for its design. Short abstract In this study, we focused on the metabolite-protein interactions (MPIs), which play pivotal roles in regulating cellular processes and metabolic pathways, and designed an effective deep-learning model for predicting MPIs. The model received the chemical and protein features yielded by large language models and refined them using a dual hypergraph convolutional network with two K-nearest-neighbor hypergraphs using different values of K. The resulting high-level features were further processed by a channel-wise attention mechanism and a one-dimensional convolutional neural network. A fully connected layer finally generated the predictions. The model shown competitive performance on four MPI datasets and outperformed several existing MPI prediction models.</p>","PeriodicalId":9209,"journal":{"name":"Briefings in bioinformatics","volume":"27 5","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13561419/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148928911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Machine learning methodology using a masked neural network for robust genetic risk score calculation from noisy and missing data.","authors":"Steven Squires, Michael N Weedon, Richard A Oram","doi":"10.1093/bib/bbag538","DOIUrl":"https://doi.org/10.1093/bib/bbag538","url":null,"abstract":"<p><strong>Purpose: </strong>Genetic risk scores (GRSs) are summaries of genetic data that can improve prediction of disease risk and progression. GRSs are increasing available but rely on high-quality input data to produce good output results; with noisy or missing inputs the GRS may be inaccurate. We aimed to develop a method to produce a robust estimate of the GRS when input data are missing, noisy or both.</p><p><strong>Approach: </strong>We developed a neural network approach, named masked-multi-layer perceptron (MLP), for robust GRS calculation trained on a set of GRS scores calculated on clean data. The masked-MLP includes additional input data and has noise inserted during training, both which make the model more robust.</p><p><strong>Results: </strong>A GRS for type 1 diabetes (T1D) calculated on input data with 10% of the data corrupted had a Spearman rank correlation to the clean GRS of 0.669 (0.665-0.674) while the equivalent for the masked-MLP was 0.951 (0.950-0.952). For the same data, the area under the receiver operating characteristic curve for separation of T1D from population samples fell from 0.919 (0.904-0.932) to 0.808 (0.787-0.827) for the GRS while the masked-MLP fell to 0.910 (0.895-0.924).</p><p><strong>Conclusions: </strong>The masked-MLP was more robust to noise when calculating a GRS than using standard approaches. Our approach has the potential to enable GRS calculations which are more robust to noise.</p>","PeriodicalId":9209,"journal":{"name":"Briefings in bioinformatics","volume":"27 5","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13630461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149104278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Anwen Zhao, Yu Li, Zixuan Wang, Tianhao Wu, Ran Fu, Yuxuan Lou, Yanfen Xu, Xuliang Han, Wenying Wang, Jun Yan, Xiangfeng Wang
{"title":"Surf2Spot: a surface-informed geometry-aware model for predicting partner-independent binder and nanobody design hotspots.","authors":"Anwen Zhao, Yu Li, Zixuan Wang, Tianhao Wu, Ran Fu, Yuxuan Lou, Yanfen Xu, Xuliang Han, Wenying Wang, Jun Yan, Xiangfeng Wang","doi":"10.1093/bib/bbag542","DOIUrl":"10.1093/bib/bbag542","url":null,"abstract":"<p><p>Protein-protein interactions (PPIs) and nanobody-antigen interactions (NAIs) play essential roles in cellular function, yet potential hotspot prediction remains challenging. We present Surf2Spot, a deep learning framework that integrates sequence embeddings, structural features, and protein surface properties to predicts surface regions with a high propensity to contain PPI hotspot residues. Unlike complex-prediction approaches that require predefined binding partners, Surf2Spot identifies interaction-prone regions directly from target sequences or predicted monomeric structures, enabling partner-independent hotspot prediction. By jointly modeling structural and physicochemical determinants, Surf2Spot achieves strong hotspot prediction performance on curated PPI and NAI datasets, outperforming existing methods in terms of F1-scores and the area under the precision-recall curve (AUPRC). Case studies on NbPDS1 and VdPDA1 demonstrate that Surf2Spot can identify putative hotspot residues within functional domains that are enriched in experimentally validated binder designs. For the tested targets, Surf2Spot-guided designs (with RFdiffusion and BindCraft) yielded a four-fold increase in successful design throughput and enhanced binding affinities compared to baseline strategies in a target-dependent manner. These results establish Surf2Spot as a powerful tool for hotspot discovery and rational protein engineering.</p>","PeriodicalId":9209,"journal":{"name":"Briefings in bioinformatics","volume":"27 5","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13647275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149135218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Phuong Lam Tran, Chi-Nga Chow, Yun Tang, Michael Anekson Widjaya, You Sheng Paik, Yann-Jen Ho, Wei-Chih Huang, Chia-Ru Chung, Wen-Chi Chang, Muh-Hwa Yang, Tzong-Yi Lee
{"title":"An integrative multi-omics modeling framework for chemotherapy response prediction through microRNA-target regulatory signatures.","authors":"Phuong Lam Tran, Chi-Nga Chow, Yun Tang, Michael Anekson Widjaya, You Sheng Paik, Yann-Jen Ho, Wei-Chih Huang, Chia-Ru Chung, Wen-Chi Chang, Muh-Hwa Yang, Tzong-Yi Lee","doi":"10.1093/bib/bbag560","DOIUrl":"https://doi.org/10.1093/bib/bbag560","url":null,"abstract":"<p><p>Chemotherapy remains a cornerstone of cancer treatment, yet therapeutic resistance continues to limit durable clinical responses. MicroRNAs (miRNAs) are key post-transcriptional regulators of gene expression that orchestrate diverse cellular processes implicated in drug sensitivity and resistance. However, the contribution of miRNA regulatory networks to chemotherapy response has not been systematically characterized using clinical patient cohorts. Here we present DrugMiR, an integrative multi-omics modeling framework that integrates drug response-associated miRNAs with experimentally validated target genes to identify regulatory signatures predictive of chemotherapy response. Using 1015 patient samples from The Cancer Genome Atlas, we identified differentially expressed miRNAs (DEmiRs) associated with response to five widely used chemotherapeutic agents (cisplatin, carboplatin, gemcitabine, paclitaxel, and fluorouracil) and constructed predictive models using multiple machine learning algorithms. DrugMiR achieved robust predictive performance, particularly for platinum-based therapies, with area under the receiver operating characteristic curves of 0.81 for cisplatin and 0.79 for carboplatin. Integration of validated miRNA targets consistently improved predictive performance while substantially enhancing biological interpretability. Integrative network and pathway analyses identified recurrent miRNA-target regulatory programs shared across chemotherapy cohorts, particularly involving the miR-200 family and target genes such as BMP2, ITGA3, EGFR, FGFR1, MET, and IL6, implicating growth factor signaling, focal adhesion, extracellular matrix remodeling, and adaptive survival pathways in chemotherapy response. Together, these findings establish patient-derived miRNA-target regulatory signatures as robust predictors of chemotherapy response and provide a multi-omics framework for elucidating molecular mechanisms underlying therapeutic sensitivity and resistance across diverse cancer types.</p>","PeriodicalId":9209,"journal":{"name":"Briefings in bioinformatics","volume":"27 5","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13660478/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149179467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"ST-ConMa: a multimodal foundation framework for spatial transcriptomics via image-gene contrastive and matching learning.","authors":"Taelim Yeom, Dongha Choi, Hyunju Lee","doi":"10.1093/bib/bbag535","DOIUrl":"10.1093/bib/bbag535","url":null,"abstract":"<p><p>Spatial transcriptomics (ST) enables the spatial mapping of gene expression by combining tissue images with spot-level gene expression profiles, allowing for the analysis of gene distribution and interactions between adjacent regions. Although numerous deep learning models have been developed for ST, most existing approaches are task-specific, and multimodal foundation models with broad knowledge of ST remain scarce. While a few ST multimodal models currently exist, they have been either trained on low-resolution tissue images or developed for a specific platform, thereby limiting their generalizability when applied to diverse ST data. To address this gap, we propose ST-ConMa, a multimodal foundation model pretrained on large-scale spot-level tissue images paired with corresponding gene expression profiles using contrastive and matching learning. While conventional task-specific and foundation models generate modality-specific embeddings for images and genes separately, our model jointly learns image-gene fusion representations using a multimodal encoder equipped with cross-attention and a matching objective. Through extensive evaluations on histopathology image classification benchmarks and domain-specific tasks including gene expression prediction and spatial clustering, we demonstrate that ST-ConMa learns high-quality multimodal representations and consistently outperforms existing methods. These results indicate that ST-ConMa serves as a generalizable backbone for diverse ST approaches.</p>","PeriodicalId":9209,"journal":{"name":"Briefings in bioinformatics","volume":"27 5","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13617578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mikhail M Khandokhin, Aleksandr Sokolov, Nikolay Oskolkov, Robert Fredriksson, Olga E Titova, Helgi B Schiöth
{"title":"Metabolomics workbench: data-driven classification and correlation analysis between metabolite classes, biomarkers, and drugs.","authors":"Mikhail M Khandokhin, Aleksandr Sokolov, Nikolay Oskolkov, Robert Fredriksson, Olga E Titova, Helgi B Schiöth","doi":"10.1093/bib/bbag576","DOIUrl":"10.1093/bib/bbag576","url":null,"abstract":"<p><p>Public repositories now accumulate an unprecedented amount of metabolomics data. Despite the opportunities for large-scale meta-analyses opened by these repositories, the deposited data rarely becomes systematically re-analyzed. We conducted a systematic metadata-based re-analysis of all human blood metabolomics studies in the Metabolomics Workbench performed using Orbitrap or QTOF mass spectrometry, encompassing 44 165 samples. After harmonizing metabolites with PubChem identifiers and embedding them using SMILES representations, we generated a map of 6752 blood metabolites forming 25 structural clusters, and subsequently performed correlation analysis between these clusters, biomarkers, and drugs. Analysis of 337 120 metabolite pairs detected in at least 10 studies showed that structurally related clusters display correlated abundances (ρ up to 0.6). Correlation patterns among established clinical biomarkers revealed candidate metabolic correlates, several with ρ > 0.7. We also developed open-source software enabling similar analyses for any metabolite across the Workbench data explored. Additionally, curating drug-containing datasets enabled meta-analyses for compounds such as acetaminophen, metoprolol, and atenolol, identifying both known and novel metabolic signatures. Besides the biological insights, we have found that Orbitrap and QTOF tend to detect different metabolites, but they give quantitatively coherent results on overlapping compounds. Overall, the present study provides the methodology and software to perform large-scale mining of public metabolomics data enabling its re-analysis to obtain novel biomedical insights.</p>","PeriodicalId":9209,"journal":{"name":"Briefings in bioinformatics","volume":"27 5","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13677790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149219776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}