Circos > Citations > Scientific

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Circos has been used and referenced in many scientific publications (9,378 as of January 2024, Google Scholar citations).

I also keep a list of published images.

Circos in Scientific Literature

1Aboukhalil R, Fendler B, Atwal GS 2013 ArXiv e-prints
4Albertsen M, Hansen LB, Saunders AM et al. 2011 A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal The ISME journal
5Albertsen M, Hugenholtz P, Skarshewski A et al. 2013 Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Nature biotechnology
6Alexander RP, Fang G, Rozowsky J et al. 2010 Annotating non-coding regions of the genome Nat Rev Genet 11:559-571.
7Ali A, Soares S, Barbosa E et al. 2013 Microbial Comparative Genomics: An Overview of Tools and Insights Into The Genus Corynebacterium J Bacteriology & Parasitology 4:167.
8Alnemer LM, Seetan RI, Bassi FM et al. 2013 Wheat Zapper: a flexible online tool for colinearity studies in grass genomes Funct Integr Genomics 13:11-17.
9AlNoamany Y, AlSum A, Weigle MC et al. 2013 Who and What Links to the Internet Archive arxiv 1309.4016:
12Angelakis E, Million M, D’Amato F et al. 2012 Q fever and pregnancy: disease, prevention, and strain specificity European Journal of Clinical Microbiology & Infectious Diseases 1-8.
13Aury JM, Jaillon O, Duret L et al. 2006 Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia Nature 444:171-178.
14Baker M 2010 Epigenome: Mapping in Motion Nature Methods 7:181-186.
15Barnard RT, Loftis KL, Martin RS et al. 2013 Development of a robust mapping between AIS 2+ and ICD-9 injury codes Accident Analysis & Prevention 52:133-143.
16Bass AJ, Lawrence MS, Brace LE et al. 2011 Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion Nat Genet 43:964-968.
17Batelli G, Oh D-H, D’Urzo M et al. 2014 Using Arabidopsis-Related Model Species (ARMS): Growth, Genetic Transformation, and Comparative Genomics In Arabidopsis Protocols, (ed. JJ Sanchez-Serrano, J Salinas), p. 27-51. Humana Press.
18Beck J, Hennecke S, Bornemann-Kolatzki K et al. 2013 Genome Aberrations in Canine Mammary Carcinomas and Their Detection in Cell-Free Plasma DNA PLoS One 8:e75485.
20Bekele WA, Fiedler K, Shiringani A et al. 2013 Unravelling the genetic complexity of sorghum seedling development under low temperature conditions Plant, cell & environment
21Bekele WA, Wieckhorst S, Friedt W et al. 2013 High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array Plant biotechnology journal
24Bello JP, Grosche P, Muller M et al. 2011 ACM Computers in Entertainment 1:
26Bhatt AS, Freeman SS, Herrera AF et al. 2013 Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome The New England journal of medicine 369:517-528.
27Bhavani SK, Drake J, Bellela G et al.. 2013. How Complimentary Bipartite Visual Analytical Representations Reveal Patterns in Cytokine Expression: A Case Study in Rickettsioses. In AMIA Proceedings.
28Bhavnani S, Drake J, Divekar R 2014 The Role of Visual Analytics in Asthma Phenotyping and Biomarker Discovery In Heterogeneity in Asthma, (ed. AR Brasier), p. 289-305. Springer US.
29Bhavnani SK, Bellala G, Victor S et al. 2012 The role of complementary bipartite visual analytical representations in the analysis of SNPs: a case study in ancestral informative markers Journal of the American Medical Informatics Association 19:e5-e12.
33Bollongino R, Nehlich O, Richards MP et al. 2013 2000 years of parallel societies in Stone Age Central Europe Science 342:479-481.
34Borkin MA, Yeh CS, Boyd M et al.. 2013. Evaluation of Filesystem Provenance Visualization Tools. In IEEE Information Visualization 2013, Atlanta, GA.
35Bornelöv S, Enroth S, Komorowski J 2012 Visualization of Rules in Rule-Based Classifiers Intelligent Decision Technologies In J Watada, T Watanabe, G Phillips-Wren, RJ Howlett, LC Jain), p. 329-338. Springer Berlin Heidelberg.
36Borst L, Wesolowska A, Joshi T et al. 2012 Genome-wide analysis of cytogenetic aberrations in ETV6/RUNX1-positive childhood acute lymphoblastic leukaemia British journal of haematology
37Bossen C, Mansson R, Murre C 2012 Chromatin topology and the regulation of antigen receptor assembly Annual review of immunology 30:337-356.
40Branham MT, Marzese DM, Laurito SR et al. 2012 Methylation profile of triple-negative breast carcinomas Oncogenesis 1:e17.
41Brastianos PK, Horowitz PM, Santagata S et al. 2013 Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations Nat Genet
42Brown AM, Huynh LY, Bolender CM et al. 2013 Population genomics of a symbiont in the early stages of a pest invasion Mol Ecol
43Bunting SF, Nussenzweig A 2013 End-joining, translocations and cancer Nat Rev Cancer
44Burkart-Waco D, Josefsson C, Dilkes BR et al. 2011 Hybrid incompatibility in Arabidopsis is determined by a multi-locus genetic network Plant physiology
45Busemeyer L, Ruckelshausen A, Moller K et al. 2013 Precision phenotyping of biomass accumulation in triticale reveals temporal genetic patterns of regulation Scientific reports 3:2442.
47Bzhalava D, Johansson H, Ekstrom J et al. 2013 Unbiased approach for virus detection in skin lesions PLoS One 8:e65953.
49Campbell SJ, Gaulton A, Marshall J et al. 2009 Visualizing the drug target landscape Drug Discov Today 15:3-15.
50Cannon EK, Cannon SB 2011 Chromosome visualization tool: a whole genome viewer International journal of plant genomics 2011:373875.
52Carless MA, Griffiths LR 2011 Cytogenetics of Primary Skin Tumors In Molecular Diagnostics in Dermatology and Dermatopathology, (ed. MJ Murphy), p. 57-72. Humana Press.
54Carver T, Thomson N, Bleasby A et al. 2009 DNAPlotter: circular and linear interactive genome visualization Bioinformatics 25:119-120.
55Catchen JM, Conery JS, Postlethwait JH 2009 Automated identification of conserved synteny after whole-genome duplication Genome research 19:1497-1505.
56Cattoir V, Narasimhan G, Skurnik D et al. 2013 Transcriptional response of mucoid Pseudomonas aeruginosa to human respiratory mucus mBio 3:e00410-00412.
57Cer RZ, Donohue DE, Mudunuri US et al. 2012 Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools Nucleic Acids Res
58Chagne D, Crowhurst RN, Troggio M et al. 2012 Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple PLoS One 7:e31745.
59Chang VY, Federman N, Martinez-Agosto J et al. 2012 Whole exome sequencing of pediatric gastric adenocarcinoma reveals an atypical presentation of Li-Fraumeni syndrome Pediatric blood & cancer
60Che D, Wang H 2013 GIV: A Tool for Genomic Islands Visualization Bioinformation 9:879-882.
63Chen R, Giliani S, Lanzi G et al. 2013 Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias The Journal of allergy and clinical immunology 132:656-664 e617.
64Cheng J, Zeng X, Ren G et al. 2013 CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes BMC Bioinformatics 14:95.
66Chin CS, Sorenson J, Harris JB et al. 2011 The origin of the Haitian cholera outbreak strain The New England journal of medicine 364:33-42.
67Cho BK, Zengler K, Qiu Y et al. 2009 The transcription unit architecture of the Escherichia coli genome Nature biotechnology 27:1043-1049.
68Claessen JHT. 2011. Visualization of Multivariate Data. In Department of Mathematics and Computer Science, Vol Masters. Eidhoven University of Technology, Eidhoven.
69Clark MJ, Homer N, O'Connor BD et al. 2010 U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line PLoS Genet 6:e1000832.
71Clark TA, Murray IA, Morgan RD et al. 2011 Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing Nucleic Acids Research
73Cockram J, Thiel T, Steuernagel B et al. 2012 Genome Dynamics Explain the Evolution of Flowering Time CCT Domain Gene Families in the Poaceae PLoS One 7:e45307.
74Coelho AC, Boisvert S, Mukherjee A et al. 2012 Multiple Mutations in Heterogeneous Miltefosine-Resistant Leishmania major Population as Determined by Whole Genome Sequencing PLoS neglected tropical diseases 6:e1512.
75Cooke T, Horberry T, Burgess-Limerick R. 2012. Revisiting injury narratives to pinpoint human factor issues associated with surface mobile mining equipment. In Occupational Safety in Transport Conference 2012, Gold Coast, QLD, Australia.
76Costello JF, Krzywinski M, Marra MA 2009 A first look at entire human methylomes Nature biotechnology 27:1130-1132.
77Cruz J, Liu Y, Liang Y et al. 2011 BacMap: an up-to-date electronic atlas of annotated bacterial genomes Nucleic Acids Res
78Curtin SJ, Kantar MB, Yoon HW et al. 2012 Co-expression of soybean Dicer-like genes in response to stress and development Funct Integr Genomics
79D'Hont A, Denoeud F, Aury J-M et al. 2012 The banana (Musa acuminata) genome and the evolution of monocotyledonous plants Nature 488:213-217.
80Damas J, Carneiro J, Goncalves J et al. 2012 Mitochondrial DNA deletions are associated with non-B DNA conformations Nucleic Acids Res
81Darzentas N 2010 Circoletto: visualizing sequence similarity with Circos Bioinformatics 26:2620-2621.
82Daub JT, Hofer T, Cutivet E et al. 2013 Evidence for Polygenic Adaptation to Pathogens in the Human Genome Mol Biol Evol
84Dayem Ullah AZ, Cutts RJ, Ghetia M et al. 2013 The pancreatic expression database: recent extensions and updates Nucleic Acids Res
85De Fazio S, Bartonicek N, Di Giacomo M et al. 2011 The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements Nature advanced online:-.
86Demaere MZ, Williams TJ, Allen MA et al. 2013 High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake Proc Natl Acad Sci U S A
87Demare LE, Leng J, Cotney J et al. 2013 The genomic landscape of cohesin-associated chromatin interactions Genome research
88Demiralp C, Hayden E, Hammerbacher J et al.. 2013. invis: Exploring High-Dimensional RNA Sequences from In Vitro Selection. In IEEE Symposium on Biological Data Visualization, Atlanta, GA.
90den Bakker HC, Desjardins CA, Griggs AD et al. 2013 Evolutionary Dynamics of the Accessory Genome of Listeria monocytogenes PLoS One 8:e67511.
94Dhillon BK, Chiu TA, Laird MR et al. 2013 IslandViewer update: improved genomic island discovery and visualization Nucleic Acids Res
96Ding L, Ellis MJ, Li S et al. 2010 Genome remodelling in a basal-like breast cancer metastasis and xenograft Nature 464:999-1005.
97Disanto G, Sandve GK, Berlanga-Taylor AJ et al. 2012 Vitamin D receptor binding, chromatin states and association with multiple sclerosis Human molecular genetics
98Dittwald P, Gambin T, Gonzaga-Jauregui C et al. 2012 Inverted low-copy repeats and genome instability-A genome-wide analysis Human mutation
99Djebali S, Lagarde J, Kapranov P et al. 2012 Evidence for transcript networks composed of chimeric RNAs in human cells PLoS One 7:e28213.
100Dobbins SE, Sherborne AL, Ma YP et al. 2013 The silent mutational landscape of infant MLL-AF4 pro-B acute lymphoblastic leukemia Genes Chromosomes Cancer 52:954-960.
103Duan Z, Andronescu M, Schutz K et al. 2010 A three-dimensional model of the yeast genome Nature 465:363-367.
104Durrens P, Nikolski M, Sherman D 2008 Fusion and fission of genes define a metric between fungal genomes PLoS Comput Biol 4:e1000200.
105Edgren H, Murumagi A, Kangaspeska S et al. 2011 Identification of fusion genes in breast cancer by paired-end RNA-sequencing Genome Biol 12:R6.
106Editorial board of I 2013 Perspectives on design creativity and innovation research International Journal of Design Creativity and Innovation 1:1-42.
108Eichten SR, Briskine R, Song J et al. 2013 Epigenetic and genetic influences on DNA methylation variation in maize populations Plant Cell 25:2783-2797.
109Ellis MJ, Ding L, Shen D et al. 2012 Whole-genome analysis informs breast cancer response to aromatase inhibition Nature 486:353-360.
110Ellwood SR, Liu Z, Syme RA et al. 2010 A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres Genome Biol 11:R109.
111Enroth S, Bornelov S, Wadelius C et al. 2012 Combinations of histone modifications mark exon inclusion levels PLoS One 7:e29911.
112Enyeart PJ, Chirieleison SM, Dao MN et al. 2013 Generalized bacterial genome editing using mobile group II introns and Cre-lox Mol Syst Biol 9:
113Eswaran J, Cyanam D, Mudvari P et al. 2012 Transcriptomic landscape of breast cancers through mRNA sequencing Scientific reports 2:264.
114Etherington GJ, MacLean D 2013 SVGenes: a library for rendering genomic features in scalable vector graphic format Bioinformatics 29:1890-1892.
119Feichtinger J, Thallinger GG, McFarlane RJ et al. 2012 Microarray Meta-Analysis: From Data to Expression to Biological Relationships Computational Medicine In Z Trajanoski), p. 59-77. Springer Vienna.
123Flannery MC 2009 Writing Across Rome The American Biology Teacher 71:52-55.
124Flint A, Butcher J, Clarke C et al. 2010 Use of a rabbit soft tissue chamber model to investigate campylobacter jejuni-host interactions Front Microbiol 1:126.
125Flot JF, Hespeels B, Li X et al. 2013 Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga Nature 500:453-457.
129Freeman JD, Warren RL, Webb JR et al. 2009 Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing Genome research 19:1817-1824.
130Furney SJ, Turajlic S, Fenwick K et al. 2012 Genomic Characterisation of Acral Melanoma Cell Lines Pigment cell & melanoma research
131Gamwell LF, Gambaro K, Merziotis M et al. 2013 Small cell ovarian carcinoma: genomic stability and responsiveness to therapeutics Orphanet journal of rare diseases 8:33.
132Gao D, Middleton R, Rasko JE et al. 2013 miREval 2.0: a web tool for simple microRNA prediction in genome sequences Bioinformatics
133Gao F, Wei Z, An W et al. 2013 The interactomes of POU5F1 and SOX2 enhancers in human embryonic stem cells Scientific reports 3:1588.
135Gedye K, Gonzalez-Hernandez J, Ban Y et al. 2010 Investigation of the Transcriptome of Prairie Cord Grass, a New Cellulosic Biomass Crop Plant Gen 3:69-80.
136Gherman A, Chen PE, Teslovich TM et al. 2007 Population bottlenecks as a potential major shaping force of human genome architecture PLoS Genet 3:e119.
137Ghosh S, Matsuoka Y, Asai Y et al. 2013 Toward an integrated software platform for systems pharmacology Biopharmaceutics & drug disposition
138Giannuzzi G, Cardone MF, Ventura M et al. 2013 Read-depth Methodology for the Analysis of Recent Segmental Duplications in the Grapevine Genome In Sequence and Genome Analysis I - Humans, Animals and Plants, (ed. i Press), p. iConcept Press.
139Giannuzzi G, D'Addabbo P, Gasparro M et al. 2011 Analysis of high-identity segmental duplications in the grapevine genome BMC Genomics 12:436.
141Goecks J, Eberhard C, Too T et al. 2013 Web-based visual analysis for high-throughput genomics BMC Genomics 14:397.
147Gutierrez-Gonzalez JJ, Garvin DF 2011 The Plant Genome 4:178-190.
151Hallin PF, Staerfeldt H-H, Rotenberg E et al. 2009 GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes Stand Genomic Sci 1:204-215.
153Hayden KE 2012 Human centromere genomics: now it's personal Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 20:621-633.
154Hayden KE, Strome ED, Merrett SL et al. 2013 Sequences associated with centromere competency in the human genome Molecular and cellular biology 33:763-772.
156Hegedusova E, Brejova B, Tomaska L et al. 2013 Mitochondrial genome of the basidiomycetous yeast Jaminaea angkorensis Curr Genet
157Hennemann S 2013 Information-rich visualisation of dense geographical networks Journal of Maps 1-8.
158Herbig A, Jager G, Battke F et al. 2012 GenomeRing: alignment visualization based on SuperGenome coordinates Bioinformatics 28:i7-i15.
160Heyn H, Moran S, Hernando-Herraez I et al. 2013 DNA methylation contributes to natural human variation Genome research 23:1363-1372.
161Heyn H, Vidal E, Sayols S et al. 2012 Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient Epigenetics : official journal of the DNA Methylation Society 7:
164Hiltemann S, McClellan EA, van Nijnatten J et al. 2013 iFUSE: integrated FUSion gene Explorer Bioinformatics
165Hirsch D, Kemmerling R, Davis S et al. 2013 Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma Cancer research 73:1454-1460.
166Ho AS, Kannan K, Roy DM et al. 2013 The mutational landscape of adenoid cystic carcinoma Nat Genet
167Holmfeldt L, Wei L, Diaz-Flores E et al. 2013 The genomic landscape of hypodiploid acute lymphoblastic leukemia Nat Genet
170Hsueh A, Rauch R 2012 Ovarian Kaleidoscope Database: 10 Years and Beyond Biology of reproduction
172Hu Y, Wang K, He X et al. 2010 A probabilistic framework for aligning paired-end RNA-seq data Bioinformatics 26:1950-1957.
173Hur M, Campbell AA, Almeida-de-Macedo M et al. 2013 A global approach to analysis and interpretation of metabolic data for plant natural product discovery Natural product reports
177Imielinski M, Berger AH, Hammerman PS et al. 2012 Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing Cell 150:1107-1120.
178Irimia A, Chambers MC, Torgerson CM et al. 2012 Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury Frontiers in Neurology 3:
182Jaillon O, Aury JM, Noel B et al. 2007 The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Nature 449:463-467.
184Jain 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.
185Jankovic M, Feldhahn N, Oliveira TY et al. 2013 53BP1 Alters the Landscape of DNA Rearrangements and Suppresses AID-Induced B Cell Lymphoma Molecular cell
187Jiang 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.
189Jon 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
190Jones SJ, Laskin J, Li YY et al. 2010 Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors Genome Biol 11:R82.
192Joshi 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.
194Kabekkodu SP, Bhat S, Mascarenhas R et al. 2013 Mitochondrial DNA variation analysis in cervical cancer Mitochondrion
195Kanemoto K, Moran D, Lenzen M et al. 2013 International trade undermines national emission reduction targets: New evidence from air pollution Global Environmental Change
196Karlebach 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.
197Kasaian K, Wiseman SM, Thiessen N et al. 2013 Complete Genomic Landscape of a Recurring Sporadic Parathyroid Carcinoma J Pathol
200Keane TM, Goodstadt L, Danecek P et al. 2011 Mouse genomic variation and its effect on phenotypes and gene regulation Nature 477:289-294.
204Kim 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
205Kim S, Medvedev P, Paton TA et al. 2013 Reprever: resolving low-copy duplicated sequences using template driven assembly Nucleic Acids Res
207Kimbrel 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.
208Kobow K, Kaspi A, Harikrishnan KN et al. 2013 Deep sequencing reveals increased DNA methylation in chronic rat epilepsy Acta neuropathologica
209Koch M, Wiese M 2012 Quality Visualization of Microarray Datasets Using Circos Microarrays 1:84-94.
210Koks S, Lilleoja R, Reimann E et al. 2013 Sequencing and annotated analysis of the Holstein cow genome Mamm Genome 24:309-321.
211Kowarsch A, Fuchs A, Frishman D et al. 2010 Correlated mutations: a hallmark of phenotypic amino acid substitutions PLoS Comput Biol 6:e1000923.
212Koytiger G, Kaushansky A, Gordus A et al. 2013 Phosphotyrosine signaling proteins that drive oncogenesis tend to be highly interconnected Molecular & Cellular Proteomics
213Kristian O 2012 Genomic Region Operation Kit for Flexible Processing of Deep Sequencing Data IEEE/ACM Transactions on Computational Biology and Bioinformatics 99:1-1.
214Krzywinski M, Birol I, Jones SJ et al. 2011 Hive plots - A rational approach to visualizing networks Briefings in Bioinformatics
215Krzywinski M, Schein J, Birol I et al. 2009 Circos: an information aesthetic for comparative genomics Genome research 19:1639-1645.
219Kwei KA, Kung Y, Salari K et al. 2010 Genomic instability in breast cancer: pathogenesis and clinical implications Mol Oncol 4:255-266.
222Lam 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.
224Landry JJ, Pyl PT, Rausch T et al. 2013 The Genomic and Transcriptomic Landscape of a HeLa Cell Line G3
226Langridge 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.
228Le Marechal C, Seyffert N, Jardin J et al. 2011 Molecular Basis of Virulence in Staphylococcus aureus Mastitis PLoS One 6:e27354.
230Ledford H 2010 Big science: The cancer genome challenge Nature 464:972-974.
232Lee J, Kim D, Park J et al.. 2013. Flow circle: circular visualization of wiki revision history. In ACM SIGGRAPH 2013 Posters, pp. 1-1. ACM, Anaheim, California.
236Lee 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.
240Letzel AC, Pidot SJ, Hertweck C 2012 A genomic approach to the cryptic secondary metabolome of the anaerobic world Natural product reports
243Li JL, Mazar J, Zhong C et al. 2013 Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network Scientific reports 3:2962.
247Lilleoja R, Sarapik A, Reimann E et al. 2011 Sequencing and annotated analysis of an Estonian human genome Gene
250Lin 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.
251Liu B, Faller LL, Klitgord N et al. 2012 Deep sequencing of the oral microbiome reveals signatures of periodontal disease PLoS One 7:e37919.
252Liu CC, Tang CY, Kuo HY et al. 2013 The origin of Acinetobacter baumannii TYTH-1: a comparative genomics study International journal of antimicrobial agents
253Liu H, Chen Y, Lv J et al. 2013 Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes Scientific reports 3:2576.
255Liu 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.
256Lluch-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.
257Lo I, Denef VJ, Verberkmoes NC et al. 2007 Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria Nature 446:537-541.
260Love C, Sun Z, Jima D et al. 2012 The genetic landscape of mutations in Burkitt lymphoma Nat Genet
261Lucas MR, Diop N-N, Wanamaker S et al. 2011 Cowpea-Soybean Synteny Clarified through an Improved Genetic Map The Plant Genome 4:218-225.
262Lucas MR, Ehlers JD, Roberts PA et al. 2012 Markers For Quantitative Inheritance Of Resistance To Foliar Thrips In Cowpea Crop Sci 52:2075-2081.
263Lucchi 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.
264Lucker 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.
265Lynch KH, Stothard P, Dennis JJ 2012 Characterization of DC1, a broad-host-range Bcep22-like podovirus Appl Environ Microbiol 78:889-891.
268Mace ES, Tai S, Gilding EK et al. 2013 Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum Nature communications 4:2320.
270Makanju 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.
272Mallo 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
273Mameaux 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:-.
274Mandakova T, Joly S, Krzywinski M et al. 2010 Fast diploidization in close mesopolyploid relatives of Arabidopsis Plant Cell 22:2277-2290.
275Mandakova T, Kovarik A, Zozomova-Lihova J et al. 2013 The More the Merrier: Recent Hybridization and Polyploidy in Cardamine Plant Cell
276Mandlik 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.
277Mann 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.
278Markovets A, Herman D 2011 Analysis of cancer metabolism with high-throughput technologies BMC Bioinformatics 12:S8.
280Martin 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.
281Martis MM, Zhou R, Haseneyer G et al. 2013 Reticulate Evolution of the Rye Genome Plant Cell
282Mayer KF, Martis M, Hedley PE et al. 2011 Unlocking the barley genome by chromosomal and comparative genomics Plant Cell 23:1249-1263.
283McBride 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.
284McGraw 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.
287Mehine M, Kaasinen E, Makinen N et al. 2013 Characterization of uterine leiomyomas by whole-genome sequencing The New England journal of medicine 369:43-53.
289Mewis K, Armstrong Z, Song YC et al. 2013 Biomining active cellulases from a mining bioremediation system Journal of biotechnology 167:462-471.
290Meyer C, Kowarz E, Hofmann J et al. 2009 New insights to the MLL recombinome of acute leukemias Leukemia 23:1490-1499.
291Meyer M, Munzner T, Pfister H 2009 MizBee: a multiscale synteny browser IEEE Trans Vis Comput Graph 15:897-904.
292Meyerson M, Gabriel S, Getz G 2010 Advances in understanding cancer genomes through second-generation sequencing Nat Rev Genet 11:685-696.
293Miga KH, Newton Y, Jain M et al. 2013 Complete sequence representation across human X and Y centromeric regions arXiv 1307.0035:
294Milczarski PÇ, Bolibok-Bragoszewska H, Myskow B et al. 2011 A High Density Consensus Map of Rye (Secale cereale L.) Based on DArT Markers PLoS One 6:e28495.
295Ming R, Vanburen R, Liu Y et al. 2013 Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Genome Biol 14:R41.
296Miousse IR, Gomez-Acevedo H, Sharma N et al. 2013 Mammary gland morphology and gene expression signature of weanling male and female rats following exposure to exogenous estradiol Experimental biology and medicine 238:1033-1046.
297Moere AV 2007 Aesthetic Data Visualization as a Resource for Educating Creative Design In Computer-Aided Architectural Design Futures 2007: Proceedings of the 12th International CAADFutures Conference, (ed. A Dong, AV Moere, JS Gero), p. 71-84. Springer.
300Monsieurs P, Moors H, Van Houdt R et al. 2011 Heavy metal resistance in <i>Cupriavidus metallidurans</i> CH34 is governed by an intricate transcriptional network Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine 1-19.
302Mun JH, Yu HJ, Shin JY et al. 2012 Auxin response factor gene family in Brassica rapa: genomic organization, divergence, expression, and evolution Molecular genetics and genomics : MGG
303Muthamilarasan M, Venkata Suresh B, Pandey G et al. 2013 Development of 5123 Intron-Length Polymorphic Markers for Large-Scale Genotyping Applications in Foxtail Millet DNA research : an international journal for rapid publication of reports on genes and genomes
309Neph S, Stergachis AB, Reynolds A et al. 2012 Circuitry and dynamics of human transcription factor regulatory networks Cell 150:1274-1286.
310Network TCGAR 2013 Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia The New England journal of medicine 368:2059-2074.
311Newman S, Howarth KD, Greenman CD et al. 2013 The relative timing of mutations in a breast cancer genome PLoS One 8:e64991.
312Nickerson ML, Im KM, Misner KJ et al. 2013 Somatic Alterations Contributing to Metastasis of a Castration Resistant Prostate Cancer Human mutation
314Nielsen C, Wong B 2012 Points of view: Representing genomic structural variation Nat Meth 9:631-631.
315Nielsen CB, Cantor M, Dubchak I et al. 2010 Visualizing genomes: techniques and challenges Nat Methods 7:S5-S15.
316Nijkamp JF, Pop M, Reinders MJ et al. 2013 Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold Bioinformatics
317Nussbaumer T, Martis MM, Roessner SK et al. 2012 MIPS PlantsDB: a database framework for comparative plant genome research Nucleic Acids Res
318O'Huallachain M, Karczewski KJ, Weissman SM et al. 2012 Extensive genetic variation in somatic human tissues Proc Natl Acad Sci U S A 109:18018-18023.
319O'Quin KE, Yoshizawa M, Doshi P et al. 2013 Quantitative Genetic Analysis of Retinal Degeneration in the Blind Cavefish Astyanax mexicanus PLoS One 8:e57281.
322Omodei D, Licastro D, Salvatore F et al. 2013 Serum from humans on long-term calorie restriction enhances stress resistance in cell culture Aging (Albany NY) 5:599-606.
323Orlova IA, Alexander GM, Qureshi RA et al. 2011 MicroRNA modulation in complex regional pain syndrome Journal of translational medicine 9:195.
324Orsi W, Song YC, Hallam S et al. 2012 Effect of oxygen minimum zone formation on communities of marine protists The ISME journal
325Ostrander EA 2007 Genetics and the Shape of Dogs American Scientist 95:406-413.
326Pabinger S, Dander A, Fischer M et al. 2013 A survey of tools for variant analysis of next-generation genome sequencing data Brief Bioinform
327Padmanabhan S, Newton-Cheh C, Dominiczak AF 2012 Genetic basis of blood pressure and hypertension Trends in genetics : TIG
328Page JT, Huynh MD, Liechty ZS et al. 2013 Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing G3: Genes|Genomes|Genetics 3:1809-1818.
330Palmieri F, Pierri CL, De Grassi A et al. 2011 Evolution, structure and function of mitochondrial carriers: a review with new insights Plant J 66:161-181.
332Park R, Gehlenborg N, Park P. 2011. Seqeyes: A multi-scale interactive visualization tool for structural variations. In 1st IEEE Symposium on Biological Data Visualization, Providence, RI.
333Park W, Oh HS, Kim H 2013 Acceleration of X-chromosome gene order evolution in the cattle lineage BMB reports 46:310-315.
334Partipilo G, D'Addabbo P, Lacalandra GM et al. 2011 Refinement of Bos taurus sequence assembly based on BAC-FISH experiments BMC Genomics 12:639.
335Paten B, Diekhans M, Earl D et al. 2010 Cactus Graphs for Genome Comparisons In Lecture notes in Computer Science, (ed. 410-425. Springer Berlin.
336Paterson T, Law A 2013 ArkMAP: integrating genomic maps across species and data sources BMC Bioinformatics 14:246.
337Pavlopoulos GA, Kumar P, Sifrim A et al. 2013 Meander: visually exploring the structural variome using space-filling curves Nucleic Acids Res
340Peregrin-Alvarez JM, Xiong X, Su C et al. 2009 The Modular Organization of Protein Interactions in Escherichia coli PLoS Comput Biol 5:e1000523.
345Pimiento JM, Larkin EM, Smalley KS et al. 2013 Melanoma genotypes and phenotypes get personal Laboratory investigation; a journal of technical methods and pathology 93:858-867.
346Pleasance ED, Cheetham RK, Stephens PJ et al. 2010 A comprehensive catalogue of somatic mutations from a human cancer genome Nature 463:191-196.
347Pleasance ED, Stephens PJ, O'Meara S et al. 2010 A small-cell lung cancer genome with complex signatures of tobacco exposure Nature 463:184-190.
348Prasad TS, Harsha HC, Keerthikumar S et al. 2011 Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry Journal of proteome research
349Procter JB, Thompson J, Letunic I et al. 2010 Visualization of multiple alignments, phylogenies and gene family evolution Nat Methods 7:S16-25.
350Pugh TJ, Morozova O, Attiyeh EF et al. 2013 The genetic landscape of high-risk neuroblastoma Nat Genet
351Quinlan AR, Hall IM 2012 Characterizing complex structural variation in germline and somatic genomes Trends in genetics : TIG 28:43-53.
353Rafael-Palou X, Schroeder MP, Lopez-Bigas N 2011 SVGMap: configurable image browser for experimental data Bioinformatics
354Rafelsberger W, Schari A. 2009. Games with a purpose for social networking platforms. In Conference on Hypertext and Hypermedia, Vol 1, pp. 193-198. ACM, Torino, Italy.
356Rajaraman A, Tannier E, Chauve C 2013 FPSAC: fast phylogenetic scaffolding of ancient contigs Bioinformatics
357Rangkuti FGA. 2011. Genome Assembly and Computational Analysis Pipelines for Bacterial Pathogens. Vol M.Sc. King Abdullah University of Science and Technology, Thuwal.
358Rasko 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:-.
360Rawal HC, Singh NK, Sharma TR 2013 Conservation, Divergence, and Genome-Wide Distribution of PAL and POX A Gene Families in Plants International Journal of Genomics 2013:10.
361Raychaudhuri S 2011 VIZ-GRAIL: visualizing functional connections across disease loci Bioinformatics 27:1589-1590.
362Rebich-Hespanha S, Rice RE, Montello DR et al.. 2013. Political Framing of Climate Change in US News Imagery. In Environmental Politics Conference, University of California, Santa Barbara, CA.
363Reith F, Etschmann B, Grosse C et al. 2009 Mechanisms of gold biomineralization in the bacterium Cupriavidus metallidurans Proc Natl Acad Sci U S A 106:17757-17762.
364Riley DR, Angiuoli SV, Crabtree J et al. 2012 Using Sybil for interactive comparative genomics of microbes on the web Bioinformatics 28:160-166.
365Riley DR, Sieber KB, Robinson KM et al. 2013 Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples PLoS Comput Biol 9:e1003107.
368Roest Crollius H, Weissenbach J 2005 Fish genomics and biology Genome research 15:1675-1682.
371Rossello FJ, Tothill RW, Britt K et al. 2013 Next-Generation Sequence Analysis of Cancer Xenograft Models PLoS One 8:e74432.
372Roulin A, Auer PL, Libault M et al. 2012 The fate of duplicated genes in a polyploid plant genome Plant J
373Roychowdhury S, Iyer MK, Robinson DR et al. 2011 Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study Science Translational Medicine 3:111ra121.
375Ruddle RA, Fateen W, Treanor D 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.
378Sakai R, Moisse M, Reumers J et al. 2013 Pipit: visualising functional impacts of structural variations Bioinformatics
379Sakarya O, Breu H, Radovich M et al. 2012 RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm PLoS Comput Biol 8:e1002464.
380Salse J, Abrouk M, Murat F et al. 2009 Improved criteria and comparative genomics tool provide new insights into grass paleogenomics Brief Bioinform 10:619-630.
383Sarkies P, Sale JE 2012 Cellular epigenetic stability and cancer Trends in genetics : TIG 28:118-127.
385Saxena RK, Varma Penmetsa R, Upadhyaya HD et al. 2012 Large-Scale Development of Cost-Effective Single-Nucleotide Polymorphism Marker Assays for Genetic Mapping in Pigeonpea and Comparative Mapping in Legumes DNA research : an international journal for rapid publication of reports on genes and genomes
386Sboner A, Habegger L, Pflueger D et al. 2010 FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data Genome Biol 11:R104.
387Schenk TL, Jr. 2011 Measuring Transitions into the Workforce as a Form of Accountability SSRN eLibrary ID 1831967:-.
388Schmutz J, Cannon SB, Schlueter J et al. 2010 Genome sequence of the palaeopolyploid soybean Nature 463:178-183.
389Schnable PS Ware D Fulton RS et al. 2009 The B73 maize genome: complexity, diversity, and dynamics Science 326:1112-1115.
390Schroeder MP, Gonzalez-Perez A, Lopez-Bigas N 2013 Visualizing multidimensional cancer genomics data Genome medicine 5:9.
391Schultz AK, Bulla I, Abdou-Chekaraou M et al. 2012 jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus Nucleic Acids Res
392Secrier M, Schneider R 2013 Visualizing time-related data in biology, a review Brief Bioinform
395Seshagiri S, Stawiski EW, Durinck S et al. 2012 Recurrent R-spondin fusions in colon cancer Nature 488:660-664.
396Shankar K, Zhong Y, Kang P et al. 2012 RNA-seq Analysis of the Functional Compartments within the Rat Placentation Site Endocrinology 153:1999-2011.
399Shih AH, Abdel-Wahab O, Patel JP et al. 2012 The role of mutations in epigenetic regulators in myeloid malignancies Nat Rev Cancer 12:599-612.
400Shin SC, Ahn do H, Kim SJ et al. 2013 Advantages of Single-Molecule Real-Time Sequencing in High-GC Content Genomes PLoS One 8:e68824.
401Shirasawa K, Bertioli DJ, Varshney RK et al. 2013 Integrated Consensus Map of Cultivated Peanut and Wild Relatives Reveals Structures of the A and B Genomes of Arachis and Divergence of the Legume Genomes DNA research : an international journal for rapid publication of reports on genes and genomes
403Sierra R, Rodriguez RL, Chaves D et al. 2010 Discovery of phytophthora infestans genes expressed in planta through mining of cDNA libraries PLoS One 5:e9847.
404Silva IT, Rosales RA, Holanda AJ et al. 2013 Identification of chromosomal translocation hotspots via scan statistics arXivorg arXiv:1310.3291:
407Simonetti FL, Teppa E, Chernomoretz A et al. 2013 MISTIC: mutual information server to infer coevolution Nucleic Acids Res
408Singh N, Gupta D, Jayaswal P et al. 2011 The first draft of the pigeonpea genome sequence Journal of Plant Biochemistry and Biotechnology 1-15.
410Sirand-Pugnet P, Citti C, Barre A et al. 2007 Evolution of mollicutes: down a bumpy road with twists and turns Res Microbiol 158:754-766.
413Sloan DB, Moran NA 2012 Endosymbiotic bacteria as a source of carotenoids in whiteflies Biology Letters
415Smith JJ, Miller LR, Kreisberg R et al. 2011 Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing Mol Syst Biol 7:455.
416Soderlund C, Bomhoff M, Nelson WM 2011 SyMAP v3.4: a turnkey synteny system with application to plant genomes Nucleic Acids Res 39:e68.
419Spans L, Atak ZK, Van Nieuwerburgh F et al. 2011 Variations in the exome of the LNCaP prostate cancer cell line The Prostate
420Sperling E, Rosengarten R, Moreno M et al. 2011 The complete mitochondrial genome of the verongid sponge Aplysina cauliformi: implications for DNA barcoding in demosponges Hydrobiologia advanced online:1-9.
421Srinivas G, Moller S, Wang J et al. 2013 Genome-wide mapping of gene-microbiota interactions in susceptibility to autoimmune skin blistering Nature communications 4:2462.
426Stein LD 2011 An introduction to the informatics of "next-generation" sequencing Current protocols in bioinformatics / editoral board, Andreas D Baxevanis [et al] Chapter 11:Unit11 11.
428Stephens PJ, McBride DJ, Lin ML et al. 2009 Complex landscapes of somatic rearrangement in human breast cancer genomes Nature 462:1005-1010.
430Stintzi A, Flint A, Butcher J et al. 2010 Use of a Rabbit Soft Tissue Chamber Model to Investigate Campylobacter jejuni - Host Interactions Frontiers in Microbiology 1:126.
432Taiwo O, Wilson GA, Emmett W et al. 2013 DNA methylation analysis of murine hematopoietic side population cells during aging Epigenetics : official journal of the DNA Methylation Society 8:
435Throude M, Bolot S, Bosio M et al. 2009 Structure and expression analysis of rice paleo duplications Nucleic Acids Res 37:1248-1259.
436Tobias CM, Sarath G, Twigg P et al. 2008 Comparative Genomics in Switchgrass Using 61,585 High-Quality Expressed Sequence Tags The Plant Genome 1:111-124.
437Tobias NJ, Doig KD, Medema MH et al. 2013 Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans Ecovar Liflandii J Bacteriol 195:556-564.
438Tomljenovic-Berube AM. 2013. SsrB-dependent regulation during Salmonella pathogenesis. Vol PhD. McMaster University.
439Tomljenovic-Berube AM, Mulder DT, Whiteside MD et al. 2010 Identification of the regulatory logic controlling Salmonella pathoadaptation by the SsrA-SsrB two-component system PLoS Genet 6:e1000875.
441Turajlic S, Furney SJ, Lambros MB et al. 2012 Whole genome sequencing of matched primary and metastatic acral melanomas Genome research 22:196-207.
442Turchaninova MA, Britanova OV, Bolotin DA et al. 2013 Pairing of T-cell receptor chains via emulsion PCR European journal of immunology
443Ugalde JA, Gallardo MJ, Belmar C et al. 2013 Microbial life in a fjord: metagenomic analysis of a microbial mat in chilean patagonia PLoS One 8:e71952.
444Valdes C, Seo P, Tsinoremas N et al. 2013 Characteristics of cross-hybridization and cross-alignment of expression in pseudo-xenograft samples by RNA-Seq and microarrays Journal of clinical bioinformatics 3:8.
445Van Bel M, Proost S, Wischnitzki E et al. 2012 Dissecting plant genomes with the PLAZA comparative genomics platform Plant physiology 158:590-600.
446Van der Aa N, Cheng J, Mateiu L et al. 2013 Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains Nucleic Acids Res
447Van Horn JD, Irimia A, Torgerson CM et al. 2012 Mapping connectivity damage in the case of phineas gage PLoS One 7:e37454.
449Van K, Rastogi K, Kim K-H et al. 2013 Next-generation Sequencing Technology for Crop Improvement SABRAO Journal of Breeding and Genetics 45:84-99.
450van Ooijen G, Hindle M, Martin SF et al. 2013 Functional analysis of Casein Kinase 1 in a minimal circadian system PLoS One 8:e70021.
451Vanburen R, Ming R 2013 Organelle DNA accumulation in the recently evolved papaya sex chromosomes Molecular genetics and genomics : MGG 288:277-284.
452Varala K, Swaminathan K, Li Y et al. 2011 Rapid Genotyping of Soybean Cultivars Using High Throughput Sequencing PLoS One 6:e24811.
453Varela I, Klijn C, Stephens PJ et al. 2010 Somatic structural rearrangements in genetically engineered mouse mammary tumors Genome Biol 11:R100.
456Vergara IA, Frech C, Chen N 2012 CooVar: Co-occurring variant analyzer BMC research notes 5:615.
457Voet T, Kumar P, Van Loo P et al. 2013 Single-cell paired-end genome sequencing reveals structural variation per cell cycle Nucleic Acids Res
458Vonholdt BM, Pollinger JP, Lohmueller KE et al. 2010 Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication Nature 464:898-902.
463Wang J, de Villena F, McMillan L 2012 Comparative analysis and visualization of multiple collinear genomes BMC Bioinformatics 13:S13.
468Wang YE, Marinov GK, Wold BJ et al. 2013 Genome-Wide Analysis Reveals Coating of the Mitochondrial Genome by TFAM PLoS One 8:e74513.
469Wartman LD, Larson DE, Xiang Z et al. 2011 Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression J Clin Invest 121:1445-1455.
472Weier C, Haffner MC, Mosbruger T et al. 2013 Nucleotide resolution analysis of TMPRSS2 and ERG rearrangements in prostate cancer J Pathol 230:174-183.
473Weiss GJ, Liang WS, Izatt T et al. 2012 Paired tumor and normal whole genome sequencing of metastatic olfactory neuroblastoma PLoS One 7:e37029.
474Westphal-Fitch G, Oh J, Fitch WT 2013 Psychology of Aesthetics, Creativity, and the Arts 7:13-26.
478Wilson GA, Lechner M, Koferle A et al. 2013 Integrated virus-host methylome analysis in head and neck squamous cell carcinoma Epigenetics : official journal of the DNA Methylation Society 8:
480Wohlgemuth SE, Gorochowski TE, Roubos JA 2013 Translational sensitivity of the Escherichia coli genome to fluctuating tRNA availability Nucleic Acids Res 41:8021-8033.
481Wong B 2012 Points of view: Visualizing biological data Nat Meth 9:1131-1131.
482Wozniak M, Wong L, Tiuryn J 2011 CAMBerVis: visualization software to support comparative analysis of multiple bacterial strains Bioinformatics 27:3313-3314.
483Wright JJ, Mewis K, Hanson NW et al. 2013 Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle The ISME journal
484Wu C, Wyatt AW, McPherson A et al. 2012 Poly-gene fusion transcripts and chromothripsis in prostate cancer Genes Chromosomes Cancer
485Wu K, Chen J, Pruett WA et al.. 2013. HumMod Browser: An Exploratory Visualization Tool for the Analysis of Whole-Body Physiology Simulation Data. In IEEE Symposium on Biological Data Visualization, Atlanta, GA.
486Wu S, Li N, Ma J et al. 2013 First proteomic exploration of protein-encoding genes on chromosome 1 in human liver, stomach, and colon Journal of proteome research 12:67-80.
487Wu S, Li N, Ma J et al. 2013 First proteomic exploration of protein-encoding genes on chromosome 1 in human liver, stomach, and colon Journal of proteome research 12:67-80.
492Yang J, Osman K, Iqbal M et al. 2013 Inferring the Brassica rapa interactome using protein-protein interaction data from Arabidopsis thaliana Frontiers in Plant Science 3:
495Yang Y, Li B, Ju F et al. 2013 Exploring Variation of Antibiotic Resistance Genes in Activated Sludge over a Four-Year Period through a Metagenomic Approach Environmental science & technology 47:10197-10205.
496Yasmin A, Kenny JG, Shankar J et al. 2010 Comparative genomics and transduction potential of Enterococcus faecalis temperate bacteriophages J Bacteriol 192:1122-1130.
498Yen K, Vinayachandran V, Pugh BF 2013 SWR-C and INO80 Chromatin Remodelers Recognize Nucleosome-free Regions Near +1 Nucleosomes Cell 154:1246-1256.
499Ying CY, Dominguez-Sola D, Fabi M et al. 2013 MEF2B mutations lead to deregulated expression of the oncogene BCL6 in diffuse large B cell lymphoma Nature immunology 14:1084-1092.
502Yoshida K, Toki T, Okuno Y et al. 2013 The landscape of somatic mutations in Down syndrome-related myeloid disorders Nat Genet
504Youens-Clark K, Faga B, Yap IV et al. 2009 CMap 1.01: a comparative mapping application for the Internet Bioinformatics 25:3040-3042.
505Young ND, Bharti AK 2011 Genome-Enabled Insights into Legume Biology Annual Review of Plant Biology
506Young ND Debelle F Oldroyd GE et al. 2011 The Medicago genome provides insight into the evolution of rhizobial symbioses Nature 480:520-524.
507Yu SC, Jiang P, Choy KW et al. 2013 Noninvasive prenatal molecular karyotyping from maternal plasma PLoS One 8:e60968.
508Yuan H, Qin F, Movassagh M et al. 2013 A Chimeric RNA Characteristic of Rhabdomyosarcoma in Normal Myogenesis Cancer discovery
509Yuan H, Zhao K, Lei H et al. 2013 Genome-wide analysis of the GH3 family in apple (Malus x domestica) BMC Genomics 14:297.
510Yuan Z, Sun X, Jiang D et al. 2010 Origin and evolution of a placental-specific microRNA family in the human genome BMC Evol Biol 10:346.
511Zavou A, Pappas V, Kemerlis V et al.. 2013. Cloudopsy: an Autopsy of Data Flows in the Cloud. In International Conference on Human-Computer Interaction, Las Vegas, NV.
512Zeitouni B, Boeva V, Janoueix-Lerosey I et al. 2010 SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data Bioinformatics 26:1895-1896.
513Zhang D, Guo H, Kim C et al. 2012 CSGRqtl, a comparative QTL database for Saccharinae grasses Plant physiology
514Zhang H, Meltzer P, Davis S 2013 RCircos: an R package for Circos 2D track plots BMC Bioinformatics 14:244.
515Zhang J, Grubor V, Love CL et al. 2013 Genetic heterogeneity of diffuse large B-cell lymphoma Proc Natl Acad Sci U S A 110:1398-1403.
518Zhao F, Zhang X, Tung AKH et al. 2011 BROAD: Diversified Keyword Search in Databases NUS SOC Technical Report TRD3/11:1-15.
521Zhou Z, Deng F, Han N et al. 2013 Reassortment and migration analysis of Crimean-Congo haemorrhagic fever virus The Journal of general virology 94:2536-2548.