Samuel Talbot

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/arti…

Finally using pixi to write up all code for a project. Multiple sub environments, with underlying tasks and scripts + singularity container calls within. Excited to just include the .toml + .lock with publication and be done with it. Should have done this months ago!

@BTIscience Testing weightless environments and measuring gravitropic responses! Pretty cool.

Throwback science! 🌿We found this fascinating piece of equipment while digging into the BTI archives. Think you know what it was used for? Take a guess in the comments!

It’s a great tune. But I might be biased🧬

Can we make it easier to submit gff files to genbank? It is so convoluted and time consuming compared to a genome upload. I’m still seeing papers say “check figshare” tempting me to do the same.

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

@agus3260 Ahh minisplice! It is a great example, thanks for the suggestion.! Have to emphasize GPUs for our supercomputer😆

@SamCTalbot You thought about including minisplice, it doesn't run on GPU, but in my humble opinion, I think it's a good example. Cheers!!

Preparing a 20min talk for a broad audience interested in AI and GPUs. Three case studies: metagenome assembly binning (LORBIN), gene prediction model generation (Tiberius) and pangenome variant calling (DeepVariant). Yes, I will be speaking fast. 1 slide for installs though!

@jcamthrash Ohhh I needed this. Great timing, thank you!

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning nature.com/articles/s4158…

@acarroll_ATG @EBPgenome @Googleorg Excited about this for the VGL! What would be really cool is to use trio assemblies to support a truth set model for implementing deepvariant calls across some of these specific endangered species of interest. Might be hard to get that parental data but still !

This blog talks about the great work of the @EBPgenome. To support it @Googleorg has funded sequencing and open release of 13 genomes, with a $3M commit to sequence 150 more and develop methods to improve assembly finishing and other bottlenecks. blog.google/innovation-and…

Excited about this tool! The upcoming trio feature is particularly important for these complex regions

@Psy_Fer_ I can’t speak to the P2i but, it seems good? The p2S took a lot more configuring, and prices of GPU have only increased. That said p2S seems potentially more durable long term…

Okay, so is there anyone out there that has a P2S and a P2i who can give their opinion on the 2 devices, in terms of performance, ease of use, and pricing? I'll even settle for just feedback about the P2i. Are all the P2S users I know crazy or is this the best ONT product so far?

@WashUGenetics @12pm @EichlerLab @tycheleturner No zoom link 🙁

Join @WashUGenetics this Thursday Oct. 23 @12pm in Connor Auditorium when Evan Eichler, PhD,@EichlerLab presents “Complete genomes and complex structural variation”, hosted by Tychele Turner, PhD,@tycheleturner

@Psy_Fer_ Ah this is really nice. Thanks for sharing!

Ever wanted to get the query sequence from a bam using bed coordinates? How about the matching coordinates of an assembly mapped to a reference but repeats and SVs are confusing liftover? Well I did while trying to benchmark STR stuff. Nice side quest. github.com/Psy-Fer/bedpull

The complete genome of a songbird. #ReferenceGEnome #SongbirdGenome #ZebraFinchGenome #T2T #LongRead #Sequencing @biorxiv_genomic biorxiv.org/content/10.110…

@NatureRevGenet Nice paper but kind of sidesteps the question of how genotype imputation phasing is related to assembly. PB falcon phase is nearly 5 years old. The critical question is how does genotype imputation phasing compare to when an end user is given two haplotype assemblies? What then

New online! Advances in haplotype phasing and genotype imputation bit.ly/4gKo5ag

@dr_alphalyrae In a way it’s similar to the philosopher guys of the 1800s who created meta or universal theorems to explain everything in a field. It is a bubble that needs actual tech people using the models developed + validated beyond the curated model truth set — how many truly can?

Going from biotech to tech was an unexpectedly humbling experience, almost an egodeath. In biotech, doing bioinformatics during a PhD or postdoc is considered highly technical, you’re the “computer person” in a world of wet-lab scientists. But in tech, that experience doesn’t carry the same weight. If you haven’t trained a billion-parameter model or built a platform from scratch, you’re not seen as “technical” enough. The shift kinda forces you to rethink what being “technical” really means. Or perhaps we're in this bay area bubble of accusing each other of not being 'technical enough' till death takes us.

@KIGFletcher @nanopore Statistics look great until you inspect the ONT contigs and see how gappy they really are. Needs a true evaluation paper

I think I found the perfect post if @nanopore ever needed a real-world example to advertise their technology. github.com/chhylp123/hifi…

~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/10.110…

@naturepoker1 Do you have HiC data to confirm? If so i’d check contacts. Also QV. The plasmids may be very similar to another part of the chrom and falsely joined. Another good q to consider is the methods and data used to generate the refseq genome, super old refs may not be easily comparable

Is anyone aware of plasmids getting swallowed up by the chromosome during continued lab propagation? Going through new #Archaea data with 500x ONT asm suggests two of its plasmids in NCBI refseq (pub 2010) are gone, they show up as part of the chromosome. Were they ever real?

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/earthbiogenome…