Lab Meeting FAQ kamounlab.dreamhosters.com/KamounLab-Me...

Sophien Kamoun@kamounlab.bsky.social · yesterday

I just published: The lab meeting, explained Open mic, one slide, and why Joe chairs instead of me. And do check the FAQ. kamounlab.medium.com/the-lab-meet...

Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below

Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics

This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...

nature.com

This study uses phylogenetic modelling to show that #spermconjugation, a type of social cooperation among sperm, has a deep and pervasive evolutionary history, including repeated convergence of both structures and their underlying proteins. www.nature.com/articles/s41...

Pervasive convergent evolution of sperm conjugation across the Arthropoda tree of life - Nature Communications

Sperm cells evolve rapidly and have unique life histories. This study uses phylogenetic modelling to show that sperm conjugation, a type of social cooperation among sperm, has a deep and pervasive evo...

nature.com

The headlines are still covering the cyclosporiasis outbreak from lettuce, but let's talk about a different summer, long ago. The headlines in Bavaria would have called it "summer diarrhea" & it was killing babies. Enter our hero, Professor Theodor Escherich of the Julius Hospital, Würzburg.

Our study published today @science.org shows that X-chromosome inactivation (XCI) attracts L1 mutations to the human X chromosome: doi.org/10.1126/scie... With outstanding Perspective from @aurelien-doucet.bsky.social & @retrogenomics.bsky.social: doi.org/10.1126/scie...

Next summer's Epigenetics GRC (I'm co-chairing with Deborah Bouch'is) is shaping up nicely with an all-star lineup of speakers working on a broad range of organisms and systems and everything from molecular mechanisms to new phenomena. Apply and put it on your calendar! www.grc.org/epigenetics-...

wanna read the latest overview of “internal evolutionary conflicts” — scenarios where genes spread despite being organism-deleterious? and wanna learn how to model them? look at our new preprint! we introduce unifying ideas, and try hard to write accessibly. small 🧵 www.biorxiv.org/content/10.6...

It's been incredibly fun to work with @gauravathreya.bsky.social @yagmurerten.bsky.social @arvidagren.bsky.social @tom-is-kean.bsky.social on internal evolutionary conflicts (also called intragenomic/intraorganismal conflict) and how to model them! See below for Gaurav's great explainer on the paper

Gaurav Athreya@gauravathreya.bsky.social · last wk.

wanna read the latest overview of “internal evolutionary conflicts” — scenarios where genes spread despite being organism-deleterious? and wanna learn how to model them? look at our new preprint! we introduce unifying ideas, and try hard to write accessibly. small 🧵 www.biorxiv.org/content/10.6...

EEB Mentor Match is now open! But apps due soon (8/17). Mentees: get help applying for grad school or fellowships in ecology & evolution. Mentors: senior grads, post-docs, or faculty in these fields willing to give advice Org by Diversity Cmte of @asn-amnat.bsky.social Pls share! eebmentormatch.com

EEB Mentor Match

Visit the post for more.

eebmentormatch.com

⭐Postdoc position available⭐ How do symbionts evolve new beneficial functions? Join the Henry Lab to investigate how horizontal gene transfer drives host–microbe symbioses. 🦠 Apply below Enquiries: l.henry@qmul.ac.uk Please share! #Postdoc #EvolutionaryBiology #Symbiosis henry-lab.co.uk

Our paper on how better amino acid substitution matrices trained on cleaned alignments improve gene tree inference, and on best practice for cleaning MSAs more broadly, is now out academic.oup.com/mbe/advance-.... New options in both IQTree and Muscle5. @phylowheeler.bsky.social

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models

Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig

academic.oup.com

Joanna Masel@joannamasel.bsky.social · 8mo ago

Sequence alignments are notoriously prone to error. Our latest preprint offers a new tool for filtering errors out, assesses it and other filtering tools, and recommends new best practice. www.biorxiv.org/content/10.6... @phylowheeler.bsky.social 1/10

And just like that… @pravrutharaman.bsky.social is ready to leave us to start her lab at @umassboston.bsky.social We mark this occasion by the ‘solemn’ passing of the crown and specter to the next seniormost postdoc @tamanash.bsky.social; may his reign be as short as British PMs.

So much sadness, excitement, anxiety.. all the feels! This was a long journey that started with a pandemic and ended with “whatever this is”. But I am thrilled that the Raman lab will be a thing. More about our lab soon but for now, must move toddler and dog across the country. Send good vibes

Harmit Singh Malik@harmitmalik.bsky.social · 2w ago

And just like that… @pravrutharaman.bsky.social is ready to leave us to start her lab at @umassboston.bsky.social We mark this occasion by the ‘solemn’ passing of the crown and specter to the next seniormost postdoc @tamanash.bsky.social; may his reign be as short as British PMs.

In 2018, I had the opportunity as a PhD student to write a review about chemical waves with @ditalialab.bsky.social Looking back, this was such a fun and valuable experience. If you’re curious to know more about how chemical waves regulate signaling in cells and embryos, check out our review! 🌊

Journal of Cell Biology@jcb.org · 2w ago

@vdeneke.bsky.social and @ditalialab.bsky.social review how the spatiotemporal coordination of cellular functions across large distances is controlled by chemical waves. rupress.org/jcb/article/... 📕 Part of "Collective Behaviors and Self-Organization in Cells" rupress.org/jcb/collecti...

📢 #Postdoc job: I am looking for a #bioinformatician to join my lab for investigating #XchromosomeInactivation and #chromatin-mediated #epigenetic mechanisms underlying #sexbias in #MultipleSclerosis. Please RT

Gabriel Spitzer (@kuow.org) visited our lab to learn about our work to use evolutionary principles to supercharge innate immunity to (hopefully) deploy it in the face of viral infections. Gabriel is a masterful storyteller and would recommend listening to his ‘Pocket Science’ series (each ~12 min)

Fred Hutch@fredhutch.org · 2w ago

Our immune systems have evolved to overcome all kinds of flus, plagues and poxes, but the process of adaptation is slow. @basicsci.fredhutch.orgs' @harmitmalik.bsky.social looks to find ways to put evolution into overdrive to fight future diseases. 🎧 Listen to @kuow.org's Pocket Science for more.

Priscillia Lhoumaud and I were very happy to write a N&V for a monster paper about intriguing DNMT1 biology by @mafdawson.bsky.social and co, just out in @natgenet.nature.com . Check it out here (and the actual paper in the next post) (1/2) www.nature.com/articles/s41...

SUMOylation fine-tunes DNMT1 to silence viral mimicry transcripts - Nature Genetics

DNMT1 binds unmethylated CpG islands at active genes and, upon catalytic inhibition, redistributes to partially methylated, inaccessible regions, triggering viral mimicry via endogenous retroelements ...

nature.com

Sometimes the dark alleys are in fact dark alleys that we shouldn't have gone down. But sometimes the dark alleys are really the path to enlightenment. And we don't really know, ahead of time, which one is going to go, unfortunately. –@harmitmalik.bsky.social on the Night Science Podcast, episode 6

The third chapter in our coral single-cell trilogy is here. After mapping cell type diversity in Stylophora (Levy 2021) and exploring facultative symbiosis in Oculina (Levy 2025), we now uncover cell type-specific responses to heat stress. Find out more in @xgrau.bsky.social's thread below.

Cell-resolved transcriptional responses during heat-induced coral bleaching and recovery

Coral reefs depend on an intracellular symbiosis between cnidarian hosts and photosynthetic dinoflagellates that is disrupted by ocean warming, causing coral bleaching. Yet how these responses are dis...

biorxiv.org

Xavier Grau-Bové 🌾@xgrau.bsky.social · 2w ago

I'm happy to share our latest on #coral single-cell biology: a transcriptomic timecourse of heat stress in Stylophora pistillata, from bleaching to recovery 🪸🌊 This project was spearheaded by Shani Levy and carried through in @arnausebe.bsky.social's lab at @crg.eu. www.biorxiv.org/content/10.6...

I wish I did not have to bring up this old tweet from ‘that other place’ every now and again but here we are (again) and here it is…

How does an embryo generate the right cells in the right place? Delighted to share our latest findings on how neural crest cells acquire vagal or trunk identities Spoiler alert: The timing & combination of CDXs preconfigures cell identity & distinct HOX states www.biorxiv.org/content/10.6...

Temporally distinct CDX programmes preconfigure vagal and trunk neural crest

Neural crest cells (NCCs) are progenitor cells vital in establishing the head, heart, gut and peripheral nervous system of vertebrate embryos. Disruptions to NCC development underlie neurocristopathie...

biorxiv.org

Hello World ! We have another postdoc position open in the lab! Are you a freshly minted Ph.D. with a passion for chromatin and evolution ? Come join our ERC project #EvoEpi ! Inclusive environment + cool people + great science = success details 👉 tinyurl.com/3r6zk54n Repost are always appreciated

Just for fun, as a side project, Jeremy went back to his rotation project in my lab and assembled a dream team of collaborators to tackle a puzzle about the apparently missing essential centromeric histone chaperones in animals: www.science.org/doi/10.1126/... (TL;DR: they’re not really missing)

Remote homology and functional genetics unmask deeply preserved Scm3/HJURP orthologs in metazoans

Animals encode a rapidly evolving, essential cell cycle gene previously thought to be absent.

science.org

He is a remarkably gifted scientist but he is also a welcome reminder to me that the best ideas in a lab often come from the imagination of trainees. Yiu can read about his integrin work here: www.science.org/doi/10.1126/... and in a preprint we hope to post later this year (watch this space)

Molecular exaptation by the integrin αI domain

An ancient protein domain insertion seamlessly preserved conformational signaling while providing a novel surface for adaptation.

science.org

1/10 🚨Preprint! One RING to rule them all (phages)👑💍⚔️ Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇 biorxiv.org/content/10.6...

The ever amazing Steve Henikoff! @fredhutch.org @basicsci.fredhutch.org

HHMI@hhmi-science.bsky.social · 4w ago

Discoveries can hide in plain sight. #HHMIInvestigator Steven Henikoff's lab found a surprise when revisiting their old data: a region of ribosomal DNA producing microRNAs that can be associated with cancer, revealing a new role for part of the genome overlooked for decades: bit.ly/3RQwTmy.

Our new preprint @biorxivpreprint.bsky.social, led by @katsuminami.bsky.social‬ et al.! 🎉 www.biorxiv.org/content/10.6... Machine learning-assisted Repli-Histo labeling and single-nucleosome imaging reveal distinct transcription-dependent chromatin constraints across euchromatin and heterochromatin.

Our group is moving from @mpi-bio-fml.bsky.social to the maritime city of Kiel! ⛵️🩵 I will lead the Department of Marine Plant Development and Physiology @uni-kiel.de 🌱🪸🌊 Look out for opportunities to join us in this exciting & growing hub for Plant, Marine & Evolutionary Biology in North Germany 🇩🇪

New paper from the group! We were curious if the longevity of naked mole-rats has anything to do with their protein synthesis machinery. It was shown that the ribosomal 28S is split into 3 subunits Our cryo-EM study of the NMR ribosomes by @mehmetguel.bsky.social etal www.nature.com/articles/s41...

Cryo-EM structure of the naked mole-rat ribosome reveals a stabilized split 28S rRNA - Nature Communications

The long-living rodent naked mole-rat has a distinct break in its 28S ribosomal RNA. Here, the authors present cryo-EM structures showing this cleavage is stabilized by surrounding ribosomal proteins,...

nature.com

Open science before it had a name: An interview with molecular biologist Steven Henikoff (who is not on social media) @fredhutch.org @basicsci.fredhutch.org @hhmi-science.bsky.social @natprot.nature.com www.springernature.com/gp/researche...