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Chuck Herring

@chuckherring.bsky.social
219 followers 448 following 27 posts

Former US Marine, General Contractor, graduate student in Lau Lab, and current postdoc in the Lister Lab. Single cell genomics and epigenetics. Bioinformatics, and Neuronal Development 💻🧬🇦🇺

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Reposted by Chuck Herring
Arjun Raj @arjunraj.bsky.social · 11/10/2026
One of my favorite papers from our lab. Not only does it show heterogeneity is important in development, but it also points to division of labor: clones divvy up tasks in the organism based on their relative ability to perform well at a given fate! I like to think of it as "embryo economics".
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Sergiu P. Pasca @sergiuppasca.bsky.social · 16/09/2026
Today in Nature @nature.com, we report a new approach to studying human brain development and modeling disease in vivo. Open article link below 👇
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Johan Duchêne @johanduchene.bsky.social · 26/08/2026
Wow! Only Good Antibodies has developed a new tool that lets you see, directly in a paper, which antibodies were tested and validated. A tool that comes at the right time, given all the issues surrounding antibody validation. Definitively a tool to get onlygoodantibodies.co.uk/extension/
onlygoodantibodies.co.uk
Browser Extension — Only Good Antibodies
A free browser extension that marks antibodies cited in a paper with their knockout-controlled validation status, for the application they were used in.
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Stephen Turner @stephenturner.us · 20/08/2026
Terence Tao: Mathematics in the age of AI arxiv.org/abs/2608.16753
arxiv.org
Mathematics in the age of AI
An essay, based on a public lecture delivered at the 2026 International Congress of Mathematicians, on how the mathematical community might respond to the arrival of artificial intelligence tools that...
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Reposted by Chuck Herring
Ran Blekhman @blekhman.bsky.social · 26/07/2026
Everyone says AI will accelerate science. I don't think it will -- at least not in biology, and at least not soon. New post where I explain why, and how the productivity paradox can be resolved: blekhman.substack.com/p/why-ai-wil...
blekhman.substack.com
Why AI will not speed up science (yet)
You can see AI everywhere except in the productivity statistics
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Ming Tommy Tang @tommytang.bsky.social · 26/07/2026
A nice python package for creating Publication-Ready Scientific Plots github.com/faridrashid... if you use R, take a look at rpkgs.datanovia.com/ggpubr/
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Reposted by Chuck Herring
Kai Kupferschmidt @kakape.bsky.social · 23/07/2026
“Seven days after the girl’s medical team infused trillions of viruses carrying the recipe for the base editor into her spinal fluid, she died of a severe immune reaction linked to the therapy…” This, in @science.org, is an important and tragic story. (It’s also an incredibly well reported one.) 🧪
science.org
Exclusive: Death of girl in Chinese gene-editing trial was never made public
Parents want accountability after study went disastrously wrong, Science and Retraction Watch investigation reveals
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#SingleCell preprints @prepub-singlecell.bsky.social · 21/07/2026
When Simpler Models Win: A Calibration Benchmark of scGPT for Cell-Type Annotation #SingleCell 🧪🧬🖥️ www.researchsquare.com/article/rs-1…
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Andreas Gschwind @argschwind.bsky.social · 15/07/2026
Thrilled to share that our ENCODE enhancer–gene mapping paper is now out in Nature! An encyclopedia of human enhancer–gene regulatory interactions: www.nature.com/articles/s41... Thread 👇 1/
nature.com
An encyclopedia of human enhancer–gene regulatory interactions - Nature
An encyclopedia of more than 92 million enhancer–gene regulatory interactions created as part of the ENCODE4 project provides a valuable resource for future studies of gene regulation and human geneti...
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Reposted by Chuck Herring
#SingleCell preprints @prepub-singlecell.bsky.social · 13/05/2026
Spurious correlation inflates performance in single-cell perturbation prediction #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20…
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Reposted by Chuck Herring
Lorne Genome Conference, Australia @lornegenome.bsky.social · 30/04/2026
Lorne Genome 2027 will be held 14 to 17th February in Lorne Australia. Our invited speakers will include Karen Arndt, Neil Brockdorff, Laura Banaszynski and Fides Zenk.
Lorne Genome 2027 Poster: 14 to 17th February, at Lorne Australia. Background shows the coast off Lorne. Invited speakers include Karen Arndt, Neil Brockdorff, Laura Banaszynski and Fides Zenk.
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Reposted by Chuck Herring
#SingleCell preprints @prepub-singlecell.bsky.social · 07/04/2026
Comparative single cell analysis of wound and cancer identifies the metabolic dialogues between tumor initiating stem cells and macrophages #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20…
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#SingleCell preprints @prepub-singlecell.bsky.social · 03/04/2026
annbatch unlocks terabyte-scale training of biological data in anndata #SingleCell 🧪🧬🖥️ arxiv.org/abs/2604.01949
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#SingleCell preprints @prepub-singlecell.bsky.social · 03/04/2026
Generating and navigating single cell dynamics via a geodesic bridge between nonlinear transcriptional and linear latent manifolds #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20…
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Alistair Forrest @alforrest.bsky.social · 11/03/2026
Excited to share currently confirmed speakers for HCA Asia 2026 (lnkd.in/gEQPj3Gk)! #SingleCell #Genomics #SpatialBiology #SpatialOmics #HumanCellAtlas #SingleCell #transcriptomics #multiomics #Spatial_transcriptomics @ozsinglecell.bsky.social @lornegenome.bsky.social
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#SingleCell preprints @prepub-singlecell.bsky.social · 04/03/2026
GPU-accelerated single-cell analysis at scale with rapids-singlecell #SingleCell 🧪🧬🖥️ arxiv.org/abs/2603.02402
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#SingleCell preprints @prepub-singlecell.bsky.social · 19/02/2026
Differential analysis of genomics count data with edge #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20…
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#SingleCell preprints @prepub-singlecell.bsky.social · 18/02/2026
Evaluating Single-Cell Perturbation Response Models Is Far from Straightforward #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20…
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Human Cell Atlas @humancellatlas.org · 28/01/2026
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
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Alistair Forrest @alforrest.bsky.social · 31/10/2025
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
A a figure showing comparison of connectomeDB2025 to other ligand-receptor pair databases.
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A/Prof Sam Stehbens PhD (She/Her) @samstehbens.bsky.social · 01/12/2025
@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/
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ARC Tracker @arc-tracker.bsky.social · 02/12/2025
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
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Prof Gina Ravenscroft🇿🇦🇦🇺 @ginaravenscroft.bsky.social · 26/11/2024
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
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Lorne Genome Conference, Australia @lornegenome.bsky.social · 30/10/2025
Last chance! Early bird rates and oral presentation abstract submissions for Lorne Genome 𝐞𝐧𝐝 𝐍𝐨𝐯𝐞𝐦𝐛𝐞𝐫 𝟕𝐭𝐡, 𝟐𝟎𝟐𝟓 - only one week away: www.lornegenome.org/registrations We have a fantastic lineup of national and international speakers: www.lornegenome.org/speakers. Join us!
lornegenome.org
Speakers — Lorne Genome
No description found
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Reposted by Chuck Herring
#SingleCell preprints @prepub-singlecell.bsky.social · 27/10/2025
velotest: Statistical assessment of RNA velocity embeddings reveals quality differences for reliable trajectory visualizations #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.1101/202…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 20/10/2025
Igniting full-length isoform analysis in single-cell and spatial RNA-seq data with FLAMESv2 www.biorxiv.org/content/10.1101/202…
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Reposted by Chuck Herring
Lorne Genome Conference, Australia @lornegenome.bsky.social · 24/09/2025
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.
lornegenome.org
Registrations — Lorne Genome
Registrations are now open! Secure your ticket to attend Lorne Genome 2022!
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Reposted by Chuck Herring
bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 01/09/2025
The Fragile X mental retardation protein (FMRP) coordinates an epigenetic checkpoint in neural progenitor cells www.biorxiv.org/content/10.1101/202…
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#SingleCell preprints @prepub-singlecell.bsky.social · 31/08/2025
Whole-transcriptome-scale and isoform-resolved spatial imaging of single cells in complex tissues #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.1101/202…
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Reposted by Chuck Herring
Australasian Epigenetic Alliance (AEpiA) @aepia.bsky.social · 25/08/2025
🧬 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
aepia.org.au
Emma Whitelaw Publication Award — Australasian Epigenetics Alliance
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Jamie Heather @jamieheather.bsky.social · 14/08/2025
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.
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Reposted by Chuck Herring
bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 13/08/2025
Disentangling the influences of pre- and postnatal periods on human cortical microstructure www.biorxiv.org/content/10.1101/202…
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Keith Fitzgerald @keithfitzgerald.bsky.social · 26/06/2025
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.
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 19/06/2025
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
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 13/05/2025
Extrinsic biological stochasticity and technical noise normalization of single-cell RNA sequencing data www.biorxiv.org/content/10.1101/202…
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Kevin M. Kruse @kevinmkruse.bsky.social · 07/05/2025
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.
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Anshul Kundaje @anshulkundaje.bsky.social · 20/04/2025
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.
genomebiology.biomedcentral.com
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...
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Nature Portfolio @natureportfolio.nature.com · 09/04/2025
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. 🧪
go.nature.com
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.
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Nikolai Slavov @slavov-n.bsky.social · 14/04/2025
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
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 05/04/2025
MeCP2 controls dendritic morphogenesis via miR-199a-mediated Qki downregulation www.biorxiv.org/content/10.1101/202…
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 11/03/2025
Metabolic Atlas of Early Human Cortex Identifies Regulators of Cell Fate Transitions www.biorxiv.org/content/10.1101/202…
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Alistair Forrest @alforrest.bsky.social · 12/02/2025
Heading to #lornegenome25 #LorneCancerConference ? Looking for a computational postdoc to work on spatial and single nuclei transcriptomics of poor prognosis cancers, please DM me or see me at Lorne. We will be advertising soon. @ozsinglecell.bsky.social #LorneCancer2025 #Lorne2025
bsky.app
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 30/01/2025
ScaleSC: A superfast and scalable single cell RNA-seq data analysis pipeline powered by GPU. www.biorxiv.org/content/10.1101/202…
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Austin Wang @austintwang.bsky.social · 11/12/2024
(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430
arxiv.org
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA
Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn gen...
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Chuck Herring @chuckherring.bsky.social · 09/11/2024
www.nature.com/articles/s41... 💻🧬
nature.com
Uncovering functional lncRNAs by scRNA-seq with ELATUS - Nature Communications
The inaccurate annotation of long noncoding RNAs (lncRNAs) hampers their detection by scRNA-seq. The computational workflow ELATUS, based on the pseudoaligner Kallisto, addresses this problem and unco...
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Reposted by Chuck Herring
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 01/11/2024
mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysis www.biorxiv.org/content/10.1101/202…
biorxiv.org
mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysis https://www.biorxiv.org/content/10.1101/2024.10.30.621093v1
In single-cell data analysis, addressing sparsity often involves aggregating the profiles of homogen
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Chuck Herring @chuckherring.bsky.social · 26/10/2024
This is an excellent program, especially for researchers from low-income backgrounds and those who pursue a research career later in life, like me. Thank you for sharing @mehr.nz
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Chuck Herring @chuckherring.bsky.social · 24/10/2024
Turns out I was relying a bit much on Twitter to keep up with new papers. Any suggestions for how to keep up the latest publications?
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Mathieu Lupien @matlupien.bsky.social · 16/10/2024
📖 New review in Nature Reviews Cancer on how epigenomic heterogeneity drives tumour evolution! We dive into: Check it out if you're into epigenetics, single-cell tech, or the future of cancer therapy! 📖 www.nature.com/articles/s41...
nature.com
Epigenomic heterogeneity as a source of tumour evolution - Nature Reviews Cancer
Single-cell epigenomic technologies are refining our understanding of cancer evolution. Here Laisné et al. describe how epigenomic heterogeneity generates dynamic reservoirs of tumour cell states, thr...
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Chuck Herring @chuckherring.bsky.social · 25/09/2024
As a former general contractor and small business owner before the Great Recession, I found this breakdown logical—it’s primarily a supply-side issue. But found it lacking, only one presidential candidate wants to deport a significant portion of housing work force. open.spotify.com/show/3IM0lmZ...
open.spotify.com
The Daily
Podcast · [object Object] · This is what the news should sound like. The biggest stories of our time, told by the best journalists in the world. Hosted by Michael Barbaro and Sabrina Tavernise. Twenty...
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