@biocomputedaily.bsky.social
Interesting use of language in omics!
Language may be all omics needs: Harmonizing multimodal data for omics understanding with CellHermes https://www.biorxiv.org/content/10.1101/2025.11.07.687322v1
November 11, 2025 at 8:22 PM
Interesting use of language in omics!
Reposted
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
November 10, 2025 at 7:48 PM
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
Reposted
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
November 11, 2025 at 11:05 AM
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
Reposted
Leveraging Disease Association Degree for High-Accuracy MicroRNA Target Prediction https://www.biorxiv.org/content/10.1101/2025.11.06.686936v1
November 11, 2025 at 4:57 PM
Leveraging Disease Association Degree for High-Accuracy MicroRNA Target Prediction https://www.biorxiv.org/content/10.1101/2025.11.06.686936v1
Reposted
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
October 30, 2025 at 6:47 AM
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
Reposted
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
January 8, 2025 at 5:47 PM
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
Reposted
Fast and flexible minimizer digestion with digest https://www.biorxiv.org/content/10.1101/2025.01.02.631161v1
January 8, 2025 at 9:48 AM
Fast and flexible minimizer digestion with digest https://www.biorxiv.org/content/10.1101/2025.01.02.631161v1
Reposted
Multicancer analyses of short tandem repeat variations reveal shared gene regulatory mechanisms https://www.biorxiv.org/content/10.1101/2025.01.06.629343v1
January 7, 2025 at 11:47 PM
Multicancer analyses of short tandem repeat variations reveal shared gene regulatory mechanisms https://www.biorxiv.org/content/10.1101/2025.01.06.629343v1
Reposted
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
January 8, 2025 at 12:47 AM
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
Reposted
Deep Learning for Biomarker Discovery in Cancer Genomes https://www.biorxiv.org/content/10.1101/2025.01.06.631471v1
January 8, 2025 at 12:47 AM
Deep Learning for Biomarker Discovery in Cancer Genomes https://www.biorxiv.org/content/10.1101/2025.01.06.631471v1
Package name of the day
QUICHE reveals structural definitions of anti-tumor responses in triple negative breast cancer https://www.biorxiv.org/content/10.1101/2025.01.06.631548v1
January 10, 2025 at 8:37 PM
Package name of the day
Reposted
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
January 8, 2025 at 9:47 PM
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
Reposted
Improving functional protein generation via foundation model-derived latent space likelihood optimization https://www.biorxiv.org/content/10.1101/2025.01.07.631724v1
January 8, 2025 at 10:47 PM
Improving functional protein generation via foundation model-derived latent space likelihood optimization https://www.biorxiv.org/content/10.1101/2025.01.07.631724v1
Reposted
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
January 8, 2025 at 10:47 PM
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
Reposted
Transfer learning applied in predicting small molecule bioactivity https://www.biorxiv.org/content/10.1101/2025.01.09.632140v1
January 10, 2025 at 3:47 PM
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 www.biorxiv.org/content/10.1...
Subcellular Level Spatial Transcriptomics with PHOTON
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
September 15, 2024 at 11:43 AM
Subcellular Level Spatial Transcriptomics with PHOTON www.biorxiv.org/content/10.1...
Reposted
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
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
www.biorxiv.org
September 9, 2024 at 2:46 PM
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
Reposted
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
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
www.biorxiv.org
September 9, 2024 at 3:46 PM
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
Reposted
BFVD - a large repository of predicted viral protein structures https://www.biorxiv.org/content/10.1101/2024.09.08.611582v1
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
www.biorxiv.org
September 10, 2024 at 5:46 AM
BFVD - a large repository of predicted viral protein structures https://www.biorxiv.org/content/10.1101/2024.09.08.611582v1
Reposted
Unlocking cross-modal interplay of single-cell and spatial joint profiling with CellMATE https://www.biorxiv.org/content/10.1101/2024.09.06.610031v1
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
www.biorxiv.org
September 10, 2024 at 5:47 AM
Unlocking cross-modal interplay of single-cell and spatial joint profiling with CellMATE https://www.biorxiv.org/content/10.1101/2024.09.06.610031v1
Reposted
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
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
www.biorxiv.org
September 10, 2024 at 5:47 AM
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
Reposted
Reversible Transcriptomic Age Shifts from Physiological Stress in Whole Blood https://www.biorxiv.org/content/10.1101/2024.09.08.611853v1
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
www.biorxiv.org
September 10, 2024 at 5:47 AM
Reversible Transcriptomic Age Shifts from Physiological Stress in Whole Blood https://www.biorxiv.org/content/10.1101/2024.09.08.611853v1
Reposted
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
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,
www.biorxiv.org
September 6, 2024 at 5:46 AM
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
Reposted
Kontextual: Reframing analysis of spatial omics data reveals consistent cell relationships across images https://www.biorxiv.org/content/10.1101/2024.09.03.611109v1
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
www.biorxiv.org
September 6, 2024 at 6:46 PM
Kontextual: Reframing analysis of spatial omics data reveals consistent cell relationships across images https://www.biorxiv.org/content/10.1101/2024.09.03.611109v1
Reposted
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
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
www.biorxiv.org
September 6, 2024 at 6:46 PM
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