Staff scientist at the Center for Quantitative Life Sciences. Focused on genome assembly, gene annotation, and identifying R-genes. Metagenomics in WW.
Oregon State University
Joined January 2021
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I’m very proud to announce my first publication. Featured on the cover of G3 Genes | Genomes | Genetics. The haplotype-resolved genome of European hazelnut will be a valuable resource for the plant breeding program here at Oregon State University.
academic.oup.com/g3journal/a…
ALT Disease-resistant hazelnut orchard in Oregon’s Willamette Valley. Lynn Howlett Photography
I’m shocked that SingularityCE by sylabs is at end of life. No more software engineering either. Support ends October 25, 2026.
It seems so sudden, I wonder what happened?
Amazing work by the Bat 1K.
I’m happy to have played a small role in this, generating assemblies and manually curating chromosomes for over 30* different bat species!
Special shout out to the VGL team for the amazing opportunity @genomewarriors 🦇
Our new study suggests that bats originated in Europe around 65 million years ago and revises our understanding of how several major bat groups are related. Proud to be part of the international Bat1K team behind this work.
doi.org/10.1038/s41586-026-1…
Perhaps every biology field should make their own millennium challenge list, then researchers can sort through them to generate a comprehensive list that doesn’t read like an ad. Surely there are overlaps in technical limitations and ideas.
Samuel Talbot retweeted
Single-page, interactive overlap assembler for teaching purposes: lh3.github.io/teach-demo/ova… (vibe coded)
The recent HPRCV2 is so impressive, what an inspiration. Deep learning models for patching raw reads at the nucleotide level, improvements in alignment over complex rDNA arrays, a pan epigenome, and an all vs all indexable alignment lookup with localized pangenome assembly. Wow!
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
I don’t work on cancer but this figure gave me a laugh. It’s easy to follow too! G4 quadriplexes are fascinating
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…
Fascinating how many different wet lab methods and bioinformatics tools are needed to assess the astonishing complexity of centromeres! And it’s only possible thanks to the quality of these reference genomes acting as the substrate. @HumanPangenome team setting the standard !!
Nature research paper: A global view of human centromere variation and evolution
go.nature.com/4bnIAb7
The hifiasm step is flawed. It’s eval hacking, and i’d argue it’s helpful, but calling a non-model draft assembly complete by just optimizing asm statistics without understanding downstream impact on contigs/hiC map is suspect. Reviewing pubs w/ many uniq params is a nightmare.
Coding agents are helping scientists spend more time advancing research, taking on everything from routine maintenance and targeted optimization to complete redesigns and new systems.
While agents can reliably execute on ambitious projects, researchers must still define the scientific questions, verify results, and take a stance on long-term ownership.
An academics’ audience being AI and not the proverbial public is interesting. How many pubs do you read where the data is filtered tables and not complt? I’m guilty — believing tht a human reading wouldn’t sift through noise. But maybe we can do both? Publish filtered + tar full?
The preps for obtaining pacbio/nanopore reads are easy compared to generating ultralong 80-100kb + in non model plants. Why have there been such minimal advances in dna extraction chemistry?
The NSF engines program is ambitious , but doesn’t seem serious. “Up to $160M over 10 years” gives the impression that the true amount awarded will be much lower. Maybe there’s an industry partnership layer baked in that i’m missing?
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!!!
Samuel Talbot retweeted
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…
Very happy to contribute to the VGL lab and broader genomics community.
We need more high quality reference genomes across the tree of life. These public resources are fundamental in understanding modern biology and aiding global conservation efforts.
🧬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
🧬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
Awesome to see a new LiftOn github.com/Kuanhao-Chao/Lift… version 1.0.9 with big improvements to accuracy. Very helpful to see the between version benchmark comparisons. Starting to test it on some messy hop genomes ! Thanks @KuanHaoChao
