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Loyal Goff

@loyalgoff.bsky.social
232 followers 362 following 8 posts

I study neural development and cell fate commitment in cephalopods (and sometimes mammals) @ Johns Hopkins. Nice even split between computational and molecular biology.

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Reposted by Loyal Goff
Philippe Batut @philippebatut.bsky.social · 10/09/2026
🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇
science.org
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...
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Tessa Montague @tessamontague.bsky.social · 29/09/2026
I'm excited to share our new preprint: Generation of a transgenic cephalopod tinyurl.com/pc86jxz8 Cephalopods (cuttlefish, octopus & squid) are crazy critters that dynamically camouflage to their surroundings by changing the color, pattern, & texture of their skin, which they control w their brain.
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Silas Maniatis @manimota.bsky.social · 28/09/2026
In 2022 we published an open-source hardware, software, and protocols ecosystem for repurposing sequencers as automated fluidics coupled imaging instruments. On Oct 13 @yougotkunal.bsky.social & @nygenome.org will host a workshop on current applications. Register here: regenseq.github.io/meeting/
regenseq.github.io
RegenSeq Community Meeting 2026
Bringing together the RegenSeq community across multiplexed imaging, spatial transcriptomics, and optical pooled screening.
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 23/09/2026
What if any dataset, any size, any number of dimensions, opened in a browser tab from a link? 🔬🧪💻 Luxar is out today: write it in Python, share it as a link, explore it in any browser. Open source. 🧵 @biohub.org Preprint: doi.org/10.5281/zen... Code: github.com/royerlab/luxar
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Justus Kebschull @justuskebschull.bsky.social · 21/09/2026
NEW PREPRINT! An evo-devo look at how new cerebellar nuclei are made. Spoiler: it’s all driven by region-specific excitatory progenitors in the early rhombic lip; inhibitory neurons fill in later. If you care about brain evolution or cerebellar development, check it out: tinyurl.com/CNdevelopment
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Jeremiah Cohen @jeremiahycohen.bsky.social · 16/09/2026
Happy to share the version of record of our locus coeruleus paper here: www.nature.com/articles/s41... Prior thread on some of our discoveries in this study: bsky.app/profile/jere...
nature.com
Topographic structure and function of locus coeruleus noradrenaline neurons - Nature
Dorsal and ventral noradrenergic neurons in the locus coeruleus form topographic subpopulations whose projection patterns and activity encode choice switching, reward-prediction errors and disregard o...
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Kevin Thiessen, PhD @kevinthiessen.bsky.social · 05/09/2026
As a fish person, I was always jealous of the annotations/resources for the human genome. Now as a ctenophore researcher, I realize that #zebrafish people don't know how good they actually have it. A silver lining is that the struggles I had with the zebrafish genome have prepared me for this. 😵‍💫
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Dave Shechner @shechnerlab.bsky.social · 02/09/2026
📄 Our latest review is now out in Current Opinion in Chemical Biology! We discuss a growing class of oligonucleotide-directed proximity labeling strategies that use programmable DNA hybridization to target RNAs and genomic loci. This was a fun one to write—I hope you enjoy it! bit.ly/4h6KaRV
bit.ly
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Leandros Boukas @leandrosboukas.bsky.social · 16/07/2026
Together with Hans Bjornsson (and @kasperdhansen.bsky.social, and others) we have spent many years thinking about the molecular basis of Mendelian disorders caused by variants in chromatin regulators. We have written a review where we discuss our thoughts: www.tandfonline.com/doi/full/10....
tandfonline.com
Mendelian disorders of the epigenetic machinery: a decade of insights into the molecular basis
The Mendelian disorders of the Epigenetic Machinery (MDEMs), or Chromatinopathies, are now understood to be a collectively common cause of childhood neurodevelopmental delays and intellectual disab...
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James Briscoe @jamesbriscoe.bsky.social · 08/06/2026
Our latest: Minimal essential requirements for neural tube self-organisation How does a single cell give rise to a tissue with the right cell types in the right proportions? We deconstruct and rebuild a self-organising tissue from first principles A thread🧵 www.biorxiv.org/content/10.6...
biorxiv.org
Minimal essential requirements for neural tube self-organisation
The reliable generation of diverse cell types in precise proportions is essential for the formation of functional tissues during embryonic development. Three-dimensional organoid models derived from p...
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Tessa Montague @tessamontague.bsky.social · 06/06/2026
Do you know an outstanding aquarist? We're hiring a Senior Aquarist to help run our cephalopod facility at Columbia University. Our team maintains a colony of 250+ cuttlefish, develops new husbandry techniques (inc transgenics) & studies cuttlefish camouflage and social behavior. 1/3 [Pls repost!]
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Justus Kebschull @justuskebschull.bsky.social · 04/06/2026
POINTseq, now out in Neuron after peer review. Read it. There are barcodes, viruses, and dopamine. Congrats to @hyopilkim.bsky.social on leading our lab's first published paper!
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Justus Kebschull @justuskebschull.bsky.social · 17/05/2026
New from the lab: BARseq3! Barcodes + high efficiency spatial transcriptomics and translatomics in the same cells, or just a nice spatial transcriptomics assay. All in a modular, expandable system to enable truly multimodal measurements. Check it out: www.biorxiv.org/content/10.6...
biorxiv.org
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Jeremiah Cohen @jeremiahycohen.bsky.social · 13/04/2026
Delighted to share our discoveries about one of the brain's neurotransmitter systems: www.biorxiv.org/content/10.6... Together with colleagues at the @alleninstitute.org, we have learned a lot about a tiny cluster of neurons in the brainstem locus coeruleus (LC) that releases norepinephrine (NE). 1
biorxiv.org
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OneNeuro Initiative @oneneurojhu.org · 06/03/2026
The winner of OneNeuro's February #FotoFriday #FluorescenceFriday contest is "Spatial transcriptomics captures brain regions in the hummingbird bobtail squid" submitted by Alyson Hally in the @loyalgoff.bsky.social Lab at @hopkinsmedicine.bsky.social View BRAINART gallery: www.oneneurojhu.org/art/
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Lior Pachter @lpachter.bsky.social · 19/02/2026
I used Claude Opus 4.5/4.6 (and a bit of Codex GPT-5.3) to port edgeR to Python. See edgePython github.com/pachterlab/e... This allowed me to develop a single-cell DE method that extends NEBULA with edgeR Empirical Bayes. All in one week. Details in doi.org/10.64898/202...
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The Transmitter @thetransmitter.bsky.social · 16/02/2026
If neuroscience is serious about building general principles of brain function, cross-species dialogue must become a core organizing principle rather than an afterthought, writes @suthanalab.bsky.social. #neuroskyence www.thetransmitter.org/animal-model...
thetransmitter.org
Neuroscience has a species problem
If neuroscience is serious about building general principles of brain function, cross-species dialogue must become a core organizing principle.
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sina b @sina.bio · 03/02/2026
Peer review is often opaque and confusing. @elife.bsky.social worked to change that. In a new preprint, we show how eLife’s Publish, Review, Curate model makes it possible to evaluate AI-generated reviews (with OpenEval) against human peer review. w/ @lauraluebbert.com and @lpachter.bsky.social
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Rajiv McCoy @rajivmccoy.bsky.social · 21/01/2026
Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk. First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
nature.com
Common variation in meiosis genes shapes human recombination and aneuploidy - Nature
Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...
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Cris Niell @crisniell.bsky.social · 06/01/2026
Less than two weeks left to apply for the Cephalopod Neuroscience Gordon Conference! An exciting lineup of speakers and posters, and financial aid is available upon request. 🐙🦑 www.grc.org/cephalopod-n...
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Igor Ulitsky @igorulitsky.bsky.social · 13/11/2025
A preprint‼️that's bound to ruffle some 🪶 "Widespread DNA off-targeting confounds studies of RNA chromatin occupancy" led by our Micah Goldrich and Louis Delhaye from Pieter Mestdagh in Ghent. TL;DR we show that many of lncRNA chromatin occupancy obtained are flawed www.biorxiv.org/content/10.1...
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 30/09/2025
Yeah, I no longer have ESI status due to collaborative work, but because I didn't get an ESI MIRA first, I'm probably locked out of a MIRA forever, because only unicorns get NIGMS R01s these days. The "must have an NIGMS R01" requirement might have worked at the start, but definitely doesn't now.
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Drug Monkey @drugmonkey.bsky.social · 30/09/2025
On the nature of a NSF (or NIH) graduate training fellowship drugmonkey.wordpress.com/2025/09/29/o...
drugmonkey.wordpress.com
On the nature of a NSF (or NIH) graduate training fellowship
I had a thought about graduate school fellowships and added it to the prior past about the NSF GRFP limitations to first year graduate students. [ETA 09/29/2025: I forgot to mention something impor…
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The Interactive Fly @interactivefly.bsky.social · 28/08/2025
Alfonso-Gonzalez, C., Shi, M., Gorey, S., Holec, S., Carrasco, J., Rauer, M., Tsagkris, S., Mateos, F., Hilgers, V. (2025). ELAV mediates circular RNA biogenesis in neurons. Genes Dev, genesdev.cshlp.org/content/earl...
genesdev.cshlp.org
ELAV mediates circular RNA biogenesis in neurons
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
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Loyal Goff @loyalgoff.bsky.social · 26/08/2025
A few weeks ago, this beautiful and inspired mural was painted on the building behind my lab space at Johns Hopkins. I walk past it each day and honestly feel humbled by how it makes me feel. Feeling compelled to share it with others today.
A new brightly colored mural of Henrietta Lacks just outside of Johns Hopkins Hospital in Baltimore.
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Cephalopod Research Network @cephalopodanetwork.bsky.social · 16/08/2025
If you are someone actively involved in cephalopod research whether you are a Masters student, PhD student, Postdoc, Professor, Emeritus, reach out to me via the Bsky chat so we can get you invited to the Cephalopod Research Network Discord server! It's essentially a year-round CIAC!
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Marshall G Hussain Shuler Lab @hushulab.bsky.social · 28/05/2025
hub.jhu.edu/2025/05/21/u...
hub.jhu.edu
America's retreat from research risks exodus of world's 'brightest minds'
Johns Hopkins neuroscientist Uli Mueller came to the U.S. from Germany decades ago because of the unrivaled opportunities for research and discovery. He worries that cuts to research funding will upen...
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Mark Mandel @markjmandel.bsky.social · 28/02/2025
With more mollusk genomes available, a new genome-based phylogeny is featured on the cover of Science. Paper from @sigwartae.bsky.social at www.science.org/doi/10.1126/... Cover photo by Magnus Lundgren.
Science Magazine cover 28 Feb 2025; "An oval squid (Sepioteuthis lessoniana)"
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Richard Sever @richardsever.bsky.social · 26/02/2025
A mosquito cell atlas www.biorxiv.org/content/10.1... ht @leslievosshall.bsky.social
biorxiv.org
Mosquito Cell Atlas: A single-nucleus transcriptomic atlas of the adult Aedes aegypti mosquito
The female mosquito's remarkable ability to hunt humans and transmit pathogens relies on her unique biology. Here, we present the Mosquito Cell Atlas (MCA), a comprehensive single-nucleus RNA sequenci...
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Randall Munroe @xkcd.com · 26/02/2025
RNA xkcd.com/3056
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 08/02/2025
'Trans-differentiation of neutrophils from plasmablast' is an artefact caused by over-reliance on machine algorithms in single cell RNA sequencing analysis: Lesson learnt and steps ahead www.biorxiv.org/content/10.1101/202…
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Mike Schatz @mikeschatz.bsky.social · 08/02/2025
Just saw this. NIH is capping indirects at 15%. This will crush so many institutions. grants.nih.gov/grants/guide...
grants.nih.gov
NOT-OD-25-068: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates NOT-OD-25-068. OD
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Itai Yanai @itaiyanai.bsky.social · 24/11/2024
70% of scientists say they experience the imposter syndrome. I still experience it too sometimes, and what helps is talking with a science buddy with whom it’s ok to say stupid things, which may actually turn out to be good ideas.
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Rafael Irizarry @rafalab.bsky.social · 22/11/2024
New method for identifying spatially variable genes in spatial transcriptomics. We use spectral graph theory to extract 1D curves related to tissue morphology, creating a more relevant coordinate system. Improves sensitivity. with @PhillipNicol et al. www.biorxiv.org/content/10.1...
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Dan Arking @arking.bsky.social · 15/11/2024
Nice work from Nicole Lake and Monkol Lek (with a small contribution from our group): medicalxpress.com/news/2024-11...
medicalxpress.com
Decoding disease: Novel tool helps identify mutations in mitochondrial DNA
Geneticists looking inside the nuclear genome for mutations that contribute to disease have long relied on a principal known as constraint modeling, which allows researchers to assess the degree of se...
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