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circos

data viewer with comparative genomics in mind

martin krzywinski

Click on an image to view next image. Download presentation as pdf png jpg pptx ppt. More about Circos. Circos - data viewer - introduction - page 1 Circos - data viewer - introduction - page 2 Circos - data viewer - introduction - page 3 Circos - data viewer - introduction - page 4 Circos - data viewer - introduction - page 5 Circos - data viewer - introduction - page 6 Circos - data viewer - introduction - page 7 Circos - data viewer - introduction - page 8 Circos - data viewer - introduction - page 9 Circos - data viewer - introduction - page 10 Circos - data viewer - introduction - page 11 Circos - data viewer - introduction - page 12 Circos - data viewer - introduction - page 13 Circos - data viewer - introduction - page 14 Circos - data viewer - introduction - page 15 Circos - data viewer - introduction - page 16 Circos - data viewer - introduction - page 17 Circos - data viewer - introduction - page 18 Circos - data viewer - introduction - page 19 Circos - data viewer - introduction - page 20 Circos - data viewer - introduction - page 21 Circos - data viewer - introduction - page 22 Circos - data viewer - introduction - page 23 Circos - data viewer - introduction - page 24 Circos - data viewer - introduction - page 25 Circos - data viewer - introduction - page 26 Circos - data viewer - introduction - page 27 Circos - data viewer - introduction - page 28 Circos - data viewer - introduction - page 29 Circos - data viewer - introduction - page 30 Circos - data viewer - introduction - page 31 Circos - data viewer - introduction - page 32 Circos - data viewer - introduction - page 33 Circos - data viewer - introduction - page 34 Circos - data viewer - introduction - page 35 Circos - data viewer - introduction - page 36 Circos - data viewer - introduction - page 37 Circos - data viewer - introduction - page 38 Circos - data viewer - introduction - page 39 Circos - data viewer - introduction - page 40 Circos - data viewer - introduction - page 41 Circos - data viewer - introduction - page 42 Circos - data viewer - introduction - page 43 Circos - data viewer - introduction - page 44 Circos - data viewer - introduction - page 45 Circos - data viewer - introduction - page 46 Circos - data viewer - introduction - page 47 Circos - data viewer - introduction - page 48 Circos - data viewer - introduction - page 49 Circos - data viewer - introduction - page 50 Circos - data viewer - introduction - page 51 Circos - data viewer - introduction - page 52 Circos - data viewer - introduction - page 53 Circos - data viewer - introduction - page 54

news + thoughts

Neural network primer

Mon 06-02-2023

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.

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

Mon 21-11-2022

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.

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.

Gene Cultures exhibit — art at the MIT Museum

Tue 25-10-2022

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
My art at the MIT Museum Gene Cultures exhibit tells shows the scale and structure of the human genome. Pay no attention to the pink chicken.

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