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20 imperatives of information design — BioVis 2012

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 numerous scientific publications (376 as of Apr 2012, see published images).

Journals with the most papers with Circos images are

Circos in Scientific Literature

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10Baker M 2010 Epigenome: Mapping in Motion Nature Methods 7:181-186.
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13Bellgard 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.
14Bellieny-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.
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19Biggs 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.
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21Borst 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
22Bossen C, Mansson R, Murre C 2012 Chromatin topology and the regulation of antigen receptor assembly Annual review of immunology 30:337-356.
23Bossolini 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.
24Bousios 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
25Branham MT, Marzese DM, Laurito SR et al. 2012 Methylation profile of triple-negative breast carcinomas Oncogenesis 1:e17.
26Brastianos PK, Horowitz PM, Santagata S et al. 2013 Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations Nat Genet
27Burkart-Waco D, Josefsson C, Dilkes BR et al. 2011 Hybrid incompatibility in Arabidopsis is determined by a multi-locus genetic network Plant physiology
28Campbell 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.
29Campbell SJ, Gaulton A, Marshall J et al. 2009 Visualizing the drug target landscape Drug Discov Today 15:3-15.
30Cannon EK, Cannon SB 2011 Chromosome visualization tool: a whole genome viewer International journal of plant genomics 2011:373875.
31Carbone 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.
32Carless MA, Griffiths LR 2011 Cytogenetics of Primary Skin Tumors In Molecular Diagnostics in Dermatology and Dermatopathology, (ed. MJ Murphy), p. 57-72. Humana Press.
33Carlier AL, Eberl L 2012 The eroded genome of a Psychotria leaf symbiont: hypotheses about lifestyle and interactions with its plant host Environ Microbiol
34Carver T, Thomson N, Bleasby A et al. 2009 DNAPlotter: circular and linear interactive genome visualization Bioinformatics 25:119-120.
35Catchen JM, Conery JS, Postlethwait JH 2009 Automated identification of conserved synteny after whole-genome duplication Genome research 19:1497-1505.
36Cattoir V, Narasimhan G, Skurnik D et al. 2013 Transcriptional response of mucoid Pseudomonas aeruginosa to human respiratory mucus mBio 3:e00410-00412.
37Cer 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
38Chagne 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.
39Chang 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
40Chen G, Wang C, Shi L et al. 2013 Incorporating the human gene annotations in different databases significantly improved transcriptomic and genetic analyses Rna
41Chen 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.
42Cheng J, Zeng X, Ren G et al. 2013 CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes BMC Bioinformatics 14:95.
43Chiarle 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.
44Cho BK, Zengler K, Qiu Y et al. 2009 The transcription unit architecture of the Escherichia coli genome Nature biotechnology 27:1043-1049.
45Claessen JHT. 2011. Visualization of Multivariate Data. In Department of Mathematics and Computer Science, Vol Masters. Eidhoven University of Technology, Eidhoven.
46Clark 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.
47Clark 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.
48Clark TA, Murray IA, Morgan RD et al. 2011 Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing Nucleic Acids Research
49Clayton 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.
50Cockram 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.
51Coelho 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.
52Cooke 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.
53Costello JF, Krzywinski M, Marra MA 2009 A first look at entire human methylomes Nature biotechnology 27:1130-1132.
54Cruz J, Liu Y, Liang Y et al. 2011 BacMap: an up-to-date electronic atlas of annotated bacterial genomes Nucleic Acids Res
55Curtin SJ, Kantar MB, Yoon HW et al. 2012 Co-expression of soybean Dicer-like genes in response to stress and development Funct Integr Genomics
56D'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.
57Damas J, Carneiro J, Goncalves J et al. 2012 Mitochondrial DNA deletions are associated with non-B DNA conformations Nucleic Acids Res
58Darzentas N 2010 Circoletto: visualizing sequence similarity with Circos Bioinformatics 26:2620-2621.
59Davidson RM, Gowda M, Moghe G et al. 2012 Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution Plant J
60De 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:-.
61den 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.
62Deng 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
63Deng 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.
64Dere 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.
65Diguistini 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.
66Ding L, Ellis MJ, Li S et al. 2010 Genome remodelling in a basal-like breast cancer metastasis and xenograft Nature 464:999-1005.
67Disanto G, Sandve GK, Berlanga-Taylor AJ et al. 2012 Vitamin D receptor binding, chromatin states and association with multiple sclerosis Human molecular genetics
68Dittwald P, Gambin T, Gonzaga-Jauregui C et al. 2012 Inverted low-copy repeats and genome instability-A genome-wide analysis Human mutation
69Djebali S, Lagarde J, Kapranov P et al. 2012 Evidence for transcript networks composed of chimeric RNAs in human cells PLoS One 7:e28213.
70Dohm 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.
71Du 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
72Duan Z, Andronescu M, Schutz K et al. 2010 A three-dimensional model of the yeast genome Nature 465:363-367.
73Durrens P, Nikolski M, Sherman D 2008 Fusion and fission of genes define a metric between fungal genomes PLoS Comput Biol 4:e1000200.
74Edgren H, Murumagi A, Kangaspeska S et al. 2011 Identification of fusion genes in breast cancer by paired-end RNA-sequencing Genome Biol 12:R6.
75Editorial board of I 2013 Perspectives on design creativity and innovation research International Journal of Design Creativity and Innovation 1:1-42.
76Egan 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.
77Ellis MJ, Ding L, Shen D et al. 2012 Whole-genome analysis informs breast cancer response to aromatase inhibition Nature 486:353-360.
78Ellwood 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.
79Enroth S, Bornelov S, Wadelius C et al. 2012 Combinations of histone modifications mark exon inclusion levels PLoS One 7:e29911.
80Eswaran J, Cyanam D, Mudvari P et al. 2012 Transcriptomic landscape of breast cancers through mRNA sequencing Scientific reports 2:264.
81Evrony 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.
82Falentin 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.
83Fang 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.
84Feichtinger 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.
85Ferreira 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
86Feulner 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
87Flannery MC 2009 Writing Across Rome The American Biology Teacher 71:52-55.
88Flint 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.
89Forbes 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.
90Franklin 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
91Frech 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.
92Freeman 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.
93Furney SJ, Turajlic S, Fenwick K et al. 2012 Genomic Characterisation of Acral Melanoma Cell Lines Pigment cell & melanoma research
94Gamwell 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.
95Gao F, Wei Z, An W et al. 2013 The interactomes of POU5F1 and SOX2 enhancers in human embryonic stem cells Scientific reports 3:1588.
96Gedye 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.
97Gherman A, Chen PE, Teslovich TM et al. 2007 Population bottlenecks as a potential major shaping force of human genome architecture PLoS Genet 3:e119.
98Giannuzzi G, D'Addabbo P, Gasparro M et al. 2011 Analysis of high-identity segmental duplications in the grapevine genome BMC Genomics 12:436.
99Giorno F, Guerriero G, Baric S et al. 2012 Heat shock transcriptional factors in Malus domestica: identification, classification and expression analysis BMC Genomics 13:639.
100Goodwin 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.
101Grad 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:
102Grzymski 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
103Guo 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.
104Gutierrez-Gonzalez JJ, Garvin DF 2011 The Plant Genome 4:178-190.
105Guyot 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.
106Hallin PF, Staerfeldt H-H, Rotenberg E et al. 2009 GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes Stand Genomic Sci 1:204-215.
107Hampton 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.
108Hayden 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.
109Hayden KE, Strome ED, Merrett SL et al. 2013 Sequences associated with centromere competency in the human genome Molecular and cellular biology 33:763-772.
110Hennemann S 2013 Information-rich visualisation of dense geographical networks Journal of Maps 1-8.
111Herbig A, Jager G, Battke F et al. 2012 GenomeRing: alignment visualization based on SuperGenome coordinates Bioinformatics 28:i7-i15.
112Heyn 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:
113Higgs 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.
114Hillmer 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.
115Hirsch 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.
116Holmfeldt L, Wei L, Diaz-Flores E et al. 2013 The genomic landscape of hypodiploid acute lymphoblastic leukemia Nat Genet
117Hou 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.
118Howe K Clark MD Torroja CF et al. 2013 The zebrafish reference genome sequence and its relationship to the human genome Nature
119Hsueh A, Rauch R 2012 Ovarian Kaleidoscope Database: 10 Years and Beyond Biology of reproduction
120Hu FZ, Eutsey R, Ahmed A et al. 2012 In vivo capsular switch in Streptococcus pneumoniae - analysis by whole genome sequencing PLoS One 7:e47983.
121Hu Y, Wang K, He X et al. 2010 A probabilistic framework for aligning paired-end RNA-seq data Bioinformatics 26:1950-1957.
122Hur 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
123Hur M, Yeo I, Kim E et al. 2010 Correlation of FT-ICR Mass Spectra with the Chemical and Physical Properties of Associated Crude Oils Energy & Fuels 24:5524-5532.
124Illa E, Sargent DJ, Lopez Girona E et al. 2011 Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family BMC Evol Biol 11:9.
125Imielinski M, Berger AH, Hammerman PS et al. 2012 Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing Cell 150:1107-1120.
126Irimia 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:
127Irimia A, Chambers MC, Torgerson CM et al. 2012 Circular representation of human cortical networks for subject and population-level connectomic visualization NeuroImage
128Irimia A, Van Horn JD 2012 The structural, connectomic and network covariance of the human brain NeuroImage
129Jaakma U 2013 Microbial Comparative Genomics: An Overview of Tools and Insights Into The Genus Corynebacterium Bacteriology & Parasitology 4:167.
130Jaillon O, Aury JM, Noel B et al. 2007 The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Nature 449:463-467.
131Jaillon O, Aury JM, Wincker P 2009 "Changing by doubling", the impact of Whole Genome Duplications in the evolution of eukaryotes C R Biol 332:241-253.
132Jankovic M, Feldhahn N, Oliveira TY et al. 2013 53BP1 Alters the Landscape of DNA Rearrangements and Suppresses AID-Induced B Cell Lymphoma Molecular cell
133Janssen 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:e10433.
134Jiang Z, Jhunjhunwala S, Liu J et al. 2012 The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients Genome research 22:593-601.
135Jiang Z, Zhou Y, Devarajan K et al. 2012 Identifying putative breast cancer-associated long intergenic non-coding RNA loci by high density SNP array analysis Frontiers in genetics 3:299.
136Jon McIlroy S, Kristiansen R, Albertsen M et al. 2013 Metabolic model for the filamentous 'Candidatus Microthrix parvicella' based on genomic and metagenomic analyses The ISME journal
137Jones SJ, Laskin J, Li YY et al. 2010 Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors Genome Biol 11:R82.
138Joseph SJ, Didelot X, Rothschild J et al. 2012 Population Genomics of Chlamydia trachomatis: Insights on Drift, Selection, Recombination, and Population Structure Mol Biol Evol
139Joshi T, Valliyodan B, Wu J-H et al. 2013 Genomic differences between cultivated soybean, G. max and its wild relative G. soja BMC Genomics 14:S5.
140Jung S, Cestaro A, Troggio M et al. 2012 Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies BMC Genomics 13:129.
141Karlebach G, Shamir R 2012 Constructing logical models of gene regulatory networks by integrating transcription factor-DNA interactions with expression data: an entropy-based approach Journal of computational biology : a journal of computational molecular cell biology 19:30-41.
142Katapadi VK, Nambiar M, Raghavan SC 2012 Potential G-quadruplex formation at breakpoint regions of chromosomal translocations in cancer may explain their fragility Genomics
143Kazakoff SH, Imelfort M, Edwards D et al. 2012 Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia pinnata PLoS One 7:e51687.
144Keane TM, Goodstadt L, Danecek P et al. 2011 Mouse genomic variation and its effect on phenotypes and gene regulation Nature 477:289-294.
145Kelleher 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 50:1063-1078.
146Kido EA, Ferreira Neto JR, Silva RL et al. 2013 Expression dynamics and genome distribution of osmoprotectants in soybean: identifying important components to face abiotic stress BMC Bioinformatics 14 Suppl 1:S7.
147Kim B, Yu HJ, Park SG et al. 2012 Identification and profiling of novel microRNAs in the Brassica rapa genome based on small RNA deep sequencing BMC Plant Biol 12:218.
148Kim C, Zhang D, Auckland SA et al. 2012 SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum TAG Theoretical and applied genetics Theoretische und angewandte Genetik
149Kim SC, Jung Y, Park J et al. 2013 A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers PLoS One 8:e55596.
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