Michael Totty
@mictott.bsky.social
Postdoctoral neuroscientist at JHU working at the intersection of neural circuits, bioinformatics, and psychiatric disorders.
https://mictott.github.io
https://mictott.github.io
Pinned
Michael Totty
@mictott.bsky.social
· Sep 18
Transcriptomic diversity of amygdalar subdivisions across humans and nonhuman primates
Specialized cell types and links to psychiatric disorders are revealed by genetic mapping of primate amygdala neurons.
www.science.org
Very excited to share my second postdoc, now out in Science Advances! We used targeted snRNA-seq to profile four major subnuclei of the primate across three species (including humans). 1/13 www.science.org/doi/10.1126/...
Reposted by Michael Totty
So functional cell types certainly exist in the spatial system. There is no doubt about this. However, this paper shows that you cannot know that you have found them by just decoding space, or even by showing spatial selectivity! This is a very important thing to tell the field.
November 25, 2025 at 8:34 PM
So functional cell types certainly exist in the spatial system. There is no doubt about this. However, this paper shows that you cannot know that you have found them by just decoding space, or even by showing spatial selectivity! This is a very important thing to tell the field.
Reposted by Michael Totty
"The inevitability and superfluousness of cell types in spatial cognition". Intuitive cell types are found in random artificial networks using the same selection criteria neuroscientists use with actual data. elifesciences.org/reviewed-pre... 1/2
elifesciences.org
November 25, 2025 at 7:29 PM
"The inevitability and superfluousness of cell types in spatial cognition". Intuitive cell types are found in random artificial networks using the same selection criteria neuroscientists use with actual data. elifesciences.org/reviewed-pre... 1/2
Reposted by Michael Totty
A great intro to academic conferencing.
Not sure how I missed this one.
scienceforeveryone.science/getting-the-...
Not sure how I missed this one.
scienceforeveryone.science/getting-the-...
Getting the most of out a scientific conference
A slightly unconventional guide to your first time
scienceforeveryone.science
November 26, 2025 at 4:47 AM
A great intro to academic conferencing.
Not sure how I missed this one.
scienceforeveryone.science/getting-the-...
Not sure how I missed this one.
scienceforeveryone.science/getting-the-...
Reposted by Michael Totty
We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor”!
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
November 22, 2025 at 12:38 PM
We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor”!
Whether you're new to bioinformatics or a seasoned pro, OSTA covers everything that you need to know about spatial transcriptomics data analysis spanning both sequencing and imaging-based technologies within the Bioconductor framework 👨💻🧬
Congrats to all the authors on this huge effort!
Congrats to all the authors on this huge effort!
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
November 21, 2025 at 7:44 PM
Whether you're new to bioinformatics or a seasoned pro, OSTA covers everything that you need to know about spatial transcriptomics data analysis spanning both sequencing and imaging-based technologies within the Bioconductor framework 👨💻🧬
Congrats to all the authors on this huge effort!
Congrats to all the authors on this huge effort!
Reposted by Michael Totty
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
November 21, 2025 at 5:31 PM
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Reposted by Michael Totty
and there it is. the absolutely massive change in R01s funded multi-year. our perceptions that the new mandate, sorry strong suggestion, has had a dramatic effect on forward funding and therefore success rates is validated.
2025
Here the largest fraction is for R01 awards, followed by RF1s, and R21s.
In most cases, these were R01s that had not particularly reason to be forward funded except that NIH had put itself in a situation when large amounts of funding needed to be committed by the end of the fiscal year
21/25
Here the largest fraction is for R01 awards, followed by RF1s, and R21s.
In most cases, these were R01s that had not particularly reason to be forward funded except that NIH had put itself in a situation when large amounts of funding needed to be committed by the end of the fiscal year
21/25
November 5, 2025 at 4:45 PM
and there it is. the absolutely massive change in R01s funded multi-year. our perceptions that the new mandate, sorry strong suggestion, has had a dramatic effect on forward funding and therefore success rates is validated.
Learning induces persistent chromatin loops underlying robust gene expression during memory recall www.biorxiv.org/content/10.1...
Learning induces persistent chromatin loops underlying robust gene expression during memory recall
Long-term memories are stored in neuronal ensembles called engrams, but the existence of persistent molecular traces in nuclei of engram neurons remain unknown. Using activity-dependent nuclear taggin...
www.biorxiv.org
October 8, 2025 at 1:17 PM
Learning induces persistent chromatin loops underlying robust gene expression during memory recall www.biorxiv.org/content/10.1...
Locus Coeruleus-Amygdala Circuit Disrupts Prefrontal Control to Impair Fear Extinction. www.biorxiv.org/content/10.1...
Locus Coeruleus-Amygdala Circuit Disrupts Prefrontal Control to Impair Fear Extinction
Background Stress undermines extinction learning and hinders exposure-based clinical therapies for a variety of neuropsychiatric disorders. In both animals and humans, dysfunction in the ventromedial ...
www.biorxiv.org
October 6, 2025 at 9:32 PM
Locus Coeruleus-Amygdala Circuit Disrupts Prefrontal Control to Impair Fear Extinction. www.biorxiv.org/content/10.1...
Reposted by Michael Totty
Have you wondered which neuron types are conserved across mammals and amygdalar subdivisions? Check out this article from @mictott.bsky.social et al. in Science Advances bit.ly/4pKcbkO #PRF #PapersoftheWeek
October 2, 2025 at 2:00 PM
Have you wondered which neuron types are conserved across mammals and amygdalar subdivisions? Check out this article from @mictott.bsky.social et al. in Science Advances bit.ly/4pKcbkO #PRF #PapersoftheWeek
Single-cell long-read sequencing of the experience-induced transcriptome www.biorxiv.org/content/10.1...
Single-cell long-read sequencing of the experience-induced transcriptome
Neural activity drives transcriptional events that are critical for learning. Activity-induced transcript isoform expression and alternative splicing are cell-type specific events typically obscured b...
www.biorxiv.org
September 18, 2025 at 2:56 PM
Single-cell long-read sequencing of the experience-induced transcriptome www.biorxiv.org/content/10.1...
Reposted by Michael Totty
This was a really fantastic collaboration! Congratulations @mictott.bsky.social Rita Cervera Juanes,
@svitlanabach.bsky.social and all co-authors! 🧪🧬💻🧠
@svitlanabach.bsky.social and all co-authors! 🧪🧬💻🧠
Very excited to share my second postdoc, now out in Science Advances! We used targeted snRNA-seq to profile four major subnuclei of the primate across three species (including humans). 1/13 www.science.org/doi/10.1126/...
Transcriptomic diversity of amygdalar subdivisions across humans and nonhuman primates
Specialized cell types and links to psychiatric disorders are revealed by genetic mapping of primate amygdala neurons.
www.science.org
September 18, 2025 at 1:17 AM
This was a really fantastic collaboration! Congratulations @mictott.bsky.social Rita Cervera Juanes,
@svitlanabach.bsky.social and all co-authors! 🧪🧬💻🧠
@svitlanabach.bsky.social and all co-authors! 🧪🧬💻🧠
Yes, I am on the academic job market looking to start my own lab at the intersection of molecular, computational, and systems neuroscience! If you think my work may be interest to your department, please don't hesitate to reach out.
Thank you, Keri!
Thank you, Keri!
Congrats Michael! Really appreciate the brilliance & creativity you brought to the analyses and as always, sincere dedication to open science 🧪 🧠
@mictott.bsky.social is on the job market!! Amazing skillset spanning wet lab/computational at molecular, cellular + systems level - and across species!
@mictott.bsky.social is on the job market!! Amazing skillset spanning wet lab/computational at molecular, cellular + systems level - and across species!
Very excited to share my second postdoc, now out in Science Advances! We used targeted snRNA-seq to profile four major subnuclei of the primate across three species (including humans). 1/13 www.science.org/doi/10.1126/...
September 18, 2025 at 1:31 AM
Yes, I am on the academic job market looking to start my own lab at the intersection of molecular, computational, and systems neuroscience! If you think my work may be interest to your department, please don't hesitate to reach out.
Thank you, Keri!
Thank you, Keri!
Reposted by Michael Totty
Congrats Michael! Really appreciate the brilliance & creativity you brought to the analyses and as always, sincere dedication to open science 🧪 🧠
@mictott.bsky.social is on the job market!! Amazing skillset spanning wet lab/computational at molecular, cellular + systems level - and across species!
@mictott.bsky.social is on the job market!! Amazing skillset spanning wet lab/computational at molecular, cellular + systems level - and across species!
Very excited to share my second postdoc, now out in Science Advances! We used targeted snRNA-seq to profile four major subnuclei of the primate across three species (including humans). 1/13 www.science.org/doi/10.1126/...
Transcriptomic diversity of amygdalar subdivisions across humans and nonhuman primates
Specialized cell types and links to psychiatric disorders are revealed by genetic mapping of primate amygdala neurons.
www.science.org
September 18, 2025 at 1:24 AM
Congrats Michael! Really appreciate the brilliance & creativity you brought to the analyses and as always, sincere dedication to open science 🧪 🧠
@mictott.bsky.social is on the job market!! Amazing skillset spanning wet lab/computational at molecular, cellular + systems level - and across species!
@mictott.bsky.social is on the job market!! Amazing skillset spanning wet lab/computational at molecular, cellular + systems level - and across species!
Very excited to share my second postdoc, now out in Science Advances! We used targeted snRNA-seq to profile four major subnuclei of the primate across three species (including humans). 1/13 www.science.org/doi/10.1126/...
Transcriptomic diversity of amygdalar subdivisions across humans and nonhuman primates
Specialized cell types and links to psychiatric disorders are revealed by genetic mapping of primate amygdala neurons.
www.science.org
September 18, 2025 at 1:10 AM
Very excited to share my second postdoc, now out in Science Advances! We used targeted snRNA-seq to profile four major subnuclei of the primate across three species (including humans). 1/13 www.science.org/doi/10.1126/...
Reposted by Michael Totty
Congratulations to @mictott.bsky.social, Rita Cervera Juanes and @svitlanabach.bsky.social and all co-authors! Really fun collaboration w/labs of @vincentcostaphd.bsky.social and @stephaniehicks.bsky.social to better understand cell type and spatial heterogeneity across amygdala in primate 🧠!
A spatially resolved transcriptomic atlas of the primate amygdala (human, macaque, and baboon) now out in Science Advances (www.science.org/doi/10.1126/...). The amygdala contains 32 types of neurons with many neuron types specific to particular subdivisions.
Lots of updates from the preprint!
Lots of updates from the preprint!
Transcriptomic diversity of amygdalar subdivisions across humans and nonhuman primates
Specialized cell types and links to psychiatric disorders are revealed by genetic mapping of primate amygdala neurons.
www.science.org
September 17, 2025 at 9:10 PM
Congratulations to @mictott.bsky.social, Rita Cervera Juanes and @svitlanabach.bsky.social and all co-authors! Really fun collaboration w/labs of @vincentcostaphd.bsky.social and @stephaniehicks.bsky.social to better understand cell type and spatial heterogeneity across amygdala in primate 🧠!
Reposted by Michael Totty
Hot take #3: “BLA subdivisions contain specific subtypes of excitatory and inhibitory neurons.
Hot take #4: Genes downregulated in PTSD load mainly onto specific subtypes of inhibitory interneurons that are highly conserved across primates.
Hot take #4: Genes downregulated in PTSD load mainly onto specific subtypes of inhibitory interneurons that are highly conserved across primates.
September 17, 2025 at 7:31 PM
Hot take #3: “BLA subdivisions contain specific subtypes of excitatory and inhibitory neurons.
Hot take #4: Genes downregulated in PTSD load mainly onto specific subtypes of inhibitory interneurons that are highly conserved across primates.
Hot take #4: Genes downregulated in PTSD load mainly onto specific subtypes of inhibitory interneurons that are highly conserved across primates.
Reposted by Michael Totty
Hot take #1: Amygdala neuron types are highly conserved across different primate species. No human specific innovations.
Hot take #2: Canonical gene markers identified for murine amygdala neuron types are not especially informative inferring cell type identifies for the primate amygdala.
Hot take #2: Canonical gene markers identified for murine amygdala neuron types are not especially informative inferring cell type identifies for the primate amygdala.
September 17, 2025 at 7:31 PM
Hot take #1: Amygdala neuron types are highly conserved across different primate species. No human specific innovations.
Hot take #2: Canonical gene markers identified for murine amygdala neuron types are not especially informative inferring cell type identifies for the primate amygdala.
Hot take #2: Canonical gene markers identified for murine amygdala neuron types are not especially informative inferring cell type identifies for the primate amygdala.
Reposted by Michael Totty
A spatially resolved transcriptomic atlas of the primate amygdala (human, macaque, and baboon) now out in Science Advances (www.science.org/doi/10.1126/...). The amygdala contains 32 types of neurons with many neuron types specific to particular subdivisions.
Lots of updates from the preprint!
Lots of updates from the preprint!
Transcriptomic diversity of amygdalar subdivisions across humans and nonhuman primates
Specialized cell types and links to psychiatric disorders are revealed by genetic mapping of primate amygdala neurons.
www.science.org
September 17, 2025 at 7:31 PM
A spatially resolved transcriptomic atlas of the primate amygdala (human, macaque, and baboon) now out in Science Advances (www.science.org/doi/10.1126/...). The amygdala contains 32 types of neurons with many neuron types specific to particular subdivisions.
Lots of updates from the preprint!
Lots of updates from the preprint!
Reposted by Michael Totty
(1/10) We’re excited to share our new preprint (doi.org/10.1101/2025...), which uncovers the spatiomolecular landscape of the human nucleus accumbens (NAc), by integrating snRNA-seq with Visium spatial transcriptomics across 10 control donors. 🧠 #NAcLIBD #snRNAseq #10xVisium
September 15, 2025 at 5:06 PM
(1/10) We’re excited to share our new preprint (doi.org/10.1101/2025...), which uncovers the spatiomolecular landscape of the human nucleus accumbens (NAc), by integrating snRNA-seq with Visium spatial transcriptomics across 10 control donors. 🧠 #NAcLIBD #snRNAseq #10xVisium
Reposted by Michael Totty
Super excited to share this work & accompanying data resources in collab with @martinowk.bsky.social @stephaniehicks.bsky.social @alexisbattle.bsky.social! Congrats to all coauthors and big shout out to @svitlana-bach.bsky.social @prashanthi-ravi.bsky.social for leading this NIDA-funded project.
(1/10) We’re excited to share our new preprint (doi.org/10.1101/2025...), which uncovers the spatiomolecular landscape of the human nucleus accumbens (NAc), by integrating snRNA-seq with Visium spatial transcriptomics across 10 control donors. 🧠 #NAcLIBD #snRNAseq #10xVisium
September 15, 2025 at 5:41 PM
Super excited to share this work & accompanying data resources in collab with @martinowk.bsky.social @stephaniehicks.bsky.social @alexisbattle.bsky.social! Congrats to all coauthors and big shout out to @svitlana-bach.bsky.social @prashanthi-ravi.bsky.social for leading this NIDA-funded project.
Beautiful new work from Tugce Tuna, Flavio Mourao, and @stevemaren.bsky.social showing that 8 Hz stimulation of the thalamic nucleus reuniens entrains mPFC-HPC oscillations and facilitates fear extinction! www.biorxiv.org/content/10.1...
Theta-paced stimulation of the thalamic nucleus reuniens entrains mPFC-HPC oscillations and facilitates the acquisition of extinction memories
Background: The nucleus reuniens (RE) is a midline thalamic nucleus interconnecting the medial prefrontal cortex (mPFC) and the hippocampus (HPC), structures known to be involved in aversive memory pr...
www.biorxiv.org
August 18, 2025 at 5:22 PM
Beautiful new work from Tugce Tuna, Flavio Mourao, and @stevemaren.bsky.social showing that 8 Hz stimulation of the thalamic nucleus reuniens entrains mPFC-HPC oscillations and facilitates fear extinction! www.biorxiv.org/content/10.1...
Stress-Responsive Neuronal Ensembles and β-Adrenergic Signaling in the Basolateral Amygdala Modulate the Infralimbic Cortical Activity and Govern the Delayed Stress-Induced Fear Extinction Deficit www.jneurosci.org/content/45/3...
Stress-Responsive Neuronal Ensembles and β-Adrenergic Signaling in the Basolateral Amygdala Modulate the Infralimbic Cortical Activity and Govern the Delayed Stress-Induced Fear Extinction Deficit
Stress is a critical risk factor for the development of psychological disorders, including anxiety and post-traumatic stress disorder. Key brain regions, including the basolateral amygdala (BLA) and t...
www.jneurosci.org
August 7, 2025 at 2:08 PM
Stress-Responsive Neuronal Ensembles and β-Adrenergic Signaling in the Basolateral Amygdala Modulate the Infralimbic Cortical Activity and Govern the Delayed Stress-Induced Fear Extinction Deficit www.jneurosci.org/content/45/3...
Reposted by Michael Totty
Excited to share this huge team effort collaboration supervised by Stephanie Page in Translational Neuroscience @lieberinstitute.bsky.social and @stephaniehicks.bsky.social @jhubiostat.bsky.social to generate a spatio-molecular resource of the hippocampus in human 🧠
www.nature.com/articles/s41...
www.nature.com/articles/s41...
An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus - Nature Neuroscience
The topographical organization of cells in the hippocampus reflects its ability to regulate mood and cognition. Here the authors generate a spatially resolved gene expression map in the human hippocam...
www.nature.com
July 30, 2025 at 8:51 PM
Excited to share this huge team effort collaboration supervised by Stephanie Page in Translational Neuroscience @lieberinstitute.bsky.social and @stephaniehicks.bsky.social @jhubiostat.bsky.social to generate a spatio-molecular resource of the hippocampus in human 🧠
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Happy to see the last bit of data I collected during my PhD out in publication now! Congrats to grad student Tugce Tuna for leading the manuscript, as well as our co-first author Muhammad Badarnee for leading the effort to incorporate fMRI analyses of the human reuniens!
🚨New paper🚨 Excited to share this collaborative paper exploring nucleus reuniens correlates of fear conditioning in both rats and humans! Congrats @tugcettuna @F_Mourao_ @MicTott Muhammad Badarnee and Moh Milad!! rdcu.be/eyTPs
Associative coding of conditioned fear in the thalamic nucleus reuniens in rodents and humans
Communications Biology - The nucleus reuniens encodes associative value in both humans and rats. In rats, it also tracks defensive freezing states. The reuniens has a conserved role across species...
rdcu.be
August 2, 2025 at 4:38 PM
Happy to see the last bit of data I collected during my PhD out in publication now! Congrats to grad student Tugce Tuna for leading the manuscript, as well as our co-first author Muhammad Badarnee for leading the effort to incorporate fMRI analyses of the human reuniens!