Aug 1 2017

Introduction to Circos, Features and Uses #aesthetics,alignment,analysis,bioinformatics,cancer,circos,circular,comparative,conservation,data #visualization,design,evolution,evolutionary,gene,genetic,genome,genome #sciences #centre,genomic,genomics,graph,graphics,human,human #genome,infovis,martin #krzywinski,rearrangement,science,sequence,somatic,structural,synteny


Circos at the EMBO NGS workshop in Tunis, Sept 15 25. Circos is back for 4rd year at 2014 Bioinformatics and Comparative Genome Analysis course by the Pasteur Institute Athens, May 7 20 imperatives of information design BioVis 2012 Another -ome. Circos manages the connectome of 50 brains NeuroImage 28 Jan Interested in network visualization? Frustrated by hairballs? See my hive plot project. Spunky Scientific Visualization Safely learn about the plague, ebola and marburg at the deadly genomes depot. New England Journal of Medicine animation of E. coli Circos visualization.

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.

Using News Reports to 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.

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.

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.

Circos Maps America’s Restless Interstate Migration Without a Map

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.

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.

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.

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.

Circos in 54 million pixels

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

Circos Tracks CO2 Emissions

Circos Round Lotus Sacred

6.9e11 g of oil and Circos was there

Plants Love Circos

Circos for R

Circos Interchange Diagrams Networks and Flow

Circos connects to the connectome

Circos is the Method for Visualizing Translocations

Circos Paints Chromosomes of Capsella Rubella

Circos on the Cover Of Journal of Pathology

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

What is Circos?

Who should care?

What is it for?

Only for genomics? No!

How is it different?

Useful to you?

Brief History

Future of Circos

License and Use

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