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20 imperatives of information design — BioVis 2012

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, based on the Weier et al. article 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.

Hemolytic–Uremic Syndrome Outbreak

Rasko et al. use Circos to show how the E. coli strain implicated in the German outbreak of hemolytic-uremic syndrome varies from other strains in their New England Journal of Medicine paper, where they find that "the genome of the German outbreak strain can be distinguished from those of other O104:H4 strains because it contains a prophage encoding Shiga toxin 2 and a distinct set of additional virulence and antibiotic-resistance factors."

NEJM created an animation that explains the visualizations. The paper was blogged by Pacific Biosciences.

Rasko DA, Webster DR, Sahl JW et al. 2011 Origins of the E. coli Strain Causing an Outbreak of Hemolytic-Uremic Syndrome in Germany The New England journal of medicine published ahead of print:-.

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).

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

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).

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

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

Stephens et al. report on a phenomenon by which a cell accumulates a large number of rearrangements in a single catastrophic event. This phenomenon, which they call chromothripsis, can be seen in at least 2%–3% of all cancers and in about 25% of bone cancers.

1Stephens PJ, Greenman CD, Fu B et al. 2011 Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development Cell 144:27-40.

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.

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.

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.

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

Circos Sniffs out Dog Genetics in American Scientist

The completion of the draft version of the dog genome revealed large overlaps between dog and human genomes. Working with American Scientist, Martin Krzywinski generated an illustration showing blocks of similarity between the two genomes.

The illustration accompanies the article Genetics and the Shape of Dogs, by Elaine Ostrander.

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Circos has been used and referenced in many scientific publications (407 as of June 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
2Albertsen 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
3Albertsen M, Hugenholtz P, Skarshewski A et al. 2013 Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Nature biotechnology
4Alexander RP, Fang G, Rozowsky J et al. 2010 Annotating non-coding regions of the genome Nat Rev Genet 11:559-571.
5Ali 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.
6Alnemer 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.
7Alpar D, de Jong D, Holczer-Nagy Z et al. 2013 Multiplex ligation-dependent probe amplification and fluorescence in situ hybridization are complementary techniques to detect cytogenetic abnormalities in multiple myeloma Genes Chromosomes Cancer
8Alsallkah B, Aigner W, Miksch S et al. 2012 IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE VAST 2012) 18:
9Amadou C, Pascal G, Mangenot S et al. 2008 Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia Genome research 18:1472-1483.
10Angelakis 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.
11Aury JM, Jaillon O, Duret L et al. 2006 Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia Nature 444:171-178.
12Baker M 2010 Epigenome: Mapping in Motion Nature Methods 7:181-186.
13Barnard 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.
14Bass AJ, Lawrence MS, Brace LE et al. 2011 Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion Nat Genet 43:964-968.
15Bellgard 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:e4641.
16Bellieny-Rabelo D, Oliveira AE, Venancio TM 2013 Impact of whole-genome and tandem duplications in the expansion and functional diversification of the f-box family in legumes (fabaceae) PLoS One 8:e55127.
17Bello JP, Grosche P, Muller M et al. 2011 ACM Computers in Entertainment 1:
18Berger MF, Lawrence MS, Demichelis F et al. 2011 The genomic complexity of primary human prostate cancer Nature 470:214-220.
19Bhavani 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.
20Bhavnani 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.
21Biggs PJ, Fearnhead P, Hotter G et al. 2011 Whole-Genome Comparison of Two Campylobacter jejuni Isolates of the Same Sequence Type Reveals Multiple Loci of Different Ancestral Lineage PLoS One 6:e27121.
22Bornelöv 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.
23Borst 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
24Bossen C, Mansson R, Murre C 2012 Chromatin topology and the regulation of antigen receptor assembly Annual review of immunology 30:337-356.
25Bossolini E, Klahre U, Brandenburg A et al. 2011 High resolution linkage maps of the model organism Petunia reveal substantial synteny decay with the related genome of tomato Genome 54:327-340.
26Bousios A, Kourmpetis YA, Pavlidis P et al. 2011 The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story Plant J
27Branham MT, Marzese DM, Laurito SR et al. 2012 Methylation profile of triple-negative breast carcinomas Oncogenesis 1:e17.
28Brastianos PK, Horowitz PM, Santagata S et al. 2013 Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations Nat Genet
29Burkart-Waco D, Josefsson C, Dilkes BR et al. 2011 Hybrid incompatibility in Arabidopsis is determined by a multi-locus genetic network Plant physiology
30Campbell 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 40:722-729.
31Campbell SJ, Gaulton A, Marshall J et al. 2009 Visualizing the drug target landscape Drug Discov Today 15:3-15.
32Cannon EK, Cannon SB 2011 Chromosome visualization tool: a whole genome viewer International journal of plant genomics 2011:373875.
33Carbone L, Harris RA, Vessere GM et al. 2009 Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution PLoS Genet 5:e1000538.
34Carless MA, Griffiths LR 2011 Cytogenetics of Primary Skin Tumors In Molecular Diagnostics in Dermatology and Dermatopathology, (ed. MJ Murphy), p. 57-72. Humana Press.
35Carlier AL, Eberl L 2012 The eroded genome of a Psychotria leaf symbiont: hypotheses about lifestyle and interactions with its plant host Environ Microbiol
36Carver T, Thomson N, Bleasby A et al. 2009 DNAPlotter: circular and linear interactive genome visualization Bioinformatics 25:119-120.
37Catchen JM, Conery JS, Postlethwait JH 2009 Automated identification of conserved synteny after whole-genome duplication Genome research 19:1497-1505.
38Cattoir V, Narasimhan G, Skurnik D et al. 2013 Transcriptional response of mucoid Pseudomonas aeruginosa to human respiratory mucus mBio 3:e00410-00412.
39Cer 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
40Chagne 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.
41Chang 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
42Chen G, Wang C, Shi L et al. 2013 Incorporating the human gene annotations in different databases significantly improved transcriptomic and genetic analyses Rna
43Chen H, Tian Y, Shu W et al. 2012 Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome PLoS One 7:e41374.
44Cheng J, Zeng X, Ren G et al. 2013 CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes BMC Bioinformatics 14:95.
45Chiarle R, Zhang Y, Frock RL et al. 2011 Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells Cell 147:107-119.
46Cho BK, Zengler K, Qiu Y et al. 2009 The transcription unit architecture of the Escherichia coli genome Nature biotechnology 27:1043-1049.
47Claessen JHT. 2011. Visualization of Multivariate Data. In Department of Mathematics and Computer Science, Vol Masters. Eidhoven University of Technology, Eidhoven.
48Clark 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.
49Clark TA, Lu X, Luong K et al. 2013 Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation BMC biology 11:4.
50Clark TA, Murray IA, Morgan RD et al. 2011 Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing Nucleic Acids Research
51Clayton AL, Oakeson KF, Gutin M et al. 2012 A novel human-infection-derived bacterium provides insights into the evolutionary origins of mutualistic insect-bacterial symbioses PLoS Genet 8:e1002990.
52Cockram 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.
53Coelho 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.
54Cooke 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.
55Costello JF, Krzywinski M, Marra MA 2009 A first look at entire human methylomes Nature biotechnology 27:1130-1132.
56Cruz J, Liu Y, Liang Y et al. 2011 BacMap: an up-to-date electronic atlas of annotated bacterial genomes Nucleic Acids Res
57Curtin SJ, Kantar MB, Yoon HW et al. 2012 Co-expression of soybean Dicer-like genes in response to stress and development Funct Integr Genomics
58D'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.
59Damas J, Carneiro J, Goncalves J et al. 2012 Mitochondrial DNA deletions are associated with non-B DNA conformations Nucleic Acids Res
60Darzentas N 2010 Circoletto: visualizing sequence similarity with Circos Bioinformatics 26:2620-2621.
61Daub JT, Hofer T, Cutivet E et al. 2013 Evidence for Polygenic Adaptation to Pathogens in the Human Genome Mol Biol Evol
62Davidson RM, Gowda M, Moghe G et al. 2012 Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution Plant J
63De 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:-.
64Demare LE, Leng J, Cotney J et al. 2013 The genomic landscape of cohesin-associated chromatin interactions Genome research
65den Bakker HC, Cummings CA, Ferreira V et al. 2010 Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss BMC Genomics 11:688.
66Deng N, Goh LK, Wang H et al. 2012 A comprehensive survey of genomic alterations in gastric cancer reveals systematic patterns of molecular exclusivity and co-occurrence among distinct therapeutic targets Gut
67Deng N, Goh LK, Wang H et al. 2012 A comprehensive survey of genomic alterations in gastric cancer reveals systematic patterns of molecular exclusivity and co-occurrence among distinct therapeutic targets Gut 61:673-684.
68Dere E, Lo R, Celius T et al. 2011 Integration of Genome-Wide Computation DRE Search, AhR ChIP-chip and Gene Expression Analyses of TCDD-Elicited Responses in the Mouse Liver BMC Genomics 12:365.
69Dhillon BK, Chiu TA, Laird MR et al. 2013 IslandViewer update: improved genomic island discovery and visualization Nucleic Acids Res
70Diguistini 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:R94.
71Ding L, Ellis MJ, Li S et al. 2010 Genome remodelling in a basal-like breast cancer metastasis and xenograft Nature 464:999-1005.
72Disanto G, Sandve GK, Berlanga-Taylor AJ et al. 2012 Vitamin D receptor binding, chromatin states and association with multiple sclerosis Human molecular genetics
73Dittwald P, Gambin T, Gonzaga-Jauregui C et al. 2012 Inverted low-copy repeats and genome instability-A genome-wide analysis Human mutation
74Djebali S, Lagarde J, Kapranov P et al. 2012 Evidence for transcript networks composed of chimeric RNAs in human cells PLoS One 7:e28213.
75Dohm JC, Lange C, Holtgrawe D et al. 2012 Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris) Plant J 70:528-540.
76Du J, Tian Z, Sui Y et al. 2012 Pericentromeric Effects Shape the Patterns of Divergence, Retention, and Expression of Duplicated Genes in the Paleopolyploid Soybean Plant Cell
77Duan Z, Andronescu M, Schutz K et al. 2010 A three-dimensional model of the yeast genome Nature 465:363-367.
78Durrens P, Nikolski M, Sherman D 2008 Fusion and fission of genes define a metric between fungal genomes PLoS Comput Biol 4:e1000200.
79Edgren H, Murumagi A, Kangaspeska S et al. 2011 Identification of fusion genes in breast cancer by paired-end RNA-sequencing Genome Biol 12:R6.
80Editorial board of I 2013 Perspectives on design creativity and innovation research International Journal of Design Creativity and Innovation 1:1-42.
81Egan JB, Shi CX, Tembe W et al. 2012 Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides Blood 120:1060-1066.
82Ellis MJ, Ding L, Shen D et al. 2012 Whole-genome analysis informs breast cancer response to aromatase inhibition Nature 486:353-360.
83Ellwood 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.
84Enroth S, Bornelov S, Wadelius C et al. 2012 Combinations of histone modifications mark exon inclusion levels PLoS One 7:e29911.
85Eswaran J, Cyanam D, Mudvari P et al. 2012 Transcriptomic landscape of breast cancers through mRNA sequencing Scientific reports 2:264.
86Evrony GD, Cai X, Lee E et al. 2012 Single-neuron sequencing analysis of l1 retrotransposition and somatic mutation in the human brain Cell 151:483-496.
87Falentin 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:e11748.
88Fang Y, Wu H, Zhang T et al. 2012 A Complete Sequence and Transcriptomic Analyses of Date Palm (Phoenix dactylifera L.) Mitochondrial Genome PLoS One 7:e37164.
89Feichtinger 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.
90Ferreira de Carvalho J, Poulain J, Da Silva C et al. 2012 Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae) Heredity
91Feulner PG, Chain FJ, Panchal M et al. 2012 Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks Mol Ecol
92Flannery MC 2009 Writing Across Rome The American Biology Teacher 71:52-55.
93Flint 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.
94Forbes 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:D652-657.
95Franklin S, Chen H, Mitchell-Jordan S et al. 2012 Quantitative analysis of the chromatin proteome in disease reveals remodeling principles and identifies high mobility group protein B2 as a regulator of hypertrophic growth Molecular & cellular proteomics : MCP
96Frech C, Chen N 2011 Genome comparison of human and non-human malaria parasites reveals species subset-specific genes potentially linked to human disease PLoS Comput Biol 7:e1002320.
97Freeman 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.
98Furney SJ, Turajlic S, Fenwick K et al. 2012 Genomic Characterisation of Acral Melanoma Cell Lines Pigment cell & melanoma research
99Gamwell 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.
100Gao F, Wei Z, An W et al. 2013 The interactomes of POU5F1 and SOX2 enhancers in human embryonic stem cells Scientific reports 3:1588.
101Gedye 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.
102Gherman A, Chen PE, Teslovich TM et al. 2007 Population bottlenecks as a potential major shaping force of human genome architecture PLoS Genet 3:e119.
103Giannuzzi 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.
104Giannuzzi G, D'Addabbo P, Gasparro M et al. 2011 Analysis of high-identity segmental duplications in the grapevine genome BMC Genomics 12:436.
105Giorno F, Guerriero G, Baric S et al. 2012 Heat shock transcriptional factors in Malus domestica: identification, classification and expression analysis BMC Genomics 13:639.
106Goodwin SB, Ben M'barek S, Dhillon B et al. 2011 Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis PLoS Genet 7:e1002070.
107Grad YH, Godfrey P, Cerquiera GC et al. 2013 Comparative Genomics of Recent Shiga Toxin-Producing Escherichia coli O104:H4: Short-Term Evolution of an Emerging Pathogen mBio 4:
108Grzymski JJ, Riesenfeld CS, Williams TJ et al. 2012 A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters The ISME journal
109Guo Z, Tao X, Yin C et al. 2013 National borders effectively halt the spread of rabies: the current rabies epidemic in china is dislocated from cases in neighboring countries PLoS neglected tropical diseases 7:e2039.
110Gutierrez-Gonzalez JJ, Garvin DF 2011 The Plant Genome 4:178-190.
111Guyot R, Lefebvre-Pautigny F, Dubreuil-Tranchant C et al. 2012 Ancestral Synteny Shared between Distantly-Related Plant Species from the Asterid (Coffea canephora and Solanum sp.) and Rosid (Vitis vinifera) Clades BMC Genomics 13:103.
112Hacquard S, Kracher B, Maekawa T et al. 2013 Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts Proc Natl Acad Sci U S A
113Hallin PF, Staerfeldt H-H, Rotenberg E et al. 2009 GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes Stand Genomic Sci 1:204-215.
114Hampton 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 19:167-177.
115Hayden 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.
116Hayden KE, Strome ED, Merrett SL et al. 2013 Sequences associated with centromere competency in the human genome Molecular and cellular biology 33:763-772.
117Hayward MR, Jansen VA, Woodward MJ 2013 Comparative genomics of Salmonella enterica serovars Derby and Mbandaka, two prevalent serovars associated with different livestock species in the UK BMC Genomics 14:365.
118Hennemann S 2013 Information-rich visualisation of dense geographical networks Journal of Maps 1-8.
119Herbig A, Jager G, Battke F et al. 2012 GenomeRing: alignment visualization based on SuperGenome coordinates Bioinformatics 28:i7-i15.
120Heyn 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:
121Higgs BW, Zhu W, Richman L et al. 2011 Identification of activated cytokine pathways in the blood of systemic lupus erythematosus, myositis, rheumatoid arthritis, and scleroderma patients International Journal of Rheumatic Diseases no-no.
122Hillmer AM, Yao F, Inaki K et al. 2011 Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes Genome research 21:665-675.
123Hiltemann S, McClellan EA, van Nijnatten J et al. 2013 iFUSE: integrated FUSion gene Explorer Bioinformatics
124Hirsch 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.
125Ho AS, Kannan K, Roy DM et al. 2013 The mutational landscape of adenoid cystic carcinoma Nat Genet
126Holmfeldt L, Wei L, Diaz-Flores E et al. 2013 The genomic landscape of hypodiploid acute lymphoblastic leukemia Nat Genet
127Hou Y, Song L, Zhu P et al. 2012 Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm Cell 148:873-885.
128Howe K Clark MD Torroja CF et al. 2013 The zebrafish reference genome sequence and its relationship to the human genome Nature
129Hsueh A, Rauch R 2012 Ovarian Kaleidoscope Database: 10 Years and Beyond Biology of reproduction
130Hu FZ, Eutsey R, Ahmed A et al. 2012 In vivo capsular switch in Streptococcus pneumoniae - analysis by whole genome sequencing PLoS One 7:e47983.
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