Deutsche Post DHL uses Circos in a printed advertisement for the Mail & Logistics Group

I've made a new website for Circos, and updated the site for the tableviewer.

On the new site, things should be easier to find and less ugly.

In 2008, I worked with Pearson publishers to create a cover for iGenetics (3rd ed) by Peter Russell. I just received a copy of the award won by the book's cover illustration.

Nature features an article by Heidi Ledford, The Cancer Genome Challenge, which uses Circos images from the COSMIC project to illustrate the landscape of structural variation in cancer.

Figure.

6Ledford H 2010 Big science: The cancer genome challenge Nature 464 (7291) 972-974.

In collaboration with Wired, I created an infographic that illustrates the relationship between characters on the TV show Lost.

The image appears in the 22 April 2010 issue of Wired.

Last year I collaborated with Derek Baccus from Pearson Science on a cover illustration for the 3rd edition of iGenetics by Peter Russell. I have just learned that this cover has won an award from Bookbuilders West.

Circos images are used as visual signposts for bioinformatics and biological data analysis. The image below appears on a strategy document from the Harvard School of Public Health.

In a technology feature, Epigenome: mapping in motion, Monya Baker describes the current state of epigenetics and the search for epigenetic biological markers (1Baker M 2010 Epigenome: Mapping in Motion Nature Methods 7 (3) 181-186.).

The feature cites an article I wrote with Costello and Marra about epigenetics A first look at entire human methylomes, that included a figure I designed to show the richness of whole-genome epigenetic data and its variation across tissues.

Figure. Image from

24Costello JF, Krzywinski M, Marra MA 2009 A first look at entire human methylomes Nature biotechnology 27 (12) 1130-1132.

I've received a copy of the beautiful book Expedition Zukunft/Science Express. I've written previously about this great science education project.

A Circos image appears in the video Faces of Lupus II prepared by Alex Bowles for the Alliance of Lupus Research.

An illustration of genome annotations of the E coli genome appears on the cover of Nature Biotechnology (vol 27, no 11). The image accompanies the article The transcription unit architecture of the Escherichia coli genome by Cho et al.

Figure.

23Cho BK, Zengler K, Qiu Y et al. 2009 The transcription unit architecture of the Escherichia coli genome Nature biotechnology 27 (11) 1043-1049.

I've just received news that the Chromosomes exhibition by David Cronenberg, which uses Circos illustrations and my contribution to text, will be staged in Estoril (Portugal) during the film festival.

The project also toured in Rome, Turin and Lisbon

The Film Festival of Estoril and Volumina are pleased to announce the new staging of multimedia exhibition CHROMOSOMES by David Cronenberg. During the opening (november, 10) will be present Cronenberg, that for a moment abandons the role of director (he is working on the new film 'The Matarese Circle') to present himself as artist. Inside the Congress Center of Estoril, from 5 to 14 november, you can admire the images chosen and processed by David Cronenberg and the Volumina staff starting with original film frames from his most famous movies: The Fly, Videodrome, The Dead Zone, Dead Ringers, Naked Lunch, Crash, Spider, and the recent Eastern Promises. The exhibition, curated by Domenico De Gaetano is completed by two 10-minute videos with famous sequences from Cronenberg's movies and a bilingual catalogue. One room is entirely dedicated to the installation RED CARS, in homage to the Ferrari, based on the artbook that was realized in 2005 and on rare archival footage..

I am delighted and honoured to have Circos visualizations included as part of the Science Express project. Briefly, this is a public education effort lead by Max Planck institute to raise and foster science awareness and education to the public. The project is a 13 car train, lavishly repurposed into a rolling interactive science exhibition.

For those of you who can't experience the project first-hand, there is a wonderful virtual tour.

The design firm behind the exhibition is Archimedes. Visually, the project is stunning. Each car has an entirely different feel, which matches closely to the subject matter. For example, the nanotechnology car is tiled with mirrors, to give you the sense that you're inside an infinite lattice. Brilliant!

I am a strong proponent in making the product and knowledge garnered by science visually appealing &mdash for the same reason that presentations to public audiences should be both informative and engaging. Nature offers intrinsic beauty, be it as seen through its complexity (e.g. genome as an information warehouse) or reducible simplicity (e.g. supersymmetry in fundamental physical laws). Frankly, we don't need more dry and hypnogogic presentations - the facts and knowledge are there and easily accessed (though often mind-numbingly difficult to understand). What we need are more project like Science Express to attract the public, and potential future scientists, to science, and thereby persuade them that trying to understand inherently difficult things is rewarding and ... fun!

Circos is published in Genome Research. The paper comes with an attractive foldout poster! To cite circos, please use

Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomes. Genome Res (2009) 19:1639-1645.

Download the Endnote reference

Figure. Figures 1, 2, 7 and 8 from Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomes. Genome Res (2009) 19:1639-1645.

ABSTRACT We created a visualization tool, called Circos, to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line and histogram plots, heat maps, tiles, connectors and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.

An image created by Circos appears on the cover of the EMBO Journal (6 May 2009, vol 28, no 9). The image is a crop of a comparison of 4 genomes (human, chimp, mouse and zebrafish) which is available at full resolution as part of a poster.

Figure. Cover of The Embo Journal (6 May 2009, vol 28, no 9).

Circos appears in presentation "Science as Lens" by Adam Bly, Seed's editor-in-chief. Adam writes "Science as a subject is extraordinary. There is no subject bigger, there is no subject more exciting, there's no subject changing our times more profoundly. Science as a lens is our future."

Circos appears in Designing Universal Knowledge (buy at Amazon), a compilation of infographic methods by Gerlinde Schuller.

I received my copy of the Chromosomes artbook by Volumina, for which I contributed genomic visualizations. Below are the scans of the front and the back of the book. David Cronenberg's son, Brandon Cronenberg, contributed his interpretation of chromosomes as machines of genetics - each page of the book has a unique chromosome interpretation in steam punk style.

Circos is on the cover of Building Bioformatics Solutions with Perl, R and MySQL by Conrad Bessant, Ian Shadforth, and Darren Oakley (Oxford Press).

Working with NYT's Jonathan Corum, I created an image for the science section of the New York Times, to accompany an article on epigenomics.

Circos is being used in the Catalogue of Somatic Mutations in Cancer (COSMIC) to show structural variation and copy number changes.

Figure.

27Forbes SA, Tang G, Bindal N et al. 2009 COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer Nucleic Acids Res 38 (Database issue) D652-657.

In collaboration with Volumina, Circos was used to generate illustrations for Chromosomes exhibition, an art book of still images from David Cronenberg films.

I had the opportunity to contribute not only the art work, but text for this book as well.

I worked with Pearson publishers to create a cover for iGenetics (3rd ed) by Peter Russell.

Circos images appear in the October 2008 issue of the German popular science magazine Geo.

A visual guide to Circos (Circos - an information aesthetic for comparative genomics) will be presented at the Genome Informatics meeting in Hinxton, UK (September 10-14, 2008). The guide presents some of the capabilities of Circos and its application in the field of comparative genomics and genome visualization.

Download: medium bitmap (7Mb) | huge bitmap (46Mb) | PDF (40Mb) | Illustrator (20Mb)

How about a visualization of a visualization?

Jonathan Feinberg (Cambridge/IBM) created this Circos wordle (zoom). Wordles are great, and just one of the ways to see data at many-eyes.

Circos gets a mention on Flowing Data.

American Scientist cover, which I created with Circos, wins Silver EXCEL Award in the Cover Illustration category from Society of National Association Publications (SNAP).

"The cover graphic is a dramatic visual representation of some of the chromosomal connections between the dog and human genomes," Schoonmaker said. "It helps readers understand how physical differences between dogs and humans, and between one dog and another, can be so large, even though they share much genetically." (more).

Circos is used in the Nature Genetics publication Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing by Peter J Campbell et al.

Circos appears in a New York Times graphic "Naming Names" in the US Politics Section. Jonathan discusses how he used Circos in creating the image.

A large infographic appears in the Sunday edition (16 Dec 2007).

Images were prepared by Jonathan Corum and Farhana Hossain (NYT).

An image created with Circos appears in the November issue of Conde Nast Portfolio, accompanying an article on personalized genome sequencing.

Circos is used in the Nature publication The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

Circos appears on the cover of American Scientist (Sept/Oct issue). The image accompanies the article Genetics and the Shape of Dogs by Elaine Ostrander. Read about the figure.

Circos appears in a New York Times graphic "Close up of the Genome, Species by Species by Species" in the NYT Science Section.

Circos used in Nature publication Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia by J.M. Aury et al. The image

This unusual, but effective, Circos image shows successive duplications in the Paramecium genome. The exterior circle displays all chromosome-sized scaffolds, and the three interior circles show the reconstructed sequences obtained by fusion of the paired sequences from each previous step.

Figure.

57Aury JM, Jaillon O, Duret L et al. 2006 Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia Nature 444 (7116) 171-178.

Circos appears in September 2006 issue of Seed Magazine. The image is part of Manuel Lima's article Look Around You: A Visual Exploration of Complex Networks. The image that shows the synteny between the mouse genome and human chromosome 1.

Circos is included in Visual Complexity. The page also links to Schemaball, an older project that uses circular layout to visualize database schemas.