Chuck Herring

GPU-accelerated single-cell analysis at scale with rapids-singlecell #SingleCell 🧪🧬🖥️
https://arxiv.org/abs/2603.02402

Differential analysis of genomics count data with edge #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.02.16.706223v1

Evaluating Single-Cell Perturbation Response Models Is Far from Straightforward #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.02.14.705879v1

Registration for the HCA Asia Meeting on 2-4 November, 2026 is now open! The #HCA2026Asia meeting will be held in Perth, Australia, and online, and is hosted by @alforrest.bsky.social. Please register at buff.ly/gADDEnC
🖥️ 🧬 #Genomics #SingleCell #Spatial #HumanCellAtlas

This was a great read, thank you for sharing.

A a figure showing comparison of connectomeDB2025 to other ligand-receptor pair databases.

connectomeDB2025: Quality matters!
✅3,579 ligand-receptor pairs supported by 2,803 papers
✅14 vertebrates
❌ >2,900 unsupported pairs from other DBs excluded

connectomedb.org

academic.oup.com/nar/advance-...

@JARamilowski @sakura_maezono @rui_hou_ @weitao_lin @yen_yeow + team

@ginaravenscroft.bsky.social & #NARF are collecting impact statements from Australian researchers

‘ Please consider sharing your story about the impact of Australia's chronic underfunding of science and biomedical research.’
lnkd.in/g8A_PAZG

1/

Every opportunity politicians provide for you to tell them about how chronic underfunding of research in Australia is affecting your particular fields, people, working conditions etc. is extremely important.

Fill out the form here: lnkd.in/g8A_PAZG

If your #NHMRC ideas grant was unsuccessful and you have a story to share about the impact of this on your #biomedicalresearch, career, team - get in touch. Federal DOH have asked #NARF to collect stories of impact of low funding. #SaveOzScience #DiscoveriesNeedDollars #EMCRs

Speakers — Lorne Genome No description found

Last chance! Early bird rates and oral presentation abstract submissions for Lorne Genome 𝐞𝐧𝐝 𝐍𝐨𝐯𝐞𝐦𝐛𝐞𝐫 𝟕𝐭𝐡, 𝟐𝟎𝟐𝟓 - only one week away: https://www.lornegenome.org/registrations

We have a fantastic lineup of national and international speakers: https://www.lornegenome.org/speakers. Join us!

velotest: Statistical assessment of RNA velocity embeddings reveals quality differences for reliable trajectory visualizations #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.10.26.683064v1

Igniting full-length isoform analysis in single-cell and spatial RNA-seq data with FLAMESv2 https://www.biorxiv.org/content/10.1101/2025.10.19.683327v1

Don't forget to register and submit an abstract for the 𝐋𝐨𝐫𝐧𝐞 𝐆𝐞𝐧𝐨𝐦𝐞 𝟐𝟎𝟐𝟔!

𝐓𝐡𝐢𝐬 𝐰𝐞𝐞𝐤'𝐬 𝐬𝐩𝐞𝐚𝐤𝐞𝐫 𝐬𝐩𝐨𝐭𝐥𝐢𝐠𝐡𝐭: 𝐏𝐫𝐨𝐟 𝐁𝐫𝐞𝐧𝐝𝐚 𝐀𝐧𝐝𝐫𝐞𝐰𝐬, a leading systems biologist whose research focuses on mapping genetic interaction networks and protein localisation patterns in yeast and human cells.

The Fragile X mental retardation protein (FMRP) coordinates an epigenetic checkpoint in neural progenitor cells https://www.biorxiv.org/content/10.1101/2025.08.31.673358v1

Whole-transcriptome-scale and isoform-resolved spatial imaging of single cells in complex tissues #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.08.27.672533v1

🧬 The 2025 Emma Whitelaw ECR publication award is now open!

Full T&Cs and application form are on the AEpiA website www.aepia.org.au/emma-whitela...

We can't wait to see the exciting research that has been published over the last year!

#epigenetics #ECR #research #AEpiA

My generation had to deal with datasets where Excel had autocorrected gene names to dates. Future generations are going to have to deal with the hallucinations of slopbots.

Disentangling the influences of pre- and postnatal periods on human cortical microstructure https://www.biorxiv.org/content/10.1101/2025.08.12.669812v1

Especially important for all the microscopy Widdors out there.

Beautiful paper, congrats all involved.

Worth a watch:

Head of Signal, Meredith Whittaker, on so-called "agentic AI" and the difference between how it's described in the marketing and what access and control it would actually require to work as advertised.

This is a piece that I and @karsten-rippe.bsky.social discussing a lot, and a topic that is very close to my heart. The editors @naturerevgenet.bsky.social gave us the stage to do so, and the final version of our review is now available under this link: rdcu.be/erP1u

A short thread follows 1/n

Extrinsic biological stochasticity and technical noise normalization of single-cell RNA sequencing data https://www.biorxiv.org/content/10.1101/2025.05.11.653373v1

Can't remember who said it, but using ChatGPT for your college essays is like using a forklift to move the weights around at the gym.

It's the process that's important to your development, not the end product.

It was new to me and our lab as well. Thanks for sharing.

Zero-shot evaluation reveals limitations of single-cell foundation models - Genome Biology Foundation models such as scGPT and Geneformer have not been rigorously evaluated in a setting where they are used without any further training (i.e., zero-shot). Understanding the performance of mode...

genomebiology.biomedcentral.com/articles/10....

Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.

The MICrONS Project An unprecedented dataset of high resolution anatomical images of individual cells in mouse visual cortex, mapped on to their responses. This integrated view of function and structure lays a foundation for discovering the computational bases of cortical circuits.

A package of research papers from the MICrONS (Machine Intelligence from Cortical Networks) consortium in Nature and Nature Methods provides a detailed map of mouse brain cell structure and connections, offering insights into how they relate to activity in the mouse brain. 🧪

How accurate are 'gene regulatory networks' inferred from scRNA-seq data?

This comprehensive analysis in @naturemethods.bsky.social concludes:
1. The areas under the precision-recall curve are moderate
2. Methods not using pseudotime-ordered cells are more accurate

MeCP2 controls dendritic morphogenesis via miR-199a-mediated Qki downregulation https://www.biorxiv.org/content/10.1101/2025.04.04.642981v1

Transported for an instance to what it was like to read Carl Sagan many years ago. Thanks for sharing.