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Justus Kebschull @justuskebschull.bsky.social · Sep 9

Annoyed at how difficult MAPseq dissections can be? Check out the new preprint from Kebschull undergrad Rishi Koneru and grad student @mmganant.bsky.social: www.biorxiv.org/content/10.1...

DART: A GUI Pipeline for Aligning Histological Brain Sections to 3D Atlases and Automating Laser Microdissection

The precise dissection of anatomically defined brain regions is the basis of many workflows in neurobiology. Traditionally, brain regions of interest are defined by visual inspection of tissue section...

www.biorxiv.org

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Justus Kebschull @justuskebschull.bsky.social · Jul 19

Want to learn everything there is to know about barcoded connectomics, brain clearing, and modern neuroanatomy? There is still time to apply for the CSHL High Throughput Neuroanatomy course! Stipends are available. meetings.cshl.edu/courses.aspx...

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Justus Kebschull @justuskebschull.bsky.social · Jul 7

I hope you all have fun digging into this and using POINTseq and MAPseq2 for your own favorite circuits!

Justus Kebschull @justuskebschull.bsky.social · Jul 7

And even when neurons innervate the same kind of regions, they can do so in different ways. VTA and SNc DA neurons projecting to the dorsal striatum project fundamentally differently. SNc neurons innervate more subregions and broadcast randomly to these regions, while VTA neurons are highly specific

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Justus Kebschull @justuskebschull.bsky.social · Jul 7

This large number of clusters is not an effect of splitting a stochastically wired system. Co-innervation patterns and projection motifs are often far from the null model of independent projection choice.

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Justus Kebschull @justuskebschull.bsky.social · Jul 7

We find over 30 connectomic cell types, way more than would have been expected from transcriptomic cell types. Overall, our data agrees nicely with what we know, but boy, is there more structure to this system. Maybe easier to see from the dot plots.

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Justus Kebschull @justuskebschull.bsky.social · Jul 7

To showcase POINTseq's utility, we then applied it to the midbrain dopaminergic system, mapping >3,800 DA neurons in the VTA and SNc.

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Justus Kebschull @justuskebschull.bsky.social · Jul 7

We validated POINTseq in the mouse motor cortex using two cre lines and AAVretro-cre to define cell types of interest.

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Justus Kebschull @justuskebschull.bsky.social · Jul 7

This works all over the brain

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Justus Kebschull @justuskebschull.bsky.social · Jul 7

POINTseq achieves cell type specific barcoding by pseudotyping barcoded Sindbis virus with the structural proteins of Alphavirus CHIKV, and overexpressing CHIKV cellular receptor Mxra8 in target cells. Mxra8 isn't normally expressed in mouse neurons, enabling cell type specific infection.

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Justus Kebschull @justuskebschull.bsky.social · Jul 7

Finally have time to add some more meat here. MAPseq2 is what it says on the tin. Better and cheaper. Use this going forward for anything involving MAPseq, including BARseq, BRICseq, and ConnectID!

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Reposted by Justus Kebschull

Arkarup Banerjee @arkarupbanerjee.bsky.social · Jun 26

Next-generation of barcoded projection mapping techniques: MAPseq2 and POINTseq! Congratulations @justuskebschull.bsky.social and team.

Justus Kebschull @justuskebschull.bsky.social · Jun 26

Excited to share the first 2(!) preprints from the Kebschull Lab. The amazing @hyopilkim.bsky.social developed MAPseq2 & POINTseq and used them to map the dopaminergic cells of VTA and SNc. tl;dr MAPseq2=10x cheaper, 4x better; POINTseq=easy cell type specific barcoding; DA neurons=very cool.

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Justus Kebschull @justuskebschull.bsky.social · Jun 26

www.biorxiv.org/content/10.1...

Mapping the projectional architecture of the mouse midbrain dopaminergic system using cell type-specific barcoding

Brain-wide neural circuits are formed by the diverse axonal branching patterns of many individual neurons. Here we introduce POINTseq (projections of interest by sequencing), a high-throughput and use...

www.biorxiv.org

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Justus Kebschull @justuskebschull.bsky.social · Jun 26

www.biorxiv.org/content/10.1...

MAPseq2: a sensitive and cost-effective barcoded connectomics method

The barcoded connectomics tool MAPseq enables highly multiplexed projection mapping of individual neurons by translating neuroanatomy into a DNA sequencing problem. Here we present MAPseq2, a user-fri...

www.biorxiv.org

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Justus Kebschull @justuskebschull.bsky.social · Jun 26

Excited to share the first 2(!) preprints from the Kebschull Lab. The amazing @hyopilkim.bsky.social developed MAPseq2 & POINTseq and used them to map the dopaminergic cells of VTA and SNc. tl;dr MAPseq2=10x cheaper, 4x better; POINTseq=easy cell type specific barcoding; DA neurons=very cool.

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Reposted by Justus Kebschull

Paul Masset @paulmasset.bsky.social · Jun 4

Our work with Pablo Tano, @hyunggoo-kim.bsky.social Athar Malik, Alexandre Pouget and @naoshigeuchida.bsky.social exploring how dopamine neurons could enable multi-timescale reinforcement learning in the brain is out in @nature.com
www.nature.com/articles/s41...

Multi-timescale reinforcement learning in the brain - Nature

Individual dopaminergic neurons encode future rewards over distinct temporal horizons.

www.nature.com

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Reposted by Justus Kebschull

Klingenstein Philanthropies @klingensteinorg.bsky.social · Jun 2

Thank you to @xinjin.bsky.social and @justuskebschull.bsky.social for presenting their research at the recent Klingenstein Fellowship Awards in Neuroscience Conference.

📷 : SimonProPhoto

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Reposted by Justus Kebschull

Joaquina Delas @joadelas.bsky.social · May 8

Fantastic opportunity to move to Europe, and yes, it includes the UK!

But applicants can be from any nationality.

Our team at UCL is still growing. Get in touch if any of our work sounds interesting.

delaslab.com

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Reposted by Justus Kebschull

Stand Up for Science! @standupforscience.bsky.social · Feb 12

Welcome to the Bluesky account for Stand Up for Science 2025!

Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide!

#scienceforall #sciencenotsilence

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Reposted by Justus Kebschull

Cell & Systems Biology (CSB) @uoftcellsysbiol.bsky.social · Feb 10

On Friday, Feb 14 ❤️, we will welcome Prof Justus Kebschull @justuskebschull.bsky.social of Johns Hopkins Biomedical Engineering for his talk on “Understanding brain function and evolution with barcodes and sequencing”. Happening at 11am in RW432. See you there!

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Reposted by Justus Kebschull

Rick Huganir @rhuganir.bsky.social · Feb 7

This is the end of science as we know it if it stands—15% IDCs for all NIH Grants.

grants.nih.gov/grants/guide...

NOT-OD-25-068: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates

NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates NOT-OD-25-068. OD

grants.nih.gov

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Reposted by Justus Kebschull

IDDjobs @iddjobs.org · Jan 20

Postdoc (Baltimore, United States)
Viral Phylodynamics & Neuroscience
with @justuskebschull.bsky.social @rezakalhor.bsky.social
More details: http://iddjobs.org/jobs/johns-hopkins-postdoc-position-in-viral-phylodynamics-neuroscience

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Reposted by Justus Kebschull

IDDjobs @iddjobs.org · Jan 20

Bioinformatician (Baltimore, United States)
Viral Phylodynamics & Neuroscience
with @justuskebschull.bsky.social @rezakalhor.bsky.social
More details: http://iddjobs.org/jobs/hopkins-bioinformatician-position-in-viral-phylodynamics-neuroscience

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Reposted by Justus Kebschull

Seth Blackshaw @sethblackshaw.bsky.social · Jan 8

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Reposted by Justus Kebschull

Richard Sever @richardsever.bsky.social · Dec 21

Many academics point to bioRxiv as “the one thing improving science publishing”.

If so, the one thing you all can do is persuade colleagues to submit and make this a norm. 1/2

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