Interesting use of language in omics!

MetaboliteChat: A Unified Multimodal Large Language Model for Interactive Metabolite Analysis and Functional Insights https://www.biorxiv.org/content/10.1101/2025.11.07.687008v1

Preference-Based Fine-Tuning of Genomic Sequence Models for Personal Expression Prediction with Data Augmentation https://www.biorxiv.org/content/10.1101/2025.11.09.687505v1

Leveraging Disease Association Degree for High-Accuracy MicroRNA Target Prediction https://www.biorxiv.org/content/10.1101/2025.11.06.686936v1

Consensus Pituitary Atlas, a scalable resource for annotation, novel marker discovery and analyses in pituitary gland research https://www.biorxiv.org/content/10.1101/2025.10.28.685060v1

Simple controls exceed best deep learning algorithms and reveal foundation model effectiveness for predicting genetic perturbations https://www.biorxiv.org/content/10.1101/2025.01.06.631555v1

Fast and flexible minimizer digestion with digest https://www.biorxiv.org/content/10.1101/2025.01.02.631161v1

Multicancer analyses of short tandem repeat variations reveal shared gene regulatory mechanisms https://www.biorxiv.org/content/10.1101/2025.01.06.629343v1

A comprehensive benchmark and guide for sequence-function interpretable deep learning models in genomics https://www.biorxiv.org/content/10.1101/2025.01.06.631405v1

Deep Learning for Biomarker Discovery in Cancer Genomes https://www.biorxiv.org/content/10.1101/2025.01.06.631471v1

Package name of the day

Characterization and automated classification of sentences in the biomedical literature: a case study for biocuration of gene expression and protein kinase activity https://www.biorxiv.org/content/10.1101/2025.01.06.631539v1

Improving functional protein generation via foundation model-derived latent space likelihood optimization https://www.biorxiv.org/content/10.1101/2025.01.07.631724v1

The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure https://www.biorxiv.org/content/10.1101/2025.01.07.631013v1

Transfer learning applied in predicting small molecule bioactivity https://www.biorxiv.org/content/10.1101/2025.01.09.632140v1

Subcellular Level Spatial Transcriptomics with PHOTON bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Subcellular Level Spatial Transcriptomics with PHOTON www.biorxiv.org/content/10.1...

MaskMol: Knowledge-guided Molecular Image Pre-Training Framework for Activity Cliffs with Pixel Masking https://www.biorxiv.org/content/10.1101/2024.09.04.611324v1 Activity cliffs, which refer to pairs of molecules that are structurally similar but show significan

MaskMol: Knowledge-guided Molecular Image Pre-Training Framework for Activity Cliffs with Pixel Masking https://www.biorxiv.org/content/10.1101/2024.09.04.611324v1

A robust unsupervised clustering approach for high-dimensional biological imaging data reveals shared drug-induced morphological signatures https://www.biorxiv.org/content/10.1101/2024.09.05.611300v1 High-throughput analysis methods have emerged as central technologies to accelerate discovery throug

A robust unsupervised clustering approach for high-dimensional biological imaging data reveals shared drug-induced morphological signatures https://www.biorxiv.org/content/10.1101/2024.09.05.611300v1

BFVD - a large repository of predicted viral protein structures https://www.biorxiv.org/content/10.1101/2024.09.08.611582v1 The AlphaFold Protein Structure Database (AFDB) is the largest repository of accurately predicted st

BFVD - a large repository of predicted viral protein structures https://www.biorxiv.org/content/10.1101/2024.09.08.611582v1

Unlocking cross-modal interplay of single-cell and spatial joint profiling with CellMATE https://www.biorxiv.org/content/10.1101/2024.09.06.610031v1 A key advantage of single-cell multimodal joint profiling is the modality interplay, which is essent

Unlocking cross-modal interplay of single-cell and spatial joint profiling with CellMATE https://www.biorxiv.org/content/10.1101/2024.09.06.610031v1

Estimating adequate contact rates and time of Highly Pathogenic Avian Influenza virus introduction into individual United States commercial poultry flocks during the 2022/24 epizootic https://www.biorxiv.org/content/10.1101/2024.09.08.611909v1 Following confirmation of the first case of the ongoing U.S. HPAI H5N1 epizootic in commercial poult

Estimating adequate contact rates and time of Highly Pathogenic Avian Influenza virus introduction into individual United States commercial poultry flocks during the 2022/24 epizootic https://www.biorxiv.org/content/10.1101/2024.09.08.611909v1

Reversible Transcriptomic Age Shifts from Physiological Stress in Whole Blood https://www.biorxiv.org/content/10.1101/2024.09.08.611853v1 We develop a genome-wide transcriptomic clock for predicting chronological age using whole blood sam

Reversible Transcriptomic Age Shifts from Physiological Stress in Whole Blood https://www.biorxiv.org/content/10.1101/2024.09.08.611853v1

Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex https://www.biorxiv.org/content/10.1101/2024.09.03.610962v1 The field of crosslinking mass spectrometry has seen substantial advancements over the past decades,

Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex https://www.biorxiv.org/content/10.1101/2024.09.03.610962v1

Kontextual: Reframing analysis of spatial omics data reveals consistent cell relationships across images https://www.biorxiv.org/content/10.1101/2024.09.03.611109v1 State-of-the-art spatial proteomic and transcriptomic technologies can deeply pheno- type cells in t

Kontextual: Reframing analysis of spatial omics data reveals consistent cell relationships across images https://www.biorxiv.org/content/10.1101/2024.09.03.611109v1

GenoM7GNet: An Efficient N7-methylguanosine Site Prediction Approach Based on a Nucleotide Language Model https://www.biorxiv.org/content/10.1101/2024.09.03.610976v1 N7-methylguanosine (m7G), one of the mainstream post-transcriptional RNA modifications, occupies an

GenoM7GNet: An Efficient N7-methylguanosine Site Prediction Approach Based on a Nucleotide Language Model https://www.biorxiv.org/content/10.1101/2024.09.03.610976v1

Protein secondary structure and remote homology detection https://www.biorxiv.org/content/10.1101/2024.09.03.611022v1 A protein can be represented by its primary, secondary, or tertiary structure. With recent advances

Protein secondary structure and remote homology detection https://www.biorxiv.org/content/10.1101/2024.09.03.611022v1

In Silico Target Identification Reveals IL12B as a Candidate for Small Molecule Drug Development https://www.biorxiv.org/content/10.1101/2024.09.03.609261v1 Drug discovery's rising costs and complexities require innovative strategies to identify viable ther

In Silico Target Identification Reveals IL12B as a Candidate for Small Molecule Drug Development https://www.biorxiv.org/content/10.1101/2024.09.03.609261v1

Generating virtual patient data for in-silico clinical trials of medical devices during extracorporeal membrane oxygenationtreatment https://www.biorxiv.org/content/10.1101/2024.09.03.610823v1 This study introduces a virtual patient generation tool through the generation of high-quality synth

Generating virtual patient data for in-silico clinical trials of medical devices during extracorporeal membrane oxygenationtreatment https://www.biorxiv.org/content/10.1101/2024.09.03.610823v1

Analysis of 3.6 million individuals yields minimal evidence of pairwise genetic interactions for height bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Analysis of 3.6 million individuals yields minimal evidence of pairwise genetic interactions for height
www.biorxiv.org/content/10.1...

Empowering bioinformatics communities with Nextflow and nf-core bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Empowering bioinformatics communities with Nextflow and nf-core
www.biorxiv.org/content/10.1...