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One definition of consciousness is being responsible, careful, and the desire to do one's work or duty thoroughly. It is not surprising but is extremely worrisome.

Introducing Grok Imagine.

A Perspective piece on "The Somatic Mosaicism across Human Tissues Network", now published. Here is the description of the project from @TimCoorens.

Happy to have been part of the 4D Nucleome program. So much data for understanding the 3D organization of the DNA in the nucleus--all freely available, on the portal that my lab has developed:

As is the case with all CNV methods, it will take some fine-tuning of parameters for optimal results, depending on the characteristics of each dataset. Superb work by Yifan @yifnzhao with help from Joe @luquette_j and many others, collab w/ Chris Walsh and Mark Johnson labs.

With some additional work, we can do joint analysis of point mutations and copy number! Here we looked at low-coverage data from meningiomas (a slow-growing brain tumor) and identified clusters of single cells with different SNV / CNV patterns.

Applications to the copy number analysis of brain tissues: we can find smaller CNVs (both clonal and non-clonal) than before; we analyzed the difference between CNV patterns of neurons (losses more prevalent) and oligodendrocytes (mostly gains)

This may be conceptually intuitive, but @yifnzhao has several innovations to ensure that the method performs well, such as estimating the optimal bin size based on allelic dropout and joint segmentation across multiple cells.

Published last week: "High-resolution detection of copy number alterations in single cells with HiScanner" in Nat Comm. For whole-genome seq of single cells at higher depth (say, 10-30X), we should use B-allele frequency + haplotype phasing + read depth for CNV/LOH analysis!.

I am deeply saddened to hear of Atul's passing. I got to know him when he was finishing up his PhD in the HST program at MIT. What energy he had then, and how much he has accomplished at Stanford and then at UCSF!.

Thank you @CancerGrand for your support of the tissue specificity project over the last 5 years! It was a privilege to be collaborating with many wonderful colleagues on the question of tissue specificty of cancer driver mutations, as well summarized in this magazine.

To find a comprehensive set of somatic variants accurately, an individual-specific genome assembly is needed. Glad to be collaborating with @ChengChhy and @lh3lh3 for this new version of hifiasm; Flora Qu in the lab did extensive benchmarking.

Delighted to see my MIT graduate student Yifan.@yifnzhao give a terrific thesis defense. She developed an algorithm for identifying CNVs in single cells (coming out in Nat Comm) and applied it to brain development (under review at Nat).

RT @HarvardDBMI: Reminder: We're hiring! Join a team of faculty @harvardmed committed to developing AI systems that reduce rather than ampl….

So why did this mandate arise? Probably because NIH was asked to have a more stringent privacy protention rules by an elected official. This is but one example of increased federal regulatory burden that results in more administrative cost. Good intent, a terrible outcome.

The intent is to increase the privacy protection, e.g., for patients who died of cancer and agreed to have their DNA studied by researchers to better understand why some get cancer. But, the increase due to this expensive mandate is very little if any.

This means the majority of research institutions must add another layer of security to their systems and institutional lawyers must certify it. This is extremely expensive, probably costing hundreds of millions of dollars across institutions.

Totally agree! For example, my lab studies cancer and other diseases. NIH issued a new policy (Jan 25) that researchers downloading data from a public repository for human genomic data must have computer systems that satisfy "NIST 800-171," described in a 120-page document.

Interactive circos plots now on cBioportal! Superb work from @dominikglodzik and @sehi_lyi.

This Monday (10/28) at 5pm (Eastern Daylight Time): Info session about our bioinformatics/genomics PhD program! I will describe the basics and take your questions.

How wonderful to see a South Korean win the big prize! I was incredibly lucky to have had some time to speak to her throughout the Ho-Am ceremony day in Seoul this past June - she was unassuming and pensive, and gave me some tips about the Korean language!