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Circos at the EMBO NGS workshop in Tunis, Sept 15–25.
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.
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.
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.
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.
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.
et 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."
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.
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.
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.
2013 Large-scale resource development in Gossypium hirsutum L. by 454 sequencing of genic-enriched libraries from six diverse genotypes Plant biotechnology journal
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.
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.
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.
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.
2012 Circular representation of human cortical networks for subject and population-level connectomic visualization NeuroImage, 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.
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.
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."
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".
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.
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."
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.
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).
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.
1 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.
2011 Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly Nature biotechnology 29:723-730.
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 (5,562 as of July 2020, see published images). The list below is quite old (2013) and the full citations are available on Google Scholar.
Circos in Scientific Literature
2 2013 Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes PLoS One 8:e75072.
3 2013 Genome-wide profiling reveals stimulus-specific functions of p53 during differentiation and DNA damage of human embryonic stem cells Nucleic Acids Res
4 2011 A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal The ISME journal
5 2013 Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Nature biotechnology
7 2013 Microbial Comparative Genomics: An Overview of Tools and Insights Into The Genus Corynebacterium J Bacteriology & Parasitology 4:167.
8 2013 Wheat Zapper: a flexible online tool for colinearity studies in grass genomes Funct Integr Genomics 13:11-17.
10 2012 IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE VAST 2012) 18:
11 2008 Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia Genome research 18:1472-1483.
12 2012 Q fever and pregnancy: disease, prevention, and strain specificity European Journal of Clinical Microbiology & Infectious Diseases 1-8.
13 2006 Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia Nature 444:171-178.
15 2013 Development of a robust mapping between AIS 2+ and ICD-9 injury codes Accident Analysis & Prevention 52:133-143.
16 2011 Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion Nat Genet 43:964-968.
17 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.
18 2013 Genome Aberrations in Canine Mammary Carcinomas and Their Detection in Cell-Free Plasma DNA PLoS One 8:e75485.
19 2013 Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis Nat Genet
20 2013 Unravelling the genetic complexity of sorghum seedling development under low temperature conditions Plant, cell & environment
21 2013 High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array Plant biotechnology journal
22 2009 Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine PLoS One 4:e4641.
23 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.
26 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.
28 2014 The Role of Visual Analytics in Asthma Phenotyping and Biomarker Discovery In Heterogeneity in Asthma, (ed. AR Brasier), p. 289-305. Springer US.
29 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.
30 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.
31 2013 Computational detection of abundant long-range nucleotide covariation in Drosophila genomes Rna 19:1171-1182.
32 2013 Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis PLoS One 8:e72182.
34Borkin MA, Yeh CS, Boyd M et al.. 2013. Evaluation of Filesystem Provenance Visualization Tools. In IEEE Information Visualization 2013, Atlanta, GA.
35 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.
36 2012 Genome-wide analysis of cytogenetic aberrations in ETV6/RUNX1-positive childhood acute lymphoblastic leukaemia British journal of haematology
37 2012 Chromatin topology and the regulation of antigen receptor assembly Annual review of immunology 30:337-356.
38 2011 High resolution linkage maps of the model organism Petunia reveal substantial synteny decay with the related genome of tomato Genome 54:327-340.
39 2011 The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story Plant J
44 2011 Hybrid incompatibility in Arabidopsis is determined by a multi-locus genetic network Plant physiology
45 2013 Precision phenotyping of biomass accumulation in triticale reveals temporal genetic patterns of regulation Scientific reports 3:2442.
46 2013 BAC-Pool Sequencing and Analysis of Large Segments of A12 and D12 Homoeologous Chromosomes in Upland Cotton PLoS One 8:e76757.
48 2008 Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing Nat Genet 40:722-729.
50 2011 Chromosome visualization tool: a whole genome viewer International journal of plant genomics 2011:373875.
51 2009 Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution PLoS Genet 5:e1000538.
52 2011 Cytogenetics of Primary Skin Tumors In Molecular Diagnostics in Dermatology and Dermatopathology, (ed. MJ Murphy), p. 57-72. Humana Press.
53 2012 The eroded genome of a Psychotria leaf symbiont: hypotheses about lifestyle and interactions with its plant host Environ Microbiol
55 2009 Automated identification of conserved synteny after whole-genome duplication Genome research 19:1497-1505.
56 2013 Transcriptional response of mucoid Pseudomonas aeruginosa to human respiratory mucus mBio 3:e00410-00412.
57 2012 Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools Nucleic Acids Res
58 2012 Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple PLoS One 7:e31745.
59 2012 Whole exome sequencing of pediatric gastric adenocarcinoma reveals an atypical presentation of Li-Fraumeni syndrome Pediatric blood & cancer
62 2012 Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome PLoS One 7:e41374.
63 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.
64 2013 CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes BMC Bioinformatics 14:95.
65 2011 Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells Cell 147:107-119.
66 2011 The origin of the Haitian cholera outbreak strain The New England journal of medicine 364:33-42.
67 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.
69 2010 U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line PLoS Genet 6:e1000832.
70 2013 Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation BMC biology 11:4.
71 2011 Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing Nucleic Acids Research
72 2012 A novel human-infection-derived bacterium provides insights into the evolutionary origins of mutualistic insect-bacterial symbioses PLoS Genet 8:e1002990.
73 2012 Genome Dynamics Explain the Evolution of Flowering Time CCT Domain Gene Families in the Poaceae PLoS One 7:e45307.
74 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.
78 2012 Co-expression of soybean Dicer-like genes in response to stress and development Funct Integr Genomics
79 2012 The banana (Musa acuminata) genome and the evolution of monocotyledonous plants Nature 488:213-217.
83 2012 Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution Plant J
85 2011 The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements Nature advanced online:-.
86 2013 High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake Proc Natl Acad Sci U S A
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.
89 2010 Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss BMC Genomics 11:688.
92 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.
93 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.
95 2009 De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data Genome Biol 10:R94.
96 2010 Genome remodelling in a basal-like breast cancer metastasis and xenograft Nature 464:999-1005.
97 2012 Vitamin D receptor binding, chromatin states and association with multiple sclerosis Human molecular genetics
99 2012 Evidence for transcript networks composed of chimeric RNAs in human cells PLoS One 7:e28213.
100 2013 The silent mutational landscape of infant MLL-AF4 pro-B acute lymphoblastic leukemia Genes Chromosomes Cancer 52:954-960.
101 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.
102 2012 Pericentromeric Effects Shape the Patterns of Divergence, Retention, and Expression of Duplicated Genes in the Paleopolyploid Soybean Plant Cell
104 2008 Fusion and fission of genes define a metric between fungal genomes PLoS Comput Biol 4:e1000200.
105 2011 Identification of fusion genes in breast cancer by paired-end RNA-sequencing Genome Biol 12:R6.
106 2013 Perspectives on design creativity and innovation research International Journal of Design Creativity and Innovation 1:1-42.
107 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.
108 2013 Epigenetic and genetic influences on DNA methylation variation in maize populations Plant Cell 25:2783-2797.
109 2012 Whole-genome analysis informs breast cancer response to aromatase inhibition Nature 486:353-360.
110 2010 A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres Genome Biol 11:R109.
112 2013 Generalized bacterial genome editing using mobile group II introns and Cre-lox Mol Syst Biol 9:
113 2012 Transcriptomic landscape of breast cancers through mRNA sequencing Scientific reports 2:264.
114 2013 SVGenes: a library for rendering genomic features in scalable vector graphic format Bioinformatics 29:1890-1892.
115 2012 Single-neuron sequencing analysis of l1 retrotransposition and somatic mutation in the human brain Cell 151:483-496.
116 2010 The Complete Genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy Actinobacterium with Food and Probiotic Applications PLoS One 5:e11748.
117 2012 A Complete Sequence and Transcriptomic Analyses of Date Palm (Phoenix dactylifera L.) Mitochondrial Genome PLoS One 7:e37164.
118 2013 Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis Nat Genet 45:1183-1189.
119 2012 Microarray Meta-Analysis: From Data to Expression to Biological Relationships
Computational Medicine In Z Trajanoski), p. 59-77. Springer Vienna.
120 2013 Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis Plant Mol Biol
122 2012 Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks Mol Ecol
124 2010 Use of a rabbit soft tissue chamber model to investigate campylobacter jejuni-host interactions Front Microbiol 1:126.
125 2013 Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga Nature 500:453-457.
126 2009 COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer Nucleic Acids Res 38:D652-657.
127 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
128 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.
129 2009 Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing Genome research 19:1817-1824.
131 2013 Small cell ovarian carcinoma: genomic stability and responsiveness to therapeutics Orphanet journal of rare diseases 8:33.
133 2013 The interactomes of POU5F1 and SOX2 enhancers in human embryonic stem cells Scientific reports 3:1588.
134 2013 Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences Proc Natl Acad Sci U S A 110:14492-14497.
135 2010 Investigation of the Transcriptome of Prairie Cord Grass, a New Cellulosic Biomass Crop Plant Gen 3:69-80.
136 2007 Population bottlenecks as a potential major shaping force of human genome architecture PLoS Genet 3:e119.
137 2013 Toward an integrated software platform for systems pharmacology Biopharmaceutics & drug disposition
138 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.
139 2011 Analysis of high-identity segmental duplications in the grapevine genome BMC Genomics 12:436.
140 2012 Heat shock transcriptional factors in Malus domestica: identification, classification and expression analysis BMC Genomics 13:639.
142 2011 Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis PLoS Genet 7:e1002070.
143 2013 Comparative Genomics of Recent Shiga Toxin-Producing Escherichia coli O104:H4: Short-Term Evolution of an Emerging Pathogen mBio 4:
144 2013 Distributive conjugal transfer in mycobacteria generates progeny with meiotic-like genome-wide mosaicism, allowing mapping of a mating identity locus PLoS Biol 11:e1001602.
145 2012 A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters The ISME journal
146 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.
149 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.
150 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
151 2009 GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes Stand Genomic Sci 1:204-215.
152 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.
153 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.
154 2013 Sequences associated with centromere competency in the human genome Molecular and cellular biology 33:763-772.
155 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.
158 2012 GenomeRing: alignment visualization based on SuperGenome coordinates Bioinformatics 28:i7-i15.
159 2013 De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads Bioinformatics
161 2012 Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient Epigenetics : official journal of the DNA Methylation Society 7:
162 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.
163 2011 Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes Genome research 21:665-675.
165 2013 Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma Cancer research 73:1454-1460.
168 2012 Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm Cell 148:873-885.
171 2012 In vivo capsular switch in Streptococcus pneumoniae - analysis by whole genome sequencing PLoS One 7:e47983.
172 2010 A probabilistic framework for aligning paired-end RNA-seq data Bioinformatics 26:1950-1957.
173 2013 A global approach to analysis and interpretation of metabolic data for plant natural product discovery Natural product reports
174 2010 Correlation of FT-ICR Mass Spectra with the Chemical and Physical Properties of Associated Crude Oils Energy & Fuels 24:5524-5532.
175 2011 Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family BMC Evol Biol 11:9.
176 2013 Inferring genome-wide recombination landscapes from advanced intercross lines: application to yeast crosses PLoS One 8:e62266.
177 2012 Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing Cell 150:1107-1120.
178 2012 Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury Frontiers in Neurology 3:
179 2012 Circular representation of human cortical networks for subject and population-level connectomic visualization NeuroImage
181 2013 Microbial Comparative Genomics: An Overview of Tools and Insights Into The Genus Corynebacterium Bacteriology & Parasitology 4:167.
182 2007 The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Nature 449:463-467.
183 2009 "Changing by doubling", the impact of Whole Genome Duplications in the evolution of eukaryotes C R Biol 332:241-253.
184 2013 A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.) Plant J 74:715-729.
185 2013 53BP1 Alters the Landscape of DNA Rearrangements and Suppresses AID-Induced B Cell Lymphoma Molecular cell
186 2010 The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments PLoS One 5:e10433.
187 2012 The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients Genome research 22:593-601.
188 2012 Identifying putative breast cancer-associated long intergenic non-coding RNA loci by high density SNP array analysis Frontiers in genetics 3:299.
189 2013 Metabolic model for the filamentous 'Candidatus Microthrix parvicella' based on genomic and metagenomic analyses The ISME journal
190 2010 Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors Genome Biol 11:R82.
191 2012 Population Genomics of Chlamydia trachomatis: Insights on Drift, Selection, Recombination, and Population Structure Mol Biol Evol
192 2013 Genomic differences between cultivated soybean, G. max and its wild relative G. soja BMC Genomics 14:S5.
193 2012 Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies BMC Genomics 13:129.
195 2013 International trade undermines national emission reduction targets: New evidence from air pollution Global Environmental Change
196 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.
198 2012 Potential G-quadruplex formation at breakpoint regions of chromosomal translocations in cancer may explain their fragility Genomics
199 2012 Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia pinnata PLoS One 7:e51687.
200 2011 Mouse genomic variation and its effect on phenotypes and gene regulation Nature 477:289-294.
201 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.
202 2013 Expression dynamics and genome distribution of osmoprotectants in soybean: identifying important components to face abiotic stress BMC Bioinformatics 14 Suppl 1:S7.
203 2012 Identification and profiling of novel microRNAs in the Brassica rapa genome based on small RNA deep sequencing BMC Plant Biol 12:218.
204 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
205 2013 Reprever: resolving low-copy duplicated sequences using template driven assembly Nucleic Acids Res
206 2013 A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers PLoS One 8:e55596.
207 2013 Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum PLoS pathogens 9:e1003204.
208 2013 Deep sequencing reveals increased DNA methylation in chronic rat epilepsy Acta neuropathologica
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