Rens Holmer @holmrenser.bsky.social · 02/10/2026BRB updating my data visualization course material 000
Reposted by Rens HolmerMarnix Medema @marnixmedema.bsky.social · 18/09/2026Excited that our @w-u-r.bsky.social Bioinformatics team is involved in three funded projects in the NWO KIC Biochemical Diversity Programme. Kudos to @jjjvanderhooft.bsky.social for his leadership on the TERRAPATH project. Looking forward to fun collaborative science! www.wur.nl/en/news/nwo-...wur.nlNWO funding for research into biochemical alternativesFour WUR projects receive NWO funding: one project investigates natural compounds for new flavours and fragrances, and two projects investigate more sustainable crop protection. 163
Reposted by Rens HolmerGenome Biology and Evolution @genomebiolevol.bsky.social · 17/09/2026Chen et al. show that a substantial fraction of predicted orphan genes lacks expression support, and they exhibit distinct sequence and evolutionary signatures from expressed orphans. 🔗 academic.oup.com/gbe/article/... #societyjournal #genome #evolutionacademic.oup.comIdentification and Classification of Expressed Orphan Genes, Spurious Orphan Genes, and Conserved Genes in the Human Gut MicrobiomeAbstract. Orphan genes (OGs)—genes lacking detectable homologs outside a species—are widespread in microbial genomes and are thought to contribute to their 143
Reposted by Rens HolmerDaniel Probst @skepteis.bsky.social · 16/09/2026If anyone is or knows a master's student in the Netherlands who fits this call and who is interesting in ML, let me know :-). www.nwo.nl/en/calls/mos...nwo.nlMosaic 3.0 | NWOThe Mosaic PhD scholarship programme encourages graduates with a non-Western migration background—a group underrepresented in the Dutch scientific community—to pursue a career in science. 154
Reposted by Rens HolmerJo Wolff @jowolff.bsky.social · 14/09/2026The fallacy that University leaders pushing AI are falling into is thinking that the point of undergraduate research is to find things out. It isn't. What students find out is typically already generally known. The point of undergraduate research is to learn how to find things out. 351443413
Rens Holmer @holmrenser.bsky.social · 29/08/2026I like to think I’m not too much of an AI doomer, but this just doesn’t look right… 100
Reposted by Rens HolmerMarnix Medema @marnixmedema.bsky.social · 04/08/2026New postdoc opportunity in our team! Topic is computational analysis of (meta)genomic data to study evolution of plant-microbiome interactions. Part of the AEGIS consortium (aegisearth.bio/en). Apply here: www.wur.nl/en/vacancy/p... Please RT!wur.nlPostdoc on computational (meta)genomic analysisClimate change is one of the greatest challenges for global food security, requiring new approaches to understand and harness the natural diversity that enables plants and their associated microbiomes... 02336
Reposted by Rens HolmerNils Homer @nilshomer.com · 31/07/2026Meritocracy and competition is great, and the moat due to implementation effort is gone, but we also have to remember the relational side of bioinformatics. 152
Reposted by Rens HolmerDaniel Probst @skepteis.bsky.social · 30/07/2026FloDR: An invertible dimensionality reduction method based on a normalising flow ... combining the advantages of PCA with those of UMAP. We also show what the map "hides" in the remaining dimensions and how wrong it is when two points with different labels are close. arxiv.org/pdf/2607.26278 173
Reposted by Rens HolmerGrace @gracekind.net · 21/07/2026> show us how good you are at exploits > no, not like that 530627
Rens Holmer @holmrenser.bsky.social · 18/07/2026EiC of Science questioning whether people use search engines for *checks notes* “searching” was not on my 2026 bingo card 120
Rens Holmer @holmrenser.bsky.social · 11/07/2026Don’t get me wrong, I think applications of fundamental science are _really_ important, but I also think this is the perfect analogy 010
Reposted by Rens HolmerSuitch @suitch-co.bsky.social · 07/07/2026🔬 Bioinformatics | Group Leader, Theoretical Biology @ MPI for Evolutionary Biology Independent group, own PhD funding included, fixed term up to six years. Apply by Sep 1, 2026. www.mpg.de/26854220/group-leader-in… #Bioinformatics #BioinfJobs 022
Rens Holmer @holmrenser.bsky.social · 29/06/2026I’m a simple man: I see a Gaussian Process, I click the like button. (Also this is awesome work on protein engineering in general) 110
Rens Holmer @holmrenser.bsky.social · 12/06/2026Happy to have played a small part in this, congrats to all involved 🎉 Studying spatiotemporal dynamics in roots is not easy, it was inspiring to see @wkohlen.bsky.social dig in for years to get to the bottom of this story! 020
Reposted by Rens HolmerWolfgang Huber @wkhuber.bsky.social · 10/06/2026One of the good things about the AI co-scientist brouhaha is that it makes us discuss what science *is*, and how to measure its value, impact, quality. — Questions that have been there all along, but many preferred to gloss over. 24611
Reposted by Rens HolmerDaniel Probst @skepteis.bsky.social · 04/06/2026New preprint out. Nice work by @jose-e.bsky.social and Baoquan Chen. In a nutshell, our architecture takes in a set of graphs (e.g. molecules in a reaction) and interleaves node-level feature propagation and cross-graph contextual modelling at every layer of a GNN. arxiv.org/abs/2606.05116 0125
Reposted by Rens HolmerPhilip Ball @philipcball.bsky.social · 18/04/2026But what is getting folks excited here is that this DRT system reveals a way in which sequence information can be read back from protein to DNA. And that is where the finding impacts on Crick's Central Dogma. /15 1182
Reposted by Rens HolmerPhil Ewels @ewels.bsky.social · 02/04/2026I'm both excited and a little terrified. It feels like a wave of AI-assisted tool rewrites is coming to bioinformatics whether we like it or not. We figured that the best we can do is to try to get ahead of it, so we wrote down some principles for doing it responsibly: rewrites.biorewrites.biorewrites.bio - A manifesto for bioinformaticsPrinciples for responsible AI-assisted rewriting of bioinformatics tools. 42612
Reposted by Rens HolmerChris Jackson @cajackson.org · 11/03/2026Pretty much the same reason all the gene regulatory network inference models don't work as well as people think they do 133
Reposted by Rens HolmerRetraction Watch @retractionwatch.com · 10/03/2026We're thrilled to announce the Ctrl-Z Award, a US$2,500 prize for researchers “who discover substantial errors in their published work and take meaningful steps to correct the scientific record." Covered by @nature.com today; read more here: centerforscientificintegrity.org/2026/03/10/a...nature.comKeep calm and be transparent: advice from scientists who retracted their papersRetractions correct the scientific record, but they have stigma attached to them. Some in the research community want that to change. 6471197
Reposted by Rens HolmerArc Institute @arcinstitute.org · 04/03/2026Evo 2, the largest fully open biological AI model to date, is now published in @nature.com youtu.be/o_w-E--u7GQyoutu.beBuilding Evo 2: A Frontier DNA Language ModelYouTube video by Arc Institute 1126
Reposted by Rens HolmerScott 𐚁 🦇 Cave 🦇 @hellabarnes.bsky.social · 02/03/2026we talk about carcinization, but never about the many, many times plants have invented the “tree.” Tree is not a kind of plant, it is a thing plats do, and they are by and large unrelated. 1441286
Reposted by Rens HolmerAndrew Rambaut (🐏🎀) @arambaut.bsky.social · 28/02/2026So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).artic-network.github.ioPearTree — Phylogenetic Tree Viewer 5166101
Reposted by Rens HolmerAnne Kupczok @annecmg.bsky.social · 25/02/2026Sounds like a great opportunity for a professor position in computational biology in the Netherlands careers.universiteitleiden.nl/job/Assistan...careers.universiteitleiden.nlAssistant/Associate/Full Professor Computational BiologyAssistant/Associate/Full Professor Computational Biology 01413
Rens Holmer @holmrenser.bsky.social · 20/02/2026Students being students: I found this when logging on to the lecture room PC this morning. Translation: “R is not fun <redacted>” 😂 010
Reposted by Rens HolmerThe Arabidopsis Information Resource (TAIR) @tairnews.bsky.social · 19/02/2026🎉📣 #TAIR12, the latest reannotation of the Arabidopsis thaliana genome, is now available under accession number PRJEB100887 on ENA and NCBI! Thank you all the volunteer researchers whose hard work has made this possible! #plantscience #plantbiology 🧪 bit.ly/3ZHtneTbit.lyAnnouncing the publication of TAIR12: Consult the fully reannotated genome on the European Nucleotide Archive - Phoenix BioinformaticsTAIR (The Arabidopsis Information Resource), together with our nonprofit host Phoenix Bioinformatics, is pleased to announce the public release of TAIR12 410361
Rens Holmer @holmrenser.bsky.social · 12/02/2026Our chairgroup Bioinformatics at Wageningen University changed leadership: prof. Dick de Ridder (@dickderidder.bsky.social) moved on to become Dean of Education and is now followed up by prof. Marnix Medema. Congrats @marnixmedema.bsky.social! www.wur.nl/en/news/marn...wur.nlMarnix Medema appointed chair of Bioinformatics at WURMarnix Medema has been appointed Chair of the Bioinformatics Group at Wageningen University & Research as of 1 February. He aims to further strengthen bioinformatics as a connecting discipline within ... 051
Rens Holmer @holmrenser.bsky.social · 12/02/2026Vibecoding when you’re a proficient programmermedia.tenor.coma knight with a helmet and a sword says " this is the way "ALT: a knight with a helmet and a sword says " this is the way " 010
Rens Holmer @holmrenser.bsky.social · 08/02/2026Nothing but respect for the authors who made the difficult call to retract published work after facing public scrutiny: www.science.org/doi/10.1126/... But also: scientific publishing is fundamentally broken if we see this case as anything other than a win for science!science.orgRETRACTED: Integrative phylogenomics positions sponges at the root of the animal treeDetermining whether sponges or ctenophores root the animal tree has important implications for understanding early animal evolution. Here, we examined support for these competing hypotheses by constru... 000
Rens Holmer @holmrenser.bsky.social · 08/02/2026Super interesting thread on vibecoding: translating an existing approach from c++ to rust. TLDR it’s not straightforward at all! Even though the information is there, many crucial parts are omitted/incorrect. 210
Rens Holmer @holmrenser.bsky.social · 28/01/2026Preprint your work! TIL I learned the animal phylogenomics paper has been asked to be retracted, which might have been avoided if it was looked at by more than a handful of rushed anonymous academics. 010
Reposted by Rens HolmerDolf Weijers @dolfweijers.bsky.social · 28/01/2026www.wur.nl/en/vacancy/f... Become our new colleague (and next door neighbor) and lead a chair/group/department of Biophysics at Wageningen University. Reach out to me for info and please spread!!!wur.nlFull Professor and Chair Laboratory of BiophysicsWe are looking for a Full Professor in the Biophysics chair group, part of Wageningen University & Research (WUR) 02348
Reposted by Rens HolmerMolly White @molly.wiki · 15/01/2026Sure. AI companies have ALWAYS been training their models on Wikipedia content, which under the free and open access model is available to anyone — including AI companies. Agreements like these require AI companies to limit and offset the strain they place on Wikimedia infrastructure. 4147361384
Reposted by Rens HolmerHeng Li @lh3lh3.bsky.social · 14/01/2026I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!hlilab.github.ioHLi Lab - VacanciesOpenings 14363
Rens Holmer @holmrenser.bsky.social · 12/01/2026It took me forever to realize this after reading Pearl’s The Book of Why 110
Reposted by Rens HolmerHeng Li @lh3lh3.bsky.social · 06/01/2026Now published in Algorithms for Molecular Biology: link.springer.com/article/10.1.... Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now. 15920
Reposted by Rens HolmerHeng Li @lh3lh3.bsky.social · 06/01/2026Now published in gigascience: academic.oup.com/gigascience/.... Key messages: SVs are highly enriched in low-complexity/tandem-repeat regions and are harder to call. They behave differently from transposon insertions. Always stratify if you study SVs.academic.oup.comValidate User 0339
Reposted by Rens HolmerThijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 05/01/2026I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻 Please repost Apply here: www.wur.nl/en/vacancy/p...wur.nlPostdoctoral researcher Phylogenomics and metagenomicsAre you just as excited as we are about the fascinating world of microorganisms? Do you want to contribute to exploring and genomically characterize novel prokaryotic lineages? Do you have a PhD degre... 04348
Reposted by Rens HolmerNina Markl 🏳️⚧️🏳️🌈 @ninamarkl.bsky.social · 05/01/2026happy ‘i will reply to your email on my return’ day to all who celebrate 411327
Rens Holmer @holmrenser.bsky.social · 05/01/2026I’m so far removed from this field that saying “there is no causal inference” for me is at least a lukewarm take. 010
Rens Holmer @holmrenser.bsky.social · 28/12/2025Apropos of nothing: I just realized serde literally derives from serializing/deserializing despite having used it a bunch. No I didn’t read the docs, yes I feel stupid 🙃 010
Reposted by Rens HolmerDr Alex Bond @thelabandfield.bsky.social · 25/12/2025On the first day of Christmas (in about 2014), @duckswabber.bsky.social gave to me - a partridge in a pear tree. Happy Christmas everyone! 212742
Reposted by Rens HolmerVandepoele lab @vandepoelelab.bsky.social · 23/12/2025We are pleased to announce the official release of PLAZA 5.1, our plant genomics platform, which comes with a major front-end redesign. This results in improved performance, enhanced visualization tools, and refined Toolboxes. Src: www.vandepoelelab.be/plaza/news#28 04223
Reposted by Rens HolmerMarnix Medema @marnixmedema.bsky.social · 13/12/2025Now available online: the new 2.0 version of gutSMASH, with capabilities to detect 12 new types of catabolic gene clusters relevant to gut microbiome ecology, as well as predictions of their regulation through transcription factor binding site detection. www.sciencedirect.com/science/arti...sciencedirect.comgutSMASH 2.0: Extended Identification of Primary Metabolic Gene Clusters From the Human Gut MicrobiotaMicrobiota-derived metabolites serve as key messengers mediating host–microbe and microbe–microbe interactions, often through specialized primary meta… 23518
