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Circos at the EMBO NGS workshop in Tunis, Sept 15–25.

The terrifying dinosaur corn genome

Amblin Entertainment and Legendary Pictures, the studios that produced Jurrasic World, try to inject genome science into the movie. Unfortunately, since we don't quite know how to construct viable genomes of extinct species, much less grow the creatures themselves, we don't know whether the depiction of the science is right. Perhaps theirs is exactly what a genome lab would look like in a dino-building facility.

But, we can get fewer things wrong. In the Creation Lab companion website, a Circos image is used to illustrate a triceratops genome.

Unfortunately, this is an image of the B73 Maize reference genome (B73 RefGen_v1), as published in Nature's The B73 Maize Genome: Complexity, Diversity, and Dynamics.

Schnable PS Ware D Fulton RS et al. 2009 The B73 maize genome: complexity, diversity, and dynamics Science 326 (5956) 1112-1115

Using News Reports to Track Wildlife Black Markets

http://www.wired.com/2015/06/using-news-reports-track-wildlife-black-markets/

THE INTERNATIONAL BLACK market in wildlife—alive or dead—is notoriously difficult to track. Hunters and smugglers don’t report their take for the same reasons that drug dealers don’t report profits to the IRS. But if you could actually track those networks, maybe you could do something about them. That’s what sent Nikkita Patel, a veterinary epidemiologist at the University of Pennsylvania, to an unusual source of data on the illegal wildlife trade: the news.

Wired

The image shows the illegal global rhinoceros trade network before (top) and after (bottom) a hypothetical targeted disruption. Created with Circos online table viewer.

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 Maps America’s Restless Interstate Migration Without a Map

Wired has a writeup about migration patterns within the US that shows the data using d3.js chord diagrams, modeled after how Circos shows tabular data.

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 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 reaches 500 literature citations

In October 2013 Circos reached a milestone - 500 citations in peer-reviewed literature.

To celebrate, I've made a commemorative poster that features over 400 Circos images from the literature.

citation list | image gallery | press highlights

Circos deals with 8 Gb Rye Genome

Because of its large 8 Gb genome, the genomic analysis of rye has lagged behind other cereals.

To address this, Martis et al. eastablished a linear gene order model for 72% of the rye genes based on synteny information from rice, sorghum and B. distachyon.

Although it appears that six major translocations shaped the modern rye genome, highly dissimilar conserved syntenic gene content, gene sequence diversity signatures, and phylogenetic networks were found for individual rye syntenic blocks.

Martis MM, Zhou R, Haseneyer G et al. 2013 Reticulate Evolution of the Rye Genome Plant Cell

Circos Stages Mesolithic to Neolithic Transition

Bollongino et al. present evidence of a slow transition between Mesolithic hunter-gatherer groups to Neolithic farmers.

Previous theories that the foragers disappeared shortly after the arrival of farmers are at odds with palaeogenetic and isotopic data analysis from Neolithic human skeletons from the Blätterhöhle burial site in Germany. Instead of an abrupt transition, the data suggest a more complex pattern of coexistence that persisted for over 2000 years.

Bollongino R, Nehlich O, Richards MP et al. 2013 2000 years of parallel societies in Stone Age Central Europe Science 342:479-481.

Circos in 54 million pixels

Ruddle et al. demonstrate their commodity hardware 54 million pixel data display in exploring copy number variation data.

Ruddle RA, Fateen W, Treanor Det al.. 2013. Leveraging Wall-sized High-Resolution Displays for Comparative Genomics Analyses of Copy Number Variation. In IEEE Symposium on Biological Data Visualization, Atlanta, GA.

Circos Tracks CO2 Emissions

Kanemoto et al. report on the disturbing trend of emissions leakage, in which developing countries are displacing emissions intensive production offshore.

The report confirms previous findings that adjusting for trade, developed countries emissions have increased, not decreased. A connection is made to the kind of emissions displacement that has already occurred for air pollution, where despite aggressive legislation in major emitters total global air pollution emissions have increased.

The conclusion warns us that "if regulatory policies do not account for embodied imports, global emissions are likely to rise even if developed countries emitters enforce strong national emissions targets."

Kanemoto K, Moran D, Lenzen M et al. 2013 International trade undermines national emission reduction targets: New evidence from air pollution Global Environmental Change

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.

6.9e11 g of oil and Circos was there

Rivers et a. describe the effects of the Deepwater Horizon blowout on the microbial blooms of petroleum-degrading bacteria.

By sequencing 66 million community transcripts, the identity of metabolically active microbes and their roles in petroleum consumption was revealed.

Rivers AR, Sharma S, Tringe SG et al. 2013 Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill The ISME journal

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 for R

Zhang et al. implement Circos in R.

Same round shape you expect. And now, in everyone's favourite open source statistics and data analysis environment.

CRAN RCircos package

Zhang H, Meltzer P, Davis S 2013 RCircos: an R package for Circos 2D track plots BMC Bioinformatics 14:244.

Circos Interchange Diagrams — Networks and Flow

Zeng et al. introduce a new type of visualization based on Circos, the interchange diagram, in their paper Visualizing Interchange Patterns in Massive Movement Data.

The design is applied to displaying movement data, such as daily trips made by passengers in a city. By incorporating interactivity, this visualization method is helpful to understand interchange patterns at different spatial (between trains, between cities) and time scales (different times of day).

Circos has been used for urban planning before. The town of Caceres in Spain has used Circos to communicate their urban planning strategy.

project website

Zeng W, Fu C-W, Arisona SM et al. 2013 Visualizing Interchange Patterns in Massive Movement Data Computer Graphics Forum 32:271-280

Circos connects to the connectome

Methods to visualize the connectome are reviewed in Craddock et al — Circos is one of them.

Craddock RC, Jbabdi S, Yan C-G et al. 2013 Imaging human connectomes at the macroscale Nat Meth 10:524-539.

The use of Circos for showing the connectome was introduced by Irimia et al. in Circular representation of human cortical networks for subject and population-level connectomic visualization.

A good layman description of the work can be found at the neurosceptic blog.

Irimia A, Chambers MC, Torgerson CM et al. 2012 Circular representation of human cortical networks for subject and population-level connectomic visualization NeuroImage, Irimia A, Chambers MC, Torgerson CM et al. 2012 Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury Frontiers in Neurology 3

Circos is the Method for Visualizing Translocations

Genomic rearrangements can cause disease and are implicated in many cancers. Being able to see the patterns in these changes across samples and patients is important.

In the review article End-joining, Translocations and Cancer, Bunting and Nussenzweig demonstrate how compositing the genome circularly adds value and clarity to the presentation.

Bunting SF, Nussenzweig A 2013 End-joining, translocations and cancer Nat Rev Cancer

Circos Paints Chromosomes of Capsella Rubella

Slotte et al. use Circos to show the genomic structures, chromosome painting and comparative genomic mapping in C. rubella, A. lyrata and A. thaliana.

Their figure illustrates how Circos is effective at showing two-way comparisons of syntenic structure. For three-way comparison, consider hive plots.

Slotte T, Hazzouri KM, Agren JA et al. 2013 The Capsella rubella genome and the genomic consequences of rapid mating system evolution Nat Genet

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.

For other references to Circos usage and items of note, see examples of published images and Circos citations.

News



11 February 2014

I just discovered a couple of Circos cover appearances in Cancer Discovery Journal.

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.

Circos - Circular Genome Data Visualization (567 x 458)

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.

Circos - Circular Genome Data Visualization (567 x 456)

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.

11 February 2014

Circos appears on the cover of Feb 2014 issue of Placenta Journal.

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

Circos - Circular Genome Data Visualization (530 x 300)
22 November 2013

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 image and design in Fall 2013 issue of UCSF magazine (702 x 813)
Circos image and design in Fall 2013 issue of UCSF magazine
31 October 2013

Circos reaches a milestone - 500 citations in peer-reviewed literature. To celebrate, I've made a commemorative poster that features over 400 Circos images from the literature.

citation list | image gallery | press highlights

Circos poster - 500 citations (400 x 517)
Circos reaches 500 citations in scientific literature.
30 October 2013

Boo! Circos appears on the cover of the Genome Informatics 2013 conference. The image is taken from Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) by Ming et al..

I had the opportunity to design the cover for the conference a few years back. The Genome Informatics 2010 cover showed a unique depiction of gene sequences mentioned in the abstract book.

Circos poster - 500 citations (300 x 474)
Circos on the cover of Genome Informatics 2013 program cover.
8 March 2013

In their 2012-2013 Global Market Forecast, Airbus uses a figure created by the Circos table viewer to visualize global migration patterns.

The image was originally generated by the UN Population division.

Region definition according to United Nations; Asia including Oceania, countries of the Middle East and countries of CIS, Europe including Russia. Source: United Nations Population division, International Migrant Stock

Circos in Airbus 2012-2013 Global Market Forecast. (600 x 415)
8 March 2013

Circos appears on the cover of February 2013 issue of Genome Biology and Evolution. The image is taken from the paper

1Ahmed I, Biggs PJ, Matthews PJ et al. 2012 Mutational dynamics of aroid chloroplast genomes Genome Biol Evol 4:1316-1323.
Circos on the cover of Genome Biology and Evolution. (268 x 347)
1 January 2013

Circos appears on the cover of Jan 2013 issue of Biotechnology Focus in an article about epigenetics.

Circos - Circular Genome Data Visualization (317 x 428)
1 January 2013

Circos appears on the cover of Nature Review's 2013 Cancer Calendar in the form of a figure taken from

Shih AH, Abdel-Wahab O, Patel JP et al. 2012 The role of mutations in epigenetic regulators in myeloid malignancies Nat Rev Cancer 12:599-612.

Nature Reviews recognizes the importance of clear and informative figures:

"Indeed, given the adage that 'a picture paints a thousand words', good figures can encapsulate entire fields of cancer research without the need for extensive explanations."

Circos - Circular Genome Data Visualization (400 x 357)
1 October 2012

Circos-based illustration 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.

Circos - Circular Genome Data Visualization (400 x 523)
3 May 2012

Scientific terminology. Longer, harder and more arcane. A Circos illustration accompanies the New York Times article ‘Ome,’ the Sound of the Scientific Universe Expanding.

The age of 'omes' is here. It began with the genome, continued with the proteome, branched out with the memome and reached full flowering with the notion of the omome.

This probably sounds like raw material for nonsense poetry, but it’s a real biological and linguistic trend that makes sense, once you get the idea of just what an 'ome' is.

Circos - Circular Genome Data Visualization (400 x 367)
29 April 2011

A Circos image appears as part of a spread in SFU's biannual AQ Magazine. The composite accompanies my photos of our laboratory and computer equipment.

The image was adapted from Figure 1 of our paper 1Jones SJ, Laskin J, Li YY et al. 2010 Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors Genome Biol 11:R82.

Circos in a spread in SFU
13 January 2011

Report on Business makes the connection between companies and perks in their January 2011 issue.

Circos on the cover of Report on Business (300 x 410)
8 December 2010

A Circos figure appears on the cover of Science Translational Medicine. I'm very happy to report that with this cover, Circos has appeared on the covers of both Nature and Science publications, the world's two top scientific journals.

Circos on the cover of Science Translational Medicine (310 x 427)
22 July 2010

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

Deutsche Post DHL uses Circos. (315 x 400)
5 May 2010

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.

Circos - Circular Genome Data Visualization (900 x 380)
28 April 2010

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.

Circos iGenetics book cover - recognized at the 39th annual Bookbuilders West Book Show (781 x 400)
14 April 2010

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.

Circos image in Nature - The Cancer Genome Challenge (969 x 431)
6Ledford H 2010 Big science: The cancer genome challenge Nature 464 (7291) 972-974.
12 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 22 April 2010 issue of Wired.

Circos - Circular Genome Data Visualization (800 x 424)
6 April 2010

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.

A book cover that I created with Circos has won the Bookbuilders West Cover Award (500 x 569)
2 April 2010

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.

Harvard School of Public Health - Bioinformatics Core Strategy Document (500 x 684)
1 March 2010

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.

Circos illustrates whole-genome epigenetic data (300 x 390)
Image from
24Costello JF, Krzywinski M, Marra MA 2009 A first look at entire human methylomes Nature biotechnology 27 (12) 1130-1132.
11 February 2010

Circos appears on the cover of Feb 11 2013 edition of Cancer Cell.

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 - Circular Genome Data Visualization (400 x 523)
11 January 2010

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

Circos - Circular Genome Data Visualization (600 x 441)

Circos - Circular Genome Data Visualization (600 x 472)
19 December 2009

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

Circos in Faces of Lupus II (1000 x 289)
3 November 2009

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.

Circos image in Nature Biotechnology - Escherichia Coli (300 x 395)
23Cho BK, Zengler K, Qiu Y et al. 2009 The transcription unit architecture of the Escherichia coli genome Nature biotechnology 27 (11) 1043-1049.
2 November 2009

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.

Circos - Circular Genome Data Visualization (600 x 600)

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..

9 September 2009

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.

Circos - Circular Genome Data Visualization (800 x 348)

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!

18 June 2009

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

Circos: an Information Aesthetic for Comparative Genomics. (971 x 240)
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.

13 May 2009

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.

Circos image on EMBO Journal cover (394 x 517)
Cover of The Embo Journal (6 May 2009, vol 28, no 9).
1 February 2009

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 in presentation by Adam Bly, Seed
7 January 2009

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

Circos - Circular Genome Data Visualization (765 x 457)
10 December 2008

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.

Chromosomes - David Cronenberg - by Volumina (600 x 793)
1 December 2008

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

Building Bioformatics Solutions (344 x 450)
11 November 2008

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.

New York Times - Circos - Mapping the Epigenome. (600 x 623)
15 October 2008

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

Circos in COSMIC (400 x 198)
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.
11 October 2008

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

Illustrations created with Circos used in Chromosomes, an exhibition by David Cronenberg. (500 x 508)

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

Illustrations created with Circos used in Chromosomes, an exhibition by David Cronenberg. (800 x 267)

We fear the unknown. Monsters and creatures are words we give to the most frightening unknown of all — the biological. Things living — primitive, unpredictable, ravenous and without recourse to emotion or reason. Clutching reason and humanity, we congratulate ourselves for having departed those base instincts.

But our departure is neither recent nor complete. Inside each of us is a history of our evolutionary ancestors, written in our chromosomes. The ant has 2. The house fly, 12. Humans have 46, a dog has 78 and in a fern, there are over 1,000. Chromosomes are the superblocks of genetic organization and heredity. They are an organism's contact list of its evolutionary ancestors.

Many of these ancestors were not different from monsters and creatures that inhabit our nightmares, our fears and our movies. And as the lights come on, and projections from the screen yield to reality, our body harbors elements from a darker past. Like the Alu genetic element, a jumping-gene which repeatedly copies itself within our genome and a constant companion to our evolution for the past 65 million years. In every part of every chromosome is our creature heritage.

Although we emerged in human from our mother's womb, as embryos we exhibited our evolutionary history: we all had gills, a tail, and body hair. Lost or absorbed before birth, these signposts remind us that our ancestors are inside us, not just in stories or movies. It is only later that the brain, our species' most prized possession, develops and transforms us. In the last minute, we pass into humanity and into the world. Today, we tell stories of monsters and creatures. Tomorrow, we may take their place. Distant from now, our progeny will see our forms during development and say "What creatures we were." Movies will frighten by showing our forms. "Look, mommy, a smooth-skinned biped with wide eyes."

2 October 2008

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

Circos book cover - iGenetics by Peter Russell, 3rd ed (331 x 450)
1 October 2008

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

Circos in Geo Magazine (688 x 447)
3 September 2008

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)

Circos - an information aesthetic for comparative genomics - presented at Genome Informatics 2008, Hinxton, UK (600 x 372)
2 September 2008

How about a visualization of a visualization?

A Circos wordle by Jonathan Feinberg (Cambridge/IBM) www.many-eyes.com (400 x 400)

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

5 August 2008

Circos gets a mention on Flowing Data.

Circos - Circular Genome Data Visualization (400 x 493)
12 June 2008

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

Circos - Circular Genome Data Visualization (150 x 184)

"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).

27 April 2008
15 December 2007

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.

Circos in New York Times - Naming Names (400 x 295)

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

Circos in New York Times - Naming Names (400 x 560)

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

9 October 2007

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

Circos in Conde Nast Portfolio (800 x 599)
9 August 2007

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 - Circular Genome Data Visualization (400 x 490)
23 November 2006

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

Circos in New York Times - Close up of the Genome, Species by Species by Species (400 x 370)
9 November 2006

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.

Circos - Circular Genome Data Visualization (400 x 400)
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.
10 August 2006

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 in SEED (483 x 600)
24 May 2005

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

Circos in Visual Complexity (500 x 366)