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/...
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...
Thanks, Stephanie!!
September 18, 2025 at 1:32 AM
Thanks, Stephanie!!
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!
A huge thank you and congrats to all of my co-first authors, Rita Cervera Juanes and @svitlanabach.bsky.social, and my mentors and collaborators @martinowk.bsky.social @vincentcostaphd.bsky.social, @stephaniehicks.bsky.social.
September 18, 2025 at 1:10 AM
A huge thank you and congrats to all of my co-first authors, Rita Cervera Juanes and @svitlanabach.bsky.social, and my mentors and collaborators @martinowk.bsky.social @vincentcostaphd.bsky.social, @stephaniehicks.bsky.social.
We hope that this data will be a valuable resource for the broader community. We have developed in-browser shiny apps to explore the processed data available on the github page (tinyurl.com/2jnascj9), and all raw data is currently available via GEO (GSE281366). 12/13
GitHub - LieberInstitute/BLA_crossSpecies: Collaboration between Costa, Martinowich, and Hicks labs investigating basolateral amygdala cell-types across huamn and non-human primate species.
Collaboration between Costa, Martinowich, and Hicks labs investigating basolateral amygdala cell-types across huamn and non-human primate species. - LieberInstitute/BLA_crossSpecies
tinyurl.com
September 18, 2025 at 1:10 AM
We hope that this data will be a valuable resource for the broader community. We have developed in-browser shiny apps to explore the processed data available on the github page (tinyurl.com/2jnascj9), and all raw data is currently available via GEO (GSE281366). 12/13
Finally, leveraging the human dataset, we conducted cell type enrichment for heritability of psychiatric traits (GWAS), as well as MDD and PTSD-associated transcriptomic changes. Aligning with previous literature, we found that GABAergic neurons were enriched for both. 11/13
September 18, 2025 at 1:10 AM
Finally, leveraging the human dataset, we conducted cell type enrichment for heritability of psychiatric traits (GWAS), as well as MDD and PTSD-associated transcriptomic changes. Aligning with previous literature, we found that GABAergic neurons were enriched for both. 11/13
Of importance, using the Yu et al dataset, we found amydala neuron types were markedly less conserved from humans to mice than humans to NHPs. While one to one cell type mapping could still be observed for inhibitory neurons, this was not true for excitatory cells. 10/13
September 18, 2025 at 1:10 AM
Of importance, using the Yu et al dataset, we found amydala neuron types were markedly less conserved from humans to mice than humans to NHPs. While one to one cell type mapping could still be observed for inhibitory neurons, this was not true for excitatory cells. 10/13
Leveraging the precise subregion punches in NHPs, pseudobulk differential analysis revealed highly specific marker genes for excitatory neurons found in the LA, BA, and aBA across species. We confirmed these novel markers using in situ hybridization in both humans and macaques. 9/13
September 18, 2025 at 1:10 AM
Leveraging the precise subregion punches in NHPs, pseudobulk differential analysis revealed highly specific marker genes for excitatory neurons found in the LA, BA, and aBA across species. We confirmed these novel markers using in situ hybridization in both humans and macaques. 9/13
Moving onto excitatory neurons, we found that the LA, BA, and aBA subnuclei are almost exclusively composed of distinct classes of excitatory neuron types, and these neurons display relatively strong cross-species conservation (though less than inhibitory). 8/13
September 18, 2025 at 1:10 AM
Moving onto excitatory neurons, we found that the LA, BA, and aBA subnuclei are almost exclusively composed of distinct classes of excitatory neuron types, and these neurons display relatively strong cross-species conservation (though less than inhibitory). 8/13
Within the BLA, we additionally found the aBA contains a large number of CCK+/CNR1+ interneurons, and that the LA, BA, and aBA nuclei were enriched for distinct subpopulations of SST+ and PVALB+ neurons. 7/13
September 18, 2025 at 1:10 AM
Within the BLA, we additionally found the aBA contains a large number of CCK+/CNR1+ interneurons, and that the LA, BA, and aBA nuclei were enriched for distinct subpopulations of SST+ and PVALB+ neurons. 7/13
Compositional analyses using linear mixed models (crumblr) found that the central nucleus was enriched in neurons derived from the LGE (PRKCD+, SST/TAC1+, DLK1+, etc), whereas the BLA is enriched in MGE (SST+,PVALB+) and CGE (LAMP5+, CCK+) cell types. 6/13
September 18, 2025 at 1:10 AM
Compositional analyses using linear mixed models (crumblr) found that the central nucleus was enriched in neurons derived from the LGE (PRKCD+, SST/TAC1+, DLK1+, etc), whereas the BLA is enriched in MGE (SST+,PVALB+) and CGE (LAMP5+, CCK+) cell types. 6/13
For inhibitory neurons, we found a wide variety of cell types (putatively) spanning medial, caudal, and lateral ganglionic origins - including two intercalated cell types (TSHZ1+) - which all displayed strong cross-species conservation. 5/13
September 18, 2025 at 1:10 AM
For inhibitory neurons, we found a wide variety of cell types (putatively) spanning medial, caudal, and lateral ganglionic origins - including two intercalated cell types (TSHZ1+) - which all displayed strong cross-species conservation. 5/13
This resulted in ~130,000 single nuclei across the three species, capturing a wide diversity of inhibitory and excitatory neurons, as well as non-neuronal populations. 4/13
September 18, 2025 at 1:10 AM
This resulted in ~130,000 single nuclei across the three species, capturing a wide diversity of inhibitory and excitatory neurons, as well as non-neuronal populations. 4/13
Despite the difficulties working with fresh frozen postmortem brains, @svitlanabach.bsky.social
was able to precisely capture the basolateral complex from 5 human donors. We then performed cross-species integration to decode subnuclei origins of human amygdala cell types. 3/13
was able to precisely capture the basolateral complex from 5 human donors. We then performed cross-species integration to decode subnuclei origins of human amygdala cell types. 3/13
September 18, 2025 at 1:10 AM
Despite the difficulties working with fresh frozen postmortem brains, @svitlanabach.bsky.social
was able to precisely capture the basolateral complex from 5 human donors. We then performed cross-species integration to decode subnuclei origins of human amygdala cell types. 3/13
was able to precisely capture the basolateral complex from 5 human donors. We then performed cross-species integration to decode subnuclei origins of human amygdala cell types. 3/13
In a multi-institute effort, we conducted snRNA-seq of the baboon, macaque, and human amygdala. In baboons and macaques, @vincentcostaphd.bsky.social and his lab were able to take precise punches of the lateral (LA), basal (BA), accessory basal (aBA), and central nuclei (CeA). 2/13
September 18, 2025 at 1:10 AM
In a multi-institute effort, we conducted snRNA-seq of the baboon, macaque, and human amygdala. In baboons and macaques, @vincentcostaphd.bsky.social and his lab were able to take precise punches of the lateral (LA), basal (BA), accessory basal (aBA), and central nuclei (CeA). 2/13
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/...