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...

Authors use Restricted Boltzmann machines trained on natural sequences to design new riboswitch aptamer domains and validate their functionality via chemical probing. @jorgefdcd.bsky.social www.nature.com/articles/s41...

𝘕𝘢𝘵𝘶𝘳𝘦 𝘊𝘰𝘮𝘮𝘶𝘯𝘪𝘤𝘢𝘵𝘪𝘰𝘯𝘴 @natcomms.nature.com has recently launched 𝗔𝗿𝘁𝗶𝗰𝗹𝗲𝘀 𝗶𝗻 𝗣𝗿𝗲𝘀𝘀. This provides early, citable access to accepted research, enables faster dissemination of findings, and supports a smoother publishing experience for authors. 𝗙𝗔𝗤 here: support.springernature.com/en/support/s...

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...

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...

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...

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...

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...

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...

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...

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...

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 is an endpoint-aware and task-focused compound representation learning paradigm for #Acute_Toxicity_Assessment #BiotechNatureComms doi.org/10.1038/s414...

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 detects and quantifies gene-level effects of perturbations, with uncertainty estimates, revealing complex biological interactions. @cwcyau.bsky.social doi.org/10.1038/s414...

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...

A deep learning and immune-fluorescence-guided cell labelling method for accurate cell pattern identification. #BiotechNatureComms doi.org/10.1038/s414...

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...

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...

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...

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 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 microscopy system to track mitophagic intermediates in live cells @natcomms.nature.com www.nature.com/articles/s41...

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...

Kasumi identifies local patterns in tissue patches in spatial omics data @tanevski.bsky.social, @saezlab.bsky.social #BiotechNatureComms www.nature.com/articles/s41...

A data-efficient, generative AI-based toolkit for designing a diverse set of RNA molecules. #BiotechNatureComms www.nature.com/articles/s41... alexgreenlab.org

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...

[email protected] @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+ 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...

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...

📑📑📑#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...

🧬💻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/...

Please take a look at the Springer Nature’s Opening Doors Internship Programme. It's open for applications in the UK, US and Germany as well as China and the Netherlands. The deadline is 14 March (28 February UK). Explore the available positions here: group.springernature.com/gp/group/tak...

@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...

Overview of some #Computational_Biology papers published in January 2025 in @naturecomms.bsky.social www.linkedin.com/posts/qian-c...

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...

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

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

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...

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...

Happy holidays!

Please follow our Nature Communications account @naturecomms.bsky.social Watch this space for #open-access papers with their #transparent-peer-review reports. 🎄🎄

You also can follow Nature Portfolio editors with the starter pack we have been sharing.

Browse a Focus issue from Nature Human Behaviour on menstruation. Authors discuss periods from a multidisciplinary perspective, including addressing menstrual myths, period poverty, and menstrual health management for diverse populations. https://go.nature.com/4iCnUOw 🧪

#Code_Availability_Statement! The importance of licensing code when you publishing your computational biology papers. www.linkedin.com/posts/qian-c...

The geigerlab provide the open-source 3D-cell-image analysis platform #CellDetail for quantitative spatial distribution analyses. #BiotechNatureComms www.nature.com/articles/s41...

PREVENT learns both the sequence and thermodynamic landscape of a protein and generates new functional variants. #BiotechNatureComms www.nature.com/articles/s41...

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...

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...