AAAS and the Food and Drug Law Institute (FDLI) are holding three 2-day meetings in Washington DC on personalized medicine, addressing the scientific discoveries, business models, and policy changes that are necessary to develop personalized treatments and diagnostics. All three meetings will be available via a free live webcast where viewers can use response technology to interact with speakers and session chairs.
The first meeting is June 1-2, and the agenda is available online. One session, "State of the Science: Connecting Biomarkers and Diagnostics" is chaired by Teri Manolio, who will be speaking at the CHGR's June 10 Retreat. Other sessions include topics about consumer genetics in the open market, ELSI issues, and other topics.
Personalized medicine: Planning for the Future
June 1-2 2009: Colloquium I Agenda
Highlight all the acronyms in a Word document
A tip of the hat to Lifehacker for pointing this out.
Ever been nailed by a reviewer or a thesis committee for using too many acronyms without defining them well? There's an easy way built into MS Word to find and highlight all the acronyms in a document. It's a nice check after you're done with a first draft, and you might be surprised by how many you find!
First, hit Ctrl-F to bring up a find box, and type this in exactly as written:
<[A-Z]{2,}>
Hit the "More >>" button, then check the "Use Wildcards" box. Finally, click the "Reading Highlight" box, then click "Highlight All". It should look like this:
After you do that, you'll see all your uppercase acronyms highlighted throughout the entire document. It will look something like this:
That find query basically tries to find any two or more adjacent capital letters. See the original article referenced above and the comments below it for more similar wildcard search tricks, like how to extend this idea to include numbers, or using regular expressions.
Ever been nailed by a reviewer or a thesis committee for using too many acronyms without defining them well? There's an easy way built into MS Word to find and highlight all the acronyms in a document. It's a nice check after you're done with a first draft, and you might be surprised by how many you find!
First, hit Ctrl-F to bring up a find box, and type this in exactly as written:
<[A-Z]{2,}>
Hit the "More >>" button, then check the "Use Wildcards" box. Finally, click the "Reading Highlight" box, then click "Highlight All". It should look like this:
After you do that, you'll see all your uppercase acronyms highlighted throughout the entire document. It will look something like this:
That find query basically tries to find any two or more adjacent capital letters. See the original article referenced above and the comments below it for more similar wildcard search tricks, like how to extend this idea to include numbers, or using regular expressions.
100 publications every grad student should read
Jason Moore at the previously mentioned Epistasis Blog has begun compiling a list of 100 papers every grad student should read, broken down by discipline. Right now the list is in its infancy, but it's a good start. I'll post here when the list is updated again.
100 Publications Every Graduate Student Should Read
UPDATE 2009-05-08: The list has grown substantially since yesterday. Check the link again!
100 Publications Every Graduate Student Should Read
UPDATE 2009-05-08: The list has grown substantially since yesterday. Check the link again!
Gene regulation: A new toolbox for mapping regulatory sites
Here's a paper in Nature Reviews Genetics highlighting two recently published methods for mapping regulatory sites. Most currently used procedures rely on ChIP, where you can only examine sites one protein at a time. The two methods discussed here can potentially overcome these limitations - one mostly identifies cis-regulatory sites near promoters, and the other is capable of identifying sites farther away, including long range enhancer elements.
R Reference Card (PDF)
Last week I posted a short tutorial on how to merge datasets using R. R is a free and open-source statistical computing software and programming language (get R here). The only downside is a steeper learning curve because the documentation is sparse and often difficult to understand at first. Once you start using it, you'll realize it can do anything SPSS, SAS, and Stata can do, and its graphing capabilities are light years ahead of everything else. Lately it's use is becoming more mainstream, gaining popularity in the life sciences among other fields, and knowing how to use R is a marketable skill to have on a job hunt.
If you've used R at least a few times before then this printable reference card is really handy for remembering which functions do what and how to use them. If you've never used R before, there are several online resources to teach you the basics of R, and a free book (PDF) written specifically for people who have used SPSS or SAS before and now want to learn R. Also, check back here in the future for more R tutorials or examples.
R Reference Card (PDF) via Rpad.org
If you've used R at least a few times before then this printable reference card is really handy for remembering which functions do what and how to use them. If you've never used R before, there are several online resources to teach you the basics of R, and a free book (PDF) written specifically for people who have used SPSS or SAS before and now want to learn R. Also, check back here in the future for more R tutorials or examples.
R Reference Card (PDF) via Rpad.org
Free tutorials on bioinformatics and model organisms resources
OpenHelix offers free access to a handful of their tutorials on genomics and bioinformatics resources, including the UCSC Genome Browser, Seattle SNPs, Genome Variation Server, and the VISTA Comparative Genomics tools. Below those, you can also find similar tutorials on how to use the free tools and resources for most of the major model organisms (FlyBase, ZFIN, Wormbase, etc).
Each of the tutorials has video lessons, powerpoint slides, handouts, and practice exercises available for download.
OpenHelix: Free tutorials on bioinformatics and model organisms resources
Each of the tutorials has video lessons, powerpoint slides, handouts, and practice exercises available for download.
OpenHelix: Free tutorials on bioinformatics and model organisms resources
Genetic diversity in African populations
An international team led by Sarah Tishkoff, in collaboration with our own Scott Williams, and former CHGR member Jason Moore, published yesterday in Science the largest, most comprehensive characterization of genetic variation in over 100 different African populations. The graphic below summarizes some of this regional variation by displaying the proportion of each of 14 color-coded ancestral populations that are found in modern African subpopulations.
UPDATE 2009-05-01: I didn't read through the 100+ page supplement with 40+ figures, but this has made quite a splash in the popular science journalism press. You can read about the highlights here, here, here, here, here, here, here, and here.
Science: The Genetic Structure and History of Africans and African Americans
UPDATE 2009-05-01: I didn't read through the 100+ page supplement with 40+ figures, but this has made quite a splash in the popular science journalism press. You can read about the highlights here, here, here, here, here, here, here, and here.
Science: The Genetic Structure and History of Africans and African Americans
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