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
Exciting new study led by @ekerdoncuff.bsky.social and @meaghanmarohn.bsky.social on the evolution of Lactase Persistence in South Asia.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes
Lactase persistence (LP), the ability to digest lactose from milk into adulthood, is a classic example of natural selection in humans. Multiple mutations upstream of the LCT gene are associated with L...
www.biorxiv.org
November 7, 2025 at 2:33 PM
Exciting new study led by @ekerdoncuff.bsky.social and @meaghanmarohn.bsky.social on the evolution of Lactase Persistence in South Asia.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Brandon Logeman
Nice! Whole-genome heritability estimates in the UK Biobank. Average WGS-h2 was 26%, with 21% common and 5% rare. Broadly aligns with recent sib-reg and RDR estimates.
First time on Bsky and first big announcement!
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
Estimation and mapping of the missing heritability of human phenotypes - Nature
WGS data were used from 347,630 individuals with European ancestry in the UK Biobank to obtain high-precision estimates of coding and non-coding rare variant heritability for 34 co...
www.nature.com
November 13, 2025 at 11:41 PM
Nice! Whole-genome heritability estimates in the UK Biobank. Average WGS-h2 was 26%, with 21% common and 5% rare. Broadly aligns with recent sib-reg and RDR estimates.
Reposted by Brandon Logeman
First time on Bsky and first big announcement!
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
Estimation and mapping of the missing heritability of human phenotypes - Nature
WGS data were used from 347,630 individuals with European ancestry in the UK Biobank to obtain high-precision estimates of coding and non-coding rare variant heritability for 34 co...
www.nature.com
November 12, 2025 at 5:57 PM
First time on Bsky and first big announcement!
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
Reposted by Brandon Logeman
Excited to share this preprint from first author Jon Rosen, a postdoctoral fellow in the @klmohlke.bsky.social lab and my lab. We examine eQTL study sample size and how this affects signal discovery and rates of colocalization with GWAS.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Higher eQTL power reveals signals that boost GWAS colocalization
Expression quantitative trait locus (eQTL) studies in human cohorts typically detect at least one regulatory signal per gene, and have been proposed as a way to explain mechanisms of genetic liability...
www.biorxiv.org
August 18, 2025 at 12:18 PM
Excited to share this preprint from first author Jon Rosen, a postdoctoral fellow in the @klmohlke.bsky.social lab and my lab. We examine eQTL study sample size and how this affects signal discovery and rates of colocalization with GWAS.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Brandon Logeman
Here is another way to put the paradox. If you ask, "If I had different genes, would my personality be different?" Then the answer is, "Probably, yes." If you ask, "If I had THESE genes, what would my personality be like?", the answer is, "We don't have any idea."
October 17, 2025 at 3:06 PM
Here is another way to put the paradox. If you ask, "If I had different genes, would my personality be different?" Then the answer is, "Probably, yes." If you ask, "If I had THESE genes, what would my personality be like?", the answer is, "We don't have any idea."
Reposted by Brandon Logeman
Friendly reminder that there is only one official release of ChromBPNet at our lab GitHub github.com/kundajelab/chr…
There are other versions floating around eg. in the CRESTED package that are NOT anywhere close to the official implementation. 1/
There are other versions floating around eg. in the CRESTED package that are NOT anywhere close to the official implementation. 1/
https://github.com/kundajelab/chr…
October 15, 2025 at 1:39 AM
Friendly reminder that there is only one official release of ChromBPNet at our lab GitHub github.com/kundajelab/chr…
There are other versions floating around eg. in the CRESTED package that are NOT anywhere close to the official implementation. 1/
There are other versions floating around eg. in the CRESTED package that are NOT anywhere close to the official implementation. 1/
Reposted by Brandon Logeman
Direct In-Sample Sequencing of the 3' Transcriptome Expands the Capabilities of Optical Pooled Screens https://www.biorxiv.org/content/10.1101/2025.10.11.681797v1
October 14, 2025 at 12:33 AM
Direct In-Sample Sequencing of the 3' Transcriptome Expands the Capabilities of Optical Pooled Screens https://www.biorxiv.org/content/10.1101/2025.10.11.681797v1
Reposted by Brandon Logeman
Neat trick if you polycolonal ab's suck. Incubate them with fixed cells with a KO of your protein of interest, then spin. Protocol here: www.med.upenn.edu/markslab/ass...
I was amazed how well it worked on first try (I'm sure that I can completely eliminate unspecific bands)
#WesternBlot #cellsky
I was amazed how well it worked on first try (I'm sure that I can completely eliminate unspecific bands)
#WesternBlot #cellsky
October 2, 2025 at 5:11 PM
Neat trick if you polycolonal ab's suck. Incubate them with fixed cells with a KO of your protein of interest, then spin. Protocol here: www.med.upenn.edu/markslab/ass...
I was amazed how well it worked on first try (I'm sure that I can completely eliminate unspecific bands)
#WesternBlot #cellsky
I was amazed how well it worked on first try (I'm sure that I can completely eliminate unspecific bands)
#WesternBlot #cellsky
Reposted by Brandon Logeman
Persistent hindrances to data re-use in single-cell genomics https://www.biorxiv.org/content/10.1101/2025.10.02.680150v1
October 3, 2025 at 2:35 PM
Persistent hindrances to data re-use in single-cell genomics https://www.biorxiv.org/content/10.1101/2025.10.02.680150v1
Reposted by Brandon Logeman
My Own Lab at Westlake University is OPEN! We are recruiting cool people at all levels NOW!
By tinkering behaviors and neural circuits in distinct animal species (mouse, sugar glider, etc), we are exploring new ways of doing social neuroscience in vivo, in silico and at home!
By tinkering behaviors and neural circuits in distinct animal species (mouse, sugar glider, etc), we are exploring new ways of doing social neuroscience in vivo, in silico and at home!
October 3, 2025 at 8:09 AM
My Own Lab at Westlake University is OPEN! We are recruiting cool people at all levels NOW!
By tinkering behaviors and neural circuits in distinct animal species (mouse, sugar glider, etc), we are exploring new ways of doing social neuroscience in vivo, in silico and at home!
By tinkering behaviors and neural circuits in distinct animal species (mouse, sugar glider, etc), we are exploring new ways of doing social neuroscience in vivo, in silico and at home!
Reposted by Brandon Logeman
Every single one of these leaves is a bug.
September 29, 2025 at 12:34 AM
Every single one of these leaves is a bug.
Reposted by Brandon Logeman
It's probably the deterioration of social media (I hope) but i'm exposed to a lot less cool science. It used to feel like a new cool study is being preprinted/published every week, and lately it's rare (at least so it seems). Share a recent study that's worth knowing!
September 26, 2025 at 10:26 AM
It's probably the deterioration of social media (I hope) but i'm exposed to a lot less cool science. It used to feel like a new cool study is being preprinted/published every week, and lately it's rare (at least so it seems). Share a recent study that's worth knowing!
mRNA-based sensors are now more modular, but still rely on overexpression of ADAR1 which interferes with endogenous biology. Seems to be a situation where enzyme engineering to make a bio-orthogonal ADAR-like protein that only deaminates the reporter should be within reach.
Sequence-Independent RNA Sensing in Living Mammalian Cells https://www.biorxiv.org/content/10.1101/2025.09.18.677213v1
September 23, 2025 at 10:42 AM
mRNA-based sensors are now more modular, but still rely on overexpression of ADAR1 which interferes with endogenous biology. Seems to be a situation where enzyme engineering to make a bio-orthogonal ADAR-like protein that only deaminates the reporter should be within reach.
Reposted by Brandon Logeman
The great thing about Rosh Hashanah and Fat Bear Week starting the same day is apples and honey is completely appropriate for both
September 23, 2025 at 12:21 AM
The great thing about Rosh Hashanah and Fat Bear Week starting the same day is apples and honey is completely appropriate for both
Reposted by Brandon Logeman
This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 8:34 AM
This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/
Reposted by Brandon Logeman
Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first?
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...
September 21, 2025 at 6:54 PM
Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first?
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...
Reposted by Brandon Logeman
Against my better instincts, I have written some notes on how human probability judgements work and what you should expect from surveys that ask people to guess what proportion of the population is transgender. I hope never to speak of this matter again
Some notes on probability judgement – Notes from a data witch
For the love of fuck, literally nobody thinks that 20% of the population is transgender. Please stop sharing that ridiculous YouGov statistic
blog.djnavarro.net
September 21, 2025 at 3:38 PM
Against my better instincts, I have written some notes on how human probability judgements work and what you should expect from surveys that ask people to guess what proportion of the population is transgender. I hope never to speak of this matter again
Reposted by Brandon Logeman
Jamie Drayton and I were fortunate to contribute some RCMC analyses to this beautiful paper from Eder, Moene...van Steensel that systematically maps the relationship between enhancer location and gene expression (and nice to see RCMC predict expression in Fig 2H-I):
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
September 19, 2025 at 7:41 PM
Jamie Drayton and I were fortunate to contribute some RCMC analyses to this beautiful paper from Eder, Moene...van Steensel that systematically maps the relationship between enhancer location and gene expression (and nice to see RCMC predict expression in Fig 2H-I):
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Very interesting paper from the group of Alistair Boettiger examining DNA contact using long-term live cell imaging. Generated ~75TB of data!
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Kinetic organization of the genome revealed by ultraresolution multiscale live imaging
Genome function requires regulated genome motion. However, tools to directly observe this motion in vivo have been limited in coverage and resolution. Here we introduce an approach to tile mammalian c...
www.science.org
September 19, 2025 at 8:34 PM
Very interesting paper from the group of Alistair Boettiger examining DNA contact using long-term live cell imaging. Generated ~75TB of data!
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Brandon Logeman
New preprint from our lab!
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
September 19, 2025 at 3:03 AM
New preprint from our lab!
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
🚨 Request for functional genomics / GWAS folks. I repeatedly see claims that “… 90% of GWAS identified variants lie in regulatory regions…” from reviews, but have had a hard time tracking down where this number comes from. 🧵@sashagusevposts.bsky.social @jkpritch.bsky.social @tuuliel.bsky.social
September 16, 2025 at 5:12 PM
🚨 Request for functional genomics / GWAS folks. I repeatedly see claims that “… 90% of GWAS identified variants lie in regulatory regions…” from reviews, but have had a hard time tracking down where this number comes from. 🧵@sashagusevposts.bsky.social @jkpritch.bsky.social @tuuliel.bsky.social
Reposted by Brandon Logeman
Next-generation hybridization chain reaction tools with enhanced sensitivities to detect challenging targets https://www.biorxiv.org/content/10.1101/2025.09.09.675218v1
September 11, 2025 at 11:16 PM
Next-generation hybridization chain reaction tools with enhanced sensitivities to detect challenging targets https://www.biorxiv.org/content/10.1101/2025.09.09.675218v1
@clemmensenc.bsky.social you have a very nice 🧵 on this great review over at the other site. Would love to have something similar here
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Brain control of energy homeostasis: Implications for anti-obesity pharmacotherapy
Advances in mapping how the brain regulates energy homeostasis, together with progress
in peptide-based pharmacotherapy, highlight emerging opportunities for obesity treatment
with the potential to su...
www.cell.com
August 10, 2025 at 5:16 PM
@clemmensenc.bsky.social you have a very nice 🧵 on this great review over at the other site. Would love to have something similar here
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Utilizing in silico designed protein binders to inhibit mismatch repair and increase editing efficiency of Cas9-mediated Prime Editing
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
AI-generated MLH1 small binder improves prime editing efficiency
A compact, AI-generated suppressor of DNA mismatch repair can enhance prime editing
in vivo and in vitro and can be integrated into a variety of prime editing architectures.
www.cell.com
August 9, 2025 at 6:53 PM
Utilizing in silico designed protein binders to inhibit mismatch repair and increase editing efficiency of Cas9-mediated Prime Editing
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Important paper comparing TF footprinting methods for single-cell genomics studies from Katherine Pollard’s group at UCSF
Comparative evaluation of genomic footprinting algorithms for predicting transcription factor binding sites in single-cell data https://www.biorxiv.org/content/10.1101/2025.08.07.669008v1
August 8, 2025 at 11:20 AM
Important paper comparing TF footprinting methods for single-cell genomics studies from Katherine Pollard’s group at UCSF