Chuck Herring
@chuckherring.bsky.social
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 💻🧬🇦🇺
Reposted by Chuck Herring
@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/
‘ Please consider sharing your story about the impact of Australia's chronic underfunding of science and biomedical research.’
lnkd.in/g8A_PAZG
1/
December 1, 2025 at 10:49 PM
@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/
‘ Please consider sharing your story about the impact of Australia's chronic underfunding of science and biomedical research.’
lnkd.in/g8A_PAZG
1/
Reposted by Chuck Herring
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
Fill out the form here: lnkd.in/g8A_PAZG
@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/
‘ Please consider sharing your story about the impact of Australia's chronic underfunding of science and biomedical research.’
lnkd.in/g8A_PAZG
1/
December 2, 2025 at 4:55 AM
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
Fill out the form here: lnkd.in/g8A_PAZG
Reposted by Chuck Herring
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
November 26, 2024 at 1:46 AM
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
Reposted by Chuck Herring
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!
We have a fantastic lineup of national and international speakers: https://www.lornegenome.org/speakers. Join us!
Speakers — Lorne Genome
No description found
www.lornegenome.org
October 30, 2025 at 9:30 PM
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!
We have a fantastic lineup of national and international speakers: https://www.lornegenome.org/speakers. Join us!
Reposted by Chuck Herring
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
https://www.biorxiv.org/content/10.1101/2025.10.26.683064v1
October 27, 2025 at 8:00 AM
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
https://www.biorxiv.org/content/10.1101/2025.10.26.683064v1
Reposted by Chuck Herring
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
October 20, 2025 at 8:47 PM
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
Reposted by Chuck Herring
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.
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.
Registrations — Lorne Genome
Registrations are now open! Secure your ticket to attend Lorne Genome 2022!
www.lornegenome.org
September 24, 2025 at 1:10 AM
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.
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.
Reposted by Chuck Herring
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
September 1, 2025 at 7:15 AM
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
Reposted by Chuck Herring
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
https://www.biorxiv.org/content/10.1101/2025.08.27.672533v1
August 31, 2025 at 7:00 AM
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
https://www.biorxiv.org/content/10.1101/2025.08.27.672533v1
Reposted by Chuck Herring
🧬 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
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
Emma Whitelaw Publication Award — Australasian Epigenetics Alliance
www.aepia.org.au
August 25, 2025 at 2:35 AM
🧬 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
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
Reposted by Chuck Herring
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.
Prompt-based bioinformatics: a new interface for multi-omics analysis www.nature.com/articles/s41... read free: rdcu.be/eAnf4
Vibeoinformatics... computational vibeology... 🧬🖥️🧪
Vibeoinformatics... computational vibeology... 🧬🖥️🧪
Prompt-based bioinformatics: a new interface for multi-omics analysis - Nature Reviews Genetics
Prompt-based methods, which involve the careful design of inputs to guide large language model (LLM) outputs, are beginning to reshape bioinformatic analytical workflows. The authors compare prompt-dr...
www.nature.com
August 14, 2025 at 2:03 PM
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.
Reposted by Chuck Herring
Disentangling the influences of pre- and postnatal periods on human cortical microstructure https://www.biorxiv.org/content/10.1101/2025.08.12.669812v1
August 13, 2025 at 8:15 AM
Disentangling the influences of pre- and postnatal periods on human cortical microstructure https://www.biorxiv.org/content/10.1101/2025.08.12.669812v1
Reposted by Chuck Herring
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.
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.
June 26, 2025 at 4:28 PM
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.
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.
Reposted by Chuck Herring
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
A short thread follows 1/n
June 19, 2025 at 4:37 PM
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
A short thread follows 1/n
Reposted by Chuck Herring
Extrinsic biological stochasticity and technical noise normalization of single-cell RNA sequencing data https://www.biorxiv.org/content/10.1101/2025.05.11.653373v1
May 13, 2025 at 8:46 AM
Extrinsic biological stochasticity and technical noise normalization of single-cell RNA sequencing data https://www.biorxiv.org/content/10.1101/2025.05.11.653373v1
Reposted by Chuck Herring
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's the process that's important to your development, not the end product.
May 7, 2025 at 1:13 PM
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's the process that's important to your development, not the end product.
Reposted by Chuck Herring
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.
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.
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
April 20, 2025 at 4:14 PM
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.
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.
Reposted by Chuck Herring
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. 🧪
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.
go.nature.com
April 9, 2025 at 4:36 PM
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. 🧪
Reposted by Chuck Herring
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
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
April 14, 2025 at 11:44 AM
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
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
Reposted by Chuck Herring
MeCP2 controls dendritic morphogenesis via miR-199a-mediated Qki downregulation https://www.biorxiv.org/content/10.1101/2025.04.04.642981v1
April 5, 2025 at 8:16 AM
MeCP2 controls dendritic morphogenesis via miR-199a-mediated Qki downregulation https://www.biorxiv.org/content/10.1101/2025.04.04.642981v1
Reposted by Chuck Herring
Metabolic Atlas of Early Human Cortex Identifies Regulators of Cell Fate Transitions https://www.biorxiv.org/content/10.1101/2025.03.10.642470v1
March 11, 2025 at 11:16 AM
Metabolic Atlas of Early Human Cortex Identifies Regulators of Cell Fate Transitions https://www.biorxiv.org/content/10.1101/2025.03.10.642470v1
Reposted by Chuck Herring
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
February 12, 2025 at 1:28 AM
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
Reposted by Chuck Herring
ScaleSC: A superfast and scalable single cell RNA-seq data analysis pipeline powered by GPU. https://www.biorxiv.org/content/10.1101/2025.01.28.635256v1
January 30, 2025 at 10:47 AM
ScaleSC: A superfast and scalable single cell RNA-seq data analysis pipeline powered by GPU. https://www.biorxiv.org/content/10.1101/2025.01.28.635256v1
Reposted by Chuck Herring
(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
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...
arxiv.org
December 11, 2024 at 2:30 AM
(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
