Thread by @lpachter

My blog passed 3 million views today from more than 1.8 million visitors. There have been a total of 119 posts in just over 10 years.
I'm one of those visitors. The blog is an idea repository and I go back sometimes for recall. Some highlights 1/🧵 liorpachter.wordpress.com

Just today I revisited the PCA post to recall some of the properties of the transform. A student, Nick Markarian, taught me the Borel-Kolmogorov paradox today (topic for a future post) and the post was helpful in thinking about some things. 2/ liorpachter.wordpress.com/2014/05/26/wha…

I've been teaching a bit of phylogenetics this year and this post on the Golden-Thompson inequality just came up. 3/liorpachter.wordpress.com/2018/10/05/rat…

There are other posts I don't use regularly but perhaps some will find them useful. This post on Mahalanobis distance and heatmaps is very relevant for single-cell RNA-seq: 4/liorpachter.wordpress.com/2014/01/

Another post on single-cell RNA-seq that serves as a useful introduction is
I have since released a complete set of slides for a course on the topic (of which this was Lecture 2): 5/liorpachter.wordpress.com/2019/02/19/int…
github.com/pachterlab/BI-…

One of my personal favorites is this post on "number deconvolution", which breaks down the math incoherence in the "network deconvolution" (ND) method from the Kellis lab via a simple illustration. 6/ liorpachter.wordpress.com/2014/02/18/num…

Despite my three blog posts explaining in detail why the ND method is fundamentally flawed, incoherent, and poor in practice, it's still used. Then again, those who use it obtain poor results. Most recently who lament "the poor performance of ND". 🙃 7/biorxiv.org/content/10.110…

Some of my posts have been about math inspired by living in a house. This is one example: 🏡 8/liorpachter.wordpress.com/2014/03/

Another is on the Penrose tilings and my aperiodic rhombic bathroom: 💠 9/liorpachter.wordpress.com/2017/02/11/my-…

There are some posts that were really fun to write but didn't seem to be read much. That's fine, and they are still fun for me to go back to once in a while. This is a good read, I think, if you're designing genomics experiments... 10/liorpachter.wordpress.com/2015/02/23/col…

Perhaps my most impactful post was "Pachter's p-value prize". I learned more from the comments on this post than I have from many classes I've taken. Perhaps its time for another prize post..
11/liorpachter.wordpress.com/2015/05/26/pac…

BTW there was a winner and I sent them a check by mail, but I don't think they ever cashed it... 12/liorpachter.wordpress.com/2015/06/09/i-w…

A lot of my blog posts are about looking at things in computational biology "the right way". I wrote a post a few years ago about the professor who taught me the importance of this. 13/liorpachter.wordpress.com/2016/05/09/the…

Over the years a recurring theme has been the interactions between mathematics and biology, a reflection on Gian Carlo-Rota's quip that "The lack of real contact between mathematics and biology is either a tragedy, a scandal or a challenge, it is hard to decide which." 14/

On this topic I spent a lot of time writing 15/liorpachter.wordpress.com/2014/12/30/the…

Speaking of time, a single blog post can take me as long as writing a paper. I think it's time well spent. I've learned a ton writing these posts, in the same way that I've learned a ton from teaching. Sometimes I write a blog post just to learn, e.g. 16/liorpachter.wordpress.com/2013/09/18/uni…

I started the blog with the goal of writing technical posts about computational biology. I've largely stuck to that, but as the years went on I ventured into other issues which I think are important for the field. 17/liorpachter.wordpress.com/2018/05/18/jam…

I've also written some controversial posts. This one, on how Salmon copied kallisto without proper attribution is one example:
Looking back at it years later I don't understand why it was controversial. 18/liorpachter.wordpress.com/2017/08/02/how…

I've been asked if I regret any of my posts. I do wish some had been written differently and/or focused on different issues. An early post on 23andme missed the mark. But I've kept the bad work online for the record. I strive to improve. 19/liorpachter.wordpress.com/2013/11/30/23a…

My blog posts are not DOIed, but I've rarely changed them after they are posted (with the exception of correcting minor typos, or fixing errors people point out). In retrospect I wish they were DOIed, because they are cited. 82 citations on Scholar: 20/scholar.google.com/scholar?hl=en&…

I've been asked on occasion whether there were any posts that were difficult to write. This one was by far the hardest:
I still don't know the secret to writing. Sometimes I have writers block. Sometimes I can squeeze out the words. 21/liorpachter.wordpress.com/2020/06/10/bla…

One of the challenges in running the blog has been moderating the comments. Early on I decided to adopt a very lenient policy and basically let anyone who wants to comment write on the blog without censorship. The "official" policy is here:
22/liorpachter.wordpress.com/about/

The comments are not always complimentary, as in this case:
So it goes. 23/liorpachter.wordpress.com/2020/11/22/wil…

But overall I've received overwhelming support and positivity and I thank the numerous readers who have enriched my scientific life via the blog. Thanks you 🙏.

I may post a second update in another decade. 24/24