Abstract for the talks I’ve been giving

I’ve been traveling a bit. Here’s what I’ve been talking about:

How Regulatory DNA Encodes Function in Genomes and Gradients

A major function of the genome is to encode regulatory information, but how that function is physically encoded by DNA sequence is poorly understood. This hinders our ability to identify functional cis-regulatory elements in genomes and interpret the consequences of genetic variation in those elements. Regulatory DNA function is determined in part by short, degenerate sequence motifs that are bound by transcription factors, but these motifs do not, by themselves, account for the specificity of cis-regulation in large genomes. The functional role of other sources of specificity, such as chromatin context, nucleosome positioning, combinatorial transcription factor binding, and DNA shape, is unclear.

I will describe two studies aimed at understanding how regulatory DNA encodes function: 1) A massively parallel reporter gene assay reveals that very local DNA sequence features determine the function of ChIP-seq peaks in mouse photoreceptors. 2) Biophysical modeling of spatially restricted gene expression in Drosophila Hedgehog morphogen gradients explains the surprising role of low affinity Gli binding sites in Hedgehog-responsive enhancers.

My weekend vintage SF paperback finds. I picked these up purely for the giant rockets on the covers. 

Top: David Duncan’s Dark Dominion (1954), with a cover credited by ISFDB to Richard Powers.

Bottom: James Blish’s The Seedling Stars (1959), cover by Paul Lehr.

My research description, sans research

Over on my home page, I overhauled my research description, and ended up removing any actual description of my research. But it might be worth a read anyway.

Catching Up

Been busy, but in case you missed them, my Pacific Standard columns have continued apace:

Neuroscience and music:

How Language Helps Us Understand Music Without Words

Curiosity’s latest results on Martian habitability:

Our Search For Martian Life Is Really A Search For Our Place In The Universe

Imagine a world with an effective HIV vaccine. We’ll get there some day:

Why The HIV Vaccine Is Not A Pipe Dream

The FDA, the MiSeqDX, and the regulatory future:

The FDA Is Not Anti-Genetics

WTF evolution: a weird (and still questionable) theory of sexual selection that could explain why men have worse immune systems

Girls’ Immune Systems Rule, Boys’ Drool

Be sure to admire Pacific Standard's new makeover, which includes new sketches of the columnists and makes it even easier to find great content.

In case you missed it…

There’s some catching up to do here: my recent pieces for Pacific Standard include my thoughts on why the FDA does not need to protect you from your genome (but beware, nobody yet knows what harms or benefits will come from widespread direct-to-consumer genetic testing), what role microbes play in our (as in mammals) communications via odors, and how the decade-long erosion in National Institutes of Health funding has entirely wiped out all trace of the previously doubled budget. We’re well below where the pre-doubling trend would put us, with disastrous consequences for how science is done in this country. (You can check out more details on this in my write-up at the Finch & Pea).

asker

tgoodwin95 asked: Hello Dr. White, I just recently read your article in the Pacific Standard, "The Scientific Debate About GM Foods Is Over: They're Safe." As a student, this is an area that interests me, and I'm doing a simple project on the benefits and the costs of GMOs. That being said could I send you a few questions that I had regarding your position? Is this an appropriate place to ask? Thank you!

Sure - you’re welcome to ask here. Or, if you’d rather contact me by email, you can find my contact info on my CV page (link in the sidebar).

- Mike