So excited to have received probably the first P2 solo in the greater China region today. Gonna use it for developing a somatic variant caller and many more exciting projects! Oxford Nanopore #precisionmedicine

Excited to share our findings training GPN, a DNA language model for Arabidopsis thaliana, with @sanjitsbatra and Yun S. Song:
DNA language models are powerful predictors of non-coding variant effects, without the need for any labeled data.
doi.org/10.1101/2022.0…
1/n

A retrospective of our experience at #epi2melabs of using Nextflow to deliver bioinformatic workflows for Oxford Nanopore data analysis

labs.epi2me.io/two-years-of-n…

I am trilled to share my first PhD paper! We are releasing Han1, the first gapless, fully annotated Southern Han Chinese genome. We also conducted the first-ever direct comparison between the gene content of two complete individual human genomes. 1/6

biorxiv.org/content/10.110…

Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks academic.oup.com/bib/advance-ar…

Please RT: We are looking for talented #Bioinformatics #postdocjobs who want to work on Oxford Nanopore & PacBio data from human population to diseases ( #Cancer , #Parkinsons , ..). Develop your own research and methods at scale. Apply: jobs.bcm.edu/job/Houston-Po… BCM HGSC From the Labs at Baylor College of Medicine

We have started collecting and uploading #RECOMBSeq2022 presentation videos to our official YouTube channel. More will be added as we receive them. The playlist is here: youtube.com/playlist?list=…

Duet: SNP-Assisted Structural Variant Calling and Phasing Using Oxford Nanopore Sequencing biorxiv.org/content/10.110…

Two openings from my group: a) postdoc either on developing methods for sequencing and pangenomic data, OR on the analysis of these data types. b) staff scientist on high-performance algorithm development. For details, see hlilab.github.io/vacancies

Kit14 on the Oxford Nanopore #PromethION bringing back kit10 like yields with kit12 like accuracy and sensitivity. Need a bigger GPU 🤣 60 ng of DNA loaded onto the flowcell.

The exciting reveal of Ultima Genomics last week was accompanied by the publication of four preprints. Intrigued by the potential of the technology, Sina Booeshaghi & I decided to take a look at the data. A 🧵 about our findings & a preprint we posted: biorxiv.org/content/10.110… 1/

90% of bioinformatics tool users more often don't have sudo permissions. Think about that when you develop tools or write documentations.

After many months, I'm proud to share our work on untangling genome assembly graphs with GNNs. Or, GNNome Assembly (sorry not sorry)🧬

Paper: arxiv.org/abs/2206.00668
Code/Data: github.com/lvrcek/GNNome-…

with Xavier Bresson, T. Laurent, Martin Schmitz, and Mile Sikic.
Read more in 🧵

Image fraud gets a boost from AI
* Deepfakes in the biomedical literature are coming, if they aren't here already.
* GAN technology can easily create fake photos of Western blots or cancer cells.
Bradley van Paridon reports for Advanced Sci News
advancedsciencenews.com/image-fraud-ge…

hello #BoG22 attendees, I'm recruiting postdocs. See a list of former lab members at salzberg-lab.org/lab-members/ incl @carlk Martin Steinegger 🇺🇦 Cole Trapnell Michael Schatz Ben Langmead Daehwan Kim Ruibang Luo and others. If you want to join this group someday, email me!