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Explore the land of Neradia and meet the snowflake named Arenh Jerrus of Bosmen in the wintertime tale In Silico Flurries: Computing the world of snow in Scientific American's SA Visual story about beauty, imagination and machine learning. A collaboration with Jake Lever.
This project uses unwords.
Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca

Working with Senior Graphics Editor Jen Christiansen, Senior Editors Mark Fischetti and Clara Moskowitz, I have designed these Graphic Science visualizations for Scientific American.

Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
3,117,275,501 BASES, 0 GAPS | The history of the sequence assembly of the human genome showing when each region was completed between 2000 and 2022. August 2022 (vol 327 issue 2).
Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
HOW COVID-19 SPREAD LIKE WILDFIRE | A phylogenetic tree of SARS-Cov-2 genomes, showing how the virus mutated during its spread June 2020 (vol 322 issue 6).
Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
TAKE YOUR MEDICINE... NOW | Expression of cardiovascular genes that cycle across 24 hours. January 2019 (vol 320 issue 1).
Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
MENTAL ILLNESS OVERLAP | A distinct set of genes may underlie several psychiatric disorders. July 2018 (vol 319 issue 1).
Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
THE BACTERIA GAME | An analysis of dust reveals how the presence of men, women, dogs and cats affects the variety of bacteria in a household. December 2015 (vol 313 issue 6).
Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
TWISTS OF FATE | Genes, traits and disease are linked in complex and surprising ways June 2015 (vol 312 issue 6).
Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
THE 1 PERCENT DIFFERENCE | Genome comparisons reveal the DNA that distinguishes Homo sapiens from its kin September 2014 (vol 311 issue 3).
Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca

See how scientists put together the complete human genome

For the first time, researchers have sequenced all 3,117,275,501 bases of our genetic code.

Scientific American August 2022, volume 327 issue 2

Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
3,117,275,501 BASES, 0 GAPS | The history of the sequence assembly of the human genome showing when each region was completed between 2000 and 2022. August 2022 (vol 327 issue 2).

text by Clara Moskowitz | graphic by Martin Krzywinski

I visually track the progress of the human genome assembly from its inception in 2000 to the gapless telomere-to-telomere CHM13v2 assembly. The graphic was published in Scientific American Graphic Science.
Here, I describe in detail the inspiration and process behind the design of this information graphic.

source

assembly sequence from UCSC Genome Browser (assembly history), Nurk et al. The complete sequence of a human genome (2022) Science 376:44–53.

News

Filling in the Gaps by Laura Zahn, Most complete human genome yet reveals previously indecipherable DNA by Elizabeth Pennisi

Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca

How COVID-19 spread like wildfire

Mutations in the SARS-Cov-2 virus reveal the story.

Scientific American June 2020, volume 322 issue 6

Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
HOW COVID-19 SPREAD LIKE WILDFIRE | A phylogenetic tree of SARS-Cov-2 genomes, showing how the virus mutated during its spread June 2020 (vol 322 issue 6).

text by Mark Fischetti | graphic by Martin Krzywinski

Source

Nextstrain

Interested in more COVID-19 and SARS-Cov-2 graphics? Check out my projects below.

Discover all the things that are not trying to make you stronger.
Short emissions from piku actual during the coronavirus outbreak. Not just the pandemic, but also about other feelings. As they come.
The COVID Charts are case studies of data visualization and science communication of the coronavirus outbreak. If fix the inaccurate, the sloppy and the illegible.
Visual representations of differences in SARS Cov-2 genomes across variants."
Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca

Take your medicine... now

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

Scientific American January 2019, volume 320 issue 1

Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
TAKE YOUR MEDICINE... NOW | Expression of cardiovascular genes that cycle across 24 hours. January 2019 (vol 320 issue 1).
An original composition by the artist Segue that uses audio recordings from the GSC's laboratory equipment, robots and computers—to make music from the noise they produce. This album was commissioned as part of the celebration of GSC's 20th anniversary.
This visualization of cycling gene expression was used for artwork on the vinul version of the album Gene Machines.

text by Mark Fischetti | graphic by Martin Krzywinski

A compelling overview figure of periodicity in a quantity. Before you even think about it, you already know what you're looking it.

Source

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.

Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca

The same genes may underlie different psychiatric disorders

A distinct set of genes may underlie several psychiatric conditions.

Scientific American July 2018, volume 319 issue 1

Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
MENTAL ILLNESS OVERLAP | A distinct set of genes may underlie several psychiatric disorders. July 2018 (vol 319 issue 1).

text by Mark Fischetti | graphic by Martin Krzywinsk

The dataset is challenging: expression, correlation and network module membership of 11,000+ genes. Getting it onto one page was an exercise in restraint and calm.

source

Gandal M.J. et al. Shared Molecular Neuropathology Across Major Psychiatric Disorders Parallels Polygenic Overlap Science 359 693–697 (2018)

Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca

Men and women alter a home's bacteria differently

An analysis of dust reveals how the presence of men, women, dogs and cats affects the variety of bacteria in a household.

Scientific American December 2015, volume 313 issue 6

Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
THE BACTERIA GAME | An analysis of dust reveals how the presence of men, women, dogs and cats affects the variety of bacteria in a household. December 2015 (vol 313 issue 6).

text by Mark Fischetti | graphic by Martin Krzywinski and Barbara Jeanine Hunnicutt

Catalogue of bacteria shapes by Barbara Jeanine Hunnicutt.

We explored differences in household dust bacteria based on the gender and pet status of the occupants.

We have also written about the making of the graphic, for those interested in how these things come together.

source

Barberan A et al. (2015) The ecology of microscopic life in household dust. Proc. R. Soc. B 282: 20151139.

Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca

A roadmap to the "volume control" of genes

Genes, traits and disease are linked in complex and surprising ways.

Scientific American June 2015, volume 312 issue 6

Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
TWISTS OF FATE | Genes, traits and disease are linked in complex and surprising ways June 2015 (vol 312 issue 6).

text by Dina Fine Maron | graphic by Martin Krzywinski

Because sometimes only a network hairball will do.

source

Integrative analysis of 111 reference human epigenomes. (2015) Nature 518:317.

Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca

Tiny genetic differences between humans and other primates pervade the genome

Genome comparisons reveal the DNA that distinguishes Homo sapiens from its kin.

Scientific American September 2014, volume 311 issue 3

Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
THE 1 PERCENT DIFFERENCE | Genome comparisons reveal the DNA that distinguishes Homo sapiens from its kin September 2014 (vol 311 issue 3).

text by Kate Wong | illustrations by Portia Sloan Rollings | graphic by Martin Krzywinski

A Scientific American blog entry "A Monkey's Blueprint" accompanies this piece.

This design won a bronze award at Malofiej 23. For more information about Malofiej, see the SA Visual blog entry "There's No Infographic without Info (and other Lessons from Malofiej)".

Q: The Hilbert curve is (a) a continuous fractal space-filling curve, (b) a shape that can be used for recursive art and high-resolution data visualization, or (c) the home of the curious Hilbertonians?
A: Yes.
Here, I describe in detail the inspiration and process behind the design of this information graphic.

source

Details here.

Scientific American Graphic Science - Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
news + thoughts

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).

Error in predictor variables

Tue 02-01-2024

It is the mark of an educated mind to rest satisfied with the degree of precision that the nature of the subject admits and not to seek exactness where only an approximation is possible. —Aristotle

In regression, the predictors are (typically) assumed to have known values that are measured without error.

Practically, however, predictors are often measured with error. This has a profound (but predictable) effect on the estimates of relationships among variables – the so-called “error in variables” problem.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Error in predictor variables. (read)

Error in measuring the predictors is often ignored. In this column, we discuss when ignoring this error is harmless and when it can lead to large bias that can leads us to miss important effects.

Altman, N. & Krzywinski, M. (2024) Points of significance: Error in predictor variables. Nat. Methods 20.

Background reading

Altman, N. & Krzywinski, M. (2015) Points of significance: Simple linear regression. Nat. Methods 12:999–1000.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nat. Methods 13:541–542 (2016).

Das, K., Krzywinski, M. & Altman, N. (2019) Points of significance: Quantile regression. Nat. Methods 16:451–452.

Convolutional neural networks

Tue 02-01-2024

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

Following up on our Neural network primer column, this month we explore a different kind of network architecture: a convolutional network.

The convolutional network replaces the hidden layer of a fully connected network (FCN) with one or more filters (a kind of neuron that looks at the input within a narrow window).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Convolutional neural networks. (read)

Even through convolutional networks have far fewer neurons that an FCN, they can perform substantially better for certain kinds of problems, such as sequence motif detection.

Derry, A., Krzywinski, M & Altman, N. (2023) Points of significance: Convolutional neural networks. Nature Methods 20:1269–1270.

Background reading

Derry, A., Krzywinski, M. & Altman, N. (2023) Points of significance: Neural network primer. Nature Methods 20:165–167.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nature Methods 13:541–542.

Neural network primer

Tue 10-01-2023

Nature is often hidden, sometimes overcome, seldom extinguished. —Francis Bacon

In the first of a series of columns about neural networks, we introduce them with an intuitive approach that draws from our discussion about logistic regression.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Neural network primer. (read)

Simple neural networks are just a chain of linear regressions. And, although neural network models can get very complicated, their essence can be understood in terms of relatively basic principles.

We show how neural network components (neurons) can be arranged in the network and discuss the ideas of hidden layers. Using a simple data set we show how even a 3-neuron neural network can already model relatively complicated data patterns.

Derry, A., Krzywinski, M & Altman, N. (2023) Points of significance: Neural network primer. Nature Methods 20:165–167.

Background reading

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nature Methods 13:541–542.

Cell Genomics cover

Mon 16-01-2023

Our cover on the 11 January 2023 Cell Genomics issue depicts the process of determining the parent-of-origin using differential methylation of alleles at imprinted regions (iDMRs) is imagined as a circuit.

Designed in collaboration with with Carlos Urzua.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Our Cell Genomics cover depicts parent-of-origin assignment as a circuit (volume 3, issue 1, 11 January 2023). (more)

Akbari, V. et al. Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq (2023) Cell Genomics 3(1).

Browse my gallery of cover designs.

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

Science Advances cover

Thu 05-01-2023

My cover design on the 6 January 2023 Science Advances issue depicts DNA sequencing read translation in high-dimensional space. The image showss 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.

More details about the design.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
My Science Advances cover that encodes sequence onto hypercubes (volume 9, issue 1, 6 January 2023). (more)

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

Browse my gallery of cover designs.

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

Regression modeling of time-to-event data with censoring

Thu 17-08-2023

If you sit on the sofa for your entire life, you’re running a higher risk of getting heart disease and cancer. —Alex Honnold, American rock climber

In a follow-up to our Survival analysis — time-to-event data and censoring article, we look at how regression can be used to account for additional risk factors in survival analysis.

We explore accelerated failure time regression (AFTR) and the Cox Proportional Hazards model (Cox PH).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Regression modeling of time-to-event data with censoring. (read)

Dey, T., Lipsitz, S.R., Cooper, Z., Trinh, Q., Krzywinski, M & Altman, N. (2022) Points of significance: Regression modeling of time-to-event data with censoring. Nature Methods 19:1513–1515.

Music video for Max Cooper's Ascent

Tue 25-10-2022

My 5-dimensional animation sets the visual stage for Max Cooper's Ascent from the album Unspoken Words. I have previously collaborated with Max on telling a story about infinity for his Yearning for the Infinite album.

I provide a walkthrough the video, describe the animation system I created to generate the frames, and show you all the keyframes

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Frame 4897 from the music video of Max Cooper's Asent.

The video recently premiered on YouTube.

Renders of the full scene are available as NFTs.

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