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.
2013Sodium valproate use is associated with reduced parietal lobe thickness and brain volume Neurology 80(20):1895-1900.
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
2013 Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia New England Journal of Medicine.
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.
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."
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."
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
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.
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.
2012 Circular representation of human cortical networks for subject and population-level connectomic visualization NeuroImage, 2012 Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury Frontiers in Neurology 3
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 Nature Reviews Cancer Calendar 2013
Circos appears on the cover of Nature Review's 2013 Cancer Calendar in the form of a figure taken from2012 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, 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.
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).
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.
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."
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.
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.
2012 Mapping connectivity damage in the case of phineas gage PLoS One 7:e37454.
Circos is distribted in three independent archives.
To do anything, you'll need the Circos code distribution, which contains the main code, fonts, global configuration and an example. Tutorials are no longer included in this file.
Several, utility add-on scripts are available, such as for bundling links. These are not necessary for Circos, but helpful in carrying out common data reduction and analysis tasks. Tools are described in the Tools Tutorial.
Please direct bug reports, comments and questions to the Circos Google group.
To help resolve the problem faster, send me your conf/data files. Do not forget to include all the files, including karyotype.
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|circos-0.55-pre1.tgz||0.55||11,910,218||Thu Jun 16 16:34:30 2011||This is a pre-release candidate. It does not contain tutorials.|
|circos-0.55-pre0.tgz||0.55||11,937,893||Sun Jun 12 22:22:14 2011||This is a pre-release candidate. It does not contain tutorials.|
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|circos-0.52-3.tgz||0.52||66,262||Tue Jan 11 16:37:05 2011||circos-0.52-3.tgz is a bug release.|
|circos-0.52-2.tgz||0.52||66,173||Tue Sep 21 15:49:32 2010||circos-0.52-2.tgz is a bug release.|
|circos-0.52-1.tgz||0.52||65,628||Fri Sep 3 11:32:54 2010||circos-0.52-1.tgz is a bug release.|
|circos-0.52.tgz||0.52||43,523,958||Tue Nov 24 17:06:54 2009|
|circos-0.51-1.tgz||0.51||80,694||Wed Jul 8 15:02:27 2009||circos-0.51-1.tgz is a bug release.|
|circos-0.51.tgz||0.51||43,531,650||Tue Jul 7 10:13:23 2009|
|circos-0.50.tgz||0.50||43,239,234||Thu Jun 25 16:28:07 2009|
|circos-0.48-1.tgz||0.48||53,782||Wed Jun 17 10:51:54 2009||circos-0.48-1.tgz is a bug release.|
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|circos-0.48.tgz||0.48||60,165,323||Tue Oct 21 10:43:48 2008|
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