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Brandon Logeman

@blogeman.bsky.social
97 followers 72 following 61 posts

Assistant Professor at U of Kentucky Medicine 🐾 Functional Genomics of Neural Activity and Animal Behavior at the single cell level 🧬genes->🚥pathways->🧠circuits->🐭behavior

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Reposted by Brandon Logeman
Jesse Engreitz @jengreitz.bsky.social · 09/05/2026
Exciting study from Leonid Mirny and co: Cohesin bridging as a physical principle of enhancer-promoter communication www.biorxiv.org/content/10.6...
biorxiv.org
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Jessica Tollkuhn @tollkuhn.bsky.social · 25/02/2026
how did I only just become aware of Spicy Pepper Pokémon Scovillain, which evolves from Capsakid and has a “spicy rage attack”.
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 22/02/2026
A hypoxia-sensitive medullary nucleus modulates cerebral blood flow via a disynaptic pathway to cortex www.biorxiv.org/content/10.64898/20…
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Yarui Diao @yaruidiao.bsky.social · 20/02/2026
Happy to share scHiCAR, an ultra-high throughout (millions of cells), low cost (5 cents/cell including NGS), and trimodal platform for integrated single-cell level analysis of mRNA, open chromatin, and 5-kb resolution looping with ground-truth data the same individual cell.
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 18/02/2026
Acute threats modulate hunger circuit dynamics to instruct avoidance behaviour www.biorxiv.org/content/10.64898/20…
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 17/02/2026
Identification of target genes and regulatory networks for bone mineral density GWAS loci through systematic targeting and inhibition www.biorxiv.org/content/10.64898/20…
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 15/02/2026
A scalable approach to resolving variants of uncertain significance www.biorxiv.org/content/10.64898/20…
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 14/02/2026
Genome-wide single-cell perturbation screens with VIPerturb-seq www.biorxiv.org/content/10.64898/20…
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Camille Michèle Williams @cognitivecamz.bsky.social · 11/02/2026
Our multi-ancestry GWAS of EXTernalizing conditions (ADHD, substance use...) in ~4M people reveals neurodevelopmental risk, drug-repurposing targets, and yields one of the strongest psychiatric polygenic indices yet! 🧬🎉 doi.org/10.64898/202...
doi.org
Genomic insights into substance use and disinhibitory disorders
Externalizing spectrum disorders- spanning attention-deficit/hyperactivity disorder, conduct disorder, substance use disorders, and other disorders characterized by disinhibition - frequently co-occur...
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 10/02/2026
Identification of a neural basis for anorexia nervosa www.biorxiv.org/content/10.64898/20…
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 09/02/2026
Sex-specific control of feeding and defensive behaviors by MC3R neurons in the bed nuclei of the stria terminalis www.biorxiv.org/content/10.64898/20…
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 09/02/2026
A multi-omics atlas of human hindbrain development www.biorxiv.org/content/10.64898/20…
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Robert Warmerdam @robertwarmerdam.bsky.social · 06/02/2026
🧬 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)
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 07/02/2026
A modular transcript enrichment strategy for scalable, atlas-aligned, and clonotype-resolved single-cell transcriptomics www.biorxiv.org/content/10.64898/20…
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Davis Vaughan @davisvaughan.bsky.social · 04/02/2026
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...
tidyverse.org
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...
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Jan Broder Engler @jbengler.de · 02/02/2026
You can easily switch between magrittr pipe `%>%` and base pipe `|>` in the RStudio settings 🧰 #rstats #dataviz #phd
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 03/02/2026
Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain www.biorxiv.org/content/10.64898/20…
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 02/02/2026
A projection atlas of excitatory and inhibitory inputs to the preBötzinger Complex: substrates for multimodal breathing control www.biorxiv.org/content/10.64898/20…
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Philip Ball @philipcball.bsky.social · 30/01/2026
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...
nature.com
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...
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 29/01/2026
A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons www.biorxiv.org/content/10.64898/20…
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Konrad Kording @kordinglab.bsky.social · 28/01/2026
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 ;)
planyourscience.com
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.
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 26/01/2026
SqueakPose Studio: An end-to-end platform for pose estimation and real-time edge-AI deployment www.biorxiv.org/content/10.64898/20…
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 23/01/2026
Bright calcium-modulated bioluminescent indicators for activity imaging and red photon-assisted synaptic transmission www.biorxiv.org/content/10.64898/20…
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Thomas Norman @normanlab.bsky.social · 20/01/2026
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.
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Tuuli Lappalainen @tuuliel.bsky.social · 12/01/2026
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%.
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Luciano Martelotto @lgmartelotto.bsky.social · 10/01/2026
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...
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Jill Moore @moorejille.bsky.social · 08/01/2026
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
media.tenor.com
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 .
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 02/01/2026
Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq www.biorxiv.org/content/10.64898/20…
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Arcadia Science @arcadiascience.com · 29/12/2025
A free, open-access library of high-quality organism illustrations for science communication
doi.org
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...
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Arjun Raj @arjunraj.bsky.social · 30/12/2025
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...
open.substack.com
Just quit
Quitting projects in science is hard, but we should be doing a lot more of it.
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 27/12/2025
Multimodal spatial transcriptomics determines repeat expansion, huntingtin aggregation, and selective cortical neuron loss in Huntington Disease www.biorxiv.org/content/10.64898/20…
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Alex Stark @alex-stark.bsky.social · 24/12/2025
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)
biorxiv.org
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...
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 24/12/2025
Optimised fluorescence-activated nuclei sorting for epigenomic analysis of cortical cell types www.biorxiv.org/content/10.64898/20…
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Arrianna Marie Planey, PhD MA @arrianna-planey.bsky.social · 18/12/2025
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.
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Job Dekker @jobdekker.bsky.social · 17/12/2025
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...
nature.com
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...
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Catherine Dulac @dulaclab.bsky.social · 13/12/2025
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...
biorxiv.org
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...
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Jonathan Pritchard @jkpritch.bsky.social · 11/12/2025
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🧵:
nature.com
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.
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Jacob Schreiber @jmschreiber91.bsky.social · 10/12/2025
After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out! In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells. www.biorxiv.org/content/10.1...
biorxiv.org
Programmatic design and editing of cis-regulatory elements
The development of modern genome editing and DNA synthesis has enabled researchers to edit DNA sequences with high precision but has left unsolved the problem of designing these edits. We introduce Le...
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Marson Lab @marsonlab.bsky.social · 10/12/2025
Our latest collaboration with @jkpritch.bsky.social – led by joint post-doc Mineto Ota – is in @nature.com today: www.nature.com/articles/s41...
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Serge Ahmed @sergeahmed.bsky.social · 05/12/2025
Hunger increases exploration and risk-taking behavior, allowing an animal to forage for food despite risks Hunger-induced changes in exploration result from the modulation of dopamine signaling in the tail of the striatum via the following circuit: 1/2 www.cell.com/neuron/fullt...
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Masahiro Kanai @masakanai.bsky.social · 01/12/2025
Excited to share our new FinnGen single-nucleus multiome preprint! 🧬 We profiled ~10M PBMCs (snRNA-seq + snATAC-seq) from 1,108 Finnish donors to map how genetic variants drive complex disease through chromatin and gene regulation 🧵👇 🔗 Link: www.medrxiv.org/content/10.1...
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 02/12/2025
We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n
quinlanlab.org
Intro to Bedder – The Quinlan Lab
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medRxivpreprint @medrxivpreprint.bsky.social · 24/11/2025
Design and interpretation of eQTL-GWAS colocalisation studies: lessons from a large-scale evaluation www.medrxiv.org/content/10.1101/202…
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 25/11/2025
The architecture of allele-specific regulatory variant effects across five human genomes www.biorxiv.org/content/10.1101/202…
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Sasha Gusev @sashagusevposts.bsky.social · 13/11/2025
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.
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loic-yengo.bsky.social @loic-yengo.bsky.social · 12/11/2025
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....
nature.com
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...
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Michael Love @mikelove.bsky.social · 18/08/2025
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...
biorxiv.org
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...
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Eric Turkheimer @ent3c.bsky.social · 17/10/2025
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."
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Anshul Kundaje @anshulkundaje.bsky.social · 15/10/2025
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/
github.com
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