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MIEN: a deep-learning model for pocket-conditioned glycan pose and conformation discrimination

MIEN improves glycan pose ranking by distinguishing experimentally observed conformations from non-native ones in protein-carbohydrate interactions.

Determinants of cysteine coverage by chemoproteomics

This study identifies factors governing cysteine detection in chemoproteomics using machine learning and statistical filtering, showing that peptide properties and abundance are key determinants.

Auditing Confidence-Calibrated Benchmarking of Single-Cell Perturbation Models

The paper audits a benchmarking framework for single-cell perturbation models, revealing flaws in metric interpretation and calibration, and identifies a specific calibration failure in split-conformal prediction.

CytoRipple: Mapping Tissue Polarization through Subcellular Cytoskeleton Dynamics

CytoRipple identifies tissue-level polarization vector fields from spatial multi-omic data to reveal multi-cellular structures and their functional associations.

Predicting Lifespan-Extending Compounds Using Supervised Machine Learning

This study uses supervised machine learning to predict lifespan-extending compounds in C. elegans by comparing different feature representations and models.

Metabolite-centric Knowledge Graph Unveils Predictive and Mechanistic Insights through Self-supervised Multimodal Learning

This paper introduces MetaKG, a metabolite-centric knowledge graph with self-supervised learning that improves representation learning and uncovers biochemical relationships.

HyARQ: a Snakemake workflow for allele-specific read counting and quality control in F1 hybrids

HyARQ is a Snakemake workflow for allele-specific read counting and quality control across multiple assays in F1 hybrids, showing accurate recovery of parental proportions.

Interactive Data Integrator for Uniform Data Processing in the MorPhiC Program

The paper introduces an interactive Data Integrator for uniform processing and integration of bulk RNA-seq datasets from the MorPhiC program and external sources.

CROSS-PLATFORM CONCORDANCE ANALYSIS REVEALS ROBUST AND CLINICALLY RELEVANT GENE SIGNATURES IN BREAST CANCER

The paper identifies robust and clinically relevant gene signatures in breast cancer by integrating two RNA-seq workflows and validating them across multiple datasets and analyses.

N-Zinclopedia: A database of predicted transition metal-binding sites and metalloenzymes

N-Zinclopedia predicts transition metal-binding sites and candidate metalloenzymes across protein folds, expanding the known landscape of metal utilization.

Variable sparsity non-negative matrix and tensor factorization algorithms and their applications in cancer genomics

This paper introduces variable-sparsity matrix and tensor factorization algorithms for cancer genomics to improve biological interpretability and modeling of cancer subtypes and pathways.

Phase-Based Frequency Tracking and Analysis of Vocalisations in the Genus Saxicola

The paper introduces a phase-based frequency tracking method to analyze vocalizations in Saxicola species, revealing structured acoustic patterns and demonstrating the method's effectiveness through PCA analysis.

LineageFlow: Growth-Corrected State Dynamics for Probabilistic Cell-Fate Prediction

LineageFlow predicts clonal fate and transcriptional profiles by integrating growth dynamics and state transitions in single-cell lineage data.

mixKIN: An ancestry-aware kinship estimation method for low coverage genomes

mixKIN improves kinship estimation from low-coverage genomes by accounting for ancestry, outperforming existing methods in admixed and heterogeneous populations.

ClonoDeconv: reference-based α - β paired recurrent clonotype proportion estimation from bulk-TCR sequencing

ClonoDeconv estimates paired TCR clonotype proportions from bulk-TCR sequencing using a single-cell reference, capturing longitudinal T-cell clonal dynamics.

RDEmbed: A Sentence-Embedding Framework for Rare Disease Phenotype Representation and Phenotypic Similarity Analysis

RDEmbed uses sentence embeddings to analyze rare disease phenotypes from clinical text, outperforming ontology-based methods in similarity analysis and clustering.

Spatial proteomic profiling of cardiac stromal populations and microenvironments in systemic sclerosis-associated primary myocardial involvement

The paper uses spatial proteomic profiling to analyze cardiac stromal populations and microenvironments in systemic sclerosis-associated myocarditis, identifying distinct fibroblast subtypes and their spatial interactions.

TiSAM: fusing spatial and histopathology foundation models for whole-slide image segmentation

TiSAM improves whole-slide image segmentation by fusing spatial and histopathology features, achieving high accuracy across diverse datasets and scanners.

Integrated 16S rRNA Bioinformatics Analysis of Gut Microbiota, Predicted Pathways, and Candidate Biomarkers in Inflammatory Bowel Disease

This study analyzes gut microbiota and predicted functions in IBD patients and healthy controls, identifying microbial signatures and pathway associations.

Determining cellular phylogeny and migration at high resolution in spatial genomics

StarTrak infers cellular migration and phylogeny by integrating somatic variants, spatial data, and transcriptomics at single-pixel resolution in spatial genomics.