Single-page, interactive overlap assembler for teaching purposes: lh3.github.io/teach-demo/ova… (vibe coded)
Samuel Talbot retweeted
Excited to share Fold on Tight! 🎉
We distil recent advances in plant immunity into 10 lessons for using AI structure prediction critically and effectively, in plants and beyond.
With @amiralito_ Alex McClelland @YuSugiharaY @mpcontreras4 @KamounLab
📝zenodo.org/records/22100279
Samuel Talbot retweeted
We are pleased to share our paper in @PLOSCompBiol where we reveal patterns of position-dependent codon usage that we call "POSCO". POSCO is a score that describes biases in codon occurrence relative to the start codon. High POSCO is associated with increased translational efficiency and changes in ribosomal occupancy.
journals.plos.org/ploscompbi…
Samuel Talbot retweeted
Oregon State University's Department of Integrative Biology is currently hiring up to three tenure-track faculty members, with an emphasis on organismal biology.
Note: Previous links are no longer active due to a change in our hiring system.
oregonstate.wd501.myworkdayj…
Samuel Talbot retweeted
Singapore offers a generous package for Visiting Professorships. If you are excited about AI in biology and would like to join us at the @astar_gis for 20% of your time, contact me directly. We plan to tightly integrate AI with wet-lab experiments for training and validation.
The Visiting Professorship is open to AI researchers (either in academia or industry) who currently reside outside Singapore. The requirements for the Visiting Professorship are as follows:
A willingness to engage meaningfully with Singapore, including a commitment to spend at least 20% of time to support the collaboration, of which a substantive amount of time should be spent physically in Singapore.
The deadline is soon!! Please share!!!
1/n
We introduce new open benchmarks for ab initio gene annotation from DNA sequence alone:
Gene segmentation only benchmark:
huggingface.co/spaces/AIRI-I…
Complete annotation benchmark:
huggingface.co/spaces/AIRI-I…
Paper:
biorxiv.org/content/10.64898…
Samuel Talbot retweeted
🧬Possibly one of the most important genetics preprints of 2026 has just been published: the flagship paper of the Vertebrate Genomes Project.
An ambitious effort to generate near-complete and near-error-free reference genomes for all living vertebrate species.
The authors present 816 high-quality reference genomes covering around 95% of major vertebrate evolutionary lineages. Most assemblies are at chromosome-level quality and some are fully diploid telomere-to-telomere genomes.
Using this resource the authors reconstructed the genome of the last common ancestor of vertebrates, studied the evolution of sex chromosomes, explored 3D genome organization and compared epigenetic landscapes across hundreds of species.
This dataset will likely become a foundational platform for evolutionary biology and comparative genomics.
biorxiv.org/content/10.64898…
#VGP #evolution #ComparativeGenomics #vertebrates #genomes
Samuel Talbot retweeted
Pleased to share this free link to our new review of genome annotation in @NatureRevGenet, which just appeared today. Co-authored with Hyunjoo (Hayden) Ji and Mihaela Pertea @elapertea. We focus particularly on human annotation: rdcu.be/e4mI1
Samuel Talbot retweeted
The complete genome of a songbird. #ReferenceGEnome #SongbirdGenome #ZebraFinchGenome #T2T #LongRead #Sequencing @biorxiv_genomic
biorxiv.org/content/10.1101/…
Samuel Talbot retweeted
~25% of human candidate cis-regulatory elements (cCREs) are derived from transposable elements, further shaping gene regulation, TF binding, and GWAS variant enrichment.
Uncover the science behind it: biorxiv.org/content/10.1101/…
Samuel Talbot retweeted
The growing library of vertebrate genomes is already transforming scientific exploration and enabling research that would have been impossible just six years ago. We look forward to more collaborative insights from this stellar team as they continue generating reference genomes for species with backbones!
Across the globe, EBP groups are sequencing vertebrate genomes — both locally and globally — to contribute to the growing database of high-quality reference genomes! 🧬🌍
The Vertebrate Genomes Project, an EBP genomic powerhouse, collaborates with other EBP initiatives, including the B10K project at BGI Group (10,000 Bird Genomes), the Amphibian Genomics Project, the Tree of Life Programme, DAISEA AfricaBP, the Cetacean Genomes Project (whales and dolphins), and many more. Together, these projects show how global collaboration can overcome challenges, sequence rare or hard-to-find species, and develop shared methods that benefit researchers worldwide.
@genomeark | @DAISEA_AfricaBP | @erga_biodiv European Reference Genome Atlas | @PEPR_ATLASea : atlas of marine genomes | @sangerinstitute | @BioplatformsAus Australia | Wise Ancestors | and many more groups!
Several EBP groups are now on BlueSky, please find us there to follow updates: linktr.ee/earthbiogenomeproj…
Samuel Talbot retweeted
This morning Mark Blaxter, Head of the Tree of Life Programme, was on BBC Radio 4 Today discussing the importance of sequencing all life, including those in our oceans 🌊
Catch up here (starting at 2hrs 26 mins) ⤵️
bbc.co.uk/sounds/play/m002hb…
Samuel Talbot retweeted
Pangenome-guided sequence assembly via binary optimisation. #GenomeAssembly #PangenomeGuiedeAssembly @biorxiv_genomic
biorxiv.org/content/10.1101/…
Samuel Talbot retweeted
New preprint shows that DALI, TM-align and Foldseek overestimate protein structure alignment significance by 5-6 orders of magnitude
biorxiv.org/content/10.1101/…](biorxiv.org/content/10.1101/…
Samuel Talbot retweeted
Evaluation of sequencing reads at scale using rdeval. #SequencingData #ReadsSummary #Bioinformatics
academic.oup.com/bioinformat…
Samuel Talbot retweeted
🌍 Hear from Erich Jarvis, chair of the EBP-affiliated Vertebrate Genomes Project at the Rockefeller University, as he explains why high-quality reference genomes across the Tree of Life are essential for conservation. 🦜🐋🐒
🧬He also shares how the VGP is helping to coordinate a nationwide platform to ensure the continued generation of reference genomes across the United States.
👉 bit.ly/401IbWl
@genomeark @RockefellerUniv @erichjarvis
#Conservation #Genomics #DNA #scienceinnovation #fundingnews #sciencenews
Samuel Talbot retweeted
Slides from my talk (with Kamil Jaron) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-k…
Samuel Talbot retweeted
I start to screen for interview candidates. If you are interested, please hurry up!
Samuel Talbot retweeted
🌾 Excited to share that our research on plant tandem kinase proteins (TKPs)! nature.com/articles/s41588-0… We found wheat TKP RWT4 directly binds to the fungal effector AvrPWT4 to trigger immune responses against the devastating Magnaporthe oryzae.
Samuel Talbot retweeted
Hello world! I have a postdoc position immediately available in my lab. It will focus on identifying high-quality transposons in many genomes and finding their impacts in evolution and traits. Most works, including EDTA2 development and annotation of 400+ genomes, are done! 1/n




























