% my $url_root = $m->comp("SELF:url_root");

My images created with Circos have appeared in a variety of publications. Wired, New York Times, Conde Nast Portfolio, and American Scientist.

In genomics, scientific journals like Science, Nature, PLoS, Genome Research and others have published papers that used Circos images (Circos citations).

Wired

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.

New York Times

<% $m->comp("SELF:show_image", float=>"left", file=>"circos-nyt-epigenome.png", alt=>"Circos in the New York Times illustrating epigenetic data.", caption=>"11 Nov 2008 | In collaboration with Jonathan Corum from the NYT, Martin Krzywinski created an illustration of data showing methylation on chromosome 22 in a variety of tissues. The illustration accompanies the article Now: The Rest of the Genome, by Carl Zimmer (graphic).", width=>310, link=>"http://www.nytimes.com/imagepages/2008/11/11/science/20081111_EPIGENETICS_GRAPHIC.html") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-nyt-species.png", alt=>"Circos in the New York Times illustrating how genomes are compared.", caption=>"22 Jan 2007 | Working with David Constantine, this figure introduced NYT readers to Circos and how genomes are compared (graphic).", width=>310, link=>"http://www.nytimes.com/imagepages/2007/01/22/science/20070123_SCI_ILLO.html") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-nyt-string-of-debates.png", alt=>"Circos in the New York Times illustrating the dynamics of debates.", caption=>"15 Dec 2007 | Circos first appeared in the New York Times in a String of Debates infographic, designed by Jonathan Corum. Jonathan discusses how he used Circos in creating the image (full article graphic interactive graphic)", width=>310, link=>"http://www.nytimes.com/imagepages/2007/12/15/us/politics/16debates.web.html") %>

Conde Nast Portfolio

<% $m->comp("SELF:show_image", file=>"circos-conde-nast.png", alt=>"Circos in Conde Nast Portfolio accompanies an article about personalized genome sequencing.", caption=>"15 Oct 2007 | Working with John Grimwade, I designed this image to illustrates genomic variation, self-similarity and gene position, relevant characteristics to the accompanying article about 23andMe article interactive graphic.", width=>825, link=>"http://www.portfolio.com/news-markets/national-news/portfolio/2007/10/15/23andMe-Web-Site") %>

Covers

<% $m->comp("SELF:show_image", float=>"left", file=>"circos-igenetics.png", alt=>"", caption=>"2 Oct 2008 | In a collaboration with Derek Baccus from Pearson Science, I designed a cover illustration for the 3rd edition of iGenetics by Peter Russell. This cover won the cover award at 39th Annual 2009 Bookbuilders West Book Show. ", width=>310, link=>"http://www.amazon.com/s/ref=nb_sb_noss?field-keywords=978-0321569769") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-embo.png", alt=>"", caption=>"13 May 2009 | The image from my Circos Visual Guide Poster was used for the cover of the Embo Journal", width=>310, link=>"http://www.nature.com/emboj/journal/v28/n9/index.html") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-americanscientist.png", alt=>"", caption=>"9 Aug 2007 | I designed an image for the cover of the American Scientist to accompany an article about dog genetics by Elaine Ostrander (read more).", width=>310, link=>"http://www.americanscientist.org/issues/id.67/past.aspx") %>
<% $m->comp("SELF:show_image", float=>"left", file=>"circos-natbiotech.png", alt=>"Article by Cho et al about E coli genome uses a Circos image, which makes it to the cover of Nature Biotechnology.", caption=>"3 Nov 2009 | The cover of Nature Biotechnology uses a Circos image that appears in a paper about the genome of E. coli.", width=>310, link=>"http://www.nature.com/nbt/journal/v27/n11/abs/nbt.1582.html") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-chromosomes.png", alt=>"Circos used for illustrating Chromosomes - an art book featuring stills from movies by David Cronenberg", caption=>"10 Dec 2008 | Working with Domenico De Gaetano from Volumina, I created illustrations for Chromosomes, an exhibition and art book about films of David Cronenberg.", width=>310, link=>"http://www.volumina.net/exhibitions/exhibitions.php?id=118&meta=Chromosomes_Cronenberg") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-rmysql.png", alt=>"Oxford Biology uses a Circos image for the cover of Building Bioinformatics Solutions", caption=>"1 Dec 2008 | I initially designed the image as an example of the capabilities of Circos. It was eventuall picked up by the Science Photo Library and subsequently used by Oxford Press.", width=>310, link=>"http://www.bixsolutions.net/") %>
<% $m->comp("SELF:show_image", float=>"left", file=>"circos-knowledge.png", alt=>"Circos on the cover of Designing Universal Knowledge", caption=>"7 Jan 2009 | Gerlinde Schuller used the image that previously appeared in the New York Times on the cover of her Designing Universal Knowledge.", width=>310, link=>"http://www.theworldasflatland.net/report1.htm") %>

Advertising

<% $m->comp("SELF:show_image", float=>"left", file=>"circos-dhl.png", alt=>"Circos in a Deutsche Post DHL Ad", caption=>"22 July 2010 | The figure shows international connections serviced by DHL.", width=>900, link=>"") %>

Scientific Literature

<% $m->comp("SELF:show_image", float=>"left", file=>"circos-cancer-genome-challenge.png", alt=>"", caption=>"14 Apr 2010 |
6Ledford H 2010 Big science: The cancer genome challenge Nature 464 (7291) 972-974.
", width=>900, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20393534") %>
<% $m->comp("SELF:show_image", float=>"left", file=>"circos-3dyeast.png", alt=>"", caption=>"2 May 2010 |
1Duan Z, Andronescu M, Schutz K et al. 2010 A three-dimensional model of the yeast genome Nature ", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20436457") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-barley.png", alt=>"", caption=>"22 Aug 2009 |
42Thiel T, Graner A, Waugh R et al. 2009 Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice BMC Evol Biol 9 (209.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19698139") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-doubling.png", alt=>"", caption=>"29 Nov 2008 |
30Jaillon O, Aury JM, Wincker P 2009 'Changing by doubling', the impact of Whole Genome Duplications in the evolution of eukaryotes C R Biol 332 (2-3) 241-253.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19281955") %>
<% $m->comp("SELF:show_image", float=>"left", file=>"circos-doubling-2.png", alt=>"", caption=>"29 Nov 2008 |
30Jaillon O, Aury JM, Wincker P 2009 'Changing by doubling', the impact of Whole Genome Duplications in the evolution of eukaryotes C R Biol 332 (2-3) 241-253.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19281955") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-maize.png", alt=>"", caption=>"20 Nov 2009 |
40Schnable PS Ware D Fulton RS et al. 2009 The B73 maize genome: complexity, diversity, and dynamics Science 326 (5956) 1112-1115.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19965430") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-breast-cancer.png", alt=>"", caption=>"24 Dec 2009 |
41Stephens PJ, McBride DJ, Lin ML et al. 2009 Complex landscapes of somatic rearrangement in human breast cancer genomes Nature 462 (7276) 1005-1010.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20033038") %>
<% $m->comp("SELF:show_image", float=>"left", file=>"circos-methylomes.png", alt=>"", caption=>"Dec 2009 |
24Costello JF, Krzywinski M, Marra MA 2009 A first look at entire human methylomes Nature biotechnology 27 (12) 1130-1132.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20010593") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-u87mg.png", alt=>"", caption=>"29 Jan 2010 |
2Clark MJ, Homer N, O'Connor BD et al. 2010 U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line PLoS Genet 6 (1) e1000832.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20126413") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-microbial-fragments.png", alt=>"", caption=>"25 Jan 2010 |
9Perry SC, Beiko RG 2010 Distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives Genome Biol Evol 2010 (117-131.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20333228") %>
<% $m->comp("SELF:show_image", float=>"left", file=>"circos-soybean.png", alt=>"", caption=>"14 Jan 2010 |
14Schmutz J, Cannon SB, Schlueter J et al. 2010 Genome sequence of the palaeopolyploid soybean Nature 463 (7278) 178-183.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20075913") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-salmonella.png", alt=>"", caption=>"12 Mar 2010 |
16Tomljenovic-Berube AM, Mulder DT, Whiteside MD et al. 2010 Identification of the regulatory logic controlling salmonella pathoadaptation by the SsrA-SsrB two-component system PLoS Genet 6 (3) e1000875.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20300643") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-acidophilic.png", alt=>"", caption=>"7 Mar 2007 |
53Lo I, Denef VJ, Verberkmoes NC et al. 2007 Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria Nature 446 (7135) 537-541.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17344860") %>
<% $m->comp("SELF:show_image", float=>"left", file=>"circos-bottleneck.png", alt=>"", caption=>"Jul 2007 |
51Gherman A, Chen PE, Teslovich TM et al. 2007 Population bottlenecks as a potential major shaping force of human genome architecture PLoS Genet 3 (7) e119.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17658953") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-switchgrass.png", alt=>"", caption=>"Nov 2008 |
49Tobias CM, Sarath G, Twigg P et al. 2008 Comparative Genomics in Switchgrass Using 61,585 High-Quality Expressed Sequence Tags The Plant Genome 1 (2) 111-124.
", width=>310, link=>"http://plantgenome.scijournals.org/content/1/2/111.full") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-leptospirillum.png", alt=>"", caption=>"22 Jul 2008 |
48Simmons SL, Dibartolo G, Denef VJ et al. 2008 Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation PLoS Biol 6 (7) e177.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18651792") %>
<% $m->comp("SELF:show_image", float=>"left", file=>"circos-fusion.png", alt=>"", caption=>"24 Oct 2008 |
46Durrens P, Nikolski M, Sherman D 2008 Fusion and fission of genes define a metric between fungal genomes PLoS Comput Biol 4 (10) e1000200.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18949021") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-microbial-community.png", alt=>"", caption=>"4 May 2009 |
44Wilmes P, Bond PL 2009 Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth's biogeochemical cycles Curr Opin Microbiol 12 (3) 310-317.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19414280") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-plasticity.png", alt=>"", caption=>"6 Nov Aug 2009 |
35McMurdie PJ, Behrens SF, Muller JA et al. 2009 Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides PLoS Genet 5 (11) e1000714.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19893622") %>
<% $m->comp("SELF:show_image", float=>"left", file=>"circos-mcf7.png", alt=>"", caption=>"3 Dec 2008 |
29Hampton OA, Den Hollander P, Miller CA et al. 2009 A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome Genome research 19 (2) 167-177.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19056696") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-tcell.png", alt=>"", caption=>"18 June 2009 |
28Freeman JD, Warren RL, Webb JR et al. 2009 Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing Genome research 19 (10) 1817-1824.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19541912") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-gibbon.png", alt=>"", caption=>"26 Jun 2009 |
21Carbone L, Harris RA, Vessere GM et al. 2009 Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution PLoS Genet 5 (6) e1000538.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19557196") %>
<% $m->comp("SELF:show_image", float=>"left", file=>"circos-enterococcus.png", alt=>"", caption=>"Feb 2010 |
18Yasmin A, Kenny JG, Shankar J et al. 2010 Comparative genomics and transduction potential of Enterococcus faecalis temperate bacteriophages J Bacteriol 192 (4) 1122-1130.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20008075") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-planta.png", alt=>"", caption=>"24 Mar 2010 |
15Sierra R, Rodriguez RL, Chaves D et al. 2010 Discovery of phytophthora infestans genes expressed in planta through mining of cDNA libraries PLoS One 5 (3) e9847.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20352100") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-ring.png", alt=>"", caption=>"3 Dec 2009 |
7Lim SD, Yim WC, Moon JC et al. 2010 A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes Plant Mol Biol 72 (4-5) 369-380.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19957018") %>
<% $m->comp("SELF:show_image", float=>"left", file=>"circos-genome-remodelling.png", alt=>"", caption=>"15 April 2010 |
3Ding L, Ellis MJ, Li S et al. 2010 Genome remodelling in a basal-like breast cancer metastasis and xenograft Nature 464 (7291) 999-1005.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20393555") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-cosmic.png", alt=>"", caption=>"16 Dec 2009 |
10Pleasance ED, Cheetham RK, Stephens PJ et al. 2010 A comprehensive catalogue of somatic mutations from a human cancer genome Nature 463 (7278) 191-196.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20016485") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-grapevine.png", alt=>"", caption=>"26 Aug 2007 |
52Jaillon O, Aury JM, Noel B et al. 2007 The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Nature 449 (7161) 463-467.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17721507") %>
<% $m->comp("SELF:show_image", float=>"left", file=>"circos-cupriavidus.png", alt=>"", caption=>"5 May 2010 |
1Janssen PJ, Van Houdt R, Moors H et al. 2010 The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments PLoS One 5 (5) e10433.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20463976") %> <% $m->comp("SELF:show_image", float=>"left", file=>"circos-diatom.png", alt=>"", caption=>"22 March 2010 |
1Ravin NV, Galachyants YP, Mardanov AV et al. 2010 Complete sequence of the mitochondrial genome of a diatom alga Synedra acus and comparative analysis of diatom mitochondrial genomes Curr Genet 56 (3) 215-223.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20309551") %> <% $m->comp('SELF:show_image', float=>"left", file=>"circos-pin.png", alt=>"", caption=>"2 June 2010 |
1Shen C, Bai Y, Wang S et al. 2010 Expression profile of PIN, AUX/LAX and PGP auxin transporter gene families in Sorghum bicolor under phytohormone and abiotic stress FEBS J 277 (14) 2954-2969.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20528920") %>
<% $m->comp('SELF:show_image', float=>"left", file=>"circos-gibbon.png", alt=>"", caption=>"27 May 2010 |
1Lee W, Jiang Z, Liu J et al. 2010 The mutation spectrum revealed by paired genome sequences from a lung cancer patient Nature 465 (7297) 473-477.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20505728") %> <% $m->comp('SELF:show_image', float=>"left", file=>"circos-salmonella-ssra.png", alt=>"", caption=>"6 Feb 2010 |
1Tomljenovic-Berube AM, Mulder DT, Whiteside MD et al. 2010 Identification of the regulatory logic controlling Salmonella pathoadaptation by the SsrA-SsrB two-component system PLoS Genet 6 (3) e1000875.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20300643") %> <% $m->comp('SELF:show_image', float=>"left", file=>"circos-plasticity-dehalococcoides.png", alt=>"", caption=>"6 Nov 2009 |
1McMurdie PJ, Behrens SF, Muller JA et al. 2009 Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides PLoS Genet 5 (11) e1000714.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19893622") %>
<% $m->comp('SELF:show_image', float=>"left", file=>"circos-populus.png", alt=>"", caption=>"23 Feb 2007 |
1Kelleher CT, Chiu R, Shin H et al. 2007 A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation Plant J 50 (6) 1063-1078.
", width=>310, link=>"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17488239") %> <% $m->comp('SELF:show_image', float=>"left", file=>"circos-propionibacterium.png", alt=>"Circos - The Complete Genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy Actinobacterium with Food and Probiotic Applications", caption=>"23 Jul 2010 |
1Falentin H, Deutsch S-M, Jan G et al. 2010 The Complete Genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy Actinobacterium with Food and Probiotic Applications PLoS One 5 (7) e11748.
", width=>310, link=>"http://dx.doi.org/10.1371%2Fjournal.pone.0011748") %> <%doc> <% $m->comp('SELF:show_image', float=>"left", file=>"circos-gibbon.png", alt=>"", caption=>"Feb 2010 | ", width=>310, link=>"") %>
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