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data visualization + art
The information graphic showing the history of the human genome assembly is part of my series of designs created for the Scientific American Graphic Science page. Together with Senior Graphics Editor Jen Christiansen, we've looked at everything from the evolution of the genomes of SARS-Cov-2 strains to how pets contribute to the bacterial flora in your home.
Most of the art is available for purchase as framed prints and, yes, even pillows. Sleep's never been more important — I take custom requests.

History of the Human Genome Assembly

22 years, 3,117,275,501 bases and 0 gaps later

Round numbers are always false.
— Samuel Johnson

buy artwork Gap size and location in hg38 human genome assembly by Martin Krzywinski
MY DATA + SCIENCE ART ON A WALL | Most of my artwork is available for sale as prints and other items. (buy artwork / see all my art)
buy artwork Year-by-year history of the human genome assembly (5Mb bins) by Martin Krzywinski
MY DATA + SCIENCE ART ON A WALL | Let's talk genomes and what makes us. (buy artwork / see all my art)

1 · History of the human genome assembly — year by year

These are based on the Scientific American Graphic Science illustration, which used 1,000,000 base regions. The mitochondrial chromosome is not shown because it is much smaller (16,569 bases) than a region.

how big are things on the image?

Imperial units
If the poster is printed at 24" × 24" then the scale is 0.24" per 10,000,000 bases and the total length of all chromosomes is 74" or 6.2'.
SI units
If the poster is printed at 50 cm × 50 cm, the scale is 0.49 cm per 10,000,000 bases and the total length of all chromosomes is 154.2 cm or 1.54 m.

1.1 · in 1,000,000 base regions

History of the Human Genome Assembly (22 years, 3,117,275,501 bases and 0 gaps later) -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
THE HISTORY OF THE HUMAN GENOME ASSEMBLY — YEAR BY YEAR | Each chromosome is divided into 1,000,000 base regions, colored to indicate when the region reached 50, 90 or 99%+ completion. Completion from previous years is carried over in grey. Chromosomes 1–22, X and Y are shown. Mitochondrial chromosome is not shown. (BUY ARTWORK)

1.2 · in 250,000 base regions

History of the Human Genome Assembly (22 years, 3,117,275,501 bases and 0 gaps later) -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
THE HISTORY OF THE HUMAN GENOME ASSEMBLY — YEAR BY YEAR | Each chromosome is divided into 250,000 base regions, colored to indicate when the region reached 50, 90 or 99%+ completion. Completion from previous years is carried over in grey. Chromosomes 1–22, X and Y are shown. Mitochondrial chromosome is not shown. (BUY ARTWORK)

1.3 · in 5,000,000 base regions

History of the Human Genome Assembly (22 years, 3,117,275,501 bases and 0 gaps later) -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
THE HISTORY OF THE HUMAN GENOME ASSEMBLY — YEAR BY YEAR | Each chromosome is divided into 5,000,000 base regions, colored to indicate when the region reached 50, 90 or 99%+ completion. Completion from previous years is carried over in grey. Chromosomes 1–22, X and Y are shown. Mitochondrial chromosome is not shown. (BUY ARTWORK)
See how much you can see with my modern interpretation of the Snellen eye chart. Test yourself with mathematical operators, physical constants, chemical elements and nautical flags. There's even a version for the sightless.
The charts use my SnellenMK optotype font.

2 · History of the human genome assembly — when was it completed?

buy artwork History of the human genome assembly (250kb bins) by Martin Krzywinski
MY DATA + SCIENCE ART ON A WALL | Let's talk genomes and what makes us. (buy artwork / see all my art)

how big are things on the image?

Imperial units
If the poster is printed at 24" × 24" then the scale is 0.41" per 1,000,000 bases and the total length of all chromosomes is 1,272.4" or 106.0'.
SI units
If the poster is printed at 50 cm × 50 cm, the scale is 0.85 cm per 1,000,000 bases and the total length of all chromosomes is 2,650.7 cm or 26.51 m.

2.1 · in 50,000 base regions

History of the Human Genome Assembly (22 years, 3,117,275,501 bases and 0 gaps later) -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
THE HISTORY OF THE HUMAN GENOME ASSEMBLY — WHEN WAS IT COMPLETED? | The human genome is shown chromosome by chromosome (1—22, X, Y), with color representing the assembly version in which each 50,000 base region reached 99%+ completion. The mitochondrial chromosome is not shown. (BUY ARTWORK)

2.2 · in 250,000 base regions

History of the Human Genome Assembly (22 years, 3,117,275,501 bases and 0 gaps later) -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
THE HISTORY OF THE HUMAN GENOME ASSEMBLY — WHEN WAS IT COMPLETED? | The human genome is shown chromosome by chromosome (1—22, X, Y), with color representing the assembly version in which each 250,000 base region reached 99%+ completion. The mitochondrial chromosome is not shown. (BUY ARTWORK)

3 · Structure of the Dec 2013 hg38 human genome assembly

buy artwork Gap size and location in hg38 human genome assembly by Martin Krzywinski
MY DATA + SCIENCE ART ON A WALL | Let's talk genomes and what makes us. (buy artwork / see all my art)

how big are things on the image?

Imperial units
If the poster is printed at 24" × 24" then the scale is 0.28" per 1,000,000 bases and the total length of all chromosomes is 859.1" or 71.6'.
SI units
If the poster is printed at 50 cm × 50 cm, the scale is 0.57 cm per 1,000,000 bases and the total length of all chromosomes is 1,789.8 cm or 17.90 m.
History of the Human Genome Assembly (22 years, 3,117,275,501 bases and 0 gaps later) -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
FILLING IN THE GAPS | Before the March 2022 telomere-to-telomere assembly, the most recent humang enome assembly was from 2013 (hg38). This assembly had 1,001 gaps in chromosomes 1–22, X and Y. This panel shows the size, location and distribution of these gaps. To make small regions visible, those smaller than 230 kb are shown at a fixed size. The mitochondrial chromosome is included in the image and includes a single gap. (BUY ARTWORK)
History of the Human Genome Assembly (22 years, 3,117,275,501 bases and 0 gaps later) -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
FILLING IN THE GAPS | Before the March 2022 telomere-to-telomere assembly, the most recent humang enome assembly was from 2013 (hg38). This assembly had 1,001 gaps in chromosomes 1–22, X and Y. This panel shows the size, location and distribution of these gaps. To make small regions visible, those smaller than 230 kb are shown at a fixed size. The mitochondrial chromosome is included in the image and includes a single gap. (BUY ARTWORK)
See how much you can see with my modern interpretation of the Snellen eye chart. Test yourself with mathematical operators, physical constants, chemical elements and nautical flags. There's even a version for the sightless.
The charts use my SnellenMK optotype font.

4 · Chromosome spirals — sequence length in CHM13v2

buy artwork Chromosome spirals (CHM13v2 human genome assembly) by Martin Krzywinski
MY DATA + SCIENCE ART ON A WALL | Let's talk genomes and what makes us. (buy artwork / see all my art)
buy artwork Chromosome spirals (CHM13v2 human genome assembly) by Martin Krzywinski
MY DATA + SCIENCE ART ON A WALL | Let's talk genomes and what makes us. (buy artwork / see all my art)

These posters are based on a design I made for the 20th anniversary of Canada's Michael Smith Genome Sciences Center, but with chromosome lengths updated to the CHM13v2 (Mar 2022) assembly.

how big are things on the image?

Imperial units
If the poster is printed at 24" × 24" then the scale is 0.46" per 1,000,000 bases and the total length of all spirals is 1,428.3" or 119.0'.
SI units
If the poster is printed at 50 cm × 50 cm, the scale is 0.95 cm per 1,000,000 bases and the total length of all spirals is 2,975.6 cm or 29.76 m.
History of the Human Genome Assembly (22 years, 3,117,275,501 bases and 0 gaps later) -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Human chromosomes 1–22, X, Y and M are shown as spirals, whose length corresponds to the number of bases (A, T, G, or C) in their sequence in the first gapless telomere-to-telomere assembly of the human genome (CHM13v2, March 2022). (BUY ARTWORK)
History of the Human Genome Assembly (22 years, 3,117,275,501 bases and 0 gaps later) -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Human chromosomes 1–22, X, Y and M are shown as spirals, whose length corresponds to the number of bases (A, T, G, or C) in their sequence in the first gapless telomere-to-telomere assembly of the human genome (CHM13v2, March 2022). (BUY ARTWORK)
news + thoughts

Convolutional neural networks

Thu 17-08-2023

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:.

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.


© 1999–2023 Martin Krzywinski | contact | Canada's Michael Smith Genome Sciences CentreBC Cancer Research CenterBC CancerPHSA