James Hawley @jrhawley@scholar.social

I'm a PhD candidate in Medical Biophysics at the University of Toronto studying epigenetics and cancer. Math and physics background taking a step into bioinformatics and evolution #introductions

For a tl;dr, skip to the last section.

https://jrhawley.github.io/2020/10/15/diff-seq-analysis#4-summarizing-the-model

I often need to jump back to my notes when reading a new paper on this

A big blog post about DNA sequencing analysis!

https://jrhawley.github.io/2020/10/15/diff-seq-analysis

I often find papers describing "differential analysis" methods too complicated and don't talk about the forest from the trees.
I've tried to address the motivation and reasoning behind common statistical models for differential analysis and where some of the complication comes from.

Hopefully something like this will make it easier to see the forest.

Inspired by this earlier blog post^, I discuss more in depth a proof of the Central Limit Theorem. I also talk about something less often discussed, which is the convergence of the sample variance.

https://jrhawley.github.io/2020/10/08/clt-variance

I found that using the notation I described earlier helped sort out some points of confusion that I and others have run into when trying to talk about just what the CLT is and does. Maybe this can help others understand it a bit better, too.

I wrote some thoughts on mathematical notation and why I think certain concepts in stats are confusing as a result of bad notation.

https://jrhawley.github.io/2020/10/04/stats-notation

I go through a couple examples that I've seen many people learning stats struggle with. Maybe this will be of use to somebody

My lab is looking for new postdocs and grad students!

If anyone is interested in functional epigenomics and cancer, consider applying!

https://twitter.com/MatLupien/status/1307071139676663808

Feel free to boost.

This issue still remains, worse now than before.

A good blog post on science making

https://blog.cbs.dk/inframethodology/?p=2913

Recent trends in COVID-19 cases does not look great. Stay vigilant out there

This is a cool model for sharing code snippets.

http://gitlet.maryrosecook.com/docs/gitlet.html

It feels a lot like modern Shakespeare books, oddly enough.
Text on one side and interpretations, references, and explanations on the other

Here are some tips I've come up with for academics giving remote presentations.

https://jrhawley.github.io/2020/09/11/remote-teaching

Feel free to let me know what you'd add to this!

This is of course not an end-all-be-all solution for tackling the spread of COVID on campus this year, but seems a reasonable first step that involves the community and isn't a data-hungry software service, from what I can tell

1. It doesn't require you to create a separate account
2. Its privacy policy and terms of service are clear and in plain language
3. It is well designed with a clear flow of information, bold colours for recommendations, and provides information from the University and public health organizations for those who have questions.

The University of Toronto has contracted a Canadian health company to give students, faculty, and other employees a way to check their symptoms and receive recommendations on what to do.

https://ucheck.utoronto.ca/

This is a pretty good review of the state of SARS-CoV-2 vaccines being developed right now, how they work, and where they are at in clinical trial phases.

Coronavirus Vaccine Roundup, Early September

https://blogs.sciencemag.org/pipeline/archives/2020/09/03/coronavirus-vaccine-roundup-early-september

This is a great resource for #bioinformatics tools:

https://github.com/j-andrews7/awesome-bioinformatics-benchmarks

e.g. want to try something like calling structural variants from sequencing data? Here are 3 benchmark papers comparing 88 different tools for short read and nanopore sequencing and the summary of their findings