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My science art has appeared on the covers of many journals, including Nature, Science, PNAS, Cancer Cell and American Scientist.

EMBO Journal 2011 Cover Contest

1 · EMBO Journal — best scientific cover of 2010

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Four genomes — The illustration, originally part of a poster, shows syntenic relationships between human, chimpanzee, mouse and zebrafish genomes. Curved links encode sequence similarity and outer data tracks represent consensus similarity statistics and orthologous genes. The cover image shows a detail of a visualization prepared with the free genome comparison tool, Circos.

For its 6 May 2009 issue, the EMBO Journal selected my submission of a large Circos figure for its cover. At the time, front page exposure of this sort has made Circos a very popular tool for visualization in genomics, and in particular, in cancer research where there is a need to illustrate differences between genomes.

Below I describe a couple of subsequent submissions for the EMBO Journal 2011 Cover Contest — a scientific entry and a non-scientific entry.

For the EMBO Journal 2011 Cover Contest, I prepared two entries, one for the scientific category and one for the non-scientific category.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The non-scientific entry is abstract photo of fiber optics. The scientific entry was an information graphic showing a hive panel of genomic annotations in human, mouse and dog genomes. The hive panel is based on the use of the newly introduced hive plot.

2 · About the EMBO Journal cover contest

The EMBO Journal non-scientific cover prize is awarded for the most interesting and beautiful image made outside the lab. Contestants may submit, for example, photos or artistic impressions of wildlife animals, plants or landscapes. Particularly welcome will also be hand or computer-generated paintings or drawings (or photographs of other works of art) related to a biological or molecular biological topic.

The EMBO Journal scientific cover prize is awarded for the most captivating and thought-provoking contribution depicting a piece of molecular biology research. Entries can include light or electron micrographs, 3D reconstructions or models of biological specimen or molecules, spectacular artefacts collected in the lab, original new views of lab equipment (but not of colleagues!), or other research-based images to be of interest to molecular biologists.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Examples of scientific cover image winners from previous years. My Circos image (top left) won the 2010 scientfic image cover category.

3 · Scientific image entry — a hive panel

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Final EMBO Journal cover submissions. (More about hive plots.)

4 · Current state of network visualization

A large number of layout algorithms already exist to attempt to visualize networks. In an attempt to create attractive layouts, node and edge positions are optimized to minimize some fitness function, such as overlap or force (if edges are treated as springs). Unfortunately, as a result it is impossible to relate the position of a node (or the distance between any two nodes in the layout) to their connected neighbourhood in the network. This particularly holds for large networks, where nodes and edge overlap in the layout is unavoidable.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Hairballs are irrational network visualizations. Shown here are 8 different layouts of the same network — it is impossible to identify that these images correspond to the same network. More importantly, it is very difficult to extract meaningful and quantitative information from these layouts.

5 · The hive plot

The hive plot is a rational approach to visualizing networks. It is designed to complement (at times, replace) the network hairball.

5.1 · Hive plots for networks

In a hive plot, network nodes are assigned to and placed on axes using rational rules. These rules typically are a function of local network structure around the node (connectivity, density, centrality, etc). The resulting plot is interpretable.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
In a hive plot, nodes in a network are assigned and placed on axes using properties of the node and its relationship to its neighbours. The resulting layout is rational and easily interpreted, because the rules are based on meaningful quantities. (Hive plots rationalize network visualization.)

5.2 · Hive plots for ratios

The hive plot can be applied to visualize a large number of ratios between three or more scales.

Instead of network edges, the lines in a hive plot now correspond to an (x,y) data pair, which can be interpreted as a ratio (x/y). This approach is particularly effective when lines are drawn as ribbons, which are then stacked. This is shown in the figure below.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A hive plot can be used to visualize ratios by rendering individual ratios as stacked ribbons. The result is the circular equivalent of a stacked bar plot

The resulting visualization bears resemblance to a stacked bar plot. The circular layout grants the advantage of being able to instantly compare all pair-wise comparisons between the axes (when three axes are used). This layout also gives the image a compare compact feel and is particularly suitable for tiling.

In the examples below, a 3-axis hive plot is shown with 8 ratios between each axis. The ratios are independent, in the sense that corresponding ribbons (e.g. blue) may have different thickness on either side of an axis. For example, if x:z = 2:3 and x:y = 1:3 then the ribbon on the left of the x axis will be twice as thick as on the right (see black arrow in figure below).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
In a dual scale hive plot, each axis supports two groups of independent ribbons. Axes can be hidden (A), shown (B), or split by various amounts (C 20deg, D 30deg, E 40deg, F 60deg) to explicitly show the transition between ribbons on either side of the axis. Download high-resolution panels A B C D E F

The axes in a hive plot can be arranged arbitrarily. In the figure above panels A and B show 24 ratios — 8 each between x/y, x/z, and y/x axes. In panels C-F each axis is split to create a single 6-axis plot from a dual 3-axis plot. The split axes reveal the transition between ribbons from the left and right sides.

The dual 3-axis plot appears more stylized and mathematical, whereas the single 6-axis plot is softer and organic. As the axis split distance is increased, the plots begin to look like surface density maps, which to some degree occludes the relationships between the ratio ribbons.

5.3 · Comparing genome annotations

For each of human (hg18), mouse (mm8) and dog (canfam2) genome assemblies, UCSC annotations, available for each genome from the table browser, were used to hierarchically organize each base in the assembly using the following criteria: gene, repeat and gene+repeat. For each of these, bases were further categorized as conserved or not.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Each base in the genome assembly was assigned to one of eight disjoint categories.

By exhaustively intersecting each of the annotation regions, the assembly was divided into disjoint segments, each with its annotation states. For example, below are a few adjacent regions from hg18 chr1 (a assembly, r repeat, c-cf conserved with dog, c-mm conserved with mouse).

...
hg 1 120,942,663 120,945,658 2,996 a r
hg 1 120,945,659 120,945,665     7 a
hg 1 120,945,666 120,947,239 1,574 a c-cf c-mm
hg 1 120,947,240 120,947,243     4 a c-cf c-mm r
hg 1 120,947,244 120,947,268    25 a c-mm r
hg 1 120,947,269 120,950,367 3,099 a r
hg 1 120,950,368 120,950,386    19 a
...

Next, the total size of regions for each combination of annotation was calculated for each pairwise combination of genomes. The second genome in the pair dictates which conservation is used. For example, for the human-mouse pair, the relative fractions of the human genome that fall into each of the categories are

hg mm a        1,839,255,050 0.643542044483869
hg mm a,c-mm     757,027,260 0.264878365091574
hg mm a,r        206,719,589 0.0723296896425132
hg mm a,c-mm,r    42,358,464 0.0148209203088807
hg mm a,g          8,139,587 0.00284798264342638
hg mm a,c-mm,g     4,435,658 0.0015520046651231
hg mm a,g,r           48,994 1.71426463814481e-05
hg mm a,c-mm,g,r      33,869 1.18505182327074e-05

thus categorizing all the 2.86 Gb of the assembled human genome. The corresponding ratios for the mouse genome are

mm hg a          1,388,193,028 0.544355712823795
mm hg a,c-hg       892,892,218 0.350132128602082
mm hg a,r          196,173,508 0.0769260237089193
mm hg a,c-hg,r      62,305,053 0.0244318411447455
mm hg a,g            6,377,904 0.00250098394691097
mm hg a,c-hg,g       4,076,727 0.00159861747416369
mm hg a,g,r             81,889 3.21113447973805e-05
mm hg a,c-hg,g,r        57,585 2.2580954586784e-05

Using these two lists, all the ratios between the human and mouse axes can be determined. For example, for the conserved/gene/non-repeat regions the ratio of human:mouse is 0.00155:0.00160 (lines are bolded above). The corresponding ribbon for this ratio is shown below.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The ratio of conserved gene regions not in repeats between human and mouse genomes.

Category assignment into repeat, gene and conserved region was parametrized into three ranges for each criteria. These values were selected heuristically, to obtain a reasonable sample for each combination.

  • gene g1 <4kb, g2 4kb-22kb, g3 >22kb
  • repeat r1 simple, r2 LTR, r3 LINE/SINE
  • conservation c1 <45%, c2 45%-58%, c3 >58%

Given 3 parameters for each of the categories, the full comparison is represented by 27 hive plots. These plots are arranged on the cover as follows

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The ratio of conserved gene regions not in repeats between human and mouse genomes.

The scale of the axes was logarithmic to maintain visibility of all categories.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The ratio of conserved gene regions not in repeats between human and mouse genomes.

6 · Non-scientific image entry

My 2011 non-scientific fiber optic entry received an honorouable mention. Oh well, we can't always have nice things.

My photography aims to create create fashion, beauty, and editorial images with strong elements of geometry, story-telling, and contoured light and shadow. My process is analytical, cerebral and askew.
I am the former owner of the world's most popular rat. See the photos and be adjacent to fame.

6.1 · Fibre optic lamp photos

Some time ago, I photographed fiber optic strands. These worked out well. I had not done anything with these images, and thought they would make a competitive entry into the cover contest.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
My first attempt at photographing fiber optic lamp strands. These images were bundled into a set called Diving Horror, because of their likeness to creepy tentacles of creatures of the deep.

I revisited the fiber optic lamp with a higher resolution camera (Canon 5D — original images were from a Canon 20D) and a dedicated macro lens (Sigma 150mm f2.8 EX APO DG HSM Macro) (original images were shot with the Canon EF 24-70L).

From these new images, shown below, I created five EMBO Journal cover submissions.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Second attempt at photographing fiber optic lamp strands.

The submissions would render on the cover as shown below.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2011 EMBO Cover contest submission — macro photograph of fiber optic lamp strands.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2011 EMBO Cover contest submission — macro photograph of fiber optic lamp strands.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2011 EMBO Cover contest submission — macro photograph of fiber optic lamp strands.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2011 EMBO Cover contest submission — macro photograph of fiber optic lamp strands.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2011 EMBO Cover contest submission — macro photograph of fiber optic lamp strands.
news + thoughts

Annals of Oncology cover

Wed 14-09-2022

My cover design on the 1 September 2022 Annals of Oncology issue shows 570 individual cases of difficult-to-treat cancers. Each case shows the number and type of actionable genomic alterations that were detected and the length of therapies that resulted from the analysis.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
An organic arrangement of 570 individual cases of difficult-to-treat cancers showing genomic changes and therapies. Apperas on Annals of Oncology cover (volume 33, issue 9, 1 September 2022).

Pleasance E et al. Whole-genome and transcriptome analysis enhances precision cancer treatment options (2022) Annals of Oncology 33:939–949.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
My Annals of Oncology 570 cancer cohort cover (volume 33, issue 9, 1 September 2022). (more)

Browse my gallery of cover designs.

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

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

Sun 21-08-2022

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)

© 1999–2022 Martin Krzywinski | contact | Canada's Michael Smith Genome Sciences CentreBC Cancer Research CenterBC CancerPHSA