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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.

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.

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
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.
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.
17Bello JP, Grosche P, Muller M et al. 2011 ACM Computers in Entertainment 1:
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.
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.
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
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.
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.
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
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.
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.
50Clark TA, Murray IA, Morgan RD et al. 2011 Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing Nucleic Acids Research
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
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
69Dhillon BK, Chiu TA, Laird MR et al. 2013 IslandViewer update: improved genomic island discovery and visualization Nucleic Acids Res
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.
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.
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.
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.
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.
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.
110Gutierrez-Gonzalez JJ, Garvin DF 2011 The Plant Genome 4:178-190.
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.
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.
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:
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
129Hsueh A, Rauch R 2012 Ovarian Kaleidoscope Database: 10 Years and Beyond Biology of reproduction
131Hu Y, Wang K, He X et al. 2010 A probabilistic framework for aligning paired-end RNA-seq data Bioinformatics 26:1950-1957.
132Hur 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
136Imielinski M, Berger AH, Hammerman PS et al. 2012 Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing Cell 150:1107-1120.
137Irimia 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:
141Jaillon O, Aury JM, Noel B et al. 2007 The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Nature 449:463-467.
143Jain M, Misra G, Patel RK et al. 2013 A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.) Plant J 74:715-729.
144Jankovic M, Feldhahn N, Oliveira TY et al. 2013 53BP1 Alters the Landscape of DNA Rearrangements and Suppresses AID-Induced B Cell Lymphoma Molecular cell
146Jiang 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.
148Jon 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
149Jones SJ, Laskin J, Li YY et al. 2010 Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors Genome Biol 11:R82.
151Joshi 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.
153Karlebach 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.
154Kasaian K, Wiseman SM, Thiessen N et al. 2013 Complete Genomic Landscape of a Recurring Sporadic Parathyroid Carcinoma J Pathol
157Keane TM, Goodstadt L, Danecek P et al. 2011 Mouse genomic variation and its effect on phenotypes and gene regulation Nature 477:289-294.
161Kim 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
162Kim S, Medvedev P, Paton TA et al. 2013 Reprever: resolving low-copy duplicated sequences using template driven assembly Nucleic Acids Res
164Kimbrel JA, Thomas WJ, Jiang Y et al. 2013 Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum PLoS pathogens 9:e1003204.
165Koch M, Wiese M 2012 Quality Visualization of Microarray Datasets Using Circos Microarrays 1:84-94.
166Kowarsch A, Fuchs A, Frishman D et al. 2010 Correlated mutations: a hallmark of phenotypic amino acid substitutions PLoS Comput Biol 6:e1000923.
167Koytiger G, Kaushansky A, Gordus A et al. 2013 Phosphotyrosine signaling proteins that drive oncogenesis tend to be highly interconnected Molecular & Cellular Proteomics
168Kristian O 2012 Genomic Region Operation Kit for Flexible Processing of Deep Sequencing Data IEEE/ACM Transactions on Computational Biology and Bioinformatics 99:1-1.
169Krzywinski M, Birol I, Jones SJ et al. 2011 Hive plots - A rational approach to visualizing networks Briefings in Bioinformatics
170Krzywinski M, Schein J, Birol I et al. 2009 Circos: an information aesthetic for comparative genomics Genome research 19:1639-1645.
173Kwei KA, Kung Y, Salari K et al. 2010 Genomic instability in breast cancer: pathogenesis and clinical implications Mol Oncol 4:255-266.
176Lam HY, Mu XJ, Stutz AM et al. 2010 Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library Nature biotechnology 28:47-55.
178Landry JJ, Pyl PT, Rausch T et al. 2013 The Genomic and Transcriptomic Landscape of a HeLa Cell Line G3
180Langridge GC, Phan MD, Turner DJ et al. 2009 Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants Genome research 19:2308-2316.
182Le Marechal C, Seyffert N, Jardin J et al. 2011 Molecular Basis of Virulence in Staphylococcus aureus Mastitis PLoS One 6:e27354.
183Ledford H 2010 Big science: The cancer genome challenge Nature 464:972-974.
188Lee W, Jiang Z, Liu J et al. 2010 The mutation spectrum revealed by paired genome sequences from a lung cancer patient Nature 465:473-477.
191Letzel AC, Pidot SJ, Hertweck C 2012 A genomic approach to the cryptic secondary metabolome of the anaerobic world Natural product reports
197Lilleoja R, Sarapik A, Reimann E et al. 2011 Sequencing and annotated analysis of an Estonian human genome Gene
200Lin Z, Wang X, Strong MJ et al. 2013 Whole-genome sequencing of the akata and mutu epstein-barr virus strains Journal of virology 87:1172-1182.
201Liu B, Faller LL, Klitgord N et al. 2012 Deep sequencing of the oral microbiome reveals signatures of periodontal disease PLoS One 7:e37919.
202Liu CC, Tang CY, Kuo HY et al. 2013 The origin of Acinetobacter baumannii TYTH-1: a comparative genomics study International journal of antimicrobial agents
204Liu X, Cheung D, Ting H-F et al.. 2013. LCR_Finder: A de novo low copy repeat finder for human genome. In 9th International Symposium, ISBRA 2013, (ed. Z Cai, O Eulenstein, D Janies, D Schwartz), Charlotte, NC.
205Lluch-Senar M, Luong K, Lloréns-Rico V et al. 2013 Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution PLoS Genet 9:e1003191.
206Lo I, Denef VJ, Verberkmoes NC et al. 2007 Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria Nature 446:537-541.
208Love C, Sun Z, Jima D et al. 2012 The genetic landscape of mutations in Burkitt lymphoma Nat Genet
209Lucas MR, Diop N-N, Wanamaker S et al. 2011 Cowpea-Soybean Synteny Clarified through an Improved Genetic Map The Plant Genome 4:218-225.
210Lucas MR, Ehlers JD, Roberts PA et al. 2012 Markers For Quantitative Inheritance Of Resistance To Foliar Thrips In Cowpea Crop Sci 52:2075-2081.
211Lucchi NW, Poorak M, Oberstaller J et al. 2012 A New Single-Step PCR Assay for the Detection of the Zoonotic Malaria Parasite Plasmodium knowlesi PLoS One 7:e31848.
212Lucker S, Wagner M, Maixner F et al. 2010 A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria Proc Natl Acad Sci U S A 107:13479-13484.
213Lynch KH, Stothard P, Dennis JJ 2012 Characterization of DC1, a broad-host-range Bcep22-like podovirus Appl Environ Microbiol 78:889-891.
217Makanju T, Zincir-Heywood N, Milios E. 2012. Interactive Learning of Alert Signatures in High Performance Cluster System Logs. In 13th IEEE/IFIP Network Operations and Management Symposium (NOMS), Maui, Hawaii, USA.
219Mallo M, Del Rey M, Ibanez M et al. 2013 Response to lenalidomide in myelodysplastic syndromes with del(5q): influence of cytogenetics and mutations British journal of haematology
220Mameaux S, Cockram J, Thiel T et al. 2011 Molecular, phylogenetic and comparative genomic analysis of the cytokinin oxidase/dehydrogenase gene family in the Poaceae Plant biotechnology journal in press:-.
221Mandakova T, Joly S, Krzywinski M et al. 2010 Fast diploidization in close mesopolyploid relatives of Arabidopsis Plant Cell 22:2277-2290.
222Mandlik A, Livny J, Robins WP et al. 2011 RNA-Seq-Based Monitoring of Infection-Linked Changes in Vibrio cholerae Gene Expression Cell host & microbe 10:165-174.
223Mann KM, Ward JM, Yew CC et al. 2012 Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma Proc Natl Acad Sci U S A 109:5934-5941.
224Markovets A, Herman D 2011 Analysis of cancer metabolism with high-throughput technologies BMC Bioinformatics 12:S8.
225Martin JW, Yoshimoto M, Ludkovski O et al. 2010 Analysis of segmental duplications, mouse genome synteny and recurrent cancer-associated amplicons in human chromosome 6p21-p12 Cytogenet Genome Res 128:199-213.
226Mayer KF, Martis M, Hedley PE et al. 2011 Unlocking the barley genome by chromosomal and comparative genomics Plant Cell 23:1249-1263.
227McBride DJ, Etemadmoghadam D, Cooke SL et al. 2012 Tandem duplication of chromosomal segments is common in ovarian and breast cancer genomes The Journal of Pathology n/a-n/a.
228McGraw LA, Davis JK, Young LJ et al. 2011 A genetic linkage map and comparative mapping of the prairie vole (Microtus ochrogaster) genome BMC genetics 12:60.
232Meyer C, Kowarz E, Hofmann J et al. 2009 New insights to the MLL recombinome of acute leukemias Leukemia 23:1490-1499.
233Meyer M, Munzner T, Pfister H 2009 MizBee: a multiscale synteny browser IEEE Trans Vis Comput Graph 15:897-904.
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