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 2013 Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers Cancer discovery 3:770-781.
Sep 2012 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.
2014 A comprehensive analysis of the human placenta transcriptome Placenta 35:125-131.
Circos on cover of UCSF Magazine
The Fall 2013 issue of UCSF Magazine has my Circos illustration of personalized medicine. The human outline motif is incorporated into other design elements in the issue.
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.
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.
2013 Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Genome Biol 14:R41.
Plants Love Circos
Circos frequently appears in plant literature, twice on the cover of Plant Biotechnology Journal in the last year.
2013 Large-scale resource development in Gossypium hirsutum L. by 454 sequencing of genic-enriched libraries from six diverse genotypes Plant biotechnology journal
2013 High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array Plant biotechnology journal
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."
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".
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.
2013Sodium valproate use is associated with reduced parietal lobe thickness and brain volume Neurology 80(20):1895-1900.
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.
1 2011 Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study Science Translational Medicine 3:111ra121.
Circos Used in a David Cronenberg project about
Chromosomes is a David Cronenberg project which presents 70 images from his films, each accompanied by a text piece written by people from the world of art and science. I had the opportunity to contribute text to accompany the red bathtub photo.
The artbook is available for sale.
Little Fly, Thy Summer's Play...
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.
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.23 2009 The transcription unit architecture of the Escherichia coli genome Nature biotechnology 27 (11) 1043-1049.
Oxford Biology Uses Circos for Book Cover
A Circos image designed by Martin Krzywinski appears on the cover of Building Bioformatics Solutions with Perl, R and MySQL by Conrad Bessant, Ian Shadforth, and Darren Oakley (Oxford Press).
Circos 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).