Circos > in_literature > scientific

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.

// aury-paramecium

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).

6Ledford H 2010 Big science: The cancer genome challenge Nature 464 (7291) 972-974.

// cancer-genome-challenge

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).

6Ledford H 2010 Big science: The cancer genome challenge Nature 464 (7291) 972-974.

// cancer-genome-challenge

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.

// nat-biotech-cho

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.

// vonholdt-dogs

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

// maize
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Below are Circos' citations in the scientific literature (see published images).

Circos in Scientific Literature

1Alexander RP, Fang G, Rozowsky J et al. 2010 Annotating non-coding regions of the genome Nat Rev Genet 11 (8) 559-571.
2Baker M 2010 Epigenome: Mapping in Motion Nature Methods 7 (3) 181-186.
3Clark 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.
4Ding L, Ellis MJ, Li S et al. 2010 Genome remodelling in a basal-like breast cancer metastasis and xenograft Nature 464 (7291) 999-1005.
5Duan Z, Andronescu M, Schutz K et al. 2010 A three-dimensional model of the yeast genome Nature
6Falentin 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.
7Hu Y, Wang K, He X et al. 2010 A Probabilistic Framework for Aligning Paired-end RNA-seq Data Bioinformatics
8Janssen 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.
9Kwei KA, Kung Y, Salari K et al. 2010 Genomic instability in breast cancer: pathogenesis and clinical implications Mol Oncol 4 (3) 255-266.
10Lam HY, Mu XJ, Stutz AM et al. 2010 Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library Nature biotechnology 28 (1) 47-55.
11Ledford H 2010 Big science: The cancer genome challenge Nature 464 (7291) 972-974.
12Lee 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.
13Lepp D, Roxas B, Parreira VR et al. 2010 Identification of novel pathogenicity loci in Clostridium perfringens strains that cause avian necrotic enteritis PLoS One 5 (5) e10795.
14Lim 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.
15Lucker S, Wagner M, Maixner F et al. 2010 A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria Proc Natl Acad Sci U S A 107 (30) 13479-13484.
16Mandakova T, Joly S, Krzywinski M et al. 2010 Fast Diploidization in Close Mesopolyploid Relatives of Arabidopsis Plant Cell
17Martin JW, Yoshimoto M, Ludkovski O et al. 2010 Analysis of segmental duplications, mouse genome synteny and recurrent cancer-associated amplicons in human chromosome 6p21-p12 Cytogenet Genome Res 128 (4) 199-213.
18Nielsen CB, Cantor M, Dubchak I et al. 2010 Visualizing genomes: techniques and challenges Nat Methods 7 (3 Suppl) S5-S15.
19Paten B, Diekhans M, Earl D et al. 2010 Cactus Graphs for Genome Comparisons In Lecture notes in Computer Science, (ed. 410-425. Springer Berlin (Heidelberg).
20Perry SC, Beiko RG 2010 Distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives Genome Biol Evol 2010 (117-131.
21Pleasance ED, Cheetham RK, Stephens PJ et al. 2010 A comprehensive catalogue of somatic mutations from a human cancer genome Nature 463 (7278) 191-196.
22Pleasance ED, Stephens PJ, O'Meara S et al. 2010 A small-cell lung cancer genome with complex signatures of tobacco exposure Nature 463 (7278) 184-190.
23Procter JB, Thompson J, Letunic I et al. 2010 Visualization of multiple alignments, phylogenies and gene family evolution Nat Methods 7 (3 Suppl) S16-25.
24Ravin 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
25Schmutz J, Cannon SB, Schlueter J et al. 2010 Genome sequence of the palaeopolyploid soybean Nature 463 (7278) 178-183.
26Shen 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.
27Sierra 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.
28Tomljenovic-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.
29Vonholdt 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.
30Yasmin A, Kenny JG, Shankar J et al. 2010 Comparative genomics and transduction potential of Enterococcus faecalis temperate bacteriophages J Bacteriol 192 (4) 1122-1130.
31Zeitouni B, Boeva V, Janoueix-Lerosey I et al. 2010 SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data Bioinformatics 26 (15) 1895-1896.
32Bellgard MI, Wanchanthuek P, La T et al. 2009 Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine PLoS One 4 (3) e4641.
33Campbell SJ, Gaulton A, Marshall J et al. 2009 Visualizing the drug target landscape Drug Discov Today 15 (1-2) 3-15.
34Carbone 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.
35Carver T, Thomson N, Bleasby A et al. 2009 DNAPlotter: circular and linear interactive genome visualization Bioinformatics 25 (1) 119-120.
36Catchen JM, Conery JS, Postlethwait JH 2009 Automated identification of conserved synteny after whole-genome duplication Genome research 19 (8) 1497-1505.
37Cho BK, Zengler K, Qiu Y et al. 2009 The transcription unit architecture of the Escherichia coli genome Nature biotechnology 27 (11) 1043-1049.
38Costello JF, Krzywinski M, Marra MA 2009 A first look at entire human methylomes Nature biotechnology 27 (12) 1130-1132.
39Diguistini S, Liao NY, Platt D et al. 2009 De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data Genome Biol 10 (9) R94.
40Flannery MC 2009 Writing Across Rome The American Biology Teacher 71 (1) 52-55.
41Forbes SA, Tang G, Bindal N et al. 2009 COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer Nucleic Acids Res 38 (Database issue) D652-657.
42Freeman 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.
43Hampton 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.
44Jaillon 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.
45Krzywinski M, Schein J, Birol I et al. 2009 Circos: an information aesthetic for comparative genomics Genome research 19 (9) 1639-1645.
46Langille MG, Brinkman FS 2009 IslandViewer: an integrated interface for computational identification and visualization of genomic islands Bioinformatics 25 (5) 664-665.
47Langridge GC, Phan MD, Turner DJ et al. 2009 Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants Genome research 19 (12) 2308-2316.
48Lelandais-Briere C, Naya L, Sallet E et al. 2009 Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules Plant Cell 21 (9) 2780-2796.
49McMurdie PJ, Behrens SF, Muller JA et al. 2009 Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides PLoS Genet 5 (11) e1000714.
50Meyer C, Kowarz E, Hofmann J et al. 2009 New insights to the MLL recombinome of acute leukemias Leukemia 23 (8) 1490-1499.
51Meyer M, Munzner T, Pfister H 2009 MizBee: a multiscale synteny browser IEEE Trans Vis Comput Graph 15 (6) 897-904.
52Peregrin-Alvarez JM, Xiong X, Su C et al. 2009 The Modular Organization of Protein Interactions in Escherichia coli PLoS Comput Biol 5 (10) e1000523.
53Quraishi UM, Abrouk M, Bolot S et al. 2009 Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection Funct Integr Genomics 9 (4) 473-484.
54Reith F, Etschmann B, Grosse C et al. 2009 Mechanisms of gold biomineralization in the bacterium Cupriavidus metallidurans Proc Natl Acad Sci U S A 106 (42) 17757-17762.
55Salse J, Abrouk M, Murat F et al. 2009 Improved criteria and comparative genomics tool provide new insights into grass paleogenomics Brief Bioinform 10 (6) 619-630.
56Schnable PS Ware D Fulton RS et al. 2009 The B73 maize genome: complexity, diversity, and dynamics Science 326 (5956) 1112-1115.
57Stephens PJ, McBride DJ, Lin ML et al. 2009 Complex landscapes of somatic rearrangement in human breast cancer genomes Nature 462 (7276) 1005-1010.
58Thiel 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.
59Throude M, Bolot S, Bosio M et al. 2009 Structure and expression analysis of rice paleo duplications Nucleic Acids Res 37 (4) 1248-1259.
60Wang X, Tang H, Bowers JE et al. 2009 Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization Genome research 19 (6) 1026-1032.
61Wilmes 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.
62Winstanley C, Langille MG, Fothergill JL et al. 2009 Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa Genome research 19 (1) 12-23.
63Amadou C, Pascal G, Mangenot S et al. 2008 Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia Genome research 18 (9) 1472-1483.
64Campbell PJ, Stephens PJ, Pleasance ED et al. 2008 Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing Nat Genet
65Durrens P, Nikolski M, Sherman D 2008 Fusion and fission of genes define a metric between fungal genomes PLoS Comput Biol 4 (10) e1000200.
66Salse J, Bolot S, Throude M et al. 2008 Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution Plant Cell 20 (1) 11-24.
67Simmons 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.
68Tobias 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.
69Watanabe M, Mochida K, Kato T et al. 2008 Comparative genomics and reverse genetics analysis reveal indispensable functions of the serine acetyltransferase gene family in Arabidopsis Plant Cell 20 (9) 2484-2496.
70Gherman 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.
71Jaillon O, Aury JM, Noel B et al. 2007 The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Nature 449 (7161) 463-467.
72Kelleher 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.
73Lo I, Denef VJ, Verberkmoes NC et al. 2007 Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria Nature 446 (7135) 537-541.
74Moere AV 2007 Aesthetic Data Visualization as a Resource for Educating Creative Design In Computer-Aided Architectural Design Futures 2007: Proceedings of the 12th International CAADFutures Conference, (ed. A Dong, AV Moere, JS Gero), p. 71-84. Springer (Dordrecht).
75Ostrander EA 2007 Genetics and the Shape of Dogs American Scientist 95 (5) 406-413.
76Sirand-Pugnet P, Citti C, Barre A et al. 2007 Evolution of mollicutes: down a bumpy road with twists and turns Res Microbiol 158 (10) 754-766.
77Aury 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.
78Roest Crollius H, Weissenbach J 2005 Fish genomics and biology Genome research 15 (12) 1675-1682.