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Integrative Computational Analysis of VCX2 in Hepatocellular Carcinoma: From Potential Biomarker Discovery to Therapeutic Targeting with Peruvian Natural Products https://www.biorxiv.org/content/10.1101/2025.02.20.639333v1

submitted 45 minutes ago • 0 comments

A framework for evaluating predicted sperm trajectories in crowded microscopy videos https://www.biorxiv.org/content/10.1101/2025.02.20.639342v1

submitted 45 minutes ago • 0 comments

gyoza: a Snakemake workflow for modular analysis of deep-mutational scanning data https://www.biorxiv.org/content/10.1101/2025.02.19.639168v1

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Unveiling Candidate Drivers in Cancer Progression Using Somatic-IV Analysis https://www.biorxiv.org/content/10.1101/2025.02.20.638369v1

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Single-Cell Resolution of Cellular Damage Illuminates Disease Progression https://www.biorxiv.org/content/10.1101/2025.02.20.639269v1

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Multi-omics dissection of Parkinson's patient subgroups associated with motor and cognitive severity https://www.biorxiv.org/content/10.1101/2025.02.20.638984v1

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PEAKQC: Periodicity Evaluation in scATAC-seq data for quality assessment https://www.biorxiv.org/content/10.1101/2025.02.20.639146v1

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AstraPTM: Context-Aware PTM Prediction Model for Large-Scale Proteins https://www.biorxiv.org/content/10.1101/2025.02.20.639276v1

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Multi-view gene panel characterization for spatially resolved omics https://www.biorxiv.org/content/10.1101/2025.02.19.639174v1

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Literature-scaled immunological gene set annotation using AI-powered immune cell knowledge graph (ICKG) https://www.biorxiv.org/content/10.1101/2025.02.19.639172v1

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Exploring PBP2a resistance in MRSA by comparison between molecular covalent docking and non-covalent docking https://www.biorxiv.org/content/10.1101/2025.02.20.639213v1

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A Comprehensive Benchmark of Tools for Efficient Genomic Interval Querying https://www.biorxiv.org/content/10.1101/2025.02.19.639167v1

submitted 21 hours ago • 0 comments

Deep Learning based deconvolution methods: a systematic review https://www.biorxiv.org/content/10.1101/2025.02.18.638595v1

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Transcription Factor Driven Gene Regulation in Autism Spectrum Disorder https://www.biorxiv.org/content/10.1101/2025.02.24.639835v1

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Widespread occurrence of botulinum and tetanus neurotoxin genes in ancient DNA https://www.biorxiv.org/content/10.1101/2025.02.24.639866v1

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Computational modeling of human genetic variants in mice https://www.biorxiv.org/content/10.1101/2025.02.23.639784v1

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Nearest-neighbor nonnegative spatial factorization to study spatial and temporal transcriptomics https://www.biorxiv.org/content/10.1101/2025.02.19.639134v1

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MolGene-E: Inverse Molecular Design to Modulate Single Cell Transcriptomics https://www.biorxiv.org/content/10.1101/2025.02.19.638723v1

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BADDADAN: Mechanistic Modelling of Time Series Gene Module Expression https://www.biorxiv.org/content/10.1101/2025.02.18.638670v1

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ESMStabP: A Regression Model for Protein Thermostability Prediction https://www.biorxiv.org/content/10.1101/2025.02.18.638450v1

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Label Noise in Pathological Segmentation is Overlooked, Leading to Potential Overestimation of Artificial Intelligence Models https://www.biorxiv.org/content/10.1101/2025.02.18.638843v1

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Tracing the function expansion for a primordial protein fold in the era of fold-based function prediction: beta-trefoil https://www.biorxiv.org/content/10.1101/2025.02.18.638835v1

submitted 3 days ago • 0 comments

Growth vs. Diversity: A Time-Evolution Analysis of the Chemical Space https://www.biorxiv.org/content/10.1101/2025.02.18.638937v1

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Graph-based Contrastive Learning Enables Unified Integration and Niche Transfer Across Single-Cell and Spatial Multi-Omics https://www.biorxiv.org/content/10.1101/2025.02.19.638965v1

submitted 3 days ago • 0 comments

From literature to biodiversity data: mining arthropod organismal and ecological traits with machine learning https://www.biorxiv.org/content/10.1101/2025.02.18.638830v1

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scWGBS-GPT: A Foundation Model for Capturing Long-Range CpG Dependencies in Single-Cell Whole-Genome Bisulfite Sequencing to Enhance Epigenetic Analysis https://www.biorxiv.org/content/10.1101/2025.02.19.638959v1

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TISSLET Tissues-based Learning Estimation for Transcriptomics https://www.biorxiv.org/content/10.1101/2025.02.18.638832v1

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Protein-ligand affinity prediction via Jensen-Shannon divergence of molecular dynamics simulation trajectories https://www.biorxiv.org/content/10.1101/2025.02.17.638772v1

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ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads https://www.biorxiv.org/content/10.1101/2025.02.15.638440v1

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Is Tanimoto a metric? https://www.biorxiv.org/content/10.1101/2025.02.18.638904v1

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BENDER DB: a database of protein binding sites across neglected disease proteomes https://www.biorxiv.org/content/10.1101/2025.02.18.638856v1

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Conservation and discovery of regulatory motifs across oomycetes through comparative genomic analysis https://www.biorxiv.org/content/10.1101/2025.02.18.638864v1

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Dynamic Lipidome Reorganization in Response to Heat Shock Stress https://www.biorxiv.org/content/10.1101/2025.02.18.638884v1

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Impact of Long-Term Integrated Nutrient Management Practices on Soil Bacterial Diversity: A 16S rRNA-Based Metagenomic Approach https://www.biorxiv.org/content/10.1101/2025.02.19.639006v1

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CombDNF: Disease-specific drug combination predictions with network-based features on clinically validated data https://www.biorxiv.org/content/10.1101/2025.02.18.637825v1

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Machine learning ensemble identifies distinct age-related response to spaceflight in mammary tissue https://www.biorxiv.org/content/10.1101/2025.02.17.638732v1

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C.La.P.: Enhancing transformer-based genomic signal modeling by integrating DNA sequences and chromatin accessibility data https://www.biorxiv.org/content/10.1101/2025.02.19.638643v1

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Decoding Host-Pathogen Interactions in Staphylococcus aureus: Insights into Allelic Variation and Antimicrobial Resistance Prediction Using Artificial Intelligence and Machine Learning based approaches https://www.biorxiv.org/content/10.1101/2025.02.18.638850v1

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Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graph https://www.biorxiv.org/content/10.1101/2025.02.18.638852v1

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Collisional cross-section prediction for multiconformational peptide ions with IM2Deep https://www.biorxiv.org/content/10.1101/2025.02.18.638865v1

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EPIraction - an atlas of candidate enhancer-gene interactions in human tissues and cell lines. https://www.biorxiv.org/content/10.1101/2025.02.18.638885v1

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Boosting metaproteomics identification rates and taxonomic specificity with MS2Rescore https://www.biorxiv.org/content/10.1101/2025.02.17.638783v1

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Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database https://www.biorxiv.org/content/10.1101/2025.02.17.638570v1

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Accurate Identification and Mechanistic Evaluation of Pathogenic Missense Variants with Rhapsody-2 https://www.biorxiv.org/content/10.1101/2025.02.17.638727v1

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Decoding DNA methylation and non-coding RNAs mediated regulatory landscape of breast tumor and adjacent normal tissues https://www.biorxiv.org/content/10.1101/2025.02.17.638770v1

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SpliceSelectNet: A Hierarchical Transformer-Based Deep Learning Model for Splice Site Prediction https://www.biorxiv.org/content/10.1101/2025.02.17.638749v1

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hERG-LTN: A New Paradigm in hERG Cardiotoxicity Assessment Using Neuro-Symbolic and Generative AI Embedding (MegaMolBART, Llama3.2, Gemini, DeepSeek) Approach https://www.biorxiv.org/content/10.1101/2025.02.17.638731v1

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A comparative study of statistical methods for identifying differentially expressed genes in spatial transcriptomics https://www.biorxiv.org/content/10.1101/2025.02.17.638726v1

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Generation of appropriate protein structures for virtual screening using AlphaFold3 predicted protein-ligand complexes https://www.biorxiv.org/content/10.1101/2025.02.17.638750v1

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Learning molecular traits of human pain disease via voltage-gated sodium channel structure renormalization https://www.biorxiv.org/content/10.1101/2025.02.19.639033v1

submitted 4 days ago • 0 comments