Daniel V Brown
@dviousmind.bsky.social
Genomics technologist, SynBio enthusiast and AI hacker at the WEHI Advanced Genomics Facility. Views and opinions are my own.
Pinned
Daniel V Brown
@dviousmind.bsky.social
· Nov 25
TIRE-seq: an Integrated Sample Extraction and Transcriptomics Workflow for High Throughput Perturbation Studies
RNA sequencing is widely used in biomedical research, advancing our understanding of gene expression across biological systems. Traditional methods require upstream RNA extraction from biological inpu...
www.biorxiv.org
Tired of tedious RNA extractions for your transcriptomic studies? Introducing TIRE-seq, a novel protocol that streamlines bulk RNA-seq by integrating sample extraction with library preparation. The whole process can be completed in a day and a half. (1/5) www.biorxiv.org/content/10.1...
Reposted by Daniel V Brown
🧑🔬📰🚀 #RxivMaker is here! A framework automating the creation of publication-ready scientific #preprints from simple Markdown. Goodbye manual formatting, and hello gorgeous manuscripts! A great adventure with @guijacquemet.bsky.social's lab
📜: zenodo.org/records/1575...
👨💻: github.com/HenriquesLab...
📜: zenodo.org/records/1575...
👨💻: github.com/HenriquesLab...
June 27, 2025 at 12:34 PM
🧑🔬📰🚀 #RxivMaker is here! A framework automating the creation of publication-ready scientific #preprints from simple Markdown. Goodbye manual formatting, and hello gorgeous manuscripts! A great adventure with @guijacquemet.bsky.social's lab
📜: zenodo.org/records/1575...
👨💻: github.com/HenriquesLab...
📜: zenodo.org/records/1575...
👨💻: github.com/HenriquesLab...
Reposted by Daniel V Brown
We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!
github.com/martinpacesa...
github.com/martinpacesa...
June 30, 2025 at 7:45 PM
We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!
github.com/martinpacesa...
github.com/martinpacesa...
Reposted by Daniel V Brown
Barcoded viral tracing identifies immunosuppressive astrocyte–glioma interactions @quintanalabhms.bsky.social @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
June 25, 2025 at 5:57 PM
Barcoded viral tracing identifies immunosuppressive astrocyte–glioma interactions @quintanalabhms.bsky.social @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Daniel V Brown
Introducing Arc Institute’s first virtual cell model: STATE
June 23, 2025 at 5:28 PM
Introducing Arc Institute’s first virtual cell model: STATE
Reposted by Daniel V Brown
@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
June 19, 2025 at 8:55 PM
@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
Reposted by Daniel V Brown
If post doc opportunities in ML for genomics were a mountain, then perched at the summit, straddling the border between impossibly alluring and actually real, sits this. You. Should. Apply.
@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
June 19, 2025 at 9:56 PM
If post doc opportunities in ML for genomics were a mountain, then perched at the summit, straddling the border between impossibly alluring and actually real, sits this. You. Should. Apply.
Reposted by Daniel V Brown
Join the @steinaerts.bsky.social Lab via the VIB.AI International PhD Call 2025!
Use ML to decode how DNA sequences control gene activity.
Work with single-cell & spatial genomics, deep learning models, and CRISPR validation.
📍 Leuven
🗓️ Apply by June 22nd → https://tinyurl.com/53nc9vnd
Use ML to decode how DNA sequences control gene activity.
Work with single-cell & spatial genomics, deep learning models, and CRISPR validation.
📍 Leuven
🗓️ Apply by June 22nd → https://tinyurl.com/53nc9vnd
May 27, 2025 at 7:57 AM
Join the @steinaerts.bsky.social Lab via the VIB.AI International PhD Call 2025!
Use ML to decode how DNA sequences control gene activity.
Work with single-cell & spatial genomics, deep learning models, and CRISPR validation.
📍 Leuven
🗓️ Apply by June 22nd → https://tinyurl.com/53nc9vnd
Use ML to decode how DNA sequences control gene activity.
Work with single-cell & spatial genomics, deep learning models, and CRISPR validation.
📍 Leuven
🗓️ Apply by June 22nd → https://tinyurl.com/53nc9vnd
Reposted by Daniel V Brown
FutureHouse's goal has been to automate scientific discovery. Now we used our agents to make a genuine discovery – a potential new treatment for one kind of blindness (dAMD). We had multiple cycles of hypotheses, experiments, and data analysis – including identify the mechanism.
May 20, 2025 at 3:35 PM
FutureHouse's goal has been to automate scientific discovery. Now we used our agents to make a genuine discovery – a potential new treatment for one kind of blindness (dAMD). We had multiple cycles of hypotheses, experiments, and data analysis – including identify the mechanism.
Reposted by Daniel V Brown
A triumph of perseverance from twitterless Tom Weber, Christine Biben and the team, our in vivo barcoding "LoxCode mouse" used to resolve epiblast fate to fetal organs is finally published in @cellpress.bsky.social and available through @jacksonlab.bsky.social www.sciencedirect.com/science/arti...
LoxCode in vivo barcoding reveals epiblast clonal fate bias to fetal organs
Much remains to be learned about the clonal fate of mammalian epiblast cells. Here, we develop high-diversity Cre recombinase-driven LoxCode barcoding…
www.sciencedirect.com
May 16, 2025 at 4:32 AM
A triumph of perseverance from twitterless Tom Weber, Christine Biben and the team, our in vivo barcoding "LoxCode mouse" used to resolve epiblast fate to fetal organs is finally published in @cellpress.bsky.social and available through @jacksonlab.bsky.social www.sciencedirect.com/science/arti...
Reposted by Daniel V Brown
Australia completely lacks a dedicated training program for clinician scientists. With the vision and support of VMIAL
@petermaccc.bsky.social is extremely proud to announce the first clinician-scientist fellowship. If you meet the eligibility criteria PLEASE APPLY!
www.nature.com/naturecareer...
@petermaccc.bsky.social is extremely proud to announce the first clinician-scientist fellowship. If you meet the eligibility criteria PLEASE APPLY!
www.nature.com/naturecareer...
Clinician Scientist Fellowship - Parkville, Melbourne (AU) job with Peter MacCallum Cancer Centre – Parkville | 12839522
Peter Mac is launching Australia’s first clinician-scientist fellowship to advance cancer care, fostering innovation and global collaboration.
www.nature.com
May 15, 2025 at 9:49 AM
Australia completely lacks a dedicated training program for clinician scientists. With the vision and support of VMIAL
@petermaccc.bsky.social is extremely proud to announce the first clinician-scientist fellowship. If you meet the eligibility criteria PLEASE APPLY!
www.nature.com/naturecareer...
@petermaccc.bsky.social is extremely proud to announce the first clinician-scientist fellowship. If you meet the eligibility criteria PLEASE APPLY!
www.nature.com/naturecareer...
Reposted by Daniel V Brown
Start a lab in Australia @wehi-research.bsky.social. and don't assume we're a scientific backwater. WEHI had Science, Cell and Nature Medicine papers among others all in the last month. Wet have a kick ass environment that values discovery, translation and spin outs.
🌏 Make your mark in Melbourne! 🌏 We are looking for innovative researchers to join WEHI as Laboratory Heads and help lead the next wave of biomedical discovery.
For more information and to apply 👇
For more information and to apply 👇
Make your future Melbourne
Lead the next wave of biomedical discovery
www.wehi.edu.au
May 15, 2025 at 9:31 PM
Start a lab in Australia @wehi-research.bsky.social. and don't assume we're a scientific backwater. WEHI had Science, Cell and Nature Medicine papers among others all in the last month. Wet have a kick ass environment that values discovery, translation and spin outs.
Reposted by Daniel V Brown
i believe there are major implications for single-cell ATAC-seq, with possibly strong cell type-dependent Tn5 activity differences making it difficult to sample heterogeneous cell populations effectively.
scATAC has been slow to take off, and variable data quality could be a big reason why
scATAC has been slow to take off, and variable data quality could be a big reason why
May 14, 2025 at 5:43 AM
i believe there are major implications for single-cell ATAC-seq, with possibly strong cell type-dependent Tn5 activity differences making it difficult to sample heterogeneous cell populations effectively.
scATAC has been slow to take off, and variable data quality could be a big reason why
scATAC has been slow to take off, and variable data quality could be a big reason why
Reposted by Daniel V Brown
Inverse folding NNs are better at predicting changes to a mutated protein's equilibrium dynamics, relative to WT, than protein folding NNs (BioEmu & AF-Cluster). This was shown on an enzyme that is more enzymatically promiscuous in the open state.
May 12, 2025 at 6:27 AM
Inverse folding NNs are better at predicting changes to a mutated protein's equilibrium dynamics, relative to WT, than protein folding NNs (BioEmu & AF-Cluster). This was shown on an enzyme that is more enzymatically promiscuous in the open state.
Reposted by Daniel V Brown
🔬 Working with #spatial biology or keen to explore its potential?
Register now for the WEHI Spatial Technology Symposium 2025!
🔎 Expert talks, poster presentations & networking
📍 At WEHI and online
👇 Event info and registration
Register now for the WEHI Spatial Technology Symposium 2025!
🔎 Expert talks, poster presentations & networking
📍 At WEHI and online
👇 Event info and registration
WEHI Spatial Technology Symposium 2025
Join us for a two day symposium exploring everything spatial!
www.eventbrite.com.au
May 13, 2025 at 2:00 AM
🔬 Working with #spatial biology or keen to explore its potential?
Register now for the WEHI Spatial Technology Symposium 2025!
🔎 Expert talks, poster presentations & networking
📍 At WEHI and online
👇 Event info and registration
Register now for the WEHI Spatial Technology Symposium 2025!
🔎 Expert talks, poster presentations & networking
📍 At WEHI and online
👇 Event info and registration
Reposted by Daniel V Brown
Our speaker next week is an amazing scientist from out of town, and this is one that you won't want to miss!
Thursday, May 15th, 7pm EDT
Cannon Room, Building C, @harvardmed.bsky.social
Sarel Fleishman
www.fleishmanlab.org
"Designing new and improved functions in natural protein folds"
bpdmc.org
Thursday, May 15th, 7pm EDT
Cannon Room, Building C, @harvardmed.bsky.social
Sarel Fleishman
www.fleishmanlab.org
"Designing new and improved functions in natural protein folds"
bpdmc.org
schedule
introduction and membership
Boston Protein Design and Modeling Club (BPDMC) is a community of computational protein engineers and modelers from both academia and industry. While we are based in Boston...
bpdmc.org
May 9, 2025 at 3:08 PM
Our speaker next week is an amazing scientist from out of town, and this is one that you won't want to miss!
Thursday, May 15th, 7pm EDT
Cannon Room, Building C, @harvardmed.bsky.social
Sarel Fleishman
www.fleishmanlab.org
"Designing new and improved functions in natural protein folds"
bpdmc.org
Thursday, May 15th, 7pm EDT
Cannon Room, Building C, @harvardmed.bsky.social
Sarel Fleishman
www.fleishmanlab.org
"Designing new and improved functions in natural protein folds"
bpdmc.org
Reposted by Daniel V Brown
Madhavi Krishnans lab with an absolutely amazing new measurement technique:
Measurements of molecular size and shape on a chip | Science www.science.org/doi/10.1126/...
Measurements of molecular size and shape on a chip | Science www.science.org/doi/10.1126/...
Measurements of molecular size and shape on a chip
Size and shape are critical discriminators between molecular species and states. We describe a microchip-based high-throughput imaging approach offering rapid and precise determination of molecular pr...
www.science.org
May 9, 2025 at 8:12 AM
Madhavi Krishnans lab with an absolutely amazing new measurement technique:
Measurements of molecular size and shape on a chip | Science www.science.org/doi/10.1126/...
Measurements of molecular size and shape on a chip | Science www.science.org/doi/10.1126/...
Reposted by Daniel V Brown
We will put forward a 500 million package for 2025-2027 to make Europe a magnet for researchers.
As well as ambitious proposals for R&I in the next EU budget.
We will also offer the best and brightest the right incentives to come to Europe ↓
As well as ambitious proposals for R&I in the next EU budget.
We will also offer the best and brightest the right incentives to come to Europe ↓
May 5, 2025 at 10:02 AM
We will put forward a 500 million package for 2025-2027 to make Europe a magnet for researchers.
As well as ambitious proposals for R&I in the next EU budget.
We will also offer the best and brightest the right incentives to come to Europe ↓
As well as ambitious proposals for R&I in the next EU budget.
We will also offer the best and brightest the right incentives to come to Europe ↓
Reposted by Daniel V Brown
Huge thanks to Koen Theunis and the brilliant collaborators: @dviousmind.bsky.social @leuccilrcb.bsky.social @jdemeul.bsky.social @marinelab.bsky.social and Thierry Voet for making this possible! (8/9)
March 27, 2025 at 11:12 AM
Huge thanks to Koen Theunis and the brilliant collaborators: @dviousmind.bsky.social @leuccilrcb.bsky.social @jdemeul.bsky.social @marinelab.bsky.social and Thierry Voet for making this possible! (8/9)
Reposted by Daniel V Brown
Reposted by Daniel V Brown
State-space models naturally model epistatic relationships in their hidden states. An SSM with 55k parameters to matches models with hundreds of millions of parameters for predicting the properties of biological sequences.
@krithik-bs.bsky.social @sameedms.bsky.social
@pardissabeti.bsky.social
@krithik-bs.bsky.social @sameedms.bsky.social
@pardissabeti.bsky.social
March 26, 2025 at 9:38 PM
State-space models naturally model epistatic relationships in their hidden states. An SSM with 55k parameters to matches models with hundreds of millions of parameters for predicting the properties of biological sequences.
@krithik-bs.bsky.social @sameedms.bsky.social
@pardissabeti.bsky.social
@krithik-bs.bsky.social @sameedms.bsky.social
@pardissabeti.bsky.social
Reposted by Daniel V Brown
Start a group with us in Melbourne at PeterMac! www.nature.com/naturecareer...
Group Leader - Melbourne (Suburb), Greater Melbourne (Inner) (AU) job with Peter MacCallum Cancer Centre | 12837590
Peter Mac is recruiting a Group Leader to increase the capacity and efficiency of our “discovery to translation” cancer research pipeline.
www.nature.com
March 22, 2025 at 8:04 AM
Start a group with us in Melbourne at PeterMac! www.nature.com/naturecareer...
Reposted by Daniel V Brown
New research article from the lab led by the amazing @amydashwood.bsky.social !
In collaboration with @vib-switch-lab.bsky.social @cbdresearch.bsky.social we engineered variants of #IL2 designed for therapeutic use. 1/11
www.sciencedirect.com/science/arti...
In collaboration with @vib-switch-lab.bsky.social @cbdresearch.bsky.social we engineered variants of #IL2 designed for therapeutic use. 1/11
www.sciencedirect.com/science/arti...
Directed disruption of IL2 aggregation and receptor binding sites produces designer biologics with enhanced specificity and improved production capacity
The pleotropic nature of interleukin-2 (IL2) has allowed it to be used as both a pro-inflammatory and anti-inflammatory therapeutic agent, through pro…
www.sciencedirect.com
March 18, 2025 at 3:02 PM
New research article from the lab led by the amazing @amydashwood.bsky.social !
In collaboration with @vib-switch-lab.bsky.social @cbdresearch.bsky.social we engineered variants of #IL2 designed for therapeutic use. 1/11
www.sciencedirect.com/science/arti...
In collaboration with @vib-switch-lab.bsky.social @cbdresearch.bsky.social we engineered variants of #IL2 designed for therapeutic use. 1/11
www.sciencedirect.com/science/arti...
Reposted by Daniel V Brown
Check out this talk from our own Garyk Brixi talking about Evo 2!
Video is up!
"Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A
With the author Garyk Brixi!
"Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A
With the author Garyk Brixi!
Genome modeling and design across all domains of life with Evo 2 | Garyk Brixi
YouTube video by Valence Labs
youtu.be
March 14, 2025 at 2:35 PM
Check out this talk from our own Garyk Brixi talking about Evo 2!
Reposted by Daniel V Brown
Labeling your axes and then explaining them slowly is perhaps the biggest bang for the buck you can get for making your slides more understandable.
March 12, 2025 at 4:38 PM
Labeling your axes and then explaining them slowly is perhaps the biggest bang for the buck you can get for making your slides more understandable.