#BiotechNatureComms

Qian Cheng

@qchengx1e3.bsky.social

1 month ago

MINT, trained on large #PPI datasets, outperforms existing protein language models in predicting binding, mutations, and immune interactions.

@bergerlab.bsky.social #BiotechNatureComms

doi.org/10.1038/s414...

Qian Cheng

@qchengx1e3.bsky.social

3 months ago

PyFuRNAce: an integrated design engine for RNA origami - Nature Communications RNA nanotechnology creates structural and functional RNA architectures for biomedicine, synthetic biology and beyond. Here, the authors introduce pyFuRNAce, an intuitive browser-based RNA design tool....

PyFuRNAce is an intuitive browser-based RNA design tool. 
@monari-luca.bsky.social @kgoepfrich.bsky.social @uniheidelberg.bsky.social realized the largest cotranscriptionally folded RNA nanostructures to date. #BiotechNatureComms

www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

3 months ago

Enhanced spatial clustering of single-molecule localizations with graph neural networks - Nature Communications Single-molecule localisation microscopy enables nanoscale mapping of molecular organisation, but clustering stochastic data remains challenging. Here, authors present a graph neural network method tha...

MIRO is a graph neural network method that enhances spatial clustering for single-molecule localisation microscopy datasets. #BiotechNatureComms

@cmanzo.bsky.social @qubilab.bsky.social @giovannivolpe.bsky.social

doi.org/10.1038/s414...

Qian Cheng

@qchengx1e3.bsky.social

5 months ago

IceQream: Quantitative chromosome accessibility analysis using physical TF models - Nature Communications Cis regulatory elements endow genomes with sequence-encoded logic to drive cellular differentiation. Here, the authors introduce a biophysically principled sequence model that characterises complex TF...

A biophysically principled sequence model IceQream characterises complex Transcription Factor-DNA interactions from chromosome accessibility analysis.
@Akhiad.bsky.social
#BiotechNatureComms
www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

6 months ago

Multi-scale and multi-context interpretable mapping of cell states across heterogeneous spatial samples - Nature Communications The alignment of heterogeneous spatial samples has become a growing challenge. Here, authors present a multi-scale, multi-context, and interpretable mapping strategy to map cells across space, time, a...

A multi-scale, multi-context, and interpretable mapping strategy to map cells across space, time, and disease. @pcnmartin.bsky.social @wonkj.bsky.social

#spatialMapping #spatialOmics #BiotechNatureComms

www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

7 months ago

Time-varying stimuli that prolong IKK activation promote nuclear remodeling and mechanistic switching of NF-κB dynamics - Nature Communications Cells rely on limited numbers of transmembrane receptors to process signals from dynamic microenvironments. Using microfluidics and endogenous reporters, the authors track single cells to reveal how t...

Using microfluidics and endogenous reporters, single cells are tracked to reveal how temporal dosing rewires chromatin in a model with near single-cell accuracy. @stevenwsmeal.bsky.social @robineclee.bsky.social #BiotechNatureComms

www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

7 months ago

Single cell and spatial alternative splicing analysis with Nanopore long read sequencing - Nature Communications Single-cell isoform quantification using Nanopore long reads remains limited by sequencing errors. Here, authors present Longcell, a computational framework that corrects these errors and uncovers spl...

A computational framework for single cell and spatial alternative splicing analysis with Nanopore long read sequencing

@nancyrzhang.bsky.social
#BiotechNatureComms

www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

8 months ago

Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...

A computational tool #SCALPEL for #isoform quantification at the single-cell level using 3’ scRNA-seq data @franzake.bsky.social @mireyaplass.bsky.social #BiotechNatureComms

doi.org/10.1038/s414...

Qian Cheng

@qchengx1e3.bsky.social

8 months ago

Highly adaptable deep-learning platform for automated detection and analysis of vesicle exocytosis - Nature Communications Activity recognition in live-cell imaging is laborious. Here, authors present, IVEA, a fully automated AI ImageJ plugin, that efficiently detects and classifies exocytosis events, from synaptic transm...

A fully automated AI ImageJ plugin that detects and classifies #exocytosis events from synaptic transmission to single-vesicle fusion. @alishaib.bsky.social #BiotechNatureComms

doi.org/10.1038/s414...

Qian Cheng

@qchengx1e3.bsky.social

8 months ago

ToxACoL: an endpoint-aware and task-focused compound representation learning paradigm for acute toxicity assessment - Nature Communications Multi-species acute systemic toxicity assessment is fundamental for chemical classification, labelling and risk management. Here, the authors propose a machine learning paradigm, Adjoint Correlation L...

ToxACoL is an endpoint-aware and task-focused compound representation learning paradigm for #Acute_Toxicity_Assessment #BiotechNatureComms

doi.org/10.1038/s414...

Qian Cheng

@qchengx1e3.bsky.social

8 months ago

Facilitate integrated analysis of single cell multiomic data by binarizing gene expression values - Nature Communications Individual data types in a single cell multi-omic assay are often processed and clustered independently before combined for further analysis. Here, authors showed that binarized gene expression d...

Binarized gene expression data can be concatenated with chromatin accessibility data for effective and integrated cell clustering @zhengdy.bsky.social @einsteinmededu.bsky.social #BiotechNatureComms

doi.org/10.1038/s414...

Qian Cheng

@qchengx1e3.bsky.social

8 months ago

Modeling heterogeneous signaling dynamics of macrophages reveals principles of information transmission in stimulus responses - Nature Communications To develop virtual cells, mathematical models must account for the heterogeneity of single cells. Here, authors develop virtual single cell NFκB signalling networks that recapitulate heterogenous expe...

A virtual single-cell NFκB signalling networks that recapitulate heterogenous experimental stimulus-response dynamics @xiaoluguo.bsky.social #BiotechNatureComms

doi.org/10.1038/s414...

Qian Cheng

@qchengx1e3.bsky.social

8 months ago

DOLPHIN: a deep learning method that enables exon- and junction-level analysis to improve cell representation and detect alternative #splicing. Ding Lab junding.lab.mcgill.ca #BiotechNatureComms

doi.org/10.1038/s414...

Qian Cheng

@qchengx1e3.bsky.social

8 months ago

Automated cell annotation and classification on histopathology for spatial biomarker discovery - Nature Communications Histopathology is essential for diagnosing cancer, but cell annotation remains unreliable and inefficient. Here, authors develop a method using deep learning and immune-fluorescence-guided cell labell...

A deep learning and immune-fluorescence-guided cell labelling method for accurate cell pattern identification. #BiotechNatureComms

doi.org/10.1038/s414...

Qian Cheng

@qchengx1e3.bsky.social

8 months ago

Cell Marker Accordion: interpretable single-cell and spatial omics annotation in health and disease - Nature Communications Accurate cell type annotation is a major challenge in single-cell and spatial omics. Here, authors present a user-friendly platform providing robust automatic annotation and enhanced biological interp...

Cell Marker Accordion is a user-friendly platform providing robust automatic cell annotation of #single_cell and spatial populations @rdds-lab.bsky.social #BiotechNatureComms

doi.org/10.1038/s414...

Qian Cheng

@qchengx1e3.bsky.social

8 months ago

Accelerating cell culture media development using Bayesian optimization-based iterative experimental design - Nature Communications Optimising operational conditions for biological systems is a complex task. Here, authors present a Bayesian optimisation-based iterative experimental design framework that integrates data generation,...

A Bayesian optimisation-based iterative experimental design framework that integrates data generation, modelling, and optimisation to accelerate cell culture media development #BiotechNatureComms

doi.org/10.1038/s414...

Qian Cheng

@qchengx1e3.bsky.social

8 months ago

Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy - Nature Communications The cell nucleus coordinates diverse functions. Here, the authors utilise multiplexed super-resolution imaging to study how nuclear proteins are distributed relative to each other from the micro to th...

A multiplexed super-resolution imaging protocol studies how nuclear proteins are distributed relative to each other from the micro to the nanoscale. #BiotechNatureComms

doi.org/10.1038/s414...

Qian Cheng

@qchengx1e3.bsky.social

9 months ago

CellFM: a large-scale foundation model pre-trained on transcriptomics of 100 million human cells - Nature Communications Single-cell sequencing reveals cellular heterogeneity but is challenged by technical noise and batch effects. Here, authors present CellFM, an 800-million-parameter foundation model trained on 100 mil...

CellFM: A 800-million-parameter foundation model pre-trained on transcriptomics of 100 million human cells. #BiotechNatureComms @natcomms.nature.com

www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

10 months ago

Learning tissue representation by identification of persistent local patterns in spatial omics data - Nature Communications Spatial omics reveal tissue structures and can aid patient stratification. The authors present a method to identify patterns in tissue patches, enabling analysis of disease progression and treatment r...

Kasumi identifies local patterns in tissue patches in spatial omics data @tanevski.bsky.social, @saezlab.bsky.social #BiotechNatureComms

www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

10 months ago

Green Laboratory Visit the post for more.

A data-efficient, generative AI-based toolkit for designing a diverse set of RNA molecules. #BiotechNatureComms

www.nature.com/articles/s41...

alexgreenlab.org

Qian Cheng

@qchengx1e3.bsky.social

1 year ago

FusOn-pLM: a fusion oncoprotein-specific language model via adjusted rate masking - Nature Communications Fusion oncoproteins drive paediatric cancers but are challenging to target due to their intrinsic disorder and lack of druggable pockets. Here, authors present FusOn-pLM, trained on FusOn-DB, which us...

@pranam.bsky.social  present FusOn-pLM, which uses dynamic masking to outperform baselines in fusion-specific tasks and predict drug-resistant mutations
#BiotechNatureComms

www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

1 year ago

Contrastive-learning of language embedding and biological features for cross modality encoding and effector prediction - Nature Communications Identifying and characterizing secreted virulence proteins are fundamental for deciphering microbial pathogenicity. Here, the authors introduce a practical training framework to improve protein langua...

Authors introduce a practical training framework to improve protein language model representations by integrating biological features and prior information through contrastive learning. #BiotechNatureComms
www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

1 year ago

Transcriptome size matters for single-cell RNA-seq normalization and bulk deconvolution - Nature Communications Existing cell type deconvolution methods, crucial for studying tumour environments, overlook some critical issues. Here, authors analyse how these issues impact on deconvolution and develop methods to...

.@jiyang_yu @StJudeResearch introduce new methods for cell type deconvolution and scRNA-seq data normalisation. #BiotechNatureComms
www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

1 year ago

Spatial integration of multi-omics single-cell data with SIMO - Nature Communications Existing tools face limitations in integrating spatial data with single-cell multi-omics datasets. Here, authors introduce a computational tool that maps diverse single-cell modalities, including RNA,...

SIMO maps diverse single-cell modalities, including RNA, chromatin accessibility, and DNA methylation, onto spatial tissues. #BiotechNatureComms
www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

1 year ago

MetaQ: fast, scalable and accurate metacell inference via single-cell quantization - Nature Communications Large-scale single-cell sequencing data brings computational barriers for downstream analysis. Here, the authors propose MetaQ, a metacell algorithm that reduces cell number while preserving biologica...

MetaQ is a metacell algorithm that supports both uni- and multi-omics data for large-scale single-cell data analyses. 
#BiotechNatureComms
www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

1 year ago

Statistical identification of cell type-specific spatially variable genes in spatial transcriptomics - Nature Communications The authors develop Celina to detect cell type-specific spatially variable genes (ct-SVGs) in spatial transcriptomics. These ct-SVGs exhibit distinct spatial expression patterns within specific cell t...

Celina detects cell type-specific spatially variable genes in spatial transcriptomics, offering insights into the transcriptomic mechanism underlying cellular heterogeneity. #BiotechNatureComms
www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

1 year ago

Quantitative determination of the spatial distribution of components in single cells with CellDetail - Nature Communications Tools to determine the spatial distribution of components and their networks inside cells are not well developed. Here, authors provide the open-source 3D-cell-image analysis platform Cell Detection a...

The geigerlab provide the open-source 3D-cell-image analysis platform #CellDetail for quantitative spatial distribution analyses. #BiotechNatureComms

www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

1 year ago

Protein engineering using variational free energy approximation - Nature Communications Generative deep learning models can generate novel proteins, but these are often not functional due to thermodynamic instability. Here, authors present a method to learn both the sequence and thermody...

PREVENT learns both the sequence and thermodynamic landscape of a protein and generates new functional variants. #BiotechNatureComms

www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

1 year ago

NiCo identifies extrinsic drivers of cell state modulation by niche covariation analysis - Nature Communications A key question in single-cell biology is how cells communicate and exchange information with neighboring cells in tissues. Here, the authors introduce NiCo to predict the downstream effect of cell-cel...

The Gruen lab introduce #NiCo to predict the downstream effect of cell-cell interactions on cellular states in tissue niches from spatial transcriptomics data. #BiotechNatureComms

www.nature.com/articles/s41...

Qian Cheng

@qchengx1e3.bsky.social

1 year ago

RNA language models predict mutations that improve RNA function - Nature Communications Generating RNA sequences with improved function remains challenging. Here, authors present an RNA database for RNA structural and functional analysis. They use this database and the RNA generative mod...

GARNET is an RNA database for RNA structural and functional analysis. Authors develop sequence- and structure-aware RNA generative models. #BiotechNatureComms

www.nature.com/articles/s41...