Working with Senior Graphics Editor Jen Christiansen, Senior Editors Mark Fischetti and Clara Moskowitz, I have designed these Graphic Science visualizations for Scientific American.
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
text by Clara Moskowitz | graphic by Martin Krzywinski
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
How COVID-19 spread like wildfire
Mutations in the SARS-Cov-2 virus reveal the story.
Scientific American June 2020, volume 322 issue 6
text by Mark Fischetti | graphic by Martin Krzywinski
Source
Interested in more COVID-19 and SARS-Cov-2 graphics? Check out my projects below.
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
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.
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
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)
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
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.
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
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.
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
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)".
A: Yes.
source
Convolutional neural networks
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).
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
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.
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
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.
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.
Science Advances cover
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.
Kijima, Y. et al. A universal sequencing read interpreter (2023) Science Advances 9.
Browse my gallery of cover designs.
Regression modeling of time-to-event data with censoring
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).
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
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
The video recently premiered on YouTube.
Renders of the full scene are available as NFTs.
Gene Cultures exhibit — art at the MIT Museum
I am more than my genome and my genome is more than me.
The MIT Museum reopened at its new location on 2nd October 2022. The new Gene Cultures exhibit featured my visualization of the human genome, which walks through the size and organization of the genome and some of the important structures.
Annals of Oncology cover
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.
Pleasance E et al. Whole-genome and transcriptome analysis enhances precision cancer treatment options (2022) Annals of Oncology 33:939–949.
Browse my gallery of cover designs.
