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20 imperatives of information design — BioVis 2012

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.

Yang D, Sun Y, Hu L et al. 2013 Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer Cancer cell 23:186-199

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.

citation list | image gallery | press highlights

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.

Bollongino R, Nehlich O, Richards MP et al. 2013 2000 years of parallel societies in Stone Age Central Europe Science 342:479-481.

Circos in 54 million pixels

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

Ruddle RA, Fateen W, Treanor Det al.. 2013. Leveraging Wall-sized High-Resolution Displays for Comparative Genomics Analyses of Copy Number Variation. In IEEE Symposium on Biological Data Visualization, Atlanta, GA.

Circos Tracks CO2 Emissions

Kanemoto et al. report on the disturbing trend of emissions leakage, in which developing countries are displacing emissions intensive production offshore.

The report confirms previous findings that adjusting for trade, developed countries emissions have increased, not decreased. A connection is made to the kind of emissions displacement that has already occurred for air pollution, where despite aggressive legislation in major emitters total global air pollution emissions have increased.

The conclusion warns us that "if regulatory policies do not account for embodied imports, global emissions are likely to rise even if developed countries emitters enforce strong national emissions targets."

Kanemoto K, Moran D, Lenzen M et al. 2013 International trade undermines national emission reduction targets: New evidence from air pollution Global Environmental Change

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.

Ming R, Vanburen R, Liu Y et al. 2013 Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Genome Biol 14:R41.

6.9e11 g of oil and Circos was there

Rivers et a. describe the effects of the Deepwater Horizon blowout on the microbial blooms of petroleum-degrading bacteria.

By sequencing 66 million community transcripts, the identity of metabolically active microbes and their roles in petroleum consumption was revealed.

Rivers AR, Sharma S, Tringe SG et al. 2013 Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill The ISME journal

Plants Love Circos

Circos frequently appears in plant literature, twice on the cover of Plant Biotechnology Journal in the last year.

Rai KM, Singh SK, Bhardwaj A et al. 2013 Large-scale resource development in Gossypium hirsutum L. by 454 sequencing of genic-enriched libraries from six diverse genotypes Plant biotechnology journal

Bekele WA, Wieckhorst S, Friedt W et al. 2013 High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array Plant biotechnology journal

Circos has appeared 8 times each in the Plant Journal and Plant Cell.

Circos for R

Zhang et al. implement Circos in R.

Same round shape you expect. And now, in everyone's favourite open source statistics and data analysis environment.

CRAN RCircos package

Zhang H, Meltzer P, Davis S 2013 RCircos: an R package for Circos 2D track plots BMC Bioinformatics 14:244.

Circos Interchange Diagrams — Networks and Flow

Zeng et al. introduce a new type of visualization based on Circos, the interchange diagram, in their paper Visualizing Interchange Patterns in Massive Movement Data.

The design is applied to displaying movement data, such as daily trips made by passengers in a city. By incorporating interactivity, this visualization method is helpful to understand interchange patterns at different spatial (between trains, between cities) and time scales (different times of day).

Circos has been used for urban planning before. The town of Caceres in Spain has used Circos to communicate their urban planning strategy.

project website

Zeng W, Fu C-W, Arisona SM et al. 2013 Visualizing Interchange Patterns in Massive Movement Data Computer Graphics Forum 32:271-280

Circos connects to the connectome

Methods to visualize the connectome are reviewed in Craddock et al — Circos is one of them.

Craddock RC, Jbabdi S, Yan C-G et al. 2013 Imaging human connectomes at the macroscale Nat Meth 10:524-539.

The use of Circos for showing the connectome was introduced by Irimia et al. in Circular representation of human cortical networks for subject and population-level connectomic visualization.

A good layman description of the work can be found at the neurosceptic blog.

Irimia A, Chambers MC, Torgerson CM et al. 2012 Circular representation of human cortical networks for subject and population-level connectomic visualization NeuroImage, Irimia A, Chambers MC, Torgerson CM et al. 2012 Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury Frontiers in Neurology 3

Circos is the Method for Visualizing Translocations

Genomic rearrangements can cause disease and are implicated in many cancers. Being able to see the patterns in these changes across samples and patients is important.

In the review article End-joining, Translocations and Cancer, Bunting and Nussenzweig demonstrate how compositing the genome circularly adds value and clarity to the presentation.

Bunting SF, Nussenzweig A 2013 End-joining, translocations and cancer Nat Rev Cancer

Circos Paints Chromosomes of Capsella Rubella

Slotte et al. use Circos to show the genomic structures, chromosome painting and comparative genomic mapping in C. rubella, A. lyrata and A. thaliana.

Their figure illustrates how Circos is effective at showing two-way comparisons of syntenic structure. For three-way comparison, consider hive plots.

Slotte T, Hazzouri KM, Agren JA et al. 2013 The Capsella rubella genome and the genomic consequences of rapid mating system evolution Nat Genet

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."

Weier C, Haffner MC, Mosbruger T et al. 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".

Wyatt AW, Mo F, Wang Y et al. 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.

Pardoe, HR, Berg, AT, and Jackson, GD 2013Sodium valproate use is associated with reduced parietal lobe thickness and brain volume Neurology 80(20):1895-1900.

Improving miR-mRNA Predictions

Rijlaarsdam et al. describe an algorithm for improving miR-mRNA predictions.

"Algorithms predicting miR-mRNA interactions generate high numbers of possible interactions, many of which might be non-existent or irrelevant in a certain biological context. It is desirable to develop a transparent, user-friendly, unbiased tool to enrich miR-mRNA predictions."

Rijlaarsdam MA, Rijlaarsdam DJ, Gillis AJ et al. 2013 miMsg: a target enrichment algorithm for predicted miR-mRNA interactions based on relative ranking of matched expression data Bioinformatics

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.

Imielinski M, Berger AH, Hammerman PS et al. 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).

Cockram J, Thiel T, Steuernagel B et al. 2012 Genome Dynamics Explain the Evolution of Flowering Time CCT Domain Gene Families in the Poaceae PLoS One 7:e45307.

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.

1Roychowdhury S, Iyer MK, Robinson DR et al. 2011 Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study Science Translational Medicine 3:111ra121.

Towards a Human Pan-Genome

As reported in Wired, Li et al. use Circos to visualize the comparison of structural variation in two sequenced human genomes: Asian and Yoruban (African). It's been over 10 years since the first reference genome (comprising DNA from multiple individuals) was reported. Technological advancements have made it possible to now sequence 1000's of human genomes to identify genetic variations for tracing evolution, determining population patterns, and assessing disease susceptibility and other phenotypic traits.

Li Y, Zheng H, Luo R et al. 2011 Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly Nature biotechnology 29:723-730.

Li R, Li Y, Zheng H et al. 2010 Building the sequence map of the human pan-genome Nature biotechnology 28:57-63.

Circos has been used and referenced in many scientific publications (522 as of October 2013, see published images).

Journals with the most papers with Circos images are

Circos in Scientific Literature

1Aboukhalil R, Fendler B, Atwal GS 2013 ArXiv e-prints
4Albertsen M, Hansen LB, Saunders AM et al. 2011 A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal The ISME journal
5Albertsen M, Hugenholtz P, Skarshewski A et al. 2013 Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Nature biotechnology
6Alexander RP, Fang G, Rozowsky J et al. 2010 Annotating non-coding regions of the genome Nat Rev Genet 11:559-571.
7Ali A, Soares S, Barbosa E et al. 2013 Microbial Comparative Genomics: An Overview of Tools and Insights Into The Genus Corynebacterium J Bacteriology & Parasitology 4:167.
8Alnemer LM, Seetan RI, Bassi FM et al. 2013 Wheat Zapper: a flexible online tool for colinearity studies in grass genomes Funct Integr Genomics 13:11-17.
9AlNoamany Y, AlSum A, Weigle MC et al. 2013 Who and What Links to the Internet Archive arxiv 1309.4016:
12Angelakis E, Million M, D’Amato F et al. 2012 Q fever and pregnancy: disease, prevention, and strain specificity European Journal of Clinical Microbiology & Infectious Diseases 1-8.
13Aury JM, Jaillon O, Duret L et al. 2006 Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia Nature 444:171-178.
14Baker M 2010 Epigenome: Mapping in Motion Nature Methods 7:181-186.
15Barnard RT, Loftis KL, Martin RS et al. 2013 Development of a robust mapping between AIS 2+ and ICD-9 injury codes Accident Analysis & Prevention 52:133-143.
16Bass AJ, Lawrence MS, Brace LE et al. 2011 Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion Nat Genet 43:964-968.
17Batelli G, Oh D-H, D’Urzo M et al. 2014 Using Arabidopsis-Related Model Species (ARMS): Growth, Genetic Transformation, and Comparative Genomics In Arabidopsis Protocols, (ed. JJ Sanchez-Serrano, J Salinas), p. 27-51. Humana Press.
18Beck J, Hennecke S, Bornemann-Kolatzki K et al. 2013 Genome Aberrations in Canine Mammary Carcinomas and Their Detection in Cell-Free Plasma DNA PLoS One 8:e75485.
20Bekele WA, Fiedler K, Shiringani A et al. 2013 Unravelling the genetic complexity of sorghum seedling development under low temperature conditions Plant, cell & environment
21Bekele WA, Wieckhorst S, Friedt W et al. 2013 High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array Plant biotechnology journal
24Bello JP, Grosche P, Muller M et al. 2011 ACM Computers in Entertainment 1:
26Bhatt AS, Freeman SS, Herrera AF et al. 2013 Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome The New England journal of medicine 369:517-528.
27Bhavani SK, Drake J, Bellela G et al.. 2013. How Complimentary Bipartite Visual Analytical Representations Reveal Patterns in Cytokine Expression: A Case Study in Rickettsioses. In AMIA Proceedings.
28Bhavnani S, Drake J, Divekar R 2014 The Role of Visual Analytics in Asthma Phenotyping and Biomarker Discovery In Heterogeneity in Asthma, (ed. AR Brasier), p. 289-305. Springer US.
29Bhavnani SK, Bellala G, Victor S et al. 2012 The role of complementary bipartite visual analytical representations in the analysis of SNPs: a case study in ancestral informative markers Journal of the American Medical Informatics Association 19:e5-e12.
33Bollongino R, Nehlich O, Richards MP et al. 2013 2000 years of parallel societies in Stone Age Central Europe Science 342:479-481.
34Borkin MA, Yeh CS, Boyd M et al.. 2013. Evaluation of Filesystem Provenance Visualization Tools. In IEEE Information Visualization 2013, Atlanta, GA.
35Bornelöv S, Enroth S, Komorowski J 2012 Visualization of Rules in Rule-Based Classifiers Intelligent Decision Technologies In J Watada, T Watanabe, G Phillips-Wren, RJ Howlett, LC Jain), p. 329-338. Springer Berlin Heidelberg.
36Borst L, Wesolowska A, Joshi T et al. 2012 Genome-wide analysis of cytogenetic aberrations in ETV6/RUNX1-positive childhood acute lymphoblastic leukaemia British journal of haematology
37Bossen C, Mansson R, Murre C 2012 Chromatin topology and the regulation of antigen receptor assembly Annual review of immunology 30:337-356.
40Branham MT, Marzese DM, Laurito SR et al. 2012 Methylation profile of triple-negative breast carcinomas Oncogenesis 1:e17.
41Brastianos PK, Horowitz PM, Santagata S et al. 2013 Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations Nat Genet
42Brown AM, Huynh LY, Bolender CM et al. 2013 Population genomics of a symbiont in the early stages of a pest invasion Mol Ecol
43Bunting SF, Nussenzweig A 2013 End-joining, translocations and cancer Nat Rev Cancer
44Burkart-Waco D, Josefsson C, Dilkes BR et al. 2011 Hybrid incompatibility in Arabidopsis is determined by a multi-locus genetic network Plant physiology
45Busemeyer L, Ruckelshausen A, Moller K et al. 2013 Precision phenotyping of biomass accumulation in triticale reveals temporal genetic patterns of regulation Scientific reports 3:2442.
47Bzhalava D, Johansson H, Ekstrom J et al. 2013 Unbiased approach for virus detection in skin lesions PLoS One 8:e65953.
49Campbell SJ, Gaulton A, Marshall J et al. 2009 Visualizing the drug target landscape Drug Discov Today 15:3-15.
50Cannon EK, Cannon SB 2011 Chromosome visualization tool: a whole genome viewer International journal of plant genomics 2011:373875.
52Carless MA, Griffiths LR 2011 Cytogenetics of Primary Skin Tumors In Molecular Diagnostics in Dermatology and Dermatopathology, (ed. MJ Murphy), p. 57-72. Humana Press.
54Carver T, Thomson N, Bleasby A et al. 2009 DNAPlotter: circular and linear interactive genome visualization Bioinformatics 25:119-120.
55Catchen JM, Conery JS, Postlethwait JH 2009 Automated identification of conserved synteny after whole-genome duplication Genome research 19:1497-1505.
56Cattoir V, Narasimhan G, Skurnik D et al. 2013 Transcriptional response of mucoid Pseudomonas aeruginosa to human respiratory mucus mBio 3:e00410-00412.
57Cer RZ, Donohue DE, Mudunuri US et al. 2012 Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools Nucleic Acids Res
58Chagne D, Crowhurst RN, Troggio M et al. 2012 Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple PLoS One 7:e31745.
59Chang VY, Federman N, Martinez-Agosto J et al. 2012 Whole exome sequencing of pediatric gastric adenocarcinoma reveals an atypical presentation of Li-Fraumeni syndrome Pediatric blood & cancer
60Che D, Wang H 2013 GIV: A Tool for Genomic Islands Visualization Bioinformation 9:879-882.
63Chen R, Giliani S, Lanzi G et al. 2013 Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias The Journal of allergy and clinical immunology 132:656-664 e617.
64Cheng J, Zeng X, Ren G et al. 2013 CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes BMC Bioinformatics 14:95.
66Chin CS, Sorenson J, Harris JB et al. 2011 The origin of the Haitian cholera outbreak strain The New England journal of medicine 364:33-42.
67Cho BK, Zengler K, Qiu Y et al. 2009 The transcription unit architecture of the Escherichia coli genome Nature biotechnology 27:1043-1049.
68Claessen JHT. 2011. Visualization of Multivariate Data. In Department of Mathematics and Computer Science, Vol Masters. Eidhoven University of Technology, Eidhoven.
69Clark 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:e1000832.
71Clark TA, Murray IA, Morgan RD et al. 2011 Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing Nucleic Acids Research
73Cockram J, Thiel T, Steuernagel B et al. 2012 Genome Dynamics Explain the Evolution of Flowering Time CCT Domain Gene Families in the Poaceae PLoS One 7:e45307.
74Coelho AC, Boisvert S, Mukherjee A et al. 2012 Multiple Mutations in Heterogeneous Miltefosine-Resistant Leishmania major Population as Determined by Whole Genome Sequencing PLoS neglected tropical diseases 6:e1512.
75Cooke T, Horberry T, Burgess-Limerick R. 2012. Revisiting injury narratives to pinpoint human factor issues associated with surface mobile mining equipment. In Occupational Safety in Transport Conference 2012, Gold Coast, QLD, Australia.
76Costello JF, Krzywinski M, Marra MA 2009 A first look at entire human methylomes Nature biotechnology 27:1130-1132.
77Cruz J, Liu Y, Liang Y et al. 2011 BacMap: an up-to-date electronic atlas of annotated bacterial genomes Nucleic Acids Res
78Curtin SJ, Kantar MB, Yoon HW et al. 2012 Co-expression of soybean Dicer-like genes in response to stress and development Funct Integr Genomics
79D'Hont A, Denoeud F, Aury J-M et al. 2012 The banana (Musa acuminata) genome and the evolution of monocotyledonous plants Nature 488:213-217.
80Damas J, Carneiro J, Goncalves J et al. 2012 Mitochondrial DNA deletions are associated with non-B DNA conformations Nucleic Acids Res
81Darzentas N 2010 Circoletto: visualizing sequence similarity with Circos Bioinformatics 26:2620-2621.
82Daub JT, Hofer T, Cutivet E et al. 2013 Evidence for Polygenic Adaptation to Pathogens in the Human Genome Mol Biol Evol
84Dayem Ullah AZ, Cutts RJ, Ghetia M et al. 2013 The pancreatic expression database: recent extensions and updates Nucleic Acids Res
85De Fazio S, Bartonicek N, Di Giacomo M et al. 2011 The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements Nature advanced online:-.
86Demaere MZ, Williams TJ, Allen MA et al. 2013 High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake Proc Natl Acad Sci U S A
87Demare LE, Leng J, Cotney J et al. 2013 The genomic landscape of cohesin-associated chromatin interactions Genome research
88Demiralp C, Hayden E, Hammerbacher J et al.. 2013. invis: Exploring High-Dimensional RNA Sequences from In Vitro Selection. In IEEE Symposium on Biological Data Visualization, Atlanta, GA.
90den Bakker HC, Desjardins CA, Griggs AD et al. 2013 Evolutionary Dynamics of the Accessory Genome of Listeria monocytogenes PLoS One 8:e67511.
94Dhillon BK, Chiu TA, Laird MR et al. 2013 IslandViewer update: improved genomic island discovery and visualization Nucleic Acids Res
96Ding L, Ellis MJ, Li S et al. 2010 Genome remodelling in a basal-like breast cancer metastasis and xenograft Nature 464:999-1005.
97Disanto G, Sandve GK, Berlanga-Taylor AJ et al. 2012 Vitamin D receptor binding, chromatin states and association with multiple sclerosis Human molecular genetics
98Dittwald P, Gambin T, Gonzaga-Jauregui C et al. 2012 Inverted low-copy repeats and genome instability-A genome-wide analysis Human mutation
99Djebali S, Lagarde J, Kapranov P et al. 2012 Evidence for transcript networks composed of chimeric RNAs in human cells PLoS One 7:e28213.
100Dobbins SE, Sherborne AL, Ma YP et al. 2013 The silent mutational landscape of infant MLL-AF4 pro-B acute lymphoblastic leukemia Genes Chromosomes Cancer 52:954-960.
103Duan Z, Andronescu M, Schutz K et al. 2010 A three-dimensional model of the yeast genome Nature 465:363-367.
104Durrens P, Nikolski M, Sherman D 2008 Fusion and fission of genes define a metric between fungal genomes PLoS Comput Biol 4:e1000200.
105Edgren H, Murumagi A, Kangaspeska S et al. 2011 Identification of fusion genes in breast cancer by paired-end RNA-sequencing Genome Biol 12:R6.
106Editorial board of I 2013 Perspectives on design creativity and innovation research International Journal of Design Creativity and Innovation 1:1-42.
108Eichten SR, Briskine R, Song J et al. 2013 Epigenetic and genetic influences on DNA methylation variation in maize populations Plant Cell 25:2783-2797.
109Ellis MJ, Ding L, Shen D et al. 2012 Whole-genome analysis informs breast cancer response to aromatase inhibition Nature 486:353-360.
110Ellwood SR, Liu Z, Syme RA et al. 2010 A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres Genome Biol 11:R109.
111Enroth S, Bornelov S, Wadelius C et al. 2012 Combinations of histone modifications mark exon inclusion levels PLoS One 7:e29911.
112Enyeart PJ, Chirieleison SM, Dao MN et al. 2013 Generalized bacterial genome editing using mobile group II introns and Cre-lox Mol Syst Biol 9:
113Eswaran J, Cyanam D, Mudvari P et al. 2012 Transcriptomic landscape of breast cancers through mRNA sequencing Scientific reports 2:264.
114Etherington GJ, MacLean D 2013 SVGenes: a library for rendering genomic features in scalable vector graphic format Bioinformatics 29:1890-1892.
119Feichtinger J, Thallinger GG, McFarlane RJ et al. 2012 Microarray Meta-Analysis: From Data to Expression to Biological Relationships Computational Medicine In Z Trajanoski), p. 59-77. Springer Vienna.
123Flannery MC 2009 Writing Across Rome The American Biology Teacher 71:52-55.
124Flint A, Butcher J, Clarke C et al. 2010 Use of a rabbit soft tissue chamber model to investigate campylobacter jejuni-host interactions Front Microbiol 1:126.
125Flot JF, Hespeels B, Li X et al. 2013 Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga Nature 500:453-457.
129Freeman JD, Warren RL, Webb JR et al. 2009 Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing Genome research 19:1817-1824.
130Furney SJ, Turajlic S, Fenwick K et al. 2012 Genomic Characterisation of Acral Melanoma Cell Lines Pigment cell & melanoma research
131Gamwell LF, Gambaro K, Merziotis M et al. 2013 Small cell ovarian carcinoma: genomic stability and responsiveness to therapeutics Orphanet journal of rare diseases 8:33.
132Gao D, Middleton R, Rasko JE et al. 2013 miREval 2.0: a web tool for simple microRNA prediction in genome sequences Bioinformatics
133Gao F, Wei Z, An W et al. 2013 The interactomes of POU5F1 and SOX2 enhancers in human embryonic stem cells Scientific reports 3:1588.
135Gedye K, Gonzalez-Hernandez J, Ban Y et al. 2010 Investigation of the Transcriptome of Prairie Cord Grass, a New Cellulosic Biomass Crop Plant Gen 3:69-80.
136Gherman A, Chen PE, Teslovich TM et al. 2007 Population bottlenecks as a potential major shaping force of human genome architecture PLoS Genet 3:e119.
137Ghosh S, Matsuoka Y, Asai Y et al. 2013 Toward an integrated software platform for systems pharmacology Biopharmaceutics & drug disposition
138Giannuzzi G, Cardone MF, Ventura M et al. 2013 Read-depth Methodology for the Analysis of Recent Segmental Duplications in the Grapevine Genome In Sequence and Genome Analysis I - Humans, Animals and Plants, (ed. i Press), p. iConcept Press.
139Giannuzzi G, D'Addabbo P, Gasparro M et al. 2011 Analysis of high-identity segmental duplications in the grapevine genome BMC Genomics 12:436.
141Goecks J, Eberhard C, Too T et al. 2013 Web-based visual analysis for high-throughput genomics BMC Genomics 14:397.
147Gutierrez-Gonzalez JJ, Garvin DF 2011 The Plant Genome 4:178-190.
151Hallin PF, Staerfeldt H-H, Rotenberg E et al. 2009 GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes Stand Genomic Sci 1:204-215.
153Hayden KE 2012 Human centromere genomics: now it's personal Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 20:621-633.
154Hayden KE, Strome ED, Merrett SL et al. 2013 Sequences associated with centromere competency in the human genome Molecular and cellular biology 33:763-772.
156Hegedusova E, Brejova B, Tomaska L et al. 2013 Mitochondrial genome of the basidiomycetous yeast Jaminaea angkorensis Curr Genet
157Hennemann S 2013 Information-rich visualisation of dense geographical networks Journal of Maps 1-8.
158Herbig A, Jager G, Battke F et al. 2012 GenomeRing: alignment visualization based on SuperGenome coordinates Bioinformatics 28:i7-i15.
160Heyn H, Moran S, Hernando-Herraez I et al. 2013 DNA methylation contributes to natural human variation Genome research 23:1363-1372.
161Heyn H, Vidal E, Sayols S et al. 2012 Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient Epigenetics : official journal of the DNA Methylation Society 7:
164Hiltemann S, McClellan EA, van Nijnatten J et al. 2013 iFUSE: integrated FUSion gene Explorer Bioinformatics
165Hirsch D, Kemmerling R, Davis S et al. 2013 Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma Cancer research 73:1454-1460.
166Ho AS, Kannan K, Roy DM et al. 2013 The mutational landscape of adenoid cystic carcinoma Nat Genet
167Holmfeldt L, Wei L, Diaz-Flores E et al. 2013 The genomic landscape of hypodiploid acute lymphoblastic leukemia Nat Genet
170Hsueh A, Rauch R 2012 Ovarian Kaleidoscope Database: 10 Years and Beyond Biology of reproduction
172Hu Y, Wang K, He X et al. 2010 A probabilistic framework for aligning paired-end RNA-seq data Bioinformatics 26:1950-1957.
173Hur M, Campbell AA, Almeida-de-Macedo M et al. 2013 A global approach to analysis and interpretation of metabolic data for plant natural product discovery Natural product reports
177Imielinski M, Berger AH, Hammerman PS et al. 2012 Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing Cell 150:1107-1120.
178Irimia A, Chambers MC, Torgerson CM et al. 2012 Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury Frontiers in Neurology 3:
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