Qian Cheng

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...

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...

A comprehensive benchmark of single-cell Hi-C embedding tools - Nature Communications Embedding is a key step in single-cell Hi-C analysis to identify cell states. Here, the authors benchmark 13 embedding methods in 10 scHi-C datasets. They find that data representation, preprocessing ...

Benchmarking scHi-C embedding methods shows that data representation, preprocessing options, and biological settings play a more important role in identifying cell states. @fulaijin.bsky.social

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

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
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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

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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

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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

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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...

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...

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...

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...

GPerturb: Gaussian process modelling of single-cell perturbation data - Nature Communications Single-cell CRISPR screens enable high-throughput analysis of how genetic changes affect individual cells. Here, authors present GPerturb, a method that accurately detects and quantifies gene-level ef...

GPerturb detects and quantifies gene-level effects of perturbations, with uncertainty estimates, revealing complex biological interactions. @cwcyau.bsky.social

doi.org/10.1038/s414...

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...

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...

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...

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...

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...

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...

Associate or Senior Editor, Nature Reviews Electrical Engineering Job title: Associate or Senior Editor, Nature Reviews Electrical Engineering Location: Shanghai or New York – hybrid working model Closing date: 1st July 2025 About Springer Nature Group Springer Natu...

My first task is to hire an Associate/Senior Editor for @natrevelectreng.nature.com. Would you be interested in joining me to shape the journal? Pls DM me if you have any questions💡Apply by 1 Jul.
@natureportfolio.nature.com @springernature.com
springernature.wd3.myworkdayjobs.com/SpringerNatu...

A versatile information retrieval framework for evaluating profile strength and similarity - Nature Communications Profiling assays measure thousands of features to uncover biological insights but lack reliable methods for quality evaluation. Here, the authors develop a versatile information retrieval framework to...

A versatile information retrieval framework to quantify sample activity and similarity in large-scale profiling data @natcomms.nature.com @alxndrkalinin.bsky.social @shantanu-singh.cc @drannecarpenter.bsky.social

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

An AI-assisted fluorescence microscopic system for screening mitophagy inducers by simultaneous analysis of mitophagic intermediates - Nature Communications Mitophagy is crucial for mitochondrial function and is implicated in Alzheimer’s disease. Here, the authors introduce an AI-assisted fluorescence microscopy system to track mitophagic intermediates in...

An AI-assisted fluorescence microscopy system to track mitophagic intermediates in live cells @natcomms.nature.com

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

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...

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

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Green Laboratory Visit the post for more.

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

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alexgreenlab.org

EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals - Nature Communications Despite having structures for most proteins, we still do not know their function. Here, authors introduce EvoWeaver, a de novo method to identify genes working together using evolutionary information....

EvoWeaver identifies genes working together using evolutionary information and infers protein functions using only genomic sequences. @ahl27.bsky.social @natcomms.nature.com
www.nature.com/articles/s41...

.@jkobject.com @cantinilab.bsky.social @gabrielpeyre.bsky.social present a foundation model trained on 50 million cells, generating a meaningful gene network with zero-shot ability. #AIxBio @natcomms.nature.com

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

MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search - Nature Communications Proteomics often misses co-fragmented peptides in DDA data. Here, the authors introduce MSFragger-DDA+, a database search tool that enhances peptide identification by searching the full isolation wind...

MSFragger-DDA+ is a database search tool that enhances peptide identification by searching the full isolation window. #Proteomics @fcyucn.bsky.social @nesvilab.bsky.social

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

Statistical analysis of spatial patterns in tumor microenvironment images - Nature Communications Immunotherapy is transforming cancer treatment, with immune cell distribution in the tumour microenvironment key to predicting outcomes. Here, authors provide a robust framework to analyse spatial pat...

Authors @biaunit.bsky.socia provide a robust framework to analyse spatial patterns within the tumour microenvironment. @naturecomms.bsky.social
#spatiopath #immunotherapy #Cancer #TME

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

Computation-aided designs enable developing auxotrophic metabolic sensors for wide-range glyoxylate and glycolate detection - Nature Communications Auxotrophic metabolic sensors (AMS) are vital for bioengineering but are often time-consuming to develop. Here, the authors present a workflow for designing versatile AMS, demonstrating their use for ...

📑📑📑#synthetic_biology @eorsi.bsky.social @pabnik.bsky.social present a workflow for designing versatile auxotrophic metabolic sensors for glyoxylate and glycolate detection @naturecomms.bsky.social
www.nature.com/articles/s41...

DNA-Based Computing and Data Storage This cross-journal Collection shines a spotlight on research exploring DNA as a scalable and sustainable medium for computing and data storage.

🧬💻Call for papers: DNA-based Computing and Data Storage

@naturecomms.bsky.social @commsbio.bsky.social @commseng.bsky.social
@natureportfolio.nature.com

The deadline is mid September 2025. Feel free to drop me a message if you want to discuss submissions.

www.nature.com/collections/...