Viewing profile — gww

A few of the older 3d MMORPGS did try to instill some of those mechanics. Examples include: 1) Asheron's Call (which had a very active mod scene and now an emulator scene). I don' …

I have worked at a sequencing center before. DNA contamination is easier to mitigate because the lab disposables aren't made out of what you are testing. Disposables are almost alw…

I haven't really read the studies but shouldn't they have negative controls to negate these effects? Wouldn't that let the author's correct for a baseline contamination level in th…

That is how I became serious about programming. I played around a bit but I never really wrote anything useful until I started playing Asheron's Call. I learned C++ to write bots a…

There are other examples of oncoviruses including: Epstein-Barr virus and Human herpes virus 8 (Kaposi's Sarcoma). Makes me wonder: Is the cancer "industry" searching for causes or…

ed was the hardest thing for 12 year old me to understand.

I played Aardwolf briefly but I mostly stuck to a nightmare/LP MUD that is still around but essentially empty. I learned to code (which ended up being a gateway to C/C++), grief, a…

There's a second paper on the same topic published in Nature [1] [1] https://www.nature.com/articles/s41586-025-09771-9

I have a different problem with my M3 Macbook Pro. If I leave chrome (sometimes other apps too) open with the macbook plugged in and the lid closed the computer will get very warm …

Reminds me of one of my favorite Simpsons lines: "Aw, you can come up with statistics to prove anything, Kent. Forty percent of all people know that"

They are used somewhat commonly in bioinformatics where lookup tables can have long keys and many entries [1]. 1. https://en.m.wikipedia.org/wiki/Bloom_filters_in_bioinformat...

This is a great analogy. One small change is that there are two ways to reassemble it. One is to try to blindly put the pieces together and fork a teacup (read assembly) vs trying …

They didn't sequence the whole human genome (~3 billion bases) for multiple reasons. I am not an expert on ancient DNA but I will try to explain the paper as best I can: 1. Contami…

The BWT based FM-index is one of my favorite data structures. It's used frequently for DNA mapping, where the 4 letter alphabet can be encoded in two bits and the occurrence functi…

Users of these kinds of tools should check that their marker genes are associated with the labelled cell types. There are known markers for many cell types across multiple organism…

Will check it out. Thanks a lot

Cool thanks

Could this also be adapted for gene set enrichment? For example, if I had a set(s) of genes from an ATAC-seq experiment would it be able to guess their function / cell types?

This is really useful thanks for sharing. My students and myself tend to waste a lot of time annotating clusters and have not found a reasonable solution yet. This will be fun to t…

It is common for human cancers to be polyploid after accumulate whole genome doublings (WGD), where a tumour cells goes from being approximately diploid to tetraploid. Different tu…

I am going to steal that name. I find that computational overcooking happens more and more because the easy questions that can be asked with sequencing datasets is starting to dry …

I would argue that these are some of the most important algorithms in bioinformatics/biology. They have a wide range of applications.

Grails test isn't for somatic mutations but cancer specific DNA methylation patterns. DNA methylation is slightly more challenging to work with due to how the methylation is identi…

Beautiful book I used it in undergrad. The only problem with the book is its size; it's terrible to lug around in a backpack.