Reposted by Chuck HerringArjun Raj @arjunraj.bsky.social · 11/10/2026One 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". 1298
Reposted by Chuck HerringSergiu P. Pasca @sergiuppasca.bsky.social · 16/09/2026Today in Nature @nature.com, we report a new approach to studying human brain development and modeling disease in vivo. Open article link below 👇 59332
Reposted by Chuck HerringJohan Duchêne @johanduchene.bsky.social · 26/08/2026Wow! 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.ukBrowser Extension — Only Good AntibodiesA free browser extension that marks antibodies cited in a paper with their knockout-controlled validation status, for the application they were used in. 13715
Reposted by Chuck HerringStephen Turner @stephenturner.us · 20/08/2026Terence Tao: Mathematics in the age of AI arxiv.org/abs/2608.16753arxiv.orgMathematics in the age of AIAn 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... 161
Reposted by Chuck HerringRan Blekhman @blekhman.bsky.social · 26/07/2026Everyone 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.comWhy AI will not speed up science (yet)You can see AI everywhere except in the productivity statistics 610445
Reposted by Chuck HerringMing Tommy Tang @tommytang.bsky.social · 26/07/2026A nice python package for creating Publication-Ready Scientific Plots github.com/faridrashid... if you use R, take a look at rpkgs.datanovia.com/ggpubr/ 092
Reposted by Chuck HerringKai 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.orgExclusive: Death of girl in Chinese gene-editing trial was never made publicParents want accountability after study went disastrously wrong, Science and Retraction Watch investigation reveals 614661
Reposted by Chuck Herring#SingleCell preprints @prepub-singlecell.bsky.social · 21/07/2026When Simpler Models Win: A Calibration Benchmark of scGPT for Cell-Type Annotation #SingleCell 🧪🧬🖥️ www.researchsquare.com/article/rs-1… 021
Reposted by Chuck HerringAndreas Gschwind @argschwind.bsky.social · 15/07/2026Thrilled 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.comAn encyclopedia of human enhancer–gene regulatory interactions - NatureAn 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... 18041
Reposted by Chuck Herring#SingleCell preprints @prepub-singlecell.bsky.social · 13/05/2026Spurious correlation inflates performance in single-cell perturbation prediction #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20… 001
Reposted by Chuck HerringLorne Genome Conference, Australia @lornegenome.bsky.social · 30/04/2026Lorne 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. 0107
Reposted by Chuck Herring#SingleCell preprints @prepub-singlecell.bsky.social · 07/04/2026Comparative 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… 011
Reposted by Chuck Herring#SingleCell preprints @prepub-singlecell.bsky.social · 03/04/2026annbatch unlocks terabyte-scale training of biological data in anndata #SingleCell 🧪🧬🖥️ arxiv.org/abs/2604.01949 011
Reposted by Chuck Herring#SingleCell preprints @prepub-singlecell.bsky.social · 03/04/2026Generating and navigating single cell dynamics via a geodesic bridge between nonlinear transcriptional and linear latent manifolds #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20… 011
Reposted by Chuck HerringAlistair Forrest @alforrest.bsky.social · 11/03/2026Excited 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 142
Reposted by Chuck Herring#SingleCell preprints @prepub-singlecell.bsky.social · 04/03/2026GPU-accelerated single-cell analysis at scale with rapids-singlecell #SingleCell 🧪🧬🖥️ arxiv.org/abs/2603.02402 032
Reposted by Chuck Herring#SingleCell preprints @prepub-singlecell.bsky.social · 19/02/2026Differential analysis of genomics count data with edge #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20… 011
Reposted by Chuck Herring#SingleCell preprints @prepub-singlecell.bsky.social · 18/02/2026Evaluating Single-Cell Perturbation Response Models Is Far from Straightforward #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20… 031
Reposted by Chuck HerringHuman Cell Atlas @humancellatlas.org · 28/01/2026Registration 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 133
Chuck Herring @chuckherring.bsky.social · 24/01/2026This was a great read, thank you for sharing. 100
Reposted by Chuck HerringAlistair Forrest @alforrest.bsky.social · 31/10/2025connectomeDB2025: 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 193
Reposted by Chuck HerringA/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/ 12014
Reposted by Chuck HerringARC Tracker @arc-tracker.bsky.social · 02/12/2025Every 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 03026
Reposted by Chuck HerringProf Gina Ravenscroft🇿🇦🇦🇺 @ginaravenscroft.bsky.social · 26/11/2024If 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 23335
Reposted by Chuck HerringLorne Genome Conference, Australia @lornegenome.bsky.social · 30/10/2025Last 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.orgSpeakers — Lorne GenomeNo description found 066
Reposted by Chuck Herring#SingleCell preprints @prepub-singlecell.bsky.social · 27/10/2025velotest: Statistical assessment of RNA velocity embeddings reveals quality differences for reliable trajectory visualizations #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.1101/202… 021
Reposted by Chuck HerringbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 20/10/2025Igniting full-length isoform analysis in single-cell and spatial RNA-seq data with FLAMESv2 www.biorxiv.org/content/10.1101/202… 032
Reposted by Chuck HerringLorne Genome Conference, Australia @lornegenome.bsky.social · 24/09/2025Don'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.orgRegistrations — Lorne GenomeRegistrations are now open! Secure your ticket to attend Lorne Genome 2022! 043
Reposted by Chuck HerringbioRxiv Neuroscience @biorxiv-neursci.bsky.social · 01/09/2025The Fragile X mental retardation protein (FMRP) coordinates an epigenetic checkpoint in neural progenitor cells www.biorxiv.org/content/10.1101/202… 021
Reposted by Chuck Herring#SingleCell preprints @prepub-singlecell.bsky.social · 31/08/2025Whole-transcriptome-scale and isoform-resolved spatial imaging of single cells in complex tissues #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.1101/202… 011
Reposted by Chuck HerringAustralasian 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 #AEpiAaepia.org.auEmma Whitelaw Publication Award — Australasian Epigenetics Alliance 047
Reposted by Chuck HerringJamie Heather @jamieheather.bsky.social · 14/08/2025My 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. 04520
Reposted by Chuck HerringbioRxiv Neuroscience @biorxiv-neursci.bsky.social · 13/08/2025Disentangling the influences of pre- and postnatal periods on human cortical microstructure www.biorxiv.org/content/10.1101/202… 033
Chuck Herring @chuckherring.bsky.social · 16/07/2025Especially important for all the microscopy Widdors out there. 110
Reposted by Chuck HerringKeith Fitzgerald @keithfitzgerald.bsky.social · 26/06/2025Worth 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. 204109314360
Reposted by Chuck HerringAkis (Argyris) Papantonis @akispapantonis.bsky.social · 19/06/2025This 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 39439
Reposted by Chuck HerringbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 13/05/2025Extrinsic biological stochasticity and technical noise normalization of single-cell RNA sequencing data www.biorxiv.org/content/10.1101/202… 032
Reposted by Chuck HerringKevin M. Kruse @kevinmkruse.bsky.social · 07/05/2025Can'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. 601887323
Chuck Herring @chuckherring.bsky.social · 23/04/2025It was new to me and our lab as well. Thanks for sharing. 020
Reposted by Chuck HerringAnshul Kundaje @anshulkundaje.bsky.social · 20/04/2025genomebiology.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.comZero-shot evaluation reveals limitations of single-cell foundation models - Genome BiologyFoundation 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... 615747
Reposted by Chuck HerringNature Portfolio @natureportfolio.nature.com · 09/04/2025A 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.comThe MICrONS ProjectAn 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. 15918
Reposted by Chuck HerringNikolai Slavov @slavov-n.bsky.social · 14/04/2025How 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 24210
Reposted by Chuck HerringbioRxiv Neuroscience @biorxiv-neursci.bsky.social · 05/04/2025MeCP2 controls dendritic morphogenesis via miR-199a-mediated Qki downregulation www.biorxiv.org/content/10.1101/202… 011
Chuck Herring @chuckherring.bsky.social · 14/03/2025Transported for an instance to what it was like to read Carl Sagan many years ago. Thanks for sharing. 080
Reposted by Chuck HerringbioRxiv Neuroscience @biorxiv-neursci.bsky.social · 11/03/2025Metabolic Atlas of Early Human Cortex Identifies Regulators of Cell Fate Transitions www.biorxiv.org/content/10.1101/202… 033
Reposted by Chuck HerringAlistair Forrest @alforrest.bsky.social · 12/02/2025Heading 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 #Lorne2025bsky.app 11012
Reposted by Chuck HerringbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 30/01/2025ScaleSC: A superfast and scalable single cell RNA-seq data analysis pipeline powered by GPU. www.biorxiv.org/content/10.1101/202… 072
Reposted by Chuck HerringAustin 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/2412.05430arxiv.orgDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNARecent 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... 17027
Chuck Herring @chuckherring.bsky.social · 09/11/2024www.nature.com/articles/s41... 💻🧬nature.comUncovering functional lncRNAs by scRNA-seq with ELATUS - Nature CommunicationsThe 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... 090