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In Silico Flurries: Computing a world of snow. Scientific American. 23 December 2017


genomics + data mining

ICDM2012 Keynote

Needles in Stacks of Needles: genomics + data mining

Download talk

visual abstract

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The talk introduces genomics and cancer biology to computer scientists and outlines areas in which data mining methods are being used to further our understanding of the genome. The theme is one of complexity and relevance — computers manage the former, but we are the ultimate judges of the latter. (download talk, ICDM2012)

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.

VIEW ALL

news + thoughts

Molecular Case Studies Cover

Fri 06-07-2018

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Cover design for Apr 2018 issue of Molecular Case Studies. (details)

Happy 2018 `\tau` Day—Art for everyone

Wed 27-06-2018
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
You know what day it is. (details)

Universe Superclusters and Voids

Mon 25-06-2018

A map of the nearby superclusters and voids in the Unvierse.

By "nearby" I mean within 6,000 million light-years.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The Universe — Superclustesr and Voids. The two supergalactic hemispheres showing Abell clusters, superclusters and voids within a distance of 6,000 million light-years from the Milky Way. (details)

Datavis for your feet—the 178.75 lb socks

Sat 23-06-2018

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Some datavis for your feet: the 178.75 lb socks. (get some)

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

Sun 24-06-2018

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
An analysis of dust reveals how the presence of men, women, dogs and cats affects the variety of bacteria in a household. Appears on Graphic Science page in December 2015 issue of Scientific American.

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)