Justin Crocker
@justinmcrocker.bsky.social
Biologist studying evolution, development, and gene-regulation. Group leader at EMBL, Heidelberg. Climber.
your starter pack for Single Molecule Genomics! Why you should do it (or not) - How you should do it. Collective effort with @vram142.bsky.social @stirlingchurchman.bsky.social @naltemose.bsky.social A Stergachis M Stadler W Greenleaf @embl.org rdcu.be/PmzSEV529GRa
🧬🔬 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... 🧵👇
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 ...
science.org
The first Danionella paper from the lab. Danionella cerebrum is transparent, so you can see all of the internal organs. But what sensory information are the organs sending to the brain? In our new preprint, Emily Bayer wanted to find out. 1/4 www.biorxiv.org/content/10.6...
I made a presentation to other faculty about recent progress in general AI, to facilitate the discussion around the impact for research and teaching in biology. It could be that the slides are useful for others trying to do that same. Feel free to re-use. docs.google.com/presentation...
generalAI_for research_intro.pptx
Recent AI developments and what they mean for us Quick primer on general AI models* State-of-the-art in AI agent capabilities AI agents in biology (examples) Discussion - what does this mean for our r...
docs.google.com
Landmark paper from @benlehner.bsky.social and colleagues: www.biorxiv.org/content/10.6...
Complete Mutagenesis of the Genome and Proteome of ΦX174
The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...
biorxiv.org
Welcome, little sister!
PLOS@plos.org · last wk.The first articles have now been published in our new journal, PLOS Ecosystems. These papers bring together open research from multiple disciplines to address the challenges facing our terrestrial, freshwater and marine ecosystems. Read the first articles: buff.ly/8rsP0Z3
Wherever we look, insect numbers are declining... but most insect life on Earth is found in locations we aren't actively monitoring. @justinmcrocker.bsky.social discusses the #insect decline and how can we build the planetary observatory that #biodiversity requires @plosbiology.org 🧪 plos.io/4qzS2yv
What drives the variation in mutation rates between seals and walruses, gulls and pelicans? Maybe selection counteracting the burden of deleterious mutations- or maybe it is a spandrel, a neutral byproduct of the diversification of development and life-history academic.oup.com/evolut/advan...
Mutation rate variation as the neutral byproduct of developmental and life history diversification
Abstract. Understanding why species differ in their rates of mutation is central to explaining patterns of molecular and phenotypic evolution. Mutation rat
academic.oup.com
Huge congrats to the many authors who over MANY years worked on this (but especially @karaehunt.bsky.social , @trevorbrandt.bsky.social, Karina, @shaharsu.bsky.social and @remenecker.bsky.social. www.nature.com/articles/s41...
Rational design of disordered proteins for sequence–function investigation - Nature
GOOSE enables the design and testing of thousands of disordered protein region sequences to reveal distinct sequence-to-function relationships.
nature.com
Alex Holehouse@alexholehouse.bsky.social · 7mo agoNew (well, very old, but 100% updated) preprint: Rational design of disordered proteins for systematic sequence-to-function investigation Work done in collaboration with @shaharsu.bsky.social lab - check out the three (3) threads from the folks who did the work!
One of the world's most tightly controlled experimental evolution projects is underway in DC, and I hope someone has had the foresight to collect a time series of algal samples. www.cnn.com/2026/06/16/p...
Reflecting Pool woes: Trump administration turns to hydrogen peroxide in latest bid to beat back algae | CNN Politics
President Donald Trump’s more than $14 million Lincoln Memorial Reflecting Pool renovation was completed just over a week ago, with its more than 300,000 square feet refilled with 6.5 million gallons ...
cnn.com
Did you know that more than 20,000 species of bees, along with birds, bats, and other animals, are wild pollinators? They are essential for biodiversity and the balance of ecosystems. Learn more in the IPBES #PollinationAssessment: https://www.ipbes.net/assessment-reports/pollinators
Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇
Delighted to share our lab's latest (w/ inimitable @genophoria.bsky.social) in final form at @nature.com. Enormous lift by Sean Wang, @palindromephd.bsky.social & @martyyang.bsky.social to address extensive & constructive reviewer comments & see this through. (1/n) www.nature.com/articles/s41...
Pervasive and programmed nucleosome distortion on single chromatin fibres - Nature
An analytical pipeline called Iteratively Defined Lengths of Inaccessibility (IDLI) maps the genome-wide occupancy of a range of nucleosome types and shows that most nucleosomes exhibit programmed ‘di...
nature.com
I’m excited to share the draft for our perspective piece on »Emergence Biases« that I wrote with @vakirlis.bsky.social on arxiv: arxiv.org/abs/2604.20477
Emergence biases in molecular evolution
Biases in molecular evolution can significantly influence evolutionary trajectories. They have been described in a variety of contexts such as development and mutation, but not for acquiring new funct...
arxiv.org
🚨3 days left❗to submit your abstract for the Society for Developmental Biology Annual Meeting 2026 in Las Vegas! 🎰🃏 Don’t miss your chance to share your science, connect with the dev bio community, and join us in Vegas ➡️ www.sdbonline.org/2026mtg_abst... ✨ #SDB2026 #DevBio #DevelopmentalBiology
Everyone from the Global South moving to the Global North for a postdoc should hear this advice:
We're sharing the tentative schedule for the upcoming #Drosophila #NewPI JEDI conference! Register now to join an outstandingly collaborative environment. We cover diverse topics including #CellBiology, #DevBio, #neuroscience, #omics, #behavior, #DiseaseModel and many more!
New Preprint! When one enhancer allele changes another's regulatory output, is that bad? We found it could be a feature — interallelic cis-regulatory dominance buffers outputs AND enables evolutionary innovation. Two for one! Led by @ottilie.bsky.social from @embl.org doi: doi.org/10.64898/202...
Interallelic cis-regulatory dominance promotes robustness and evolutionary innovation
Dominance is a central principle of genetics, yet the mechanistic basis and the evolutionary consequences of dominance arising from cis-regulatory variation remain poorly understood. We examined the evolutionary trajectories of a pleiotropic developmental enhancer in Drosophila . A genotype–phenotype map between D. melanogaster and D. simulans enhancer sequences reveals extensive epistasis, and many homozygous evolutionary paths reduce transcriptional output. In heterozygotes, however, regulatory dominance masks variants that reduce gene expression, potentially relaxing evolutionary constraints. Using allele-specific reporters and imaging, we show that this dominance arises from interallelic interactions (also known as transvection) reinforced by transcriptional hubs. Importantly, this enhancer dominance is cell-type specific, raising the possibility that it conceals deleterious effects in essential tissues while revealing novel, ectopic activity in others. Interallelic regulatory hubs may therefore expand the range of mutational paths available to diploid genomes while preserving essential transcriptional output. ### Competing Interest Statement The authors have declared no competing interest.
doi.org
Excited to share my first preprint from my PhD w/ @justinmcrocker.bsky.social. We show that cell type-specific regulatory dominance promotes robustness and evolutionary innovation through interallelic transcriptional hubs, potentially expanding the mutational paths available to diploids. (1/18)
bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 6mo agoInterallelic cis-regulatory dominance promotes robustness and evolutionary innovation https://www.biorxiv.org/content/10.64898/2026.03.17.712157v1
Interallelic cis-regulatory dominance promotes robustness and evolutionary innovation https://www.biorxiv.org/content/10.64898/2026.03.17.712157v1
Thanks to co-authors Charles C. Bell, Brendan R. Camellato, M. Joaquina Delás, Daniel M. Ibrahim, and @michaeltmont.bsky.social And also to all the participants of the 2024🤨 Company of Biologists meeting that inspired this.
Registration and abstract submission are now open for the SDB 85th Annual Meeting being held July 23-26 in Las Vegas! Submit your abstract by April 15. Travel assistance is available. Free t-shirt to the first 250 registrants! Learn more: www.sdbonline.org/2026mtg #2026SDB
Have you ever wondered 🤔... Does phenotypic variance respond to environmental perturbation? Does it have a genetic basis? Are mean and variance regulating loci exposed to different selection pressures? These and more questions are explored in our new preprint 🔥 www.biorxiv.org/content/10.6...
Happy to share a recent publication to which I contributed as a corr. author: www.nature.com/articles/s41... This work is in collaboration with Dr. Yao Yu at Fudan University, where the team managed to transfer S. cerevisiae chromosmes into K. marxianus, a species diverged from Sc ~114 mya. (1/4)
Intergeneric chromosomal transfer in yeast results in improved phenotypes and widespread transcriptional responses - Nature Communications
Transferring genetic materials between distantly related yeasts, presents technical challenges but can yield industrially interesting phenotypes. Here the authors establish a method to transfer indivi...
nature.com
The #fly community aims to achieve a comprehensive genomic study of the Drosophilidae family. @pankajd.bsky.social @bernardkim.bsky.social @petrovadmitri.bsky.social @darrenobbard.bsky.social present a comparative gene annotation for 301 #Drosophilidae species @plosbiology.org 🧪 plos.io/4c3pyrI
Rethinking insecticide toxicology for the 21st century: a review written with Philip Batterham. Led by Lautaro Gandara @embl.org and Felipe Martelli: www.sciencedirect.com/science/arti...
Rethinking insecticide toxicology for the 21st century
Insecticides remain indispensable for crop protection and food security, yet their widespread use may contribute to the global decline of beneficial i…
sciencedirect.com
Many said we were exaggerating a year ago when we argued that Trump is a clear and present danger to our democracy. A year later they are eating their words. It’s up to every single one of us to save our democracy. www.nytimes.com/2026/02/02/u...
🧬✨ New 2-part review on the evolution of regulatory DNA (enhancers & promoters)! What started as conversations between Gasper Tkačik @istaresearch.bsky.social and our group @embl.org grew into a broader synthesis. Preprints here: Part 1: arxiv.org/abs/2601.19681 Part 2: arxiv.org/abs/2601.21480
Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype-phenotype maps
Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interac...
arxiv.org
📣 Paper alert! I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today! journals.biologists.com/dev/article/...
