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  1. Current methods of measuring transcription in high-throughput have led to significant improvements in our knowledge of transcriptional regulation and Systems Biology. However, endpoint measurements obtained fr...

    Authors: Saravanan Rajan, Haig Djambazian, Huan Chu Pham Dang, Rob Sladek and Thomas J Hudson
    Citation: BMC Genomics 2011 12:115
    Content type: Methodology article Published on:

  2. DNA microarray technology has had a great impact on muscle research and microarray gene expression data has been widely used to identify gene signatures characteristic of the studied conditions. With the rapid...

    Authors: Daniel Baron, Emeric Dubois, Audrey Bihouée, Raluca Teusan, Marja Steenman, Philippe Jourdon, Armelle Magot, Yann Péréon, Reiner Veitia, Frédérique Savagner, Gérard Ramstein and Rémi Houlgatte
    Citation: BMC Genomics 2011 12:113
    Content type: Database Published on:

  3. The Chinese Taihu is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. Variation of ovulation...

    Authors: Xiaojie Sun, Shuqi Mei, Hu Tao, Guodong Wang, Lina Su, Siwen Jiang, Changyan Deng, Yuanzhu Xiong and Fenge Li
    Citation: BMC Genomics 2011 12:111
    Content type: Research article Published on:

  4. Chlamydiae are obligate intracellular bacteria that multiply in a vacuolar compartment, the inclusion. Several chlamydial proteins containing a bilobal hydrophobic domain are translocated by a type III secretion ...

    Authors: Pierre Dehoux, Rhonda Flores, Catherine Dauga, Guangming Zhong and Agathe Subtil
    Citation: BMC Genomics 2011 12:109
    Content type: Research article Published on:

  5. Mannoproteins construct the outer cover of the fungal cell wall. The covalently linked cell wall protein Ccw12p is an abundant mannoprotein. It is considered as crucial structural cell wall component since in ...

    Authors: Enrico Ragni, Heidi Piberger, Christine Neupert, Jesús García-Cantalejo, Laura Popolo, Javier Arroyo, Markus Aebi and Sabine Strahl
    Citation: BMC Genomics 2011 12:107
    Content type: Research article Published on:

  6. Recent advances in massively parallel sequencing have increased the depth at which T cell receptor (TCR) repertoires can be probed by >3log10, allowing for saturation sequencing of immune repertoires. The reso...

    Authors: Phuong Nguyen, Jing Ma, Deqing Pei, Caroline Obert, Cheng Cheng and Terrence L Geiger
    Citation: BMC Genomics 2011 12:106
    Content type: Research article Published on:

  7. The horn fly, Haematobia irritans (Linnaeus, 1758) (Diptera: Muscidae) is one of the most important ectoparasites of pastured cattle. Horn flies infestations reduce cattle weight gain and milk production. Additio...

    Authors: Lorena Torres, Consuelo Almazán, Nieves Ayllón, Ruth C Galindo, Rodrigo Rosario-Cruz, Héctor Quiroz-Romero and José de la Fuente
    Citation: BMC Genomics 2011 12:105
    Content type: Research article Published on:

  8. Cucurbita pepo belongs to the Cucurbitaceae family. The "Zucchini" types rank among the highest-valued vegetables worldwide, and other C. pepo and related Cucurbita spp., are food staples and rich sources of fat ...

    Authors: José Blanca, Joaquín Cañizares, Cristina Roig, Pello Ziarsolo, Fernando Nuez and Belén Picó
    Citation: BMC Genomics 2011 12:104
    Content type: Research article Published on:

  9. Because the Japanese native cattle Kuchinoshima-Ushi have been isolated in a small island and their lineage has been intensely protected, it has been assumed to date that numerous and valuable genomic variations ...

    Authors: Ryouka Kawahara-Miki, Kaoru Tsuda, Yuh Shiwa, Yuko Arai-Kichise, Takashi Matsumoto, Yu Kanesaki, Sen-ichi Oda, Shizufumi Ebihara, Shunsuke Yajima, Hirofumi Yoshikawa and Tomohiro Kono
    Citation: BMC Genomics 2011 12:103
    Content type: Research article Published on:

  10. In addition to determining static states of gene expression (high vs. low), it is important to characterize their dynamic status. For example, genes with H3K27me3 chromatin marks are not only suppressed but al...

    Authors: Alexei A Sharov, Akira Nishiyama, Yulan Piao, Lina S Correa-Cerro, Tomokazu Amano, Marshall Thomas, Samir Mehta and Minoru SH Ko
    Citation: BMC Genomics 2011 12:102
    Content type: Research article Published on:

  11. The large number of genetic linkage maps representing Brassica chromosomes constitute a potential platform for studying crop traits and genome evolution within Brassicaceae. However, the alignment of existing map...

    Authors: Jun Wang, Derek J Lydiate, Isobel AP Parkin, Cyril Falentin, Régine Delourme, Pierre WC Carion and Graham J King
    Citation: BMC Genomics 2011 12:101
    Content type: Research article Published on:

  12. Anthracnose (Colletotrichum gloeosporioides) is a major limiting factor in the production of yam (Dioscorea spp.) worldwide. Availability of high quality sequence information is necessary for designing molecular ...

    Authors: Satya S Narina, Ramesh Buyyarapu, Kameswara Rao Kottapalli, Alieu M Sartie, Mohamed I Ali, Asiedu Robert, Mignouna JD Hodeba, Brian L Sayre and Brian E Scheffler
    Citation: BMC Genomics 2011 12:100
    Content type: Research article Published on:

  13. Because of their phylogenetic position and unique characteristics of their biology and life cycle, ferns represent an important lineage for studying the evolution of land plants. Large and complex genomes in f...

    Authors: Joshua P Der, Michael S Barker, Norman J Wickett, Claude W dePamphilis and Paul G Wolf
    Citation: BMC Genomics 2011 12:99
    Content type: Research article Published on:

  14. Many human diseases and phenotypes are related to RNA expression, levels of which are influenced by a wide spectrum of genetic and exposure-related factors. In a large genome-wide study of muscle tissue expres...

    Authors: Clinton C Mason, Robert L Hanson, Vicky Ossowski, Li Bian, Leslie J Baier, Jonathan Krakoff and Clifton Bogardus
    Citation: BMC Genomics 2011 12:98
    Content type: Research article Published on:

  15. Several approaches have been developed for miRNA target prediction, including methods that incorporate expression profiling. However the methods are still in need of improvements due to a high false discovery ...

    Authors: Claus H Bang-Berthelsen, Lykke Pedersen, Tina Fløyel, Peter H Hagedorn, Titus Gylvin and Flemming Pociot
    Citation: BMC Genomics 2011 12:97
    Content type: Research article Published on:

  16. Divergently selected Lean and Fat mouse lines represent unique models for a polygenic form of resistance and susceptibility to obesity development. Previous research on these lines focused mainly on obesity-su...

    Authors: Matjaž Simončič, Tadeja Režen, Peter Juvan, Damjana Rozman, Gregor Fazarinc, Catherine Fievet, Bart Staels and Simon Horvat
    Citation: BMC Genomics 2011 12:96
    Content type: Research article Published on:

  17. Lactation increases energy demands four- to five-fold, leading to a two- to three-fold increase in food consumption, requiring a proportional adjustment in the ability of the lactating dam to absorb nutrients ...

    Authors: Antony Athippozhy, Liping Huang, Clavia Ruth Wooton-Kee, Tianyong Zhao, Paiboon Jungsuwadee, Arnold J Stromberg and Mary Vore
    Citation: BMC Genomics 2011 12:95
    Content type: Research article Published on:

  18. Variation within individual genomes ranges from single nucleotide polymorphisms (SNPs) to kilobase, and even megabase, sized structural variants (SVs), such as deletions, insertions, inversions, and more compl...

    Authors: Hindrik HD Kerstens, Richard PMA Crooijmans, Bert W Dibbits, Addie Vereijken, Ron Okimoto and Martien AM Groenen
    Citation: BMC Genomics 2011 12:94
    Content type: Methodology article Published on:

  19. Clostridium acetobutylicum, a gram-positive and spore-forming anaerobe, is a major strain for the fermentative production of acetone, butanol and ethanol. But a previously isolated hyper-butanol producing strain

    Authors: Shiyuan Hu, Huajun Zheng, Yang Gu, Jingbo Zhao, Weiwen Zhang, Yunliu Yang, Shengyue Wang, Guoping Zhao, Sheng Yang and Weihong Jiang
    Citation: BMC Genomics 2011 12:93
    Content type: Research article Published on:

  20. Genome-wide association studies (GWAS) of common diseases have had a tremendous impact on genetic research over the last five years; the field is now moving from microarray-based technology towards next-genera...

    Authors: Benjamin Lehne, Cathryn M Lewis and Thomas Schlitt
    Citation: BMC Genomics 2011 12:92
    Content type: Research article Published on:

  25. Small non-coding RNAs (sRNAs) are regarded as important regulators in prokaryotes and play essential roles in diverse cellular processes. Xanthomonas oryzae pathovar oryzae (Xoo) is an important plant pathogenic ...

    Authors: Hong Liang, Ying-Tao Zhao, Jie-Qiong Zhang, Xiu-Jie Wang, Rong-Xiang Fang and Yan-Tao Jia
    Citation: BMC Genomics 2011 12:87
    Content type: Research article Published on:

  26. Nocturnal insects such as moths are ideal models to study the molecular bases of olfaction that they use, among examples, for the detection of mating partners and host plants. Knowing how an odour generates a ...

    Authors: Fabrice Legeai, Sébastien Malpel, Nicolas Montagné, Christelle Monsempes, François Cousserans, Christine Merlin, Marie-Christine François, Martine Maïbèche-Coisné, Frédérick Gavory, Julie Poulain and Emmanuelle Jacquin-Joly
    Citation: BMC Genomics 2011 12:86
    Content type: Research article Published on:

  27. Among the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is...

    Authors: Minkyu Park, SungHwan Jo, Jin-Kyung Kwon, Jongsun Park, Jong Hwa Ahn, Seungill Kim, Yong-Hwan Lee, Tae-Jin Yang, Cheol-Goo Hur, Byoung-Cheorl Kang, Byung-Dong Kim and Doil Choi
    Citation: BMC Genomics 2011 12:85
    Content type: Research article Published on:

  28. A well-informed choice of genetic locus is central to the efficacy of DNA barcoding. Current DNA barcoding in animals involves the use of the 5' half of the mitochondrial cytochrome oxidase 1 gene (CO1) to diagno...

    Authors: Arong Luo, Aibing Zhang, Simon YW Ho, Weijun Xu, Yanzhou Zhang, Weifeng Shi, Stephen L Cameron and Chaodong Zhu
    Citation: BMC Genomics 2011 12:84
    Content type: Research article Published on:

  29. Zinc Finger Nucleases (ZFNs) have tremendous potential as tools to facilitate genomic modifications, such as precise gene knockouts or gene replacements by homologous recombination. ZFNs can be used to advance...

    Authors: Deepak Reyon, Jessica R Kirkpatrick, Jeffry D Sander, Feng Zhang, Daniel F Voytas, J Keith Joung, Drena Dobbs and Clark R Coffman
    Citation: BMC Genomics 2011 12:83
    Content type: Database Published on:

  30. Hematophagy is a common trait of insect vectors of disease. Extensive genome-wide transcriptional changes occur in mosquitoes after blood meals, and these are related to digestive and reproductive processes, a...

    Authors: Mariangela Bonizzoni, W Augustine Dunn, Corey L Campbell, Ken E Olson, Michelle T Dimon, Osvaldo Marinotti and Anthony A James
    Citation: BMC Genomics 2011 12:82
    Content type: Research article Published on:

  31. Variation at the level of gene expression is abundant in natural populations and is thought to contribute to the adaptive divergence of populations and species. Gene expression also differs considerably betwee...

    Authors: Lena Müller, Stephan Hutter, Rayna Stamboliyska, Sarah S Saminadin-Peter, Wolfgang Stephan and John Parsch
    Citation: BMC Genomics 2011 12:81
    Content type: Research article Published on:

  32. Due to their high level of genotypic and phenotypic variability, Mus spretus strains were introduced in laboratories to investigate the genetic determinism of complex phenotypes including quantitative trait loci....

    Authors: Nisrine Boumahrou, Claudia Bevilacqua, Christian Beauvallet, Guy Miranda, Sanda Andrei, Emmanuelle Rebours, Jean-Jacques Panthier, Sylvain Bellier and Patrice Martin
    Citation: BMC Genomics 2011 12:80
    Content type: Research article Published on:

  34. Segmental duplication and deletion were implicated for a region containing the human immunoglobulin heavy chain variable (IGHV) gene segments, 1.9III/hv3005 (possible allelic variants of IGHV3-30) and hv3019b9...

    Authors: Sreemanta Pramanik, Xiangfeng Cui, Hui-Yun Wang, Nyam-Osor Chimge, Guohong Hu, Li Shen, Richeng Gao and Honghua Li
    Citation: BMC Genomics 2011 12:78
    Content type: Research article Published on:

  35. Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence ...

    Authors: Rebekah E Oliver, Gerard R Lazo, Joseph D Lutz, Marc J Rubenfield, Nicholas A Tinker, Joseph M Anderson, Nicole H Wisniewski Morehead, Dinesh Adhikary, Eric N Jellen, P Jeffrey Maughan, Gina L Brown Guedira, Shiaoman Chao, Aaron D Beattie, Martin L Carson, Howard W Rines, Donald E Obert…
    Citation: BMC Genomics 2011 12:77
    Content type: Research article Published on:

  36. Heat shock response in eukaryotes is transcriptionally regulated by conserved heat shock transcription factors (Hsfs). Hsf genes are represented by a large multigene family in plants and investigation of the H...

    Authors: Yong-Xiang Lin, Hai-Yang Jiang, Zhang-Xin Chu, Xiu-Li Tang, Su-Wen Zhu and Bei-Jiu Cheng
    Citation: BMC Genomics 2011 12:76
    Content type: Research article Published on:

  37. The prevalence of invasive fungal infections (IFIs) has increased steadily worldwide in the last few decades. Particularly, there has been a global rise in the number of infections among immunosuppressed peopl...

    Authors: Ana Karina R Abadio, Erika S Kioshima, Marcus M Teixeira, Natalia F Martins, Bernard Maigret and Maria Sueli S Felipe
    Citation: BMC Genomics 2011 12:75
    Content type: Research article Published on:

  38. Although primarily known as the site of ribosome subunit production, the nucleolus is involved in numerous and diverse cellular processes. Recent large-scale proteomics projects have identified thousands of hu...

    Authors: Michelle S Scott, François-Michel Boisvert, Angus I Lamond and Geoffrey J Barton
    Citation: BMC Genomics 2011 12:74
    Content type: Research article Published on:

  39. Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important...

    Authors: Wang Minxiao, Sun Song, Li Chaolun and Shen Xin
    Citation: BMC Genomics 2011 12:73
    Content type: Research article Published on:

  42. M. catarrhalis is a gram-negative, gamma-proteobacterium and an opportunistic human pathogen associated with otitis media (OM) and exacerbations of chronic obstructive pulmonary disease (COPD). With direct and in...

    Authors: Jeremiah J Davie, Josh Earl, Stefan PW de Vries, Azad Ahmed, Fen Z Hu, Hester J Bootsma, Kim Stol, Peter WM Hermans, Robert M Wadowsky, Garth D Ehrlich, John P Hays and Anthony A Campagnari
    Citation: BMC Genomics 2011 12:70
    Content type: Research article Published on:

  43. Sessile bivalves of the genus Mytilus are suspension feeders relatively tolerant to a wide range of environmental changes, used as sentinels in ecotoxicological investigations and marketed worldwide as seafood. M...

    Authors: Paola Venier, Laura Varotto, Umberto Rosani, Caterina Millino, Barbara Celegato, Filippo Bernante, Gerolamo Lanfranchi, Beatriz Novoa, Philippe Roch, Antonio Figueras and Alberto Pallavicini
    Citation: BMC Genomics 2011 12:69
    Content type: Research article Published on:

  44. Eukaryotic translation initiation factor 4G (eIF4G) is thought to influence the translational efficiencies of cellular mRNAs by its roles in forming an eIF4F-mRNA-PABP mRNP that is competent for attachment of ...

    Authors: Eun-Hee Park, Fan Zhang, Jonas Warringer, Per Sunnerhagen and Alan G Hinnebusch
    Citation: BMC Genomics 2011 12:68
    Content type: Research article Published on:

  45. Chinese hamster ovary (CHO) cells are among the most widely used hosts for therapeutic protein production. Yet few genomic resources are available to aid in engineering high-producing cell lines.

    Authors: Stephanie Hammond, Jeffrey C Swanberg, Mihailo Kaplarevic and Kelvin H Lee
    Citation: BMC Genomics 2011 12:67
    Content type: Research article Published on:

  46. Methods for gene-class testing, such as Gene Set Enrichment Analysis (GSEA), incorporate biological knowledge into the analysis and interpretation of microarray data by comparing gene expression patterns to pa...

    Authors: Michael A Thomas, Luobin Yang, Barbara J Carter and Rebecca D Klaper
    Citation: BMC Genomics 2011 12:66
    Content type: Research article Published on:

  47. Scanning the genome with high density SNP markers has become a standard approach for identifying regions of the genome showing substantial between-population genetic differentiation, and thus evidence of diver...

    Authors: Pamela Wiener, Mohammad A Edriss, John L Williams, David Waddington, Andrew Law, John A Woolliams and Beatriz Gutiérrez-Gil
    Citation: BMC Genomics 2011 12:65
    Content type: Research article Published on:

  49. After several years in the juvenile phase, trees undergo flowering transition to become mature (florally competent) trees. This transition depends on the balanced expression of a complex network of genes that ...

    Authors: Jin-Zhi Zhang, Xiao-Yan Ai, Lei-Ming Sun, Dong-Liang Zhang, Wen-Wu Guo, Xiu-Xin Deng and Chun-Gen Hu
    Citation: BMC Genomics 2011 12:63
    Content type: Research article Published on:

  50. Heliconius butterflies are an excellent system for studies of adaptive convergent and divergent phenotypic traits. Wing colour patterns are used as signals to both predators and potential mates and are inherited ...

    Authors: Alison K Surridge, Sara Lopez-Gomollon, Simon Moxon, Luana S Maroja, Tina Rathjen, Nicola J Nadeau, Tamas Dalmay and Chris D Jiggins
    Citation: BMC Genomics 2011 12:62
    Content type: Research article Published on:

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BMC Genomics

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