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  1. Tissue differentiation is accompanied by genome-wide changes in the underlying chromatin structure and dynamics, or epigenome. By controlling when, where, and what regulatory factors have access to the underly...

    Authors: Ky Sha, Sam G Gu, Luiz C Pantalena-Filho, Amy Goh, Jamie Fleenor, Daniel Blanchard, Chaya Krishna and Andrew Fire
    Citation: BMC Genomics 2010 11:465
    Content type: Methodology article Published on:

  2. To date, oil-rich plants are the main source of biodiesel products. Because concerns have been voiced about the impact of oil-crop cultivation on the price of food commodities, the interest in oil plants not u...

    Authors: Gustavo GL Costa, Kiara C Cardoso, Luiz EV Del Bem, Aline C Lima, Muciana AS Cunha, Luciana de Campos-Leite, Renato Vicentini, Fábio Papes, Raquel C Moreira, José A Yunes, Francisco AP Campos and Márcio J Da Silva
    Citation: BMC Genomics 2010 11:462
    Content type: Research article Published on:

  3. Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pr...

    Authors: Manuel Stark, Simon A Berger, Alexandros Stamatakis and Christian von Mering
    Citation: BMC Genomics 2010 11:461
    Content type: Methodology article Published on:

  4. Modern biomedical research depends on a complete and accurate proteome. With the widespread adoption of new sequencing technologies, genome sequences are generated at a near exponential rate, diminishing the t...

    Authors: Samuel H Payne, Shih-Ting Huang and Rembert Pieper
    Citation: BMC Genomics 2010 11:460
    Content type: Research article Published on:

  5. Heterochromatin plays an important role in chromosome function and gene regulation. Despite the availability of polytene chromosomes and genome sequence, the heterochromatin of the major malaria vector Anopheles ...

    Authors: Maria V Sharakhova, Phillip George, Irina V Brusentsova, Scotland C Leman, Jeffrey A Bailey, Christopher D Smith and Igor V Sharakhov
    Citation: BMC Genomics 2010 11:459
    Content type: Research article Published on:

  6. The advent of cheap high through-put sequencing methods has facilitated low coverage skims of a large number of organisms. To maximise the utility of the sequences, assembly into contigs and then ordering of t...

    Authors: Abhirami Ratnakumar, Sean McWilliam, Wesley Barris and Brian P Dalrymple
    Citation: BMC Genomics 2010 11:458
    Content type: Research article Published on:

  7. Phosphoinositide metabolism is essential to membrane dynamics and impinges on many cellular processes, including phagocytosis. Modulation of phosphoinositide metabolism is important for pathogenicity and virul...

    Authors: Nicola J Beresford, Charis Saville, Hayley J Bennett, Ian S Roberts and Lydia Tabernero
    Citation: BMC Genomics 2010 11:457
    Content type: Research article Published on:

  8. Human leukocyte antigen (HLA)-B27 is strongly associated with the development of reactive arthritis (ReA) in humans after salmonellosis. Human monocytic U937 cells transfected with HLA-B27 are less able to eli...

    Authors: Shichao Ge, Vittoria Danino, Qiushui He, Jay CD Hinton and Kaisa Granfors
    Citation: BMC Genomics 2010 11:456
    Content type: Research article Published on:

  9. Haemophilus parasuis is the causative agent of Glässer's disease in pigs. Currently, little is known about the molecular mechanisms that contribute to disease susceptibility. This study used a porcine oligonucleo...

    Authors: Jamie M Wilkinson, Carole A Sargent, Lucina Galina-Pantoja and Alexander W Tucker
    Citation: BMC Genomics 2010 11:455
    Content type: Research article Published on:

  11. Alu repeats in the human transcriptome undergo massive adenosine to inosine RNA editing. This process is selective, as editing efficiency varies greatly among different adenosines. Several studies have identif...

    Authors: Yoav Kleinberger and Eli Eisenberg
    Citation: BMC Genomics 2010 11:453
    Content type: Research article Published on:

  12. Lychas mucronatus is one scorpion species widely distributed in Southeast Asia and southern China. Anything is hardly known about its venom components, despite the fact that it can often cause human accidents. In...

    Authors: Zhao Ruiming, Ma Yibao, He Yawen, Di Zhiyong, Wu Yingliang, Cao Zhijian and Li Wenxin
    Citation: BMC Genomics 2010 11:452
    Content type: Research article Published on:

  13. Pulmonary surfactant is required for lung function at birth and throughout life. Lung lipid and surfactant homeostasis requires regulation among multi-tiered processes, coordinating the synthesis of surfactant...

    Authors: Yan Xu, Minlu Zhang, Yanhua Wang, Pooja Kadambi, Vrushank Dave, Long J Lu and Jeffrey A Whitsett
    Citation: BMC Genomics 2010 11:451
    Content type: Research article Published on:

  14. Rhipicephalus sanguineus, known as the brown dog tick, is a common ectoparasite of domestic dogs and can be found worldwide. R. sanguineus is recognized as the primary vector of the etiological agent of canine mo...

    Authors: Elen Anatriello, José MC Ribeiro, Isabel KF de Miranda-Santos, Lucinda G Brandão, Jennifer M Anderson, Jesus G Valenzuela, Sandra R Maruyama, João S Silva and Beatriz R Ferreira
    Citation: BMC Genomics 2010 11:450
    Content type: Research article Published on:

  15. Genome reduction is a common evolutionary process in symbiotic and pathogenic bacteria. This process has been extensively characterized in bacterial endosymbionts of insects, where primary mutualistic bacteria...

    Authors: Eugeni Belda, Andrés Moya, Stephen Bentley and Francisco J Silva
    Citation: BMC Genomics 2010 11:449
    Content type: Research article Published on:

  16. The physiological function of the prion protein remains largely elusive while its key role in prion infection has been expansively documented. To potentially assess this conundrum, we performed a comparative t...

    Authors: Sead Chadi, Rachel Young, Sandrine Le Guillou, Gaëlle Tilly, Frédérique Bitton, Marie-Laure Martin-Magniette, Ludivine Soubigou-Taconnat, Sandrine Balzergue, Marthe Vilotte, Coralie Peyre, Bruno Passet, Vincent Béringue, Jean-Pierre Renou, Fabienne Le Provost, Hubert Laude and Jean-Luc Vilotte
    Citation: BMC Genomics 2010 11:448
    Content type: Research article Published on:

  17. Mitochondrial genomes provide a rich source of molecular variation of proven and widespread utility in molecular ecology, population genetics and evolutionary biology. The tapeworm genus Taenia includes a diversi...

    Authors: Wan-Zhong Jia, Hong-Bin Yan, Ai-Jiang Guo, Xing-Quan Zhu, Yu-Chao Wang, Wan-Gui Shi, Hao-Tai Chen, Fang Zhan, Shao-Hua Zhang, Bao-Quan Fu, D Timothy J Littlewood and Xue-Peng Cai
    Citation: BMC Genomics 2010 11:447
    Content type: Research article Published on:

  18. Brown and white adipose tissues (BAT and WAT) play critical roles in controlling energy homeostasis and in the development of obesity and diabetes. The mouse Fat-Specific protein 27 (FSP27), a member of the ce...

    Authors: De Li, Yinxin Zhang, Li Xu, Linkang Zhou, Yue Wang, Bofu Xue, Zilong Wen, Peng Li and Jianli Sang
    Citation: BMC Genomics 2010 11:446
    Content type: Research article Published on:

  19. Infection by infectious laryngotracheitis virus (ILTV; gallid herpesvirus 1) causes acute respiratory diseases in chickens often with high mortality. To better understand host-ILTV interactions at the host transc...

    Authors: Jeong Yoon Lee, Joon Jin Song, Ann Wooming, Xianyao Li, Huaijun Zhou, Walter G Bottje and Byung-Whi Kong
    Citation: BMC Genomics 2010 11:445
    Content type: Research article Published on:

  20. The rate of emergence of human pathogens is steadily increasing; most of these novel agents originate in wildlife. Bats, remarkably, are the natural reservoirs of many of the most pathogenic viruses in humans....

    Authors: Thomas B Kepler, Christopher Sample, Kathryn Hudak, Jeffrey Roach, Albert Haines, Allyson Walsh and Elizabeth A Ramsburg
    Citation: BMC Genomics 2010 11:444
    Content type: Research article Published on:

  21. The DNA repair and recombination (DRR) proteins protect organisms against genetic damage, caused by environmental agents and other genotoxic agents, by removal of DNA lesions or helping to abide them.

    Authors: Sanjay K Singh, Sujit Roy, Swarup Roy Choudhury and Dibyendu N Sengupta
    Citation: BMC Genomics 2010 11:443
    Content type: Research article Published on:

  22. Chlamydia pneumoniae is a widespread pathogen causing upper and lower respiratory tract infections in addition to a range of other diseases in humans and animals. Previous whole genome analyses have focused on fo...

    Authors: Candice M Mitchell, Kelley M Hovis, Patrik M Bavoil, Garry SA Myers, Jose A Carrasco and Peter Timms
    Citation: BMC Genomics 2010 11:442
    Content type: Research article Published on:

  23. Trichoderma reesei is the main industrial producer of cellulases and hemicellulases that are used to depolymerize biomass in a variety of biotechnical applications. Many of the production strains currently in use...

    Authors: Marika Vitikainen, Mikko Arvas, Tiina Pakula, Merja Oja, Merja Penttilä and Markku Saloheimo
    Citation: BMC Genomics 2010 11:441
    Content type: Research article Published on:

  24. Widespread sampling of vertebrates, which comprise the majority of published animal mitochondrial genomes, has led to the view that mitochondrial gene rearrangements are relatively rare, and that gene orders a...

    Authors: Timothy A Rawlings, Martin J MacInnis, Rüdiger Bieler, Jeffrey L Boore and Timothy M Collins
    Citation: BMC Genomics 2010 11:440
    Content type: Research article Published on:

  25. The chemokine and chemokine receptor families play critical roles in both the healthy and diseased organism mediating the migration of cells. The chemokine system is complex in that multiple chemokines can bin...

    Authors: Stephanie Widdison, Nazneen Siddiqui, Victoria Easton, Freya Lawrence, George Ashley, Dirk Werling, Michael Watson and Tracey J Coffey
    Citation: BMC Genomics 2010 11:439
    Content type: Research article Published on:

  26. The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of...

    Authors: Alan L Archibald, Lars Bolund, Carol Churcher, Merete Fredholm, Martien AM Groenen, Barbara Harlizius, Kyung-Tai Lee, Denis Milan, Jane Rogers, Max F Rothschild, Hirohide Uenishi, Jun Wang and Lawrence B Schook
    Citation: BMC Genomics 2010 11:438
    Content type: Correspondence Published on:

  27. Rhipicephalus (Boophilus) microplus is an obligate blood feeder which is host specific to cattle. Existing knowledge pertaining to the host or host breed effects on tick transcript expression profiles during the ...

    Authors: Manuel Rodriguez-Valle, Ala Lew-Tabor, Cedric Gondro, Paula Moolhuijzen, Megan Vance, Felix D Guerrero, Matthew Bellgard and Wayne Jorgensen
    Citation: BMC Genomics 2010 11:437
    Content type: Research article Published on:

  28. Common bean (Phaseolus vulgaris L.) is the most important legume for direct human consumption and the goal of this study was to integrate a recently constructed physical map for the species with a microsatellite ...

    Authors: Juana M Córdoba, Carolina Chavarro, Jessica A Schlueter, Scott A Jackson and Matthew W Blair
    Citation: BMC Genomics 2010 11:436
    Content type: Research article Published on:

  29. Protein phosphatases are the key components of a number of signaling pathways where they modulate various cellular responses. In plants, protein phosphatases constitute a large gene family and are reportedly i...

    Authors: Amarjeet Singh, Jitender Giri, Sanjay Kapoor, Akhilesh K Tyagi and Girdhar K Pandey
    Citation: BMC Genomics 2010 11:435
    Content type: Research article Published on:

  30. DNA barcoding is a key tool for assessing biodiversity in both taxonomic and environmental studies. Essential features of barcodes include their applicability to a wide spectrum of taxa and their ability to id...

    Authors: Gentile Francesco Ficetola, Eric Coissac, Stéphanie Zundel, Tiayyba Riaz, Wasim Shehzad, Julien Bessière, Pierre Taberlet and François Pompanon
    Citation: BMC Genomics 2010 11:434
    Content type: Methodology article Published on:

  31. Discrimination between clinical and environmental strains within many bacterial species is currently underexplored. Genomic analyses have clearly shown the enormous variability in genome composition between di...

    Authors: Ed Yzerman, Jeroen W den Boer, Martien Caspers, Arpit Almal, Bill Worzel, Walter van der Meer, Roy Montijn and Frank Schuren
    Citation: BMC Genomics 2010 11:433
    Content type: Research article Published on:

  32. Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern...

    Authors: Dilmurat Yusuf, Manja Marz, Peter F Stadler and Ivo L Hofacker
    Citation: BMC Genomics 2010 11:432
    Content type: Methodology article Published on:

  33. MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studi...

    Authors: Changnian Song, Chen Wang, Changqing Zhang, Nicholas Kibet Korir, Huaping Yu, Zhengqiang Ma and Jinggui Fang
    Citation: BMC Genomics 2010 11:431
    Content type: Research article Published on:

  34. Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many un...

    Authors: Kerstin Röske, Mark F Foecking, Shibu Yooseph, John I Glass, Michael J Calcutt and Kim S Wise
    Citation: BMC Genomics 2010 11:430
    Content type: Research article Published on:

  35. Currently, a number of yeast genomes with different physiological features have been sequenced and annotated, which provides invaluable information to investigate yeast genetics, evolutionary mechanism, struct...

    Authors: Yanhui Chu, Xiaohuan Yuan, Yanqin Guo, Yufei Zhang, Yan Wu, Haifeng Liu, Dan Wu, Haihua Bao, Lixin Guan and Xiudong Jin
    Citation: BMC Genomics 2010 11:429
    Content type: Database Published on:

  37. Rhesus monkeys (Macaca mulatta) are widely-used as experimental animals in biomedical research and are closely related to other laboratory macaques, such as cynomolgus monkeys (Macaca fascicularis), and to humans...

    Authors: Dae-Soo Kim, Jae-Won Huh, Young-Hyun Kim, Sang-Je Park, Sang-Rae Lee and Kyu-Tae Chang
    Citation: BMC Genomics 2010 11:427
    Content type: Research article Published on:

  38. Recent efforts have been made to link complex human traits and disease susceptibility to DNA copy numbers. The leptin receptor (LEPR) has been implicated in obesity and diabetes. Mutations and genetic variatio...

    Authors: Jae-Pil Jeon, Sung-Mi Shim, Hye-Young Nam, Gil-Mi Ryu, Eun-Jung Hong, Hyung-Lae Kim and Bok-Ghee Han
    Citation: BMC Genomics 2010 11:426
    Content type: Research article Published on:

  39. Long terminal repeat (LTR) retroelements represent a successful group of transposable elements (TEs) that have played an important role in shaping the structure of many eukaryotic genomes. Here, we present a g...

    Authors: Mina Rho, Sarah Schaack, Xiang Gao, Sun Kim, Michael Lynch and Haixu Tang
    Citation: BMC Genomics 2010 11:425
    Content type: Research article Published on:

  40. Giardia lamblia trophozoites colonize the intestines of susceptible mammals and cause diarrhea, which can be prolonged despite an intestinal immune response. The variable expression of the variant-specific surfac...

    Authors: Rodney D Adam, Anuranjini Nigam, Vishwas Seshadri, Craig A Martens, Gregory A Farneth, Hilary G Morrison, Theodore E Nash, Stephen F Porcella and Rima Patel
    Citation: BMC Genomics 2010 11:424
    Content type: Research article Published on:

  42. Obligate biotrophs such as rust fungi are believed to establish long-term relationships by modulating plant defenses through a plethora of effector proteins, whose most recognizable feature is the presence of ...

    Authors: David L Joly, Nicolas Feau, Philippe Tanguay and Richard C Hamelin
    Citation: BMC Genomics 2010 11:422
    Content type: Research article Published on:

  44. In today's age of genomic discovery, no attempt has been made to comprehensively sequence a gymnosperm genome. The largest genus in the coniferous family Pinaceae is Pinus, whose 110-120 species have extremely la...

    Authors: Allen Kovach, Jill L Wegrzyn, Genis Parra, Carson Holt, George E Bruening, Carol A Loopstra, James Hartigan, Mark Yandell, Charles H Langley, Ian Korf and David B Neale
    Citation: BMC Genomics 2010 11:420
    Content type: Research article Published on:

  45. Inappropriate activation of AKT signaling is a relatively common occurrence in human tumors, and can be caused by activation of components of, or by loss or decreased activity of inhibitors of, this signaling ...

    Authors: Rakesh Kumar, Stephen J Blakemore, Catherine E Ellis, Emanuel F Petricoin III, Dexter Pratt, Michael Macoritto, Andrea L Matthews, Joseph J Loureiro and Keith Elliston
    Citation: BMC Genomics 2010 11:419
    Content type: Research article Published on:

  46. The immune response is an energy demanding process, which has effects in many physiological pathways in the body including protein and lipid metabolism. During an inflammatory response the liver is required to...

    Authors: Samuel AM Martin, Alex Douglas, Dominic F Houlihan and Christopher J Secombes
    Citation: BMC Genomics 2010 11:418
    Content type: Research article Published on:

  47. Admixture mapping is a powerful approach for identifying genetic variants involved in human disease that exploits the unique genomic structure in recently admixed populations. To use existing published panels ...

    Authors: Guanjie Chen, Daniel Shriner, Jie Zhou, Ayo Doumatey, Hanxia Huang, Norman P Gerry, Alan Herbert, Michael F Christman, Yuanxiu Chen, Georgia M Dunston, Mezbah U Faruque, Charles N Rotimi and Adebowale Adeyemo
    Citation: BMC Genomics 2010 11:417
    Content type: Research article Published on:

  49. Allele frequency is one of the most important population indices and has been broadly applied to genetic/genomic studies. Estimation of allele frequency using genotypes is convenient but may lose data informat...

    Authors: Hsin-Chou Yang, Hsin-Chi Lin, Mei-Chu Huang, Ling-Hui Li, Wen-Harn Pan, Jer-Yuarn Wu and Yuan-Tsong Chen
    Citation: BMC Genomics 2010 11:415
    Content type: Research article Published on:

  50. The method of chromatin immunoprecipitation combined with microarrays (ChIP-Chip) is a powerful tool for genome-wide analysis of protein binding. However, a high background signal is a common phenomenon.

    Authors: Torsten Waldminghaus and Kirsten Skarstad
    Citation: BMC Genomics 2010 11:414
    Content type: Methodology article Published on:

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BMC Genomics

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