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Circos is coming to the EMBO NGS workshop in Tunis, Sept 15–25.

Circos Mastheads

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 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 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 Times Mutations in Breast Cancer

Understanding how tumors evolve helps to identify the changes in the genome that are critical to tumor growth. Newman et al. reconstruct the likely history of a breast cancer genome in their article The Relative Timing of Mutations in a Breast Cancer Genome.

Through creative use of highlight and scatter tracks, their figure presents a circular Gantt chart of tumor progression.

Newman S, Howarth KD, Greenman CD et al. 2013 The relative timing of mutations in a breast cancer genome PLoS One 8:e64991

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.

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.

Improving miR-mRNA Predictions

Rijlaarsdam et al. describe an algorithm for improving miR-mRNA predictions.

"Algorithms predicting miR-mRNA interactions generate high numbers of possible interactions, many of which might be non-existent or irrelevant in a certain biological context. It is desirable to develop a transparent, user-friendly, unbiased tool to enrich miR-mRNA predictions."

Rijlaarsdam MA, Rijlaarsdam DJ, Gillis AJ et al. 2013 miMsg: a target enrichment algorithm for predicted miR-mRNA interactions based on relative ranking of matched expression data Bioinformatics

Dr. Tim Ley and Circos

The NYT article Cancers Share Gene Patterns, Studies Affirm, reports on the "most telling evidence yet that cancer will increasingly be seen as a disease defined primarily by its genetic fingerprint rather than just by the organ where it originated."

The photo (by Peter Newcomb for The New York Times) shows Dr. Tim Ley of Washington University in St. Louis with a Circos image on the desktop. "It certainly sets the stage for the next era of therapy."

The two studies referenced in the article are

The Cancer Genome Atlas Research Network 2013 Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia New England Journal of Medicine.

The Cancer Genome Atlas Research Network 2013 Integrated genomic characterization of endometrial carcinoma Nature 497:67-73.

Round is peachy

The International Peach Genome Initative has ensured that peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees.

"Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes."

No mention of fuzz is made.

Verde I, Abbott AG, Scalabrin S et al. 2013 The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution Nat Genet

Circos in Wired's Best Scientific Figures of 2012

Wired's Best Scientific Figures of 2012 includes an image created with Circos.

"Though it's long been assumed that each cell in a body contains the same basic genomic blueprint, research now suggests that genomes actually vary between cells in the same body. The figure comes from a study of copy number variation, in which stretches of DNA are repeated multiple times. In all 23 chromosomes (arrayed in radial form) researchers found copy number differences unique to each cell's physical origin (color coding). Brain cells, for example, had quite different genomes from lung cells."

O'Huallachain M, Karczewski KJ, Weissman SM et al. 2012 Extensive genetic variation in somatic human tissues Proc Natl Acad Sci U S A 109:18018-18023.

Circos swims with fish

Howe et al. report on the zebrafish reference genome.

"Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease."

Howe K, Clark MD, Torroja CF et al. 2013 The zebrafish reference genome sequence and its relationship to the human genome Nature

Circos Reveals Buzz in Hive NYC

Students at the Indiana University Information Visualization MOOC course used Circos to visualize the connections within the Hive NYC Learning Network, composed of 40 informal learning organizations, including museums, libraries and community-based organizations across New York City and stewarded by Mozilla.

The goal was "to show in what projects the different organizations are involved, what kind of work they do, and how they collaborate in projects over time."

Gloria Jimenez, Carmen Ng, Chantal Melser, Kristina Simacek, Maria Maza and Elwin Koster. Visualizing HiveNYC Where’s the buzz?

Airbus uses Circos to show migration patterns

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 represents cancer genome visualization for the 2013 EMBL Cancer Genomics conference

Circos has long been used by cancer genomic project like COSMIC and consortia like TCGA. The circle has become a visual motif for representing genomic alterations, recently appearing on the cover of the Nature Reviews Cancer 2013 Calendar.

Recently, Circos appeared on the conference poster of EMBL Cancer Genomics conference, held at the Advanced Training Center in Heidelberg, Germany.

Download poster.

Circos used in Visual Motif for 2013 International Symposium: Systems Biology & the Brain

Not just for genomics, Circos is used to show the connectome in publications associated with the 2013 International Symposium: Systems Biology & the Brain, held in Seattle.

Circos has been previously used to visualize the connectome to assess differences in brain injury in patients Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury in Frontiers in Neurotrauma. 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 on Cover of Nature Reviews Cancer Calendar 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 Art — Stained Glass Mosaics

Julie from Red Squirrel Mosaics recently created a piece inspired by Circos chord diagrams.

There is art in science!

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.

From Degree to Job — Circos Visualizes Workforce Transitions

Finding the relationship between a student's major and career field is the topic of "Measuring Transitions Into The Workforce As A Form Of Accountability". The diagrams connect the flow of students from one of 17 fields of study (left) to job sectors (right).

Schenk TL, Jr. 2011 Measuring Transitions into the Workforce as a Form of Accountability SSRN eLibrary ID 1831967

Satyan L Devadoss from Williams College performed a similar analysis of Impact of Major on Career Path for 15600 Williams College Alums.

Circos, Lung Cancer and Smoking

Imielinski et al. visualize mutations in the exome and genome sequences of 183 lung adenocarcinomas to reveal recurrent somatic mutations in the splicing factor gene U2AF1 and RBM10 and ARID1A, as well as EGFR and SIK2. Grouping the data revealed clusters that correlated with smoking history.

Imielinski M, Berger AH, Hammerman PS et al. 2012 Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing Cell 150:1107-1120.

Circos and Hive Plots describe regulatory networks

One of the first uses of Circos in the literature was to visualize the grapevine genome. Since then, Circos has gained popularity in the plant literature and has been used to look at poplar, rice and wheat, prairie cord grass, Arabidopsis as well as peach, apple and strawberry.

Here, Cockram et al. describe and visualize the control exerted by genes on the flowering time of members in the true grasses family (Poaceae).

Cockram J, Thiel T, Steuernagel B et al. 2012 Genome Dynamics Explain the Evolution of Flowering Time CCT Domain Gene Families in the Poaceae PLoS One 7:e45307.

Circos visualizes transitions from fields of study to industry sectors

Schenk addresses the question "Are college graduates employed in sectors related to their major?"

An interactive poster uses Circos to explore the data.

Schenk TL, Jr. 2011 Measuring Transitions into the Workforce as a Form of Accountability SSRN eLibrary ID 1831967.

Circos and Hive Plots describe regulatory networks

Neph et al. use Circos and hive plots visualize how the core human regulatory network varies across 41 cell and tissue types. They find that, "in spite of their inherent diversity, all cell-type regulatory networks independently converge on a common architecture that closely resembles the topology of living neuronal networks."

Neph S, Stergachis AB, Reynolds A et al. 2012 Circuitry and dynamics of human transcription factor regulatory networks Cell 150:1274-1286.

Microarray QC with Circos

Koch et al. use Circos to assess quality of microarray data in the publication Quality Visualization of Microarray Datasets Using Circos. The method is tuned for the Affymetrix Human Genome platform.

Koch M, Wiese M 2012 Quality Visualization of Microarray Datasets Using Circos Microarrays 1:84-94.

Bang. That's the genomes, exploding.

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 cancer genome display in NYT article

Photo shows Dr. John Carpten, left, and Dr. David Craig with a cancer genome display. New strategies attack cancer at the genetic level. (Joshua Lott for The New York Times).

"It looked as if two genes had fused to each other in Mrs. McDaniel’s cancer cells. The result was that the cell growth signals in the cancer cells were reversed, like crossed wires. The research team theorized that every time those cancer cells, T cells of her immune system, got a signal to stop growing, they reacted as though they had gotten a signal to grow. And every time they got a signal to grow, they responded by stopping their growth."

Source: A New Treatment’s Tantalizing Promise Brings Heartbreaking Ups and Downs, New York Times

Circos contributes to Max Planck Science Gallery in Berlin

The Max Planck Science Gallery is a walk-in digital installation of science, art and their intersection.

"The Max Planck Science Gallery explores the significance of the latest scientific and technological transformations – new and complex developments which are just emerging. It not only concerns science, technology and society’s requirements, but also the multifaceted links and interactions between them."

Interactive, multi-touch displays, present all aspects of science and its relationship to society and culture. Circos was used as part of the exhibit on cancer biology.

Circos draws Phineas Gage's brain

In 1848 a railroad worker named Phineas Gage had a meter-long iron rod go through his head. He survived the accident, underwent a dramatic personality change, and became one of the most famous case studies in neuroscience.

The Van Horn group at UCLA used high-resolution CT scans of Gage's skull to reconstruct the extent of damage Gage's brain suffered at the level of neuron connections.

Circos was used to contrast the connectivity in a healthy brain to Gage's brain. The circular 'connectome' diagrams depict the brain's major white matter tracts, showing the major brain regions - the frontal lobe, insula, limbic system, temporal lobe, parietal lobe, occipital lobe, brain stem and cerebellum - as colour-coded segments outside diagram, according to their position from the front.

Phineas Gage's Connectome, theguardian.co.uk.

Van Horn JD, Irimia A, Torgerson CM et al. 2012 Mapping connectivity damage in the case of phineas gage PLoS One 7:e37454.

Circos draws Phineas Gage's brain

In 1848 a railroad worker named Phineas Gage had a meter-long iron rod go through his head. He survived the accident, underwent a dramatic personality change, and became one of the most famous case studies in neuroscience.

The Van Horn group at UCLA used high-resolution CT scans of Gage's skull to reconstruct the extent of damage Gage's brain suffered at the level of neuron connections.

Circos was used to contrast the connectivity in a healthy brain to Gage's brain. The circular 'connectome' diagrams depict the brain's major white matter tracts, showing the major brain regions - the frontal lobe, insula, limbic system, temporal lobe, parietal lobe, occipital lobe, brain stem and cerebellum - as colour-coded segments outside diagram, according to their position from the front.

Phineas Gage's Connectome, theguardian.co.uk.

Van Horn JD, Irimia A, Torgerson CM et al. 2012 Mapping connectivity damage in the case of phineas gage PLoS One 7:e37454.

Circos tackles the connectome

Irimia et al. introduce circular representation of cortical networks in Circular representation of human cortical networks for subject and population-level connectomic visualization. The scalability of this circular visualization approach is demonstrated by lucid aggregate visualizations using cortical networks of 50 individuals.

The UCLA group also used the circular connectome visualization to assess differences in brain injury in patients Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury in Frontiers in Neurotrauma.

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 + Chromatin Topology

An organism's B and T lymphocytes — cells that are part of the immune system — continually develop new receptors specific to new threats to the immune system.

These receptor loci are organized into distinct regions that contain multiple variable (V), diversity (D), and/or joining (J) and constant (C) coding elements that are scattered across large genomic regions.

Bossen et al. review the relationship between epigenetics and chromatin and its effect on the diversity of receptors.

Bossen C, Mansson R, Murre C 2012 Chromatin topology and the regulation of antigen receptor assembly Annual review of immunology 30:337-356.

Circos fruit salad

Circos demonstrates sequence synteny between genomes of peach, apple and strawberry.

Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera.

Jung S, Cestaro A, Troggio M et al. 2012 Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies BMC Genomics 13:129.

Circos visualizes a 18.2 Gb metagenome

The genomes of all members in an ecosystem compose the system's metagenome.

In A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal, Albertsen et al. use Circos to compare the genome of Accumulibacter, one of the members of the 18.2 Gb metagenome of the bacterial community attached to a EBPR plant, to its reference. The comparison reveals significant differences in gene content and metabolic potential.

Albertsen M, Hansen LB, Saunders AM et al. 2011 A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal The ISME journal

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.

Circos Helps Stomach Differences in Gut Bugs

Biggs et al. report on the evolution of Campylobacter jejuni ST-474, an important human enteric pathogen, through a comparison of two flaA SVR-14 isolates and other available C. jejuni isolates and genomes.

Biggs PJ, Fearnhead P, Hotter G et al. 2011 Whole-Genome Comparison of Two Campylobacter jejuni Isolates of the Same Sequence Type Reveals Multiple Loci of Different Ancestral Lineage PLoS One 6:e27121.

Circos on the Cover of Genome Informatics 2011 Program

The image shows a high-resolution map of chromatin interactions across five loci in Drosophila Kc cells. Created by Micheal Gehring, Jennifer Phillips, Kevin van Bortle, Victor Corces, James Taylor.

Interactive Visualization of Structural Variation

Park et al. use the Circos paradigm to explore predicted structural variation. "Seqeyes is a novel multi-scale visualization that can interactively navigate dozens of genomes down to individual sequencing reads within a web browser."

Park R, Gehlenborg N, Park P. 2011. Seqeyes: A multi-scale interactive visualization tool for structural variations. In 1st IEEE Symposium on Biological Data Visualization, Providence, RI.

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.

Towards a Human Pan-Genome

As reported in Wired, Li et al. use Circos to visualize the comparison of structural variation in two sequenced human genomes: Asian and Yoruban (African). It's been over 10 years since the first reference genome (comprising DNA from multiple individuals) was reported. Technological advancements have made it possible to now sequence 1000's of human genomes to identify genetic variations for tracing evolution, determining population patterns, and assessing disease susceptibility and other phenotypic traits.

Li Y, Zheng H, Luo R et al. 2011 Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly Nature biotechnology 29:723-730.

Li R, Li Y, Zheng H et al. 2010 Building the sequence map of the human pan-genome Nature biotechnology 28:57-63.

Hemolytic–Uremic Syndrome Outbreak

Rasko et al. use Circos to show how the E. coli strain implicated in the German outbreak of hemolytic-uremic syndrome varies from other strains in their New England Journal of Medicine paper, where they find that "the genome of the German outbreak strain can be distinguished from those of other O104:H4 strains because it contains a prophage encoding Shiga toxin 2 and a distinct set of additional virulence and antibiotic-resistance factors."

NEJM created an animation that explains the visualizations. The paper was blogged by Pacific Biosciences.

Rasko DA, Webster DR, Sahl JW et al. 2011 Origins of the E. coli Strain Causing an Outbreak of Hemolytic-Uremic Syndrome in Germany The New England journal of medicine published ahead of print:-.

Circos in Simon Fraser University's AQ magazine (Apr 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 "Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors".

Jones 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 Maps Cancer Landscapes

Nature features an article by Heidi Ledford, The Cancer Genome Challenge, which discusses the progress and challenges of identifying structural variation signatures in cancer genomes.

Circos images are used throughout the piece, taken from the COSMIC project (Catalogue of Somatic Mutations in Cancer).

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

Circos Maps Cancer Landscapes

Nature features an article by Heidi Ledford, The Cancer Genome Challenge, which discusses the progress and challenges of identifying structural variation signatures in cancer genomes.

Circos images are used throughout the piece, taken from the COSMIC project (Catalogue of Somatic Mutations in Cancer).

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

Linux kernel exploration

Răzvan Musăloiu-E. explored the Linux file system and used Circos to relate the systems (disk-based, optical mediums, flash-based, network-based, cluster-based, memory-based, ancient) to kernel symbols.

Circular Worle

Jonathan Feinberg (IBM) created this perfectly circular wordle for me, using content from the Circos site.

As far as I know, this is the only circular wordle.

Circos Citation Themes

Get a Job

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

Is your resume ready?

What about your visualization?

All Your Genes Are Belong To Us

Remembering one of the most viral internet memes.

Circos is catching on, too.

Circos at VIZBI 2011

Circos was one of the community visualization tool tutorials at VIZBI 2011, at the Broad Institute in Boston.

Circos at VIZBI 2011

Circos was one of the community visualization tool tutorials at VIZBI 2011, at the Broad Institute in Boston.

Circos Helps with Urban Planning

The town of Caceres, Spain, a UNESCO World Heritage Site, used Circos to illustrate the relationships between businesses in their urban planning strategy.

Circos Helps with Urban Planning

The town of Caceres, Spain, a UNESCO World Heritage Site, used Circos to illustrate the relationships between businesses in their urban planning strategy.

Circos Helps with Urban Planning

The town of Caceres, Spain, a UNESCO World Heritage Site, used Circos to illustrate the relationships between businesses in their urban planning strategy.

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

Stephens et al. report on a phenomenon by which a cell accumulates a large number of rearrangements in a single catastrophic event. This phenomenon, which they call chromothripsis, can be seen in at least 2%–3% of all cancers and in about 25% of bone cancers.

Hive Plots - Linear Layout for Network Visualization

Visualizing large networks is hard. Nobody wants to see another hairball, but you want to show your data.

What do you do?

Try our new linear layout for network visualization, introducing the hive plot. This plot takes a fresh approach to drawing networks. It scales well, shows topology, and makes the network layout based on meaningful properties.

Hive Plots - Linear Layout for Network Visualization

Visualizing large networks is hard. Nobody wants to see another hairball, but you want to show your data.

What do you do?

Try our new linear layout for network visualization, introducing the hive plot. This plot takes a fresh approach to drawing networks. It scales well, shows topology, and makes the network layout based on meaningful properties.

Hive Plots - Linear Layout for Network Visualization

Visualizing large networks is hard. Nobody wants to see another hairball, but you want to show your data.

What do you do?

Try our new linear layout for network visualization, introducing the hive plot. This plot takes a fresh approach to drawing networks. It scales well, shows topology, and makes the network layout based on meaningful properties.

Hive Plots - Linear Layout for Network Visualization

Visualizing large networks is hard. Nobody wants to see another hairball, but you want to show your data.

What do you do?

Try our new linear layout for network visualization, introducing the hive plot. This plot takes a fresh approach to drawing networks. It scales well, shows topology, and makes the network layout based on meaningful properties.

Hive Plots - Linear Layout for Network Visualization

Visualizing large networks is hard. Nobody wants to see another hairball, but you want to show your data.

What do you do?

Try our new linear layout for network visualization, introducing the hive plot. This plot takes a fresh approach to drawing networks. It scales well, shows topology, and makes the network layout based on meaningful properties.

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.

Circos Investigates Policy Breach in Email Conversation

Circos is ideally suited for displaying the flow of information. In this case, during an investigation into email policy abuse, Ben Reardon explored the evolution of electronic conversation to reveal the source and primary propagators.

Glyph Tracks

When a text track is rendered using a symbol font, curious results can arise.

Here, a glyph track is created by using the Wingding font to encode sequence using colored dots.

Glyph Tracks

When a text track is rendered using a symbol font, curious results can arise.

Here, a glyph track is created by using the Wingding font to encode sequence using colored dots.

Get Your Learning Organized

The Circos course was presented at the 2010 Bioinformatics and Comparative Genome Analysis workshop at the Paris Pasteur Institute.

The course is composed of four sessions: a theory lecture and three practical sessions. The practical sessions focus on the core set of Circos' features. In Session 2, you learn how to define karyotypes, and how to draw, arrange, crop, order and scale ideograms. Session 3 uses the image created in Session 2 to show how to layer 2D tracks and introduces links and rules. Session 4 demonstrates the use of rules to dynamically format and layer link and scatter plot data.

Get Your Learning Organized

The Circos course was presented at the 2010 Bioinformatics and Comparative Genome Analysis workshop at the Paris Pasteur Institute.

The course is composed of four sessions: a theory lecture and three practical sessions. The practical sessions focus on the core set of Circos' features. In Session 2, you learn how to define karyotypes, and how to draw, arrange, crop, order and scale ideograms. Session 3 uses the image created in Session 2 to show how to layer 2D tracks and introduces links and rules. Session 4 demonstrates the use of rules to dynamically format and layer link and scatter plot data.

Bubbles!

When a text track is rendered using a symbol font, curious results can arise.

Here, a bubble track is created by using the Wingding font and applying dynamic rules to scale the glyph size proportionally to local gene density.

DHL Uses Circos

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

DHL Uses Circos

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

DHL Uses Circos

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

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.

Successive Duplications in Paramecium

A visual representation of ancestry analysis of 85 dog breeds and Eurasian gray wolves.

17Vonholdt BM, Pollinger JP, Lohmueller KE et al. 2010 Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication Nature 464 (7290) 898-902.

Successive Duplications in Paramecium

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.

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 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.

Circos Illustrates Genome Structure of Maize

The Maize sequence paper uses Circos to show genome structure and annotations. Links inside the circle show homologous sites of duplicated gene blocks.

40Schnable PS Ware D Fulton RS et al. 2009 The B73 maize genome: complexity, diversity, and dynamics Science 326 (5956) 1112-1115

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 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).

Circos — a Lens for Science

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 and 23andMe

This image accompanied an article in Conde Nast Portfolio about the future of genomics, profiling 23andMe.

The figure shows the human genome annotated with locations of genes implicated in disease, regions of with self-similarity and those with structural variation within populations. This graphic layers a variety of data types (links, heat maps, tiles, histograms) and is a good example of a Circos image (...more).

Circos Part of Art of Knowledge

The October 2008 German Geo issue features Circos images in an article "Die Kunst der Erkenntnis" (The Art of Knowledge). The article features a large number of beautiful artistic renderings of large data sets, including a solid rendering of the flight profile of a bat, lexical structure of the bible and a US flight map.

You Look Around

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

Circos Collaborates with Wired

When Wired needed an inforgraphic to illustrate the complex world of relationships on the TV Series Lost, it turned to Circos.

The task was to visually represent about 60 relationships shared between 35 characters. The tableviewer utility, which applies Circos to visualizing tabular data, was perfect for creating the illustration. And thus, Circos says goodbye to the table.

Circos Collaborates with Wired

When Wired needed an inforgraphic to illustrate the complex world of relationships on the TV Series Lost, it turned to Circos.

The task was to visually represent about 60 relationships shared between 35 characters. The tableviewer utility, which applies Circos to visualizing tabular data, was perfect for creating the illustration.

Circos Collaborates with Wired

When Wired needed an inforgraphic to illustrate the complex world of relationships on the TV Series Lost, it turned to Circos.

In collaboration with Christy Sheppard, Wired's Art Director, Martin Krzywinski created the illustration for the April 22 2010 issue.

Visualizing Database Schemas

Before Circos, I created a prototype system, Schemaball, to visualize database schemas.

Relationships between tables quickly became apparent and our database administrators suddenly had more free time to play Carcassonne.

Krzywinski, M. Schemaball: A New Spin on Database Visualization (2004) Sysadmin Magazine Vol 13 Issue 08.

Circos Introduced in the New York Times

My first Circos infographic to be published in the New York Times introduces the idea of sequence similarity curves linking circularly composed ideograms.

Working with David Constantine, I illustrated the similarity between chromosome 1 of mouse, rhesus, chimp, and chicken to that of human.

One of the smaller panels in the infographic was subsequently used by the Alliance of Lupus Research in their Faces of Lupus II video.

Banish Tables

Tables are natural containers for data. Whenever information is presented, chances are excellent that it is communicated by means of a table. In many cases, however, when this information is complex (and the table, therefore, is large) a tabular presentation is difficult to parse visually and patterns in the tabulated data remain opaque.

You can use Circos to visualize tabular data. It's different, reasonably easy, available online, and sure to start a conversation.

It's also quite informative.

Naming Names - Circos Engages in Political Mudslinging

Jonathan Corum of the New York Times prepared this infographic with Circos to show the extent and timing of the use of names of by presidential candidates in a series of debates. Each arrow represents one candidate refering to another, with the start of the arrow representing the time within the candidate's speech at which the reference was made.

The figure was part of a larger graphic that identified themes during the debate. Jonathan created an interactive version of this figure and discusses how he approached its design.

Naming Names - Circos Engages in Political Mudslinging

Jonathan Corum of the New York Times prepared this infographic with Circos to show the extent and timing of the use of names of by presidential candidates in a series of debates. Each arrow represents one candidate refering to another, with the start of the arrow representing the time within the candidate's speech at which the reference was made.

The figure was part of a larger graphic that identified themes during the debate. Jonathan created an interactive version of this figure and discusses how he approached its design.

Dog vs Human Synteny Panel

The completion of the draft version of the dog genome revealed large overlaps between dog and human genomes. Working with American Scientist, Martin Krzywinski designed the cover image for the magazine's Sept/Oct 2007 issue, to accompany the article "Genetics and the Shape of Dogs" by Elaine Ostrander.

The panel shown here reveals the details in the structure of sequence similarity between each dog chromosome and the human genome (top) and each human chromosome and the dog genome (bottom).

...more details

Dog vs Human Synteny Panel

The completion of the draft version of the dog genome revealed large overlaps between dog and human genomes. Working with American Scientist, Martin Krzywinski designed the cover image for the magazine's Sept/Oct 2007 issue, to accompany the article "Genetics and the Shape of Dogs" by Elaine Ostrander.

The panel shown here reveals the details in the structure of sequence similarity between each dog chromosome and the human genome (top) and each human chromosome and the dog genome (bottom).

...more details

Dog vs Human Synteny Panel

The completion of the draft version of the dog genome revealed large overlaps between dog and human genomes. Working with American Scientist, Martin Krzywinski designed the cover image for the magazine's Sept/Oct 2007 issue, to accompany the article "Genetics and the Shape of Dogs" by Elaine Ostrander.

The panel shown here reveals the details in the structure of sequence similarity between each dog chromosome and the human genome (top) and each human chromosome and the dog genome (bottom).

...more details

Circos Sniffs out Dog Genetics in American Scientist

The completion of the draft version of the dog genome revealed large overlaps between dog and human genomes. Working with American Scientist, Martin Krzywinski generated an illustration showing blocks of similarity between the two genomes.

The illustration accompanies the article Genetics and the Shape of Dogs, by Elaine Ostrander.

Circos Sniffs out Dog Genetics in American Scientist

The completion of the draft version of the dog genome revealed large overlaps between dog and human genomes. Working with American Scientist, Martin Krzywinski generated an illustration showing blocks of similarity between the two genomes.

The illustration accompanies the article Genetics and the Shape of Dogs, by Elaine Ostrander.