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20 imperatives of information design — BioVis 2012

Circos on Cancer Discovery Covers

The July 2013 issue cover shows a Circos plot of relative copy number changes in 38 oral squamous cell carcinoma tumors.

The September 2012 issue cover shows a collection of Circos images of somatic mutations in melanoma tumors.

July 2013 Pickering CR, Zhang J, Yoo SY et al. 2013 Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers Cancer discovery 3:770-781.

Sep 2012 Dahlman KB, Xia J, Hutchinson K et al. 2012 BRAF(L597) mutations in melanoma are associated with sensitivity to MEK inhibitors Cancer discovery 2:791-797.

Circos charts the placenta transcriptome

Saben et al. use Circos to visualize the transcriptome and gene expression of placenta from 20 healthy women in their article A comprehensive analysis of the human placenta transcriptome.

Saben J, Zhong Y, McKelvey S et al. 2014 A comprehensive analysis of the human placenta transcriptome Placenta 35:125-131.

Circos on cover of UCSF Magazine

The Fall 2013 issue of UCSF Magazine has my Circos illustration of personalized medicine. The human outline motif is incorporated into other design elements in the issue.

The look of the image is inspired after Nature's Encode cover by Carl De Torres.

To learn how to generate the cover and variants, read the Circos Encode Cover Tutorial.

Circos on Cover of Biotechnology Focus

Circos appears on the cover of the Dec 2012 / Jan 2013 issue of Biotechnology Focus, a magazine about the Life Sciences sector in Canada.

The image is part of an article about epigenomics, which includes other graphics work I've done for the Genome Sciences Center.

"One of the biggest breakthroughs so far in the war on cancer was the realization that it is essentially a genetic disease. However, as we learn more about cancer, it becomes clearer that what’s written in our DNA is only part of the story; there are other factors at work that go beyond genetics."

Circos on Cover of Cancer Cell

Yang et al. used network analysis approaches characterize a subtype of ovarian cancer associated with poor overall survival.

E-cadherin is a protein encoded by the CDH1 gene and is responsible for cell-cell adhesion. Yang linked the expression of E-cadherin to specific miRNAs that influenced the regulatory network singled out in this cancer subtype.

Yang D, Sun Y, Hu L et al. 2013 Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer Cancer cell 23:186-199

Circos Round — Lotus Sacred

The pleasing roundness of Circos is used by Ming et al. to depict the Sacred Lotus genome in the publication "Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).

The Sacred lotus has religious significance in both Buddhism and Hinduism and has been used as a food and herbal medicine product in Asia for over 7,000 years. Its seeds have exceptional longevity, remaining viable for as long as 1,300 years.

The plant is known for its exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan.

Ming R, Vanburen R, Liu Y et al. 2013 Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Genome Biol 14:R41.

Plants Love Circos

Circos frequently appears in plant literature, twice on the cover of Plant Biotechnology Journal in the last year.

Rai KM, Singh SK, Bhardwaj A et al. 2013 Large-scale resource development in Gossypium hirsutum L. by 454 sequencing of genic-enriched libraries from six diverse genotypes Plant biotechnology journal

Bekele WA, Wieckhorst S, Friedt W et al. 2013 High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array Plant biotechnology journal

Circos has appeared 8 times each in the Plant Journal and Plant Cell.

Circos on the Cover Of Journal of Pathology

The June 2013 issue of the Journal of Pathology features a pair of Circos plots on the cover. The images are from the paper by Weier et al. describing TMPRSS2 and ERG rearrangements in prostate cancer.

"TMPRSS2–ERG rearrangements occur in approximately 50% of prostate cancers and therefore represent one of the most frequently observed structural rearrangements in all cancers."

Weier C, Haffner MC, Mosbruger T et al. 2013 Nucleotide resolution analysis of TMPRSS2 and ERG rearrangements in prostate cancer J Pathol 230:174-183.

Circos on the Cover Of Nature's Asian Journal of Andrology

The May 2013 Special Issue of Asian Journal of Andrology presents the outcomes from the Sixth Annual Forum on Prostate Disease (6th FPD), which was held on June 8-9, 2012 in Shanghai, China [source: nature.com]. The cover art for the issue shows a Circos plot of 90 significantly recurrent molecular alterations in prostate cancer from an analysis of 372 prostate tumors discussed in the Wyatt et al. review article.

The review summarizes the current state of understanding of prostate cancer, "including the sentinel role of copy number variation, the growing spectrum of oncogenic fusion genes, the potential influence of chromothripsis, and breakthroughs in defining mutation-associated subtypes. Increasing evidence suggests that genomic lesions frequently converge on specific cellular functions and signalling pathways, yet recurrent gene aberration appears rare".

Wyatt AW, Mo F, Wang Y et al. 2013 The diverse heterogeneity of molecular alterations in prostate cancer identified through next-generation sequencing Asian J Androl 15:301-308.

Brain Volume in Epilepsy

Pardoe et al. find that "Sodium valproate use in epilepsy is associated with parietal lobe thinning, reduced total brain volume, and reduced white matter volume."

The cover image shows antiepileptic drug combinations in intractable focal epilepsy cases. Linked drugs were being taken concurrently by an individual. Valproate cases are highlighted in orange.

Pardoe, HR, Berg, AT, and Jackson, GD 2013Sodium valproate use is associated with reduced parietal lobe thickness and brain volume Neurology 80(20):1895-1900.

Trends in Genetics Cover

Circos-based illustrator designed for the cover of Trends in Genetics human genetics special issue (Trends in Genetics October 2012, 28 (10)).

Read about how it was made.

Circle of Cancer

This Circos depiction of a tumor genome provides the cover of 30 November 2011 Science's Transitional Medicine issue in which Roychowdhury et al. describe personalized treatment for patients with colorectal and prostate cancer. By quickly sequencing normal and tumor DNA and RNA, suitable therapies can be tailored for the specific mutations identified.

1Roychowdhury S, Iyer MK, Robinson DR et al. 2011 Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study Science Translational Medicine 3:111ra121.

Visualization of Time-Oriented Data

Circos appears in Visualization of Time-Oriented Data, part of the Human–Computer Interaction Series.

Aigner W, Miksch S, Schumann H et al. 2011 Visualization of Time-Oriented Data Springer-Verlag New York Inc

Circos Helps Universal Knowledge

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

Circos Used in a David Cronenberg project about

In collaboration with Volumina, Circos was used to generate illustrations for Chromosomes exhibition, which toured in Rome, Turin and Lisbon.

Chromosomes is a David Cronenberg project which presents 70 images from his films, each accompanied by a text piece written by people from the world of art and science. I had the opportunity to contribute text to accompany the red bathtub photo.

The artbook is available for sale.

Little Fly, Thy Summer's Play...

In a collaboration with Derek Baccus from Pearson Science, Martin Krzywinski designed the cover illustration for the 3rd edition of iGenetics by Peter Russell.

The cover image shows a comparison of human and fruit fly genomes. The links indicate orthologous genes — genes in both genomes whose proteins are similar.

This cover won the cover award at 39th Annual 2009 Bookbuilders West Book Show.

Circos Takes a Train Ride

A Circos visualization is included as part of the Science Express project.

A public education effort lead by Max Planck institute, Science Express is a 13 car train, lavishly repurposed into a rolling interactive science exhibition. The purpose of the project is to raise and foster science awareness and education to the public.

A virtual tour is available. Exhibition was designed by Archimedes.

Circos Appears on the Cover of Nature Biotechnology

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.

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

Oxford Biology Uses Circos for Book Cover

A Circos image designed by Martin Krzywinski appears on the cover of Building Bioformatics Solutions with Perl, R and MySQL by Conrad Bessant, Ian Shadforth, and Darren Oakley (Oxford Press).

Circos on The Embo Journal Cover

The Embo journal chooses a Circos image by Martin Krzywinski for its 6 May 2009 cover.

The image shows sequence similarity between human, chimp, mouse and zebrafish and is part of a poster that provides a visual tour of Circos.

Circos is a Bioinformatics Visualization Archetype

The Harvard School of Public Health uses a Circos image on its Bioinformatics Core Strategy Document.

The cover of the report shows three images that represent (a) raw data (genetic sequence), (b) computing resources to transmit and analyze the data (a network switch) and (c) summary and presentation of analysis (a Circos image).

My images created with Circos have appeared in Wired, New York Times, Conde Nast Portfolio, and American Scientist as well as on book covers (iGenetics, Building Bioinformatics Solutions).

In genomics, scientific journals like Science, Nature, PLoS, Genome Research, Plant Cell and Genome Biology have published papers that used Circos images (Circos citations).

14 Apr 2010 |
1Ledford H 2010 Big science: The cancer genome challenge Nature 464:972-974.

Wired

Circos in Wired, illustrating relationships between characters on Lost TV series. (950 x 519)
22 April 2010 | In collaboration with Wired, I created an infographic that illustrates the relationship between characters on the TV show Lost. The image appears in the April 2010 issue of Wired.

New York Times

Circos in the New York Times illustrating epigenetic data. (300 x 486)
11 Nov 2008 | In collaboration with Jonathan Corum from the NYT, Martin Krzywinski created an illustration of data showing methylation on chromosome 22 in a variety of tissues. The illustration accompanies the article Now: The Rest of the Genome, by Carl Zimmer (graphic).
Circos in the New York Times illustrating how genomes are compared. (300 x 486)
22 Jan 2007 | Working with David Constantine, this figure introduced NYT readers to Circos and how genomes are compared (graphic).
Circos in the New York Times illustrating the dynamics of debates. (300 x 486)
15 Dec 2007 | Circos first appeared in the New York Times in a String of Debates infographic, designed by Jonathan Corum. Jonathan discusses how he used Circos in creating the image (full article graphic interactive graphic)

Conde Nast Portfolio

Circos in Conde Nast Portfolio accompanies an article about personalized genome sequencing. (800 x 599)
15 Oct 2007 | Working with John Grimwade, I designed this image to illustrates genomic variation, self-similarity and gene position, relevant characteristics to the accompanying article about 23andMe article interactive graphic.

Covers

2 Oct 2008 | In a collaboration with Derek Baccus from Pearson Science, I designed a cover illustration for the 3rd edition of iGenetics by Peter Russell. This cover won the cover award at 39th Annual 2009 Bookbuilders West Book Show.
13 May 2009 | The image from my Circos Visual Guide Poster was used for the cover of the Embo Journal
9 Aug 2007 | I designed an image for the cover of the American Scientist to accompany an article about dog genetics by Elaine Ostrander (read more).
Article by Cho et al about E coli genome uses a Circos image, which makes it to the cover of Nature Biotechnology. (300 x 410)
3 Nov 2009 | The cover of Nature Biotechnology uses a Circos image that appears in a paper about the genome of E. coli.
Circos used for illustrating Chromosomes - an art book featuring stills from movies by David Cronenberg (300 x 410)
10 Dec 2008 | Working with Domenico De Gaetano from Volumina, I created illustrations for Chromosomes, an exhibition and art book about films of David Cronenberg.
Oxford Biology uses a Circos image for the cover of Building Bioinformatics Solutions (300 x 410)
1 Dec 2008 | I initially designed the image as an example of the capabilities of Circos. It was eventuall picked up by the Science Photo Library and subsequently used by Oxford Press.
Circos on the cover of Designing Universal Knowledge (300 x 410)
7 Jan 2009 | Gerlinde Schuller used the image that previously appeared in the New York Times on the cover of her Designing Universal Knowledge.
Circos on the cover of Report on Business (300 x 410)
13 Jan 2011 | A circular visualization layout proves useful to relate companies to job perks.
Scanning Fetal DNA. During pregnancy, a fetus releases its DNA as short fragments into the blood of its mother. (310 x 427)
8 Dec 2010 | Scanning Fetal DNA. During pregnancy, a fetus releases its DNA as short fragments into the blood of its mother.

Advertising

Circos in a Deutsche Post DHL Ad (900 x 410)
22 July 2010 | The figure shows international connections serviced by DHL.

Popular Science

Circos in SFU AQ Magazine (900 x 621)
April 2011 | A Circos image accompanies my photos of our laboratory and computer equipment in SFU's biannual AQ Magazine.

Urban Planning

Urban Planning strategy for Caceres, Spain. (900 x 783)
17 Jan 2011 | The town of Caceres, Spain, a UNESCO World Heritage Site, used Circos to illustrate the relationships between businesses in their urban planning strategy.