Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - contact me Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert Curve
Trance opera—Spente le Stellebe dramaticmore quotes

art: what we do


DNA on 10th — street art, wayfinding and font


data visualization + art

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The BC Cancer Agency’s Personalized Oncogenomics Program (POG) is a clinical research initiative applying genomic sequencing to the diagnosis and treatment of patients with incurable cancers.

Art of the Personalized Oncogenomics Program

Nature uses only the longest threads to weave her patterns, so that each small piece of her fabric reveals the organization of the entire tapestry.
— Richard Feynman

Personalized Oncogenomics Program at Canada's Michael Smith Genome Sciences Center / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The design on the posters is being used for the Vancouver Ride to Conquer Cancer cycling jersey. (buy a jersey, tour info)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The POG art shows 545 cases studied over the course of 5 years and is freely available as posters for printing and images for your desktop and presentation slides in both bitmap and PDF formats.

 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
5 Years of Personalized Oncogenomics Project at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. Cases ordered chronologically by case number. (zoom)

 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
5 Years of Personalized Oncogenomics Project at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. Cases grouped by diagnosis (tissue type) and then by similarity within group. (zoom)

cancer is the difference of differences

As individuals, we all have slightly different genomes. If you compare the genomes of two people, you will find about 3 million base pair differences, which is about 0.1% of the genome.

This variation exists not only within the population but potentially also, to a lesser extent, among our cells, which number around 40 trillion. That's roughly 10,000 cells for each base in your 3 billion base genome. And each has a role to play.

POG cases, by tissue type
n %
Gastrointestinal 141 25
 
Breast 138 25
 
Thoracic 57 10
 
Gynecologic 45 8.3
 
Soft tissue 44 8.1
 
Skin 11 2.0
 
Urologic 8 1.5
 
Hematologic 7 1.3
 
Head and neck 6 1.1
 
Endocrine 5 0.9
 
Central nervous system 5 0.9
 
Other 78 14
 
ALL 545

One consequence of this complexity and variation is that changes in the genome (through mutation or other processes) can have very different effects, depending on both the change and the genome. Cancer is a phenomena in which cells' ability to organize themselves as they divide is altered due to changes in the genome. It is an incredibly complex biological phenomenon—considering all the genomes in the population and all the possible changes that may arise, there is truly an inexhaustible number of ways in which the genome can break.

classifying cancer

Cancers are classified according to their site of origin, such as lung, breast, liver, or colon. This is a coarse grouping—within each group there are many subtypes with differences in response to treatment and overall behaviour.

diversities among clinical cases

The design of the POG art highlights the diversity and similarity among cases. The diversity is what makes the study of cancer difficult and the similarities are what makes inference possible.

Personalized Oncogenomics Program at Canada's Michael Smith Genome Sciences Center / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca

Each case is represented by three concentric rings. The width of each ring represents the extent to which the case is similar (as measured by correlation) to cancers of the type encoded by the color of the ring (see Methods).

remixes

In additional to the posters, I've created remixes for your desktop at 4k resolution.


 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
png
5 Years of Personalized Oncogenomics Project at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. Cases ordered chronologically by case number. (zoom)

 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
png
5 Years of Personalized Oncogenomics Project at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. Cases ordered chronologically by case number. (zoom)

 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
png
5 Years of Personalized Oncogenomics Project at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. Cases ordered chronologically by case number. (zoom)

 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
png
5 Years of Personalized Oncogenomics Project at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. Cases ordered chronologically by case number. (zoom)

Ride to Conquer Cancer — Data-powered, Human-driven

This year, the cyclists in the Ride to Conquer Cancer will not only have the chance to raise money for research (as they've always done) but also do so while wearing data (as they've never done before).

You can purchase your own data-powered and human-driven cycling jersey.

VIEW ALL

news + thoughts

Analyzing outliers: Robust methods to the rescue

Sat 30-03-2019
Robust regression generates more reliable estimates by detecting and downweighting outliers.

Outliers can degrade the fit of linear regression models when the estimation is performed using the ordinary least squares. The impact of outliers can be mitigated with methods that provide robust inference and greater reliability in the presence of anomalous values.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Analyzing outliers: Robust methods to the rescue. (read)

We discuss MM-estimation and show how it can be used to keep your fitting sane and reliable.

Greco, L., Luta, G., Krzywinski, M. & Altman, N. (2019) Points of significance: Analyzing outliers: Robust methods to the rescue. Nature Methods 16:275–276.

Background reading

Altman, N. & Krzywinski, M. (2016) Points of significance: Analyzing outliers: Influential or nuisance. Nature Methods 13:281–282.

Two-level factorial experiments

Fri 22-03-2019
To find which experimental factors have an effect, simultaneously examine the difference between the high and low levels of each.

Two-level factorial experiments, in which all combinations of multiple factor levels are used, efficiently estimate factor effects and detect interactions—desirable statistical qualities that can provide deep insight into a system.

They offer two benefits over the widely used one-factor-at-a-time (OFAT) experiments: efficiency and ability to detect interactions.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Two-level factorial experiments. (read)

Since the number of factor combinations can quickly increase, one approach is to model only some of the factorial effects using empirically-validated assumptions of effect sparsity and effect hierarchy. Effect sparsity tells us that in factorial experiments most of the factorial terms are likely to be unimportant. Effect hierarchy tells us that low-order terms (e.g. main effects) tend to be larger than higher-order terms (e.g. two-factor or three-factor interactions).

Smucker, B., Krzywinski, M. & Altman, N. (2019) Points of significance: Two-level factorial experiments Nature Methods 16:211–212.

Background reading

Krzywinski, M. & Altman, N. (2014) Points of significance: Designing comparative experiments.. Nature Methods 11:597–598.

Happy 2019 `\pi` Day—
Digits, internationally

Tue 12-03-2019

Celebrate `\pi` Day (March 14th) and set out on an exploration explore accents unknown (to you)!

This year is purely typographical, with something for everyone. Hundreds of digits and hundreds of languages.

A special kids' edition merges math with color and fat fonts.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
116 digits in 64 languages. (details)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
223 digits in 102 languages. (details)

Check out art from previous years: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day, 2016 `\pi` Day, 2017 `\pi` Day and 2018 `\pi` Day.

Tree of Emotional Life

Sun 17-02-2019

One moment you're :) and the next you're :-.

Make sense of it all with my Tree of Emotional life—a hierarchical account of how we feel.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A section of the Tree of Emotional Life.

Find and snap to colors in an image

Sat 29-12-2018

One of my color tools, the colorsnap application snaps colors in an image to a set of reference colors and reports their proportion.

Below is Times Square rendered using the colors of the MTA subway lines.


Colors used by the New York MTA subway lines.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Times Square in New York City.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Times Square in New York City rendered using colors of the MTA subway lines.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Granger rainbow snapped to subway lines colors from four cities. (zoom)

Take your medicine ... now

Wed 19-12-2018

Drugs could be more effective if taken when the genetic proteins they target are most active.

Design tip: rediscover CMYK primaries.

More of my American Scientific Graphic Science designs

Ruben et al. A database of tissue-specific rhythmically expressed human genes has potential applications in circadian medicine Science Translational Medicine 10 Issue 458, eaat8806.