The method can genotype challenging medically relevant genes like SMN and PTEN as well as produce accurate HLA alleles and CYP2D star-alleles. Finally, we were able to use ctyper genotypes to study relative contributions to gene expression among copy-number variable genes.

Some highlights of the method are: Walfred developed a novel mathematical model that enables accurate and rapid alignment-free genotyping of pangenome alleles. Benchmarking shows little bias (HWE), accurate trio inheritance, and near-perfect copy-number estimation.

We initially sought out to develop a method that could answer: given a short read genome and a pangenome, which copies of a gene (paralogs, orthologs, pseudogenes, etc) are in the short read sample, and do so efficiently enough to apply to biobank-scale data.

This bucks the trend of using a graph to represent a pangenome, and instead as pangenome alleles - short heritable segments of genomes that can be genotyped as shared with a short read sample.

Happy to announce our paper on a new genotyping algorithm, ctyper. https://t.co/D9WUK4mln5 . This is amazing work by Walfred Ma, someone you will want to keep on your radar for future contributions to science.

Social media is the cancer of our society - Tadej Pogacar

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Rolled up to fancy restaurant on bike. Please meme

I will be hosting an information session for applicants to the USC Computational Biology and Bioinformatics PhD program, discussing research topics and application strategies. If you are registering with a non-institutional e-mail, please let me know https://t.co/mw1NX3Fof3

My first peleton experience was without Bluetooth connection so I assume this dude is trying to sell me on how profitable Bitcoin will be if I buy now

#ASHG24 #ASHGtrainees Are you interested in #autism and how #mutations impact the development of the brain? Do you❤️ transcription factors and networks? Want to do all the #omics and live in the beautiful #pnw? DM me to discuss a #postdoc @OHSUSOM 🙏 RT https://t.co/WXQ9INSi4j

Thrilled for #ASHG24. Please check out the cool work from our group and collaborations! Lots of exciting methods for large scale analysis of genetic data 😁

Did an hour of phone banking from LAX. There are still people who need a nudge. For those who are tweeting to their circles about the need to vote, trust me the persuadables didn't see your socials

To catch up on our lab research at ASHG, you can see Walfred Ma's talk on sequence-resolved CNV genotyping in the Decoding Structural Variation at Scale session Wed 8-9:30 4-season ballroom 1, and Bida Gu's poster on our VNTR motif database 1044T. See you there!

Really excited to have this out: a cell type-specific map of the impact of an understudied class of genetic variation (tandem repeats) on gene expression, at serious scale: nearly 1800 people with both WGS and blood scRNA-seq. So much signal!

Going to #ASHG2024 next week? I will be looking forward to talk about science (we have 1 talk and 2 posters), friendship, and my newly posted popgen informatics postdoc position:

There are plenty of opportunities to make calls this weekend. It's time. Any questions for how? dm. Repost so twitter algo sends out.

I'm scouring departmental web pages for undergraduate advisor contacts in chemistry, biochemistry, biophysics, cs, and applied math, and it is universally harder to do than I thought.

I want to try something new at #ASHG24 this year: I'm going to block some time on Friday afternoon to meet with any trainees who would be interested to chat on any topic.

Sure, ... is great, but have you ever won over an independent and a Stein voter (who will now get her friends to vote) in the same phone bank? But seriously, it's time for no regrets- just a half hour here or there making calls can make the difference.