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Reposted by Adam Phillippy

Jacob Schreiber @jmschreiber91.bsky.social · 2d

Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!

The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.

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Reposted by Adam Phillippy

Rob Patro @robp.bsky.social · 1d

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

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Reposted by Adam Phillippy

Wellcome Sanger Institute @sangerinstitute.bsky.social · 1d

Read ‘Sperm sequencing reveals extensive positive selection in the male germline’ from @sangerinstitute.bsky.social and collaborators in @nature.com below:

nature.com/articles/s41...

Sperm sequencing reveals extensive positive selection in the male germline - Nature

A combination of whole-genome NanoSeq with deep whole-exome and targeted NanoSeq is used to accurately characterize mutation rates and genes under positive selection in sperm cells.

nature.com

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Reposted by Adam Phillippy

Karyn Meltz Murphy @karynotype.bsky.social · 3d

I’m pleased as punch to share our hot off the presses article in @ajhgnews.bsky.social : A scalable approach for genomic-first rare disorder detection in a healthcare-based population

Also presenting next week at #ashg25 #ashg2025

www.cell.com/ajhg/abstrac...

A scalable approach for genomic-first rare disorder detection in a healthcare-based population

Beyond commonly screened disorders, genomic-first ascertainment of genetic disorders remains underexplored. We developed a scalable framework for 2,701 additional rare genetic disorders, identifying p...

www.cell.com

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Adam Phillippy @aphillippy.bsky.social · 10d

Calling @mrvollger.bsky.social

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Adam Phillippy @aphillippy.bsky.social · 13d

Congrats! 🎉

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Adam Phillippy @aphillippy.bsky.social · 14d

Yes, some embryos should be unaffected or balanced ROB carriers. The page I pulled that original image from lists some rates at the bottom for Downs: mymds.bham.ac.uk/genetics/rob...

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Adam Phillippy @aphillippy.bsky.social · 14d

Thanks, Harmit! My group still talks about your NHGRI seminar from a few years back. Many minds were blown that day. Changed the way we think!

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Adam Phillippy @aphillippy.bsky.social · 14d

@roneilllab.bsky.social pointed me to this amazing paper just a few days ago pmc.ncbi.nlm.nih.gov/articles/ins...

Female meiosis drives karyotypic evolution in mammals

Speciation is often accompanied by changes in chromosomal number or form even though such changes significantly reduce the fertility of hybrid intermediates. We have addressed this evolutionary parado...

pmc.ncbi.nlm.nih.gov

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Adam Phillippy @aphillippy.bsky.social · 14d

Human Chr2 was probably the result of a telomeric fusion of two (sub)metacentrics, rather than a Robertsonian fusion of two acrocentrics, but either way the explanation for how it could fix so quickly is probably meiotic drive. Summons @harmitmalik.bsky.social to correct me if I'm wrong

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Adam Phillippy @aphillippy.bsky.social · 14d

If you really want to bend your brain, consider how Robertsonians in other mammals can become fixed in a population, thanks to meiotic drive, resulting in new species 🤯 pmc.ncbi.nlm.nih.gov/articles/ins...

Female meiosis drives karyotypic evolution in mammals

Speciation is often accompanied by changes in chromosomal number or form even though such changes significantly reduce the fertility of hybrid intermediates. We have addressed this evolutionary parado...

pmc.ncbi.nlm.nih.gov

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Adam Phillippy @aphillippy.bsky.social · 14d

How Robertsonian chromosomes can lead to miscarriage or trisomy explained in one great figure from Human Molecular Genetics (Strachan and Read) that I have referred to many times

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Adam Phillippy @aphillippy.bsky.social · 14d

Also the lead story on Washington Post's Science page today, featuring Jen looking at a colorless liquid in a tube! 🧪 Thanks for the gracious quotes @glennislogsdon.bsky.social! [3/3] www.washingtonpost.com/science/2025...

For decades, scientists puzzled over a genetic anomaly. They just solved it.

By examining “junk DNA,” scientists are finding clues to understanding human biology.

www.washingtonpost.com

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Adam Phillippy @aphillippy.bsky.social · 14d

More backstory on this project here. Working with Jen and Erik on this project has been an absolute joy ☺️ Big congrats to @leogdlima.bsky.social, @andreaguarracino.bsky.social, and the whole team! Meeting with them is always a highlight of my week [2/3]
www.stowers.org/news/stowers...

Stowers scientists identify the fusion point of Robertsonian…

Robertsonian chromosomes are associated with infertility and Down syndrome, now cutting-edge DNA sequencing technology has unveiled the first…

www.stowers.org

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Adam Phillippy @aphillippy.bsky.social · 14d

🚂 The T2T train keeps rolling: "The formation and propagation of human Robertsonian chromosomes" with Gerton and Garrison labs is out! What's a Robertsonian chromosome? Let Jen tell you herself in this great video, or read our paper: [1/3]
📺 youtu.be/JmlY5omxQVc
📄 www.nature.com/articles/s41...

How Stowers Scientists Found the DNA Site Where Robertsonian Chromosomes Fuse

YouTube video by Stowers Institute for Medical Research

youtu.be

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Reposted by Adam Phillippy

Ryan Wick @rrwick.bsky.social · 16d

New blog post!

metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...

Both tools improved considerably! Time to update your conda environments 😄

Benchmark update: metaMDBG and Myloasm

a blog for miscellaneous bioinformatics stuff

rrwick.github.io

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Adam Phillippy @aphillippy.bsky.social · 16d

Yes, that's what I'm looking for. @gringene.org suggested an entropy based metric in another thread and I have also been thinking along those lines

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Adam Phillippy @aphillippy.bsky.social · 16d

I would classify this as a type of bias having to do with the sequencing chemistry. I *think* this particular example is due to a weakness of the ILMN 2-color chemistry. There are also context biases, like non-B DNA increasing the error rates of the single-molecule techs, etc. etc.

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Adam Phillippy @aphillippy.bsky.social · 16d

Yes, and I think this is what happens when people measure the accuracy of variant calls, because those calls have tried to correct the underlying error, but as a metric this confounded by depth of coverage, the variant calling model used, etc. It would be nice to have a metric closer to the data

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Adam Phillippy @aphillippy.bsky.social · 16d

Another complicating problem is the alignments. E.g. if the aligner right-justifies all the indels, it will look like "bias" in the pileup, so will need to think about this a bit more carefully

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Adam Phillippy @aphillippy.bsky.social · 16d

Yes, measuring entropy of the pileups was one of my thoughts as well. Thanks for the link. Still need to think a bit if it should be measured over the alignment columns alone (i.e. variants), or also the rows (reads), or both

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Adam Phillippy @aphillippy.bsky.social · 16d

Well, we're interested in _all_ the biases and I guess this is why we go hung up deciding which to show. Too many to choose from :) If some popular requests emerge, we will implement them in the benchmarking tool

Adam Phillippy @aphillippy.bsky.social · 16d

More from HG002: This figure shows the incredible progress of de novo assembly over the past 5 years. Ash1 was a good "collapsed haplotype" assembly from 2020. Now we have single-tech solutions (ONT 6B4) that can produce nearly perfect diploid assemblies out of the (HERRO/Verkko) box 🤯

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Adam Phillippy @aphillippy.bsky.social · 16d

A couple editorial notes: (1) Element is Aviti UltraQ, ILMN is NovaSeq PCR-Free. (2) This is showing *per read* accuracy, which doesn't capture the randomness of the errors. Random (uniform) errors are better, but we couldn't decide on a metric for showing this. Suggestions welcome

Antoine Limasset @npmalfoy.bsky.social · 16d

This figure is extremely interesting, very surprising and exciting results from current state of sequencing technologies!

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Adam Phillippy @aphillippy.bsky.social · 16d

Don't get too excited, @rakyanlab.bsky.social, rDNAs are still a problem 😅

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