💻 Category

bioinformatics

1005 papers

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., Wang, Z., Zhang, H., Fang, L., Zhao, P.2026-03-31💻 bioinformatics

Identifying Inheritance Patterns of Allelic Imbalance, using Integrative Modeling and Bayesian Inference

This paper presents a Bayesian integrative modeling approach that leverages joint inference across family trios to simultaneously improve the estimation of allelic imbalance and identify its mode of inheritance, thereby enhancing the detection of causal regulatory variants and their impact on phenotypic traits.

Hoyt, S. H., Reddy, T. E., Gordan, R., Allen, A. S., Majoros, W. H.2026-03-31💻 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., Tshuva, Y., Maiers, M., Gragert, L., Bashyal, P., Israeli, S., Louzoun, Y.2026-03-31💻 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., Luan, F., Zhang, Z., Arya, S., Wei, Z.2026-03-31💻 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., Neuhaus, F., He, X., Weissenberger, S., Schirmer, M.2026-03-31💻 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., Antony Velankanni, J. P., Mutwil, M.2026-03-30💻 bioinformatics