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Jaruwatana (Sodai) Lotharukpong

@sodail.bsky.social
216 followers 360 following 22 posts

ꙩ ꙫ ө ꚛ ꙮ :: single cell genomics postdoctoral fellow @ COS Heidelberg lotharukpongjs.github.io

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Reposted by Jaruwatana (Sodai) Lotharukpong
Eirik Lågeide @eiriklag.bsky.social · 01/10/2026
Very excited to share the first preprint from my PhD with the community! This is also the first paper from the Plant Immunogenomics group with @galofir.bsky.social, so stay tuned for more! www.biorxiv.org/content/10.6... 1/n 🧵
biorxiv.org
NO VEIN is an ancestral immunity protein involved in plant-virus interaction
The conservation of immune systems from prokaryotes to eukaryotes can guide discovery of immunity genes across the tree of life. Most studies to date have focused on metazoan systems, while the extent...
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Reposted by Jaruwatana (Sodai) Lotharukpong
Hajk-Georg Drost @hajkdrost.bsky.social · 23/09/2026
This is incredibly exciting 🤩 @anthropic.com just reported, Claude helped discover a novel CRISPR-like enzyme system. Enabled by our DIAMOND/DeepClust software 🚀: 🧬 15.8 BILLION proteins → 1.94 BILLION clusters → searched by AI agents www.anthropic.com/news/claude-...
anthropic.com
Claude discovers a novel enzyme system
In early results from our new life sciences research lab, Claude agents found an enzyme system whose function is still unknown.
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Reposted by Jaruwatana (Sodai) Lotharukpong
Alex de Mendoza @alexdemendoza.bsky.social · 03/08/2026
Sailing in @biorxivpreprint.bsky.social ready for summer, our study on the iconic Portuguese man o' war 🪼 is out: www.biorxiv.org/content/10.6.... We use (epi)genomics to understand a critter that fascinates me since childhood. Massive team effort with @obog.bsky.social, Cummins and Neely groups. 🧵
the indo-pacific bluebottle (Physalia utriculus)
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Reposted by Jaruwatana (Sodai) Lotharukpong
Sean Montgomery @seanamontgomery.bsky.social · 03/08/2026
Glad to see this out at last! Check out Arnau's summary below for all the highlights
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Reposted by Jaruwatana (Sodai) Lotharukpong
Paco Majic @hhydrochaerus.bsky.social · 09/07/2026
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...
academic.oup.com
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
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Reposted by Jaruwatana (Sodai) Lotharukpong
Alice Laigle @alicelaigle.bsky.social · 23/07/2026
📝 NEW PREPRINT It’s with an immense joy that our preprint is finally out and it’s my first first co-author paper!!! 🧬🍄 What is the diversity of 3D genome architectures in fungi? We reconstructed the 3D genome architecture of public Hi-C data from 55 fungal. Preprint: lnkd.in/enxTh2Cm
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Michael Borg @borglab.bsky.social · 07/07/2026
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 🇩🇪
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Reposted by Jaruwatana (Sodai) Lotharukpong
Carole Duchene @caroleduchene.bsky.social · 18/05/2026
Our paper is out! Giant viruses lay silent in algal genome across generations, but reactivate in reproductive cell types and under specific environnemental condition to produce virions. Thank you all for your contributions !
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Reposted by Jaruwatana (Sodai) Lotharukpong
paveltomancak.bsky.social @paveltomancak.bsky.social · 18/06/2026
Big paper from @hejnol.bsky.social lab. Title says it all. Congrats, Stanislav Kremnyov and the team. www.nature.com/articles/s41...
nature.com
A blastoporal organizer in a ctenophore - Nature
Experiments using the comb jelly Mnemiopsis leidyi and the sea anemone Nematostella vectensis reveal that the emergence of a core signalling pathway may have been a key innovation enabling the transit...
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Reposted by Jaruwatana (Sodai) Lotharukpong
Iñaki Ruiz-Trillo @multicellgenome.bsky.social · 09/06/2026
1/10 For decades, cellular aggregation was considered an evolutionary dead end. Cells could come together temporarily. But complex multicellular organisms like animals? Our study, led by JP Gerdt, with Ruibao & @jennahed.bsky.social suggests it may be time to rethink that🧵 #ProtistsOnSKy
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Toni Gabaldón @tonigabaldon.bsky.social · 10/06/2026
Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 16/04/2026
1/8 🔥 New preprint dropped: Dynamic co-existence of bacteriophages and their hosts 🦠 in the Arabidopsis thaliana 🌱 phyllosphere Work led by the indomitable @sheilaroitman.bsky.social‬ #plantscience #microbiome #holobiont www.biorxiv.org/content/10.6...
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Berta Verd @bertaverd.bsky.social · 21/04/2026
New Pre-Print Alert! Evolving initial conditions: an alternative developmental route to morphological diversity with Shannon Taylor and @jamesehammond.bsky.social www.biorxiv.org/content/10.6...
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Manuel Irimia @mirimiam.bsky.social · 20/04/2026
Thrilled to present our comparative study on the evolution of zygotic genome activation (ZGA)!! 🥚🧬 Amazing PhD work of @campobes.bsky.social together with @fedemantica.bsky.social and many collaborators! @melisupf.bsky.social @crg.eu. Thread below 1/15 www.biorxiv.org/content/10.6...
biorxiv.org
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canaztekin.bsky.social @canaztekin.bsky.social · 10/04/2026
🚨 Why can’t mammals regenerate limbs like frog tadpoles or salamanders? In our new paper in @science.org , we show that species-specific oxygen sensing acts as a gatekeeper for initiating limb regeneration 🐭🐸 🔗 www.science.org/doi/10.1126/... #EvoDevo
science.org
Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration
Why mammals cannot regenerate limbs like amphibians do presents a long-standing puzzle in biology. To uncover the underlying differences, we compared amputation responses of embryonic mouse (Mus musculus) and Xenopus laevis tadpole limbs. Lowering ...
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Reposted by Jaruwatana (Sodai) Lotharukpong
Erica Dinatale @ericadinatale.bsky.social · 03/04/2026
Behind the scenes! go.nature.com/4bYY8BM
go.nature.com
What brown algae taught me about the importance of jumping genes for genome evolution
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Michael Borg @borglab.bsky.social · 02/04/2026
Our work on chromatin evolution in brown algae is now published in @natecoevo.nature.com! We show that developmentally complex brown algae evolved without epigenetic silencing pathways long thought universal, underscoring why non-model lineages are important to study. www.nature.com/articles/s41...
Undaria pinnatifida gametophyte
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Thorsten Langner @thorstenlangner.bsky.social · 01/04/2026
Now that it's official i've got some news! Our group has moved from @mpi-bio-fml.bsky.social to @unihalle.bsky.social where I am now leading the department for phytopathology and plant protection 🍄🌾🧬
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Jaruwatana (Sodai) Lotharukpong @sodail.bsky.social · 31/03/2026
Our work on chromatin evolution in brown algae is finally out! This is also my first "co-first author" paper!! I’m excited to share what we found 👇
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Nature Ecology & Evolution @natecoevo.nature.com · 30/03/2026
Chromatin plays a central role in gene regulation, but chromatin systems are only known for a few model species. This study analyses chromatin regulatory landscapes in brown algal lineages to elucidate their structural organization and evolution 🧪 www.nature.com/articles/s41...
nature.com
Evolution of a distinct chromatin regulatory landscape in brown algae - Nature Ecology & Evolution
Chromatin plays a central role in gene regulation, but chromatin systems are only known for a few model species. This study analyses chromatin regulatory landscapes in brown algal lineages to elucidat...
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Reposted by Jaruwatana (Sodai) Lotharukpong
Romy Petroll @petrollromy.bsky.social · 26/03/2026
I am very grateful to be featured discussing my work on transcription associated proteins and TAPscan @rensingstefan.bsky.social Many thanks to @theplantjournal.bsky.social for the opportunity and recognition!
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Hajk-Georg Drost @hajkdrost.bsky.social · 24/03/2026
How much protein diversity can Life on Earth actually generate? With DIAMOND DeepClust, we show how billions of proteins across the tree of life can be clustered at low-identity for downstream analytics tasks. 📚Paper: www.nature.com/articles/s41... 💻Code: github.com/bbuchfink/di...
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Amor Damatac II @amordamatac.bsky.social · 12/03/2026
I am thrilled to share our new publication in @natcomms.nature.com showing that the vertebrate developmental hourglass has a cellular basis. We asked whether this embryonic pattern is already evident at the level of cells, the building blocks of complex organisms. rdcu.be/e70XT
rdcu.be
A cellular basis for the hourglass pattern in vertebrate embryogenesis
Nature Communications - The developmental hourglass has long been seen at the level of embryos. By zooming in to single cells, this Perspective shows that mid-embryonic conservation arises from...
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Reposted by Jaruwatana (Sodai) Lotharukpong
Gennady Gorin @goringennady.bsky.social · 03/03/2026
After years of work, the centerpiece of my PhD is published in @natmethods.nature.com! Read it to learn about the biophysical insights we can get from single-cell data! But first, I would like to talk a bit about RNA velocity and normalization. 1/
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Reposted by Jaruwatana (Sodai) Lotharukpong
James Phipps-Tan @jphippstan.bsky.social · 20/02/2026
Heya science peeps, my first first-author paper is on Biorxiv! We show how transcriptome-wide expression variability in outbred animals responds massively to an environmental stressor and is underpinned by cryptic variability- (not just mean-) controlling alleles. www.biorxiv.org/content/10.6...
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Hajk-Georg Drost @hajkdrost.bsky.social · 19/02/2026
Does hidden protein biology live in the suboptimal alignment space? When we align two divergent proteins, we usually trust a single optimal alignment. 🧬 But what if the real structural signal lies in the space of near-optimal solutions? With EMERALD-UI you can unfold this perspective.
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Reposted by Jaruwatana (Sodai) Lotharukpong
Claudia Martinho @cssmartinho.bsky.social · 30/01/2026
One protein. One pathway. A whole germline fate. New paper from my postdoc @mpi-bio-fml.bsky.social out in PNAS: Germline fate determination by a single ARGONAUTE protein in Ectocarpus www.pnas.org/doi/10.1073/...
pnas.org
Germline fate determination by a single ARGONAUTE protein in Ectocarpus | PNAS
ARGONAUTE (AGO) proteins are a highly conserved family of RNA-binding proteins that play central roles in gene regulation and developmental process...
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Reposted by Jaruwatana (Sodai) Lotharukpong
Hajk-Georg Drost @hajkdrost.bsky.social · 07/01/2026
🧵 Just out in Cell after more than 10 years in the making! 🎓 www.cell.com/cell/fulltex... Plants and animals evolve radically different body plans. Do they also operate under fundamentally different molecular evolutionary constraints during organ formation? @cellpress.bsky.social
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Claudia Martinho @cssmartinho.bsky.social · 02/01/2026
Genome editing in brown algae! 🧬🪸🌿 Now out in Cell Reports Methods! Excited to share this highly efficient, transgene-free CRISPR–Cas genome editing protocol for brown algae, requiring no cloning and no specialized equipment. doi.org/10.1016/j.cr... #CRISPR #BrownAlgae @mpi-bio-fml.bsky.social
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Benjamin J. Buchfink @bbuchfink.bsky.social · 22/12/2025
DIAMOND v2.1.17 has new output fields sRANK to print taxonomy nodes of the given rank associated with the subject sequence, where RANK can be any rank in the NCBI taxonomy, e.g. sdomain, skingdom, sphylum, sorder, sgenus, sspecies, etc. github.com/bbuchfink/di...
github.com
GitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner.
Accelerated BLAST compatible local sequence aligner. - bbuchfink/diamond
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Reposted by Jaruwatana (Sodai) Lotharukpong
Hajk-Georg Drost @hajkdrost.bsky.social · 12/12/2025
Can we tune a plant’s epigenetic toolkit to disrupt plant homeostasis in ways that enable phenotypic innovation? 🌱Check out our new Opinion Paper with @thanvisrikant.bsky.social discussing this topic in @cp-trendsplantsci.bsky.social! www.sciencedirect.com/science/arti...
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canaztekin.bsky.social @canaztekin.bsky.social · 02/12/2025
🎉 Our deconstructed, stem-cell–based approach to studying signaling centers and limb-development cell types is out! 🥳 So nice to see it in its final form after the preprint— and huge thanks to the community for all the enthusiasm and interest since then! www.science.org/doi/10.1126/...
science.org
Specialized signaling centers direct cell fate and spatial organization in a mesodermal organoid model
Stem cell–derived mesodermal organoids reveal how signaling centers guide cell fate and tissue organization.
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MPI for Biology Tübingen & Friedrich Miescher Laboratory @mpi-bio-fml.bsky.social · 01/12/2025
To launch the start of the new recruitment round for PhD positions at the institute, we're highlighting this month one of our doctoral researchers for our #WeAreMPIBio #WeAreFML series: Jaruwatana Sodai Lotharukpong who joined IMPRS in 2021. Read about his work and interests: tinyurl.com/yeysnm8w
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Philip Donoghue @phil-donoghue.bsky.social · 13/11/2025
Pleased to be a small part of this molecular palaeobiology study by Jialin Wei, led by Marta Álvarez-Presas and Jordi Paps, with help from Davide Pisani. Animals repeatedly used similar genomic solutions to the challenges of terrestrialization @bristolpalaeo.bsky.social @bristolbiosci.bsky.social
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🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 13/11/2025
NEW pub in @science.org 🥳 Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life? For over 15 years, #phylogenomic studies have been divided. We provide new evidence suggesting that... 🔗: www.science.org/doi/10.1126/...
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Hajk-Georg Drost @hajkdrost.bsky.social · 04/11/2025
🚀 philentropy v0.10.0 is on CRAN! Now with long-awaited parallel distance computation & a full speed-optimized refactor thanks to Andrew Gene Brown. Compute 50+ distances/divergences in R faster than ever. 📦 CRAN: cran.r-project.org/web/packages... 💻 Code: github.com/drostlab/phi...
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Hadley Wickham @hadley.nz · 06/11/2025
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp.... genzplyr is dplyr, but bussin fr fr no cap.
github.com
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
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Hajk-Georg Drost @hajkdrost.bsky.social · 02/10/2025
Last year, our collaboration effort with @sodail.bsky.social and Susana Coelho highlighted that Brown Algae are a promising model system to study the evolution of multicellularity and emergence of embryogenesis as a constrained developmental process shaping body plans. www.nature.com/articles/s41...
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Hajk-Georg Drost @hajkdrost.bsky.social · 02/10/2025
Thrilled to share what we learned from re-annotating the mobilome of the brown algae model [Ectocarpus] 🌊🌿🏖️ genomebiology.biomedcentral.com/articles/10.... A wonderful collaboration with @ericadinatale.bsky.social, @cssmartinho.bsky.social, @rorycraig.bsky.social, and Susana Coelho! 🎉
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Erica Dinatale @ericadinatale.bsky.social · 01/10/2025
So happy to see my first first-author paper published! 🎈 A short thread on how Ectocarpus and its TE secrets have kept me busy lately: rdcu.be/eITQH
rdcu.be
Characterization of the transposable element landscape shaping the Ectocarpus genome | Genome Biology
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Alexandra Dallaire @alexdallaire.bsky.social · 03/09/2025
I’m super happy to present the first discoveries of the RIKEN-Cambridge Joint Crop Symbiosis Research Team, based in Japan 🇯🇵 doi.org/10.1101/2025... A thread 👇
doi.org
Reductive evolution of the DNA replication machinery in endosymbiotic fungi
The molecular machinery for replicating and repairing DNA accurately is critically important for life and highly conserved across the Tree of Life. Here we show that two major lineages of fungi, Glome...
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Jaruwatana (Sodai) Lotharukpong @sodail.bsky.social · 19/09/2025
Super glad to contribute to this study on chromatin evolution in brown algae! Special thanks to Jeromine Vigneau, @borglab.bsky.social and Susana Coelho for making this happen. www.biorxiv.org/content/10.1...
biorxiv.org
Rewiring of chromatin regulation underlies the evolution of brown algal multicellularity
Chromatin structure plays a central role in regulating transcription, genome stability, and epigenetic inheritance in eukaryotes. Much of our understanding of chromatin architecture and histone post-t...
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Reposted by Jaruwatana (Sodai) Lotharukpong
Nature Methods @natmethods.nature.com · 18/09/2025
GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio www.nature.com/articles/s41...
nature.com
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
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Thomas Lin Pedersen @thomasp85.com · 11/09/2025
I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN. It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package. Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
tidyverse.org
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
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Charlotte Wright @charlottewright.bsky.social · 11/09/2025
How many chromosomes can an animal have? In our paper out now in @currentbiology.bsky.social we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact. www.cell.com/current-biol...
tinyurl.com
Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly
The genome of the Atlas blue butterfly contains ten times more chromosomes than most butterflies, and more than any other known diploid animal. Wright et al. show that this extraordinary karyotype is ...
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Max Planck Institute of Molecular Cell Biology and Genetics @mpi-cbg.de · 03/09/2025
Dresden researchers @paveltomancak.bsky.social @bruvellu.bsky.social, Carl Modes, @cuencam15.bsky.social ‬ & colleagues published in @nature.com that a tissue fold in fruit fly embryos buffers mechanical stresses & may have evolved in response to mechanical forces. www.mpi-cbg.de/news-outreac...
mpi-cbg.de
Mechanical forces drive evolutionary change
A small tissue fold present in fruit fly embryos buffers mechanical stresses and may have evolved in response to mechanical forces.
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Giulio Ermanno Pibiri @jermp.bsky.social · 28/08/2025
Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :) www.biorxiv.org/content/10.1...
biorxiv.org
AllTheBacteria - all bacterial genomes assembled, available and searchable
The bacterial sequence data publicly available via the global DNA archives is a vast potential source of information on the evolution of bacteria. However, most of this sequence data is unassembled, o...
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Yi-Jyun Luo @yjluo.bsky.social · 18/08/2025
Delighted to share the peer-reviewed version of our study led by @tomlewin.bsky.social now out in Genome Biology @bmc.springernature.com! We analyzed 64 chromosome-level genomes across 15 animal phyla and found that extensive genome rearrangements are the norm in bilaterians. doi.org/10.1186/s130...
doi.org
Conservation of bilaterian genome structure is the exception, not the rule - Genome Biology
Species from diverse animal lineages have conserved groups of orthologous genes together on the same chromosome for over half a billion years since the last common ancestor of bilaterians. Although no...
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Jaruwatana (Sodai) Lotharukpong @sodail.bsky.social · 25/08/2025
A really cool study led by Josue and @agalip.bsky.social detailing the nature of sex chromosomes in brown algae, including the origin and repeated losses of U/V sexual systems. Brown algae also has highly conserved macro-synteny, retained at least ~224 Ma!! Interesting gene age data too!
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Ferdinand Marlétaz @ferdix.bsky.social · 13/08/2025
After nearly twenty years in the making, our attempt at understanding what makes the chaetognath phylum so unique has finally been published! www.nature.com/articles/s41... with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1
nature.com
The genomic origin of the unique chaetognath body plan - Nature
Genomic, single-cell transcriptomic and epigenetic analyses show that chaetognaths, following extensive gene loss in the gnathiferan lineage, relied on newly evolved genes and lineage-specific tandem ...
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