Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - contact me Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert CurveMartin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Day 2020 - Piku
Where am I supposed to go? Where was I supposed to know?Violet Indianaget lost in questionsmore quotes

round: curious



PNAS Cover: Earth BioGenome Project


visualization + design

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Cover image for the human genetics special issue. Trends in Genetics October 2012, 28 (10) (lowres, hires, Trends in Genetics)

Creating the Trends in Genetics October 2012 Cover

Lately, I've been making a lot of square things round. So when Rhiannon Macrae, the Editor of Trends in Genetics, requested a Circos-like cover image for the human genetics special edition of the journal, I started drawing circles.

The image was published on the cover of Trends in Genetics human genetics special issue (Trends in Genetics October 2012, 28 (10)).

Tools

Circos, Circos tableviewer, Illustrator CS5, and a cup (or two) of Galileo coffee from a Rancilio Epoca.

Other Covers

Circos has appeared on covers of journals and books. Some of the images were designed by me and others were drawn from papers published in the issue.

Journals

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Cover of Blood, 2 Aug 2012, 120(5). Figure from Egan, J. B., C. X. Shi, et al. (2012). Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides. Blood 120(5): 1060-1066. (Blood)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Genomics, Aug 2012, 100(2). Figure from Katapadi, V. K., M. Nambiar, et al. (2012). Potential G-quadruplex formation at breakpoint regions of chromosomal translocations in cancer may explain their fragility. Genomics 100(2): 72-80. (Genomics)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Science Translational Medicine, December 2010, 2(61). Figure from Lo, Y. M., K. C. Chan, et al. (2010). Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci Transl Med 2(61): 61ra91 (Science Translational Medicine)

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
EMBO Journal, May 2009, 28(9). Cover design by Martin Krzywinski. (EMBO)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Biotechnology, November 2009, 27(11). Figure from Cho, B. K., K. Zengler, et al. (2009). The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol 27(11): 1043-1049. (Nature Biotechnology)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Genome Research, April 2008, 18(4). Cover design by Ryan Morin (Genome Research)

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
American Scientist, September/October 2007. Cover design by Martin Krzywinski — how it was done. (American Scientist)

Books

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
iGenetics, 3rd ed. by Peter Russell (Benjamin Cummings). Cover design by Martin Krzywinski. (iGenetics)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Building Bioinformatics Solutions with Perl, R and MySQL (Oxford University Press). Cover design by Martin Krzywinski. (Building Bioinformatics Solutions)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Designing Universal Knowledge by Gerlinde Schuller (Lars Müller Publishers) (Designing Universal Knowledge)

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Chromosomes — art book of film stills, David Cronenberg. Contribution to book design by Martin Krzywinski. (Chromosomes)

source of design

I have a collection of unpublished Circos posters and thought these might be a good starting point. Rhiannon and I narrowed the choice down to the black-and-white design that showed sequenced organisms. We also liked the complex style of a panel of hundreds of Circos images generated with the tableviewer.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
An old Circos poster. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A panel of images generated from the Circos tableviewer. (zoom)

The idea would be that the foreground would be more artistic and stylized, while the background was more technical and complex. I have thousands of images available from the tableviewer (e.g. huge 15,129 image matrix).

Rhiannon also wanted to include the quote by Henry David Thoreau, "Nature and human life are as various as our several constitutions. Who shall say what prospect life offers to another?" This reminded me of a similar but more tragic line from Shakespeare's Julius Caesar, "How many ages hence shall this our lofty scene be acted over in states unborn and accents yet unknown!"

early comps

In the early comps we played around with the idea of using non-genomics elements in the image, such as coins. We thought that we could use the variety of color and shape of the coins to communicate the idea of genetic diversity. However, after wrestling with how to do this effectively the concept was scrapped — the idea of using coins felt both arcane and arbitrary.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
First set of comps. (zoom)

I decided to go with a warm brown color scheme. It's not a color I use a lot of, which makes me think that I should try to do more with it.

Deep brown provides great contrast for saturated colors, though I had to be careful not to make the image look too kitchy with an excess of colour variation. In some of the early comps shown above, two or more different color palettes were used (e.g. grey/red/blue and false color) and this lowered to overall visual cohesion of the image.

It's always a good idea to add variety to design. After all, without any variety we'd be left with a blank page. Ok, so variety is good, but too much variety is very bad, and can make you wish for that blank page again. Think about this: one kind of variety already provides variety! A variety of variety (I run the risk of recursing myself ad infinitum) can not only compete for attention but resonate destructively (that's design-speak for "turn into visual mush").

refining the design

Everyone liked the combination of bright colors and dark background. This is an approach I favour too, which has worked well on other covers.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Experimenting with an organic look. (zoom)

Briefly I experimented with various brush and pencil filters to give the image a more hand-drawn and organic look. Most of the illustrations I generate are very digital — blocks of solid colors and high-contrast shapes — and I thought a departure from this look could work in this case. However, like with the coins, this path didn't produce anything productive.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Refining color palettes. (zoom)

final image elements

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The background is created from a matrix of about 1,400 individual Circos images created by the user community using the tableviewer. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The main element is a Circos image of a 15 x 15 table, also created with the tableviewer. (zoom)

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A watermark made up from elements in a tableviewer image that show aggregate statistics for each row and column. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A multi-crop zoom of the main element shown above. This version is colored for punch. (zoom)

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Masks showing the locations of smaller vignettes. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
An 8 x 8 tableviewer image with outlined ribbons. (zoom)

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Thoreau quote: Nature and human life are as various as our several constitutions. Who shall say what prospect life offers to another? (zoom)

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Background and midground elements. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Background and foreground elements. (zoom)

final image

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Final image with all the layers. (Trends in Genetics October 2012, 28 (10)) (zoom)

VIEW ALL

news + thoughts

Survival analysis—time-to-event data and censoring

Fri 05-08-2022

Love's the only engine of survival. —L. Cohen

We begin a series on survival analysis in the context of its two key complications: skew (which calls for the use of probability distributions, such as the Weibull, that can accomodate skew) and censoring (required because we almost always fail to observe the event in question for all subjects).

We discuss right, left and interval censoring and how mishandling censoring can lead to bias and loss of sensitivity in tests that probe for differences in survival times.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Survival analysis—time-to-event data and censoring. (read)

Dey, T., Lipsitz, S.R., Cooper, Z., Trinh, Q., Krzywinski, M & Altman, N. (2022) Points of significance: Survival analysis—time-to-event data and censoring. Nature Methods 19:906–908.

3,117,275,501 Bases, 0 Gaps

Fri 05-08-2022

See How Scientists Put Together the Complete Human Genome.

My graphic in Scientific American's Graphic Science section in the August 2022 issue shows the full history of the human genome assembly — from its humble shotgun beginnings to the gapless telomere-to-telomere assembly.

Read about the process and methods behind the creation of the graphic.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
3,117,275,501 Bases, 0 Gaps. Text by Clara Moskowitz (Senior Editor), art direction by Jen Christiansen (Senior Graphics Editor), source: UCSC Genome Browser.

See all my Scientific American Graphic Science visualizations.

Anatomy of SARS-Cov-2

Tue 31-05-2022

My poster showing the genome structure and position of mutations on all SARS-CoV-2 variants appears in the March/April 2022 issue of American Scientist.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses (zoom)

An accompanying piece breaks down the anatomy of each genome — by gene and ORF, oriented to emphasize relative differences that are caused by mutations.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses (zoom)

Cancer Cell cover

Sat 23-04-2022

My cover design on the 11 April 2022 Cancer Cell issue depicts depicts cellular heterogeneity as a kaleidoscope generated from immunofluorescence staining of the glial and neuronal markers MBP and NeuN (respectively) in a GBM patient-derived explant.

LeBlanc VG et al. Single-cell landscapes of primary glioblastomas and matched explants and cell lines show variable retention of inter- and intratumor heterogeneity (2022) Cancer Cell 40:379–392.E9.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
My Cancer Cell kaleidoscope cover (volume 40, issue 4, 11 April 2022). (more)

Browse my gallery of cover designs.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A catalogue of my journal and magazine cover designs. (more)

Nature Biotechnology cover

Sat 23-04-2022

My cover design on the 4 April 2022 Nature Biotechnology issue is an impression of a phylogenetic tree of over 200 million sequences.

Konno N et al. Deep distributed computing to reconstruct extremely large lineage trees (2022) Nature Biotechnology 40:566–575.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
My Nature Biotechnology phylogenetic tree cover (volume 40, issue 4, 4 April 2022). (more)

Browse my gallery of cover designs.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A catalogue of my journal and magazine cover designs. (more)