💻 Category

bioinformatics

974 papers

Pan-Metabolomics Repository Mapping of the Carnitine Landscape

By applying a pan-repository data mining strategy with MassQL filtering to LC-MS/MS data across major public databases, this study systematically mapped the carnitine landscape to generate a comprehensive library of over 34,000 unique MS/MS spectra representing nearly 3,000 atomic compositions, thereby enabling the discovery of novel carnitine conjugates and advancing the understanding of their roles in host metabolism, diet, and disease.

Mannochio-Russo, H., Ferreira, P. C., Kvitne, K. E. + 16 more2026-03-31💻 bioinformatics

Carafe2 enables high quality in silico spectral library generation for timsTOF data-independent acquisition proteomics

The paper introduces Carafe2, a deep learning-based tool that generates high-quality, experiment-specific in silico spectral libraries directly from native timsTOF DIA raw data by fine-tuning retention time, fragment ion intensity, and ion mobility prediction models, thereby outperforming existing DDA-trained models and enabling superior peptide detection across diverse proteomic applications.

Wen, B., Paez, J. S., Hsu, C. + 10 more2026-03-31💻 bioinformatics

Scalable Microbiome Network Inference: Mitigating Sparsity and Computational Bottlenecks in Random Effects Models

This paper introduces Parallel-REM, a scalable Python-based pipeline that utilizes batched parallelization to overcome the computational bottlenecks of traditional Random Effects Models, achieving a 26.1x speedup in inferring microbial interaction networks from large-scale metagenomic data while maintaining high statistical concordance with existing R implementations.

Roy, D., Ghosh, T. S.2026-03-31💻 bioinformatics

Condition-matched in silico prediction of drug transcriptional responses enables mechanism-guided screening and combination discovery

The paper introduces DEPICT, a deep learning framework that accurately predicts condition-matched drug-induced transcriptional responses from baseline gene expression, enabling scalable virtual screening for drug repurposing and combination discovery, as demonstrated by its superior performance over existing models and successful prioritization of clinically relevant compounds in non-small cell lung cancer.

Xiao, M., He, Y., Hu, J. + 2 more2026-03-31💻 bioinformatics

scTGCL: A Transformer-Based Graph Contrastive Learning Approach for Efficiently Clustering Single-Cell RNA-seq Data

The paper proposes scTGCL, a novel Transformer-based graph contrastive learning framework that integrates multi-head self-attention with robust augmentation strategies to achieve superior accuracy, interpretability, and computational efficiency in clustering high-dimensional single-cell RNA-seq data compared to existing state-of-the-art methods.

Khan, M. S. A., Kabir, M. H., Faisal, M. M.2026-03-31💻 bioinformatics

Decoupling Topology from Geometry: Detecting Large-Scale Conformational Changes via Conformational Scanning

This paper introduces a high-throughput "conformational scanning" method that decouples topological connectivity from geometric rigidity using a coarse-grained secondary structure representation to systematically mine the PDB for proteins sharing identical topology but exhibiting large-scale conformational changes, thereby creating a critical ground-truth dataset for bridging static structural data with dynamic protein function.

Lin, R., Ahnert, S. E.2026-03-31💻 bioinformatics

LATTE for locus-specific quantification of transposable element expression across species

The paper introduces LATTE, a high-accuracy computational framework for locus-specific quantification of transposable element (TE) expression across species, which reveals that TEs possess a distinct regulatory landscape decoupled from host genes and contribute significantly to the genetic architecture of complex traits, including Sjogren's syndrome.

He, J., Peng, C., Zhang, Y. + 4 more2026-03-31💻 bioinformatics

GRIMM-II: A Two-Stage Real-Time Algorithm for Nine-Locus HLA Imputation and Matching with Up to Three Mismatches

GRIMM-II is a scalable, real-time, two-stage algorithm that enables efficient nine-locus HLA imputation and the identification of hematopoietic stem cell donors with up to three mismatches, significantly expanding the pool of suitable candidates for transplantation while maintaining high accuracy and computational speed.

Kirshenboim, O., Kabya, A., Yehezkel-Imra, R. + 6 more2026-03-31💻 bioinformatics

CoLa-VAE: Cell-Cell Communication-aware Variational Autoencoder with Dynamic Graph Laplacian Constraints

CoLa-VAE is a deep generative framework that integrates dynamic graph Laplacian constraints derived from ligand-receptor interactions into a variational autoencoder to disentangle cell-cell communication topology from intrinsic transcriptional heterogeneity, thereby outperforming existing methods in clustering and denoising across diverse single-cell datasets.

Chen, Y., Qi, C., Fang, H. + 4 more2026-03-31💻 bioinformatics

MetaGEAR Explorer: Rapid interactive searches and cross-cohort analyses of microbiome gene associations in disease

MetaGEAR Explorer is a freely available web platform that enables rapid, interactive, and programmatic cross-cohort analysis of over 33 million microbial gene families across 9,053 metagenomic samples to facilitate the identification of disease-associated microbial genes in inflammatory bowel disease and colorectal cancer.

Rios, E., Jin, S., Zhang, C. + 4 more2026-03-31💻 bioinformatics

Constructing Gene Co-functional and Co-regulatory Networks from Public Transcriptomes using Condition-Specific Ensemble Co-expression

The paper introduces TEA-GCN, a novel method that constructs robust and explainable gene co-expression networks from diverse public RNA-seq data by leveraging unsupervised dataset partitioning and multi-metric ensemble scoring, thereby outperforming existing state-of-the-art approaches in predicting gene functions, inferring regulatory networks, and enabling cross-species comparative studies.

Lim, P. K., Wang, R., Lim, S. C. + 2 more2026-03-30💻 bioinformatics