We've launched a department Trainee Emergency Fund, to help support EVERYONE BELONGING IN SCIENCE by meeting urgent financial needs of students and postdocs. Click to learn more about our goal with this fund and to donate!
www.givecampus.com/schools/Univ...
We have a lot of plans for this tool and, in addition to docs (brentp.github.io/bedder-docs/...), we created a custom GPT (chatgpt.com/g/g-69a6027f...) to help use the tool and dev Python snippets for custom analyses. The Python snippers have direct access to the intersections from the Rust engine.
Brent Pedersen, Mitchell Vollger and I have "posted" our preprint of the manuscript describing bedder, a complement to the functionality of bedtools. The "preprint server" we have chosen is google docs because it was rejected by biorxiv.
docs.google.com/document/d/1...
Congrats to @tomsasani.bsky.social for leading this study!
This study highlights how subtle differences in motif composition can profoundly shape TR mutability, and underscores the power of long-read sequencing to reveal the full landscape of germline repeat instability.
We found that DNMs are more likely to arise at loci that are longer, purer, and heterozygous. We also discovered 43 hyper-mutable loci, including one near LINC03021 where a single 19bp motif drove recurrent mutations across generations, while a ~identical motif remained completely stable.
In collab w @hdashnow.bsky.social, we have a new preprint out on tandem repeat (TR) mutagenesis! Using HiFi sequencing, we profiled nearly 8 million TR loci across four generations of a large CEPH/Utah family and identified 1,270 de novo expansions and contractions.
www.biorxiv.org/content/10.6...
All expenses will be covered by the Department of Human Genetics at the University of Utah.
Also, please share this with your colleagues and spread the word - this has been an engaging and fun event in the past!
We are looking for postdocs with research programs in:
• Genetics of Health and Disease
• Computational Genomics
• Evolutionary Genetics and Genomics and Human Population Diversity
• Functional Genetics and Genomics
We are holding our annual Rising Stars in Genetics and Genomics Postdoc Symposium on September 24-25, 2026! Please nominate postdocs who are conducting cutting edge, creative work, and are likely to be a leader in their field. Please nominate by April 30, 2026: forms.gle/85NZaxFezUk8...
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Giving a RIP without slides for the first time in ages today. Send good vibes.
New lab photo for the first time in too many years. I am so proud of this team's curiosity, camaraderie, and collabative energy.
Reminder that the abstract deadline for the Biology of Genomes meeting at CSHL is on Feb 13! We have a fantastic lineup of keynote speakers (Janet Kelso and Jonathan Pritchard) and session chairs. Submit your best science to this exciting and engaged meeting!
meetings.cshl.edu/meetings.asp...
Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
A new preprint from Peter Mchale and Michael Goldberg in my group on the latent biases inherent to current models of non-coding constraint.
www.biorxiv.org/content/10.6...
This is an important and information rich article. I wondered about the effects by Institute. The table below (which is snipped here but is in the article) has that info. Broken down by # of grants and $ amounts.
All developed by @brent-p.bsky.social
Get bedder v0.1.8 and r𝗲𝗮𝗱 𝘁𝗵𝗲 𝗱𝗼𝗰𝘂𝗺𝗲𝗻𝘁𝗮𝘁𝗶𝗼𝗻 here: github.com/quinlan-lab/...
We are looking for researchers to kick the tires, integrate bedder into their pipelines, and provide feedback on the Python functions, performance, and overall user experience! Please share and give us your feedback.
4. 𝗦𝗶𝗺𝗽𝗹𝗶𝗳𝗶𝗲𝗱 𝘀𝘆𝗻𝘁𝗮𝘅: We've streamlined the intersection logic, replacing complex flags like -wao, -f, and -r with clearer, modular options for defining intersection requirements.
3. 𝗨𝘀𝗲 𝗼𝗳 𝗶𝗻𝗱𝗶𝗰𝗲𝘀 𝗳𝗼𝗿 𝗵𝗶𝗴𝗵 𝗽𝗲𝗿𝗳𝗼𝗿𝗺𝗮𝗻𝗰𝗲 𝗼𝗻 𝗹𝗮𝗿𝗴𝗲 𝗱𝗮𝘁𝗮 𝘀𝗲𝘁𝘀: bedder is engineered to utilize file indexing (e.g., VCF indexes), resulting in dramatically faster queries, especially when intersecting against massive indexed datasets like gnomAD.
2. 𝗩𝗖𝗙 𝗜𝗻𝘁𝗲𝗴𝗿𝗮𝘁𝗶𝗼𝗻: For the first time, you can easily update VCF INFO fields based on interval overlaps, opening up new possibilities for variant annotation and processing.
Here is a high-level summary of what is innovative about #𝗯𝗲𝗱𝗱𝗲𝗿:
𝗖𝘂𝘀𝘁𝗼𝗺 𝗟𝗼𝗴𝗶𝗰 𝘄𝗶𝘁𝗵 𝗣𝘆𝘁𝗵𝗼𝗻: bedder has a flexible Python interface that allows you to define custom functions to process intersection fragments on the fly. This enables custom analyses without the need for endless command-line options.
Developed in Rust for speed and efficiency, bedder is designed to overcome the analytical limitations of traditional interval-based tools by putting analytical flexibility directly into your hands.
Please read our detailed 𝗯𝗹𝗼𝗴 𝗽𝗼𝘀𝘁: quinlanlab.org/blogposts/be...
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We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
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I was excited to be Dept. Chair as a way to serve, grow, and improve the department I love. The first year has certainly provided ample opportunities to learn the ropes of the role!
Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen...
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Perspective on the impact of cuts to research funding from Jerry Kaplan and Dana Carroll, two science giants from the University of Utah. It highlights the storied history of the fantastic Dept. of Human Genetics that I now have the privilege of leading. www.sltrib.com/opinion/comm...
Forbes: 'Hundreds Of NIH Staff Send Strong Letter Of Dissent To Their Bosses'
'In addition to Bhattacharya, the letter was sent to U.S. Health and Human Services Secretary Robert F. Kennedy Jr. and members of Congress who oversee NIH'
www.forbes.com/sites/michae...
You may be excited, @mrvollger.bsky.social, but we are even more so! I can't wait to be your colleague!
If you’ve ever wondered about the statistical significance of differences among mutational signature profiles, check out our new Aggregate Mutation Spectrum Distance (AMSD) preprint co-led by Sam Hart and @alisonfeder.bsky.social with @nalcala.bsky.social www.biorxiv.org/cgi/content/...
