resources
visualizations
presentations
lunch break
Distractions and amusements, with a sandwich and coffee.
genomics + data mining
ICDM2012 Keynote
Needles in Stacks of Needles: genomics + data mining
visual abstract
abstract
In 2001, the first human genome sequence was published. Now, just over 10 years later, we capable of sequencing a genome in just a few days. Massive parallel sequencing projects now make it possible to study the cancers of thousands of individuals. New data mining approaches are required to robustly interrogate the data for causal relationships among the inherently noisy biology. How does one identify genetic changes that are specific and causal to a disease within the rich variation that is either natural or merely correlated? The problem is one of finding a needle in a stack of needles. I will provide a non-specialist introduction to data mining methods and challenges in genomics, with a focus on the role visualization plays in the exploration of the underlying data.
references
The title of the talk was drawn from the paper
Gregory M. Cooper & Jay Shendure Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data Nature Reviews Genetics 12, 628-640 (September 2011)
I will be posting a full list of references for the talk shortly.
news + thoughts
Molecular Case Studies Cover
The theme of the April issue of Molecular Case Studies is precision oncogenomics. We have three papers in the issue based on work done in our Personalized Oncogenomics Program (POG).
The covers of Molecular Case Studies typically show microscopy images, with some shown in a more abstract fashion. There's also the occasional Circos plot.
I've previously taken a more fine-art approach to cover design, such for those of Nature, Genome Research and Trends in Genetics. I've used microscopy images to create a cover for PNAS—the one that made biology look like astrophysics—and thought that this is kind of material I'd start with for the MCS cover.
Happy 2018 `\tau` Day—Art for everyone
Universe Superclusters and Voids
A map of the nearby superclusters and voids in the Unvierse.
By "nearby" I mean within 6,000 million light-years.
Datavis for your feet—the 178.75 lb socks
In the past, I've been tangentially involved in fashion design. I've also been more directly involved in fashion photography.
It was now time to design my first ... pair of socks.
In collaboration with Flux Socks, the design features the colors and relative thicknesses of Rogue olympic weightlifting plates. The first four plates in the stack are the 55, 45, 35, and 25 competition plates. The top 4 plates are the 10, 5, 2.5 and 1.25 lb change plates.
The perceived weight of each sock is 178.75 lb and 357.5 lb for the pair.
The actual weight is much less.
Genes Behind Psychiatric Disorders
Find patterns behind gene expression and disease.
Expression, correlation and network module membership of 11,000+ genes and 5 psychiatric disorders in about 6" x 7" on a single page.
Design tip: Stay calm.
More of my American Scientific Graphic Science designs
Gandal M.J. et al. Shared Molecular Neuropathology Across Major Psychiatric Disorders Parallels Polygenic Overlap Science 359 693–697 (2018)