π Daylatest newsbuy art
Twenty — minutes — maybe — more.Naomichoose four wordsmore quotes
very clickable
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
Year-by-year history of the human genome assembly (250kb bins) 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)

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)
I created a font to encode genomic sequence on the wayfinding signs in my DNA on 10th public art project. Download the font it and make your own creations.

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

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)
Martin Krzywinski | contact | Canada's Michael Smith Genome Sciences CentreBC Cancer Research CenterBC CancerPHSA
Google whack “vicissitudinal corporealization”
{ 10.9.234.151 }