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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  13. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  20. 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:

  21. 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:

  22. The template switching PCR (TS-PCR) method of cDNA synthesis represents one of the most straightforward approaches to generating full length cDNA for sequencing efforts. However, when applied to very small RNA...

    Authors: Jeremy Kapteyn, Ruifeng He, Eric T McDowell and David R Gang
    Citation: BMC Genomics 2010 11:413
    Content type: Methodology article Published on:

  23. With the wealth of genomic data available it has become increasingly important to assign putative protein function through functional transfer between orthologs. Therefore, correct elucidation of the evolution...

    Authors: Anna Henricson, Kristoffer Forslund and Erik LL Sonnhammer
    Citation: BMC Genomics 2010 11:412
    Content type: Research article Published on:

  24. Protein phosphorylation is an important post-translational modification influencing many aspects of dynamic cellular behavior. Site-specific phosphorylation of amino acid residues serine, threonine, and tyrosi...

    Authors: Diego Mauricio Riaño-Pachón, Sabrina Kleessen, Jost Neigenfind, Pawel Durek, Elke Weber, Wolfgang R Engelsberger, Dirk Walther, Joachim Selbig, Waltraud X Schulze and Birgit Kersten
    Citation: BMC Genomics 2010 11:411
    Content type: Research article Published on:

  25. Mobile elements (MEs) are diverse, common and dynamic inhabitants of nearly all genomes. ME transposition generates a steady stream of polymorphic genetic markers, deleterious and adaptive mutations, and subst...

    Authors: David J Witherspoon, Jinchuan Xing, Yuhua Zhang, W Scott Watkins, Mark A Batzer and Lynn B Jorde
    Citation: BMC Genomics 2010 11:410
    Content type: Methodology article Published on:

  26. MicroRNA (miRNA) play an important role in gene expression regulation. At present, the number of annotated miRNA continues to grow rapidly, in part due to advances of high-throughput sequencing techniques. Her...

    Authors: Ning-Yi Shao, Hai Yang Hu, Zheng Yan, Ying Xu, Hao Hu, Corinna Menzel, Na Li, Wei Chen and Philipp Khaitovich
    Citation: BMC Genomics 2010 11:409
    Content type: Research article Published on:

  27. More than 80% of the wheat genome is composed of transposable elements (TEs). Since active TEs can move to different locations and potentially impose a significant mutational load, their expression is suppress...

    Authors: Dario Cantu, Leonardo S Vanzetti, Adam Sumner, Martin Dubcovsky, Marta Matvienko, Assaf Distelfeld, Richard W Michelmore and Jorge Dubcovsky
    Citation: BMC Genomics 2010 11:408
    Content type: Research article Published on:

  28. The medicinal leech, Hirudo medicinalis, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently appr...

    Authors: Eduardo R Macagno, Terry Gaasterland, Lee Edsall, Vineet Bafna, Marcelo B Soares, Todd Scheetz, Thomas Casavant, Corinne Da Silva, Patrick Wincker, Aurélie Tasiemski and Michel Salzet
    Citation: BMC Genomics 2010 11:407
    Content type: Research article Published on:

  29. The domestic cat has offered enormous genomic potential in the veterinary description of over 250 hereditary disease models as well as the occurrence of several deadly feline viruses (feline leukemia virus -- ...

    Authors: James C Mullikin, Nancy F Hansen, Lei Shen, Heather Ebling, William F Donahue, Wei Tao, David J Saranga, Adrianne Brand, Marc J Rubenfield, Alice C Young, Pedro Cruz, Carlos Driscoll, Victor David, Samer WK Al-Murrani, Mary F Locniskar, Mitchell S Abrahamsen…
    Citation: BMC Genomics 2010 11:406
    Content type: Database Published on:

  30. Serine proteases (SPs) and serine proteases homologs (SPHs) are a large group of proteolytic enzymes, with important roles in a variety of physiological processes, such as cell signalling, defense and developm...

    Authors: Ping Zhao, Gen-Hong Wang, Zhao-Ming Dong, Jun Duan, Ping-Zhen Xu, Ting-Cai Cheng, Zhong-Huai Xiang and Qing-You Xia
    Citation: BMC Genomics 2010 11:405
    Content type: Research article Published on:

  31. Extreme acidic environments are characterized by their high metal content and lack of nutrients (oligotrophy). Macroscopic biofilms and filaments usually grow on the water-air interface or under the stream att...

    Authors: Mercedes Moreno-Paz, Manuel J Gómez, Aida Arcas and Víctor Parro
    Citation: BMC Genomics 2010 11:404
    Content type: Research article Published on:

  33. Thousands of plants and animals possess pharmacological properties and there is an increased interest in using these materials for therapy and health maintenance. Efficacies of the application is critically de...

    Authors: Shao-Ke Lou, Ka-Lok Wong, Ming Li, Paul Pui-Hay But, Stephen Kwok-Wing Tsui and Pang-Chui Shaw
    Citation: BMC Genomics 2010 11:402
    Content type: Database Published on:

  34. About 10% of cases of male infertility are due to the presence of microdeletions within the long arm of the Y chromosome (Yq). Despite the large literature covering this critical issue, very little is known ab...

    Authors: Valentina Gatta, Florina Raicu, Alberto Ferlin, Ivana Antonucci, Anna Paola Scioletti, Andrea Garolla, Giandomenico Palka, Carlo Foresta and Liborio Stuppia
    Citation: BMC Genomics 2010 11:401
    Content type: Research article Published on:

  35. Whitefly (Bemisia tabaci) causes extensive crop damage throughout the world by feeding directly on plants and by vectoring hundreds of species of begomoviruses. Yet little is understood about its genes involved i...

    Authors: Xiao-Wei Wang, Jun-Bo Luan, Jun-Min Li, Yan-Yuan Bao, Chuan-Xi Zhang and Shu-Sheng Liu
    Citation: BMC Genomics 2010 11:400
    Content type: Research article Published on:

  36. Alternative splicing is known to increase the complexity of mammalian transcriptomes since nearly all mammalian genes express multiple pre-mRNA isoforms. However, our knowledge of the extent and function of al...

    Authors: Timothée Revil, Daniel Gaffney, Christel Dias, Jacek Majewski and Loydie A Jerome-Majewska
    Citation: BMC Genomics 2010 11:399
    Content type: Research article Published on:

  37. Digital gene expression profiling was used to characterize the assembly of genes expressed in equine skeletal muscle and to identify the subset of genes that were differentially expressed following a ten-month...

    Authors: Beatrice A McGivney, Paul A McGettigan, John A Browne, Alexander CO Evans, Rita G Fonseca, Brendan J Loftus, Amanda Lohan, David E MacHugh, Barbara A Murphy, Lisa M Katz and Emmeline W Hill
    Citation: BMC Genomics 2010 11:398
    Content type: Research article Published on:

  38. Carbonic anhydrases (CAs) are a family of enzymes that regulate pH homeostasis in various tissues. CA IX is an exceptional member of this family because in addition to the basic CA function, it has been implic...

    Authors: Heini Kallio, Mika Hilvo, Alejandra Rodriguez, Eeva-Helena Lappalainen, Anna-Maria Lappalainen and Seppo Parkkila
    Citation: BMC Genomics 2010 11:397
    Content type: Research article Published on:

  40. Genetically anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing. Cultivated tetraploid cottons, Gossypium hirsutum and G. ba...

    Authors: Lifeng Lin, Gary J Pierce, John E Bowers, James C Estill, Rosana O Compton, Lisa K Rainville, Changsoo Kim, Cornelia Lemke, Junkang Rong, Haibao Tang, Xiyin Wang, Michele Braidotti, Amy H Chen, Kristen Chicola, Kristi Collura, Ethan Epps…
    Citation: BMC Genomics 2010 11:395
    Content type: Research article Published on:

  41. Trypanosomosis is the most economically important disease constraint to livestock productivity in Africa. A number of trypanotolerant cattle breeds are found in West Africa, and identification of the genes con...

    Authors: Joseph K Nganga, Morris Soller and Fuad A Iraqi
    Citation: BMC Genomics 2010 11:394
    Content type: Research article Published on:

  42. The genus Erwinia includes plant-associated pathogenic and non-pathogenic Enterobacteria. Important pathogens such as Erwinia amylovora, the causative agent of fire blight and E. pyrifoliae causing bacterial shoo...

    Authors: Michael Kube, Alexander M Migdoll, Isabel Gehring, Katja Heitmann, Yvonne Mayer, Heiner Kuhl, Florian Knaust, Klaus Geider and Richard Reinhardt
    Citation: BMC Genomics 2010 11:393
    Content type: Research article Published on:

  43. The zebrafish intestine is a simple tapered tube that is folded into three sections. However, whether the intestine is functionally similar along its length remains unknown. Thus, a systematic structural and f...

    Authors: Zhengyuan Wang, Jianguo Du, Siew Hong Lam, Sinnakarupan Mathavan, Paul Matsudaira and Zhiyuan Gong
    Citation: BMC Genomics 2010 11:392
    Content type: Research article Published on:

  45. Understanding the genetic basis of adaptive changes has been a major goal of evolutionary biology. In complex organisms without sequenced genomes, de novo transcriptome assembly using a longer read sequencing ...

    Authors: Wiesław Babik, Michał Stuglik, Weihong Qi, Marzanna Kuenzli, Katarzyna Kuduk, Paweł Koteja and Jacek Radwan
    Citation: BMC Genomics 2010 11:390
    Content type: Research article Published on:

  46. Clostridium difficile is a Gram-positive, anaerobic, spore-forming bacterium that is responsible for C. difficile associated disease in humans and is currently the most common cause of nosocomial diarrhoea in the...

    Authors: Gemma L Marsden, Ian J Davis, Victoria J Wright, Mohammed Sebaihia, Ed J Kuijper and Nigel P Minton
    Citation: BMC Genomics 2010 11:389
    Content type: Research article Published on:

  47. Circulating CD34+ progenitor cells have the potential to differentiate into a variety of cells, including endothelial cells. Knowledge is still scarce about the transcriptional programs used by CD34+ cells fro...

    Authors: Tineke CTM van der Pouw Kraan, Stephan H Schirmer, Joost O Fledderus, Perry D Moerland, Josefien M Baggen, Thomas A Leyen, Anja M van der Laan, Jan J Piek, Niels van Royen and Anton JG Horrevoets
    Citation: BMC Genomics 2010 11:388
    Content type: Research article Published on:

  48. Emerging methods of massive sequencing that allow for rapid re-sequencing of entire genomes at comparably low cost are changing the way biological questions are addressed in many domains. Here we propose a nov...

    Authors: Julien Portela, Christoph Grunau, Céline Cosseau, Sophie Beltran, Christelle Dantec, Hugues Parrinello and Jérôme Boissier
    Citation: BMC Genomics 2010 11:387
    Content type: Methodology article Published on:

  49. Chromatin in the nucleus of all eukaryotes is organized into a system of loops and domains. These loops remain fastened at their bases to the fundamental framework of the nucleus, the matrix or the scaffold. T...

    Authors: Sushma S Padmaja, Jagannathan Lakshmanan, Ravi Gupta, Santanu Banerjee, Pennathur Gautam and Sulagna Banerjee
    Citation: BMC Genomics 2010 11:386
    Content type: Research article Published on:

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BMC Genomics

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