Brandon Logeman
@blogeman.bsky.social
Assistant Professor at U of Kentucky Medicine 🐾
Functional Genomics of Neural Activity and Animal Behavior at the single cell level
🧬genes->🚥pathways->🧠circuits->🐭behavior
Functional Genomics of Neural Activity and Animal Behavior at the single cell level
🧬genes->🚥pathways->🧠circuits->🐭behavior
Reposted by Brandon Logeman
🧬 New preprint alert! After years of collaborative work across 52 datasets we are presenting eQTLGen phase 2: a genome-wide eQTL meta-analysis covering 43,301 blood samples: www.medrxiv.org/content/10.6... (1/8)
February 6, 2026 at 10:14 AM
🧬 New preprint alert! After years of collaborative work across 52 datasets we are presenting eQTLGen phase 2: a genome-wide eQTL meta-analysis covering 43,301 blood samples: www.medrxiv.org/content/10.6... (1/8)
Reposted by Brandon Logeman
A modular transcript enrichment strategy for scalable, atlas-aligned, and clonotype-resolved single-cell transcriptomics https://www.biorxiv.org/content/10.64898/2026.02.06.703342v1
February 7, 2026 at 6:33 AM
A modular transcript enrichment strategy for scalable, atlas-aligned, and clonotype-resolved single-cell transcriptomics https://www.biorxiv.org/content/10.64898/2026.02.06.703342v1
Reposted by Brandon Logeman
dplyr 1.2.0 is out now and we are SO excited!
- `filter_out()` for dropping rows
- `recode_values()`, `replace_values()`, and `replace_when()` that join `case_when()` as a complete family of recoding/replacing tools
These are huge quality of life wins for #rstats!
tidyverse.org/blog/2026/02...
- `filter_out()` for dropping rows
- `recode_values()`, `replace_values()`, and `replace_when()` that join `case_when()` as a complete family of recoding/replacing tools
These are huge quality of life wins for #rstats!
tidyverse.org/blog/2026/02...
dplyr 1.2.0
dplyr 1.2.0 fills in some important gaps in dplyr's API: we've added a new complement to `filter()` focused on dropping rows, and we've expanded the `case_when()` family with three new recoding and re...
tidyverse.org
February 4, 2026 at 11:39 AM
dplyr 1.2.0 is out now and we are SO excited!
- `filter_out()` for dropping rows
- `recode_values()`, `replace_values()`, and `replace_when()` that join `case_when()` as a complete family of recoding/replacing tools
These are huge quality of life wins for #rstats!
tidyverse.org/blog/2026/02...
- `filter_out()` for dropping rows
- `recode_values()`, `replace_values()`, and `replace_when()` that join `case_when()` as a complete family of recoding/replacing tools
These are huge quality of life wins for #rstats!
tidyverse.org/blog/2026/02...
Reposted by Brandon Logeman
Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain https://www.biorxiv.org/content/10.64898/2026.02.02.703166v1
February 3, 2026 at 8:32 AM
Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain https://www.biorxiv.org/content/10.64898/2026.02.02.703166v1
Reposted by Brandon Logeman
A projection atlas of excitatory and inhibitory inputs to the preBötzinger Complex: substrates for multimodal breathing control https://www.biorxiv.org/content/10.64898/2026.02.02.703188v1
February 2, 2026 at 5:16 PM
A projection atlas of excitatory and inhibitory inputs to the preBötzinger Complex: substrates for multimodal breathing control https://www.biorxiv.org/content/10.64898/2026.02.02.703188v1
Reposted by Brandon Logeman
I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Advancing regulatory variant effect prediction with AlphaGenome - Nature
AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...
www.nature.com
January 30, 2026 at 9:47 AM
I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Brandon Logeman
A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons https://www.biorxiv.org/content/10.64898/2026.01.28.702385v1
January 29, 2026 at 9:31 PM
A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons https://www.biorxiv.org/content/10.64898/2026.01.28.702385v1
Reposted by Brandon Logeman
First week where planyourscience.com had more than 1000 organic users. I know this is nothing by software standards but it is quite something by academic standards. And to everyone using it - tell me what could/should be better. And use it to export a first draft ;)
Scientific Paper Planner - AI-Powered Research Planning
Structure your scientific research with AI-powered guidance. From hypothesis to methodology, plan your research paper with intelligent mentoring.
planyourscience.com
January 28, 2026 at 3:36 PM
First week where planyourscience.com had more than 1000 organic users. I know this is nothing by software standards but it is quite something by academic standards. And to everyone using it - tell me what could/should be better. And use it to export a first draft ;)
Reposted by Brandon Logeman
SqueakPose Studio: An end-to-end platform for pose estimation and real-time edge-AI deployment https://www.biorxiv.org/content/10.64898/2026.01.24.700912v1
January 26, 2026 at 11:15 PM
SqueakPose Studio: An end-to-end platform for pose estimation and real-time edge-AI deployment https://www.biorxiv.org/content/10.64898/2026.01.24.700912v1
Reposted by Brandon Logeman
Bright calcium-modulated bioluminescent indicators for activity imaging and red photon-assisted synaptic transmission https://www.biorxiv.org/content/10.64898/2026.01.20.700092v1
January 23, 2026 at 10:15 AM
Bright calcium-modulated bioluminescent indicators for activity imaging and red photon-assisted synaptic transmission https://www.biorxiv.org/content/10.64898/2026.01.20.700092v1
Reposted by Brandon Logeman
New preprint on technologies to scale up CRISPR screens.
We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.
We also introduce an approach for cloning lentiviral libraries with billions of elements.
We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.
We also introduce an approach for cloning lentiviral libraries with billions of elements.
January 20, 2026 at 1:42 PM
New preprint on technologies to scale up CRISPR screens.
We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.
We also introduce an approach for cloning lentiviral libraries with billions of elements.
We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.
We also introduce an approach for cloning lentiviral libraries with billions of elements.
Reposted by Brandon Logeman
TL;DR: Indirect costs as a percentage of total costs - like the private sector tends to calculate it - for NIH grants is typically around 30-35%.
A short Bluetorial about indirect cost rates and indirect cost recovery.
1/14
1/14
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
January 12, 2026 at 7:57 PM
TL;DR: Indirect costs as a percentage of total costs - like the private sector tends to calculate it - for NIH grants is typically around 30-35%.
Reposted by Brandon Logeman
New revolutionary hack about to change our molecular tool-box!
Thanks @ioavlachos.bsky.social for sharing this!
Rapid evolution of a highly efficient RNA polymerase by homologous recombination
www.nature.com/articles/s41...
Thanks @ioavlachos.bsky.social for sharing this!
Rapid evolution of a highly efficient RNA polymerase by homologous recombination
www.nature.com/articles/s41...
January 10, 2026 at 8:18 PM
New revolutionary hack about to change our molecular tool-box!
Thanks @ioavlachos.bsky.social for sharing this!
Rapid evolution of a highly efficient RNA polymerase by homologous recombination
www.nature.com/articles/s41...
Thanks @ioavlachos.bsky.social for sharing this!
Rapid evolution of a highly efficient RNA polymerase by homologous recombination
www.nature.com/articles/s41...
Reposted by Brandon Logeman
Our paper on the Expanded Registry of candidate cis-Regulatory Elements (cCREs) is out 🎉
www.nature.com/articles/s41...
To celebrate, here’s a "meme-torial" walkthrough of the science.
Let’s get started 🧵 1/11
www.nature.com/articles/s41...
To celebrate, here’s a "meme-torial" walkthrough of the science.
Let’s get started 🧵 1/11
a man wearing a plaid shirt and a purple hat is saying here we go .
ALT: a man wearing a plaid shirt and a purple hat is saying here we go .
media.tenor.com
January 8, 2026 at 2:04 AM
Our paper on the Expanded Registry of candidate cis-Regulatory Elements (cCREs) is out 🎉
www.nature.com/articles/s41...
To celebrate, here’s a "meme-torial" walkthrough of the science.
Let’s get started 🧵 1/11
www.nature.com/articles/s41...
To celebrate, here’s a "meme-torial" walkthrough of the science.
Let’s get started 🧵 1/11
Reposted by Brandon Logeman
Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq https://www.biorxiv.org/content/10.64898/2026.01.01.697286v1
January 2, 2026 at 11:32 PM
Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq https://www.biorxiv.org/content/10.64898/2026.01.01.697286v1
Reposted by Brandon Logeman
A free, open-access library of high-quality organism illustrations for science communication
A free, open-access library of high-quality organism illustrations for science communication
We create vector graphics of model organisms and emerging biological research organisms to enhance our publications. We’re sharing these editable graphics under a CC0 license for other scientists to...
doi.org
December 29, 2025 at 6:03 PM
A free, open-access library of high-quality organism illustrations for science communication
Reposted by Brandon Logeman
Blog post: Just quit
Quitting projects in science is hard, but we should be doing a lot more of it.
open.substack.com/pub/arjunraj...
Quitting projects in science is hard, but we should be doing a lot more of it.
open.substack.com/pub/arjunraj...
Just quit
Quitting projects in science is hard, but we should be doing a lot more of it.
open.substack.com
December 30, 2025 at 3:02 PM
Blog post: Just quit
Quitting projects in science is hard, but we should be doing a lot more of it.
open.substack.com/pub/arjunraj...
Quitting projects in science is hard, but we should be doing a lot more of it.
open.substack.com/pub/arjunraj...
Reposted by Brandon Logeman
Multimodal spatial transcriptomics determines repeat expansion, huntingtin aggregation, and selective cortical neuron loss in Huntington Disease https://www.biorxiv.org/content/10.64898/2025.12.26.696622v1
December 27, 2025 at 9:15 PM
Multimodal spatial transcriptomics determines repeat expansion, huntingtin aggregation, and selective cortical neuron loss in Huntington Disease https://www.biorxiv.org/content/10.64898/2025.12.26.696622v1
Reposted by Brandon Logeman
Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)
Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo
Enhancers control tissue-specific gene expression across metazoans. Although deep learning has enabled enhancer prediction and design in mammalian cell lines and invertebrate systems, it remains uncle...
www.biorxiv.org
December 24, 2025 at 3:06 PM
Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)
Reposted by Brandon Logeman
Optimised fluorescence-activated nuclei sorting for epigenomic analysis of cortical cell types https://www.biorxiv.org/content/10.64898/2025.12.22.695789v1
December 24, 2025 at 5:33 AM
Optimised fluorescence-activated nuclei sorting for epigenomic analysis of cortical cell types https://www.biorxiv.org/content/10.64898/2025.12.22.695789v1
Reposted by Brandon Logeman
I love past me for developing the habit of simultaneously drafting presentation slides when I write papers and/or grant proposals. It makes things sooooo much easier when people ask me to give a talk.
December 18, 2025 at 10:46 PM
I love past me for developing the habit of simultaneously drafting presentation slides when I write papers and/or grant proposals. It makes things sooooo much easier when people ask me to give a talk.
Reposted by Brandon Logeman
A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
An integrated view of the structure and function of the human 4D nucleome - Nature
The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...
www.nature.com
December 17, 2025 at 8:59 PM
A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Brandon Logeman
New paper alert!!...🤩 Led by @blogeman.bsky.social, we identify how cell type-specific hormonal responses in the hypothalamus tunes parenting behavior in males and females 🐭🧠🍼. Highlights in thread 👇 1/6
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Cell Type-Specific Hormonal Signaling Configures Hypothalamic Circuits for Parenting
Parenting behavior emerges from hormonally sensitive circuits, but how distinct circuit components are affected by, and contribute to, sex and state dependent changes in infant caregiving remains uncl...
www.biorxiv.org
December 13, 2025 at 2:03 PM
New paper alert!!...🤩 Led by @blogeman.bsky.social, we identify how cell type-specific hormonal responses in the hypothalamus tunes parenting behavior in males and females 🐭🧠🍼. Highlights in thread 👇 1/6
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Brandon Logeman
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Causal modelling of gene effects from regulators to programs to traits - Nature
Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.
www.nature.com
December 11, 2025 at 5:54 PM
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵: