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Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Elements of the cover design.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
data visualization + art

Science Advances Cover

6 January 2023, Issue 9, Volume 1

1 · The cover

Kijima, Y. et al. A universal sequencing read interpreter (2023) Science Advances 9.

The cover depicts three sets of 672 bases of barcode sequences, which are encoded onto 7-dimensional cubes. Three overlapping cubes are shown, one for each of the three sequencing platforms: 10X Chromium v3 scRNA-seq, Quartz-seq2, and Drop-seq.

Individual bases are encoded by oriented triangles on each of the 2-dimensional faces of the cube (of which there are 672). I created various designs and in the one chosen by Science Advances, the triangles are 7.5% of their full size (more details).

Science Advances caption: DNA sequencing read translation in high-dimensional space. The cover image was created when 672 bases of sequencing barcodes generated by three different single-cell RNA sequencing platforms were encoded as oriented triangles on the faces of three 7-dimensional cubes. Kijima et al. have developed a software tool that interprets DNA sequences to extract encoded information for additional biological analysis. The tool called, INTERSTELLAR, will facilitate development of sequencing-based experiments and sharing of data analysis pipelines.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A Rosetta Stone for DNA sequencing read translation in high-dimensional space: 672 bases of sequencing barcodes generated by three different single-cell RNA sequencing platforms are encoded as oriented triangles on the faces of three 7-dimensional cubes. Cubes encode DNA barcodes from 10X Chromium v3 scRNA-seq, Quartz-seq2 v3.1, and Drop-seq.
My animation of the scale and structure of the human genome is part of the MIT Museum Gene Cultures exhibit.
I've encoded DNA in other ways — in a museum exhibit.

2 · Inspiration

We wanted to create some kind of high-dimensional encoding of sequences. For this, I looked back to my collaboration with Max Cooper's for his Ascent video from his Unspoken Words album.

My animation of 5 dimensions sets the stage for Max Cooper's track Ascent from his new album Unspoken Words.

In ascent, we animated multiple 5-dimensional cubes to create a flurries of lines and shapes — a promising direction for encoding sequences.

3 · Other covers

Browse my gallery of cover designs.

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

Propensity score matching

Mon 16-09-2024

I don’t have good luck in the match points. —Rafael Nadal, Spanish tennis player

In many experimental designs, we need to keep in mind the possibility of confounding variables, which may give rise to bias in the estimate of the treatment effect.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Propensity score matching. (read)

If the control and experimental groups aren't matched (or, roughly, similar enough), this bias can arise.

Sometimes this can be dealt with by randomizing, which on average can balance this effect out. When randomization is not possible, propensity score matching is an excellent strategy to match control and experimental groups.

Kurz, C.F., Krzywinski, M. & Altman, N. (2024) Points of significance: Propensity score matching. Nat. Methods 21:1770–1772.

Nasa to send our human genome discs to the Moon

Sat 23-03-2024

We'd like to say a ‘cosmic hello’: mathematics, culture, palaeontology, art and science, and ... human genomes.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
SANCTUARY PROJECT | A cosmic hello of art, science, and genomes. (details)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
SANCTUARY PROJECT | Benoit Faiveley, founder of the Sanctuary project gives the Sanctuary disc a visual check at CEA LeQ Grenoble (image: Vincent Thomas). (details)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
SANCTUARY PROJECT | Sanctuary team examines the Life disc at INRIA Paris Saclay (image: Benedict Redgrove) (details)

Comparing classifier performance with baselines

Fri 22-03-2024

All animals are equal, but some animals are more equal than others. —George Orwell

This month, we will illustrate the importance of establishing a baseline performance level.

Baselines are typically generated independently for each dataset using very simple models. Their role is to set the minimum level of acceptable performance and help with comparing relative improvements in performance of other models.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Comparing classifier performance with baselines. (read)

Unfortunately, baselines are often overlooked and, in the presence of a class imbalance, must be established with care.

Megahed, F.M, Chen, Y-J., Jones-Farmer, A., Rigdon, S.E., Krzywinski, M. & Altman, N. (2024) Points of significance: Comparing classifier performance with baselines. Nat. Methods 21:546–548.

Happy 2024 π Day—
sunflowers ho!

Sat 09-03-2024

Celebrate π Day (March 14th) and dig into the digit garden. Let's grow something.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2024 π DAY | A garden of 1,000 digits of π. (details)

How Analyzing Cosmic Nothing Might Explain Everything

Thu 18-01-2024

Huge empty areas of the universe called voids could help solve the greatest mysteries in the cosmos.

My graphic accompanying How Analyzing Cosmic Nothing Might Explain Everything in the January 2024 issue of Scientific American depicts the entire Universe in a two-page spread — full of nothing.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
How Analyzing Cosmic Nothing Might Explain Everything. Text by Michael Lemonick (editor), art direction by Jen Christiansen (Senior Graphics Editor), source: SDSS

The graphic uses the latest data from SDSS 12 and is an update to my Superclusters and Voids poster.

Michael Lemonick (editor) explains on the graphic:

“Regions of relatively empty space called cosmic voids are everywhere in the universe, and scientists believe studying their size, shape and spread across the cosmos could help them understand dark matter, dark energy and other big mysteries.

To use voids in this way, astronomers must map these regions in detail—a project that is just beginning.

Shown here are voids discovered by the Sloan Digital Sky Survey (SDSS), along with a selection of 16 previously named voids. Scientists expect voids to be evenly distributed throughout space—the lack of voids in some regions on the globe simply reflects SDSS’s sky coverage.”

voids

Sofia Contarini, Alice Pisani, Nico Hamaus, Federico Marulli Lauro Moscardini & Marco Baldi (2023) Cosmological Constraints from the BOSS DR12 Void Size Function Astrophysical Journal 953:46.

Nico Hamaus, Alice Pisani, Jin-Ah Choi, Guilhem Lavaux, Benjamin D. Wandelt & Jochen Weller (2020) Journal of Cosmology and Astroparticle Physics 2020:023.

Sloan Digital Sky Survey Data Release 12

constellation figures

Alan MacRobert (Sky & Telescope), Paulina Rowicka/Martin Krzywinski (revisions & Microscopium)

stars

Hoffleit & Warren Jr. (1991) The Bright Star Catalog, 5th Revised Edition (Preliminary Version).

cosmology

H0 = 67.4 km/(Mpc·s), Ωm = 0.315, Ωv = 0.685. Planck collaboration Planck 2018 results. VI. Cosmological parameters (2018).

Martin Krzywinski | contact | Canada's Michael Smith Genome Sciences CentreBC Cancer Research CenterBC CancerPHSA
Google whack “vicissitudinal corporealization”
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