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  1. Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was dev...

    Authors: Joseph R Shaw, John K Colbourne, Jennifer C Davey, Stephen P Glaholt, Thomas H Hampton, Celia Y Chen, Carol L Folt and Joshua W Hamilton
    Citation: BMC Genomics 2007 8:477
  2. Iron is one of fourteen mineral elements required for proper plant growth and development of soybean (Glycine max L. Merr.). Soybeans grown on calcareous soils, which are prevalent in the upper Midwest of the Uni...

    Authors: Jamie A O'Rourke, Dirk V Charlson, Delkin O Gonzalez, Lila O Vodkin, Michelle A Graham, Silvia R Cianzio, Michael A Grusak and Randy C Shoemaker
    Citation: BMC Genomics 2007 8:476
  3. Ice, snow and temperatures of -14°C are conditions which most animals would find difficult, if not impossible, to survive in. However this exactly describes the Arctic winter, and the Arctic springtail Onychiurus...

    Authors: Melody S Clark, Michael AS Thorne, Jelena Purać, Gordana Grubor-Lajšić, Michael Kube, Richard Reinhardt and M Roger Worland
    Citation: BMC Genomics 2007 8:475
  4. The xylem-inhabiting bacterium Xylella fastidiosa (Xf) is the causal agent of Pierce's disease (PD) in vineyards and citrus variegated chlorosis (CVC) in orange trees. Both of these economically-devastating disea...

    Authors: Vivian S da Silva, Cláudio S Shida, Fabiana B Rodrigues, Diógenes CD Ribeiro, Alessandra A de Souza, Helvécio D Coletta-Filho, Marcos A Machado, Luiz R Nunes and Regina Costa de Oliveira
    Citation: BMC Genomics 2007 8:474
  5. The corn smut fungus Ustilago maydis is a well-established model system for molecular phytopathology. In addition, it recently became evident that U. maydis and humans share proteins and cellular processes that a...

    Authors: Martin Münsterkötter and Gero Steinberg
    Citation: BMC Genomics 2007 8:473
  6. NOD2 is an innate immune receptor for the bacterial cell wall component muramyl-dipeptide. Mutations in the leucine-rich repeat region of NOD2, which lead to an impaired recognition of muramyl-dipeptide, have ...

    Authors: Philip Rosenstiel, Klaus Huse, Andre Franke, Jochen Hampe, Kathrin Reichwald, Cornelia Platzer, Roland G Roberts, Christopher G Mathew, Matthias Platzer and Stefan Schreiber
    Citation: BMC Genomics 2007 8:472
  7. The Oomycete genus Aphanomyces comprises devastating plant and animal pathogens. However, little is known about the molecular mechanisms underlying pathogenicity of Aphanomyces species. In this study, we report o...

    Authors: Mohammed-Amine Madoui, Elodie Gaulin, Catherine Mathé, Hélène San Clemente, Arnaud Couloux, Patrick Wincker and Bernard Dumas
    Citation: BMC Genomics 2007 8:471
  8. Recent studies using high-throughput methods have revealed that transposable elements (TEs) are a comprehensive target for DNA methylation. However, the relationship between TEs and their genomic environment r...

    Authors: Miwako Takata, Akihiro Kiyohara, Atsuko Takasu, Yuji Kishima, Hisako Ohtsubo and Yoshio Sano
    Citation: BMC Genomics 2007 8:469
  9. The soybean (Glycine max) cotyledon is a specialized tissue whose main function is to serve as a nutrient reserve that supplies the needs of the young plant throughout seedling development. During this process th...

    Authors: Delkin O Gonzalez and Lila O Vodkin
    Citation: BMC Genomics 2007 8:468
  10. Small untranslated RNAs (sRNAs) seem to be far more abundant than previously believed. The number of sRNAs confirmed in E. coli through various approaches is above 70, with several hundred more sRNA candidate gen...

    Authors: Vincent M Ulvé, Emeric W Sevin, Angélique Chéron and Frédérique Barloy-Hubler
    Citation: BMC Genomics 2007 8:467
  11. The invasion of Anopheles salivary glands by Plasmodium sporozoites is an essential step for transmission of the parasite to the vertebrate host. Salivary gland sporozoites undergo a developmental programme to ex...

    Authors: Isabelle Rosinski-Chupin, Thomas Chertemps, Bertrand Boisson, Sylvie Perrot, Emmanuel Bischoff, Jérôme Briolay, Pierre Couble, Robert Ménard, Paul Brey and Patricia Baldacci
    Citation: BMC Genomics 2007 8:466
  12. Tomato has excellent genetic and genomic resources including a broad set of Expressed Sequence Tag (EST) data and high-density genetic maps. In addition, emerging physical maps and bacterial artificial clone s...

    Authors: Allen Van Deynze, Kevin Stoffel, C Robin Buell, Alexander Kozik, Jia Liu, Esther van der Knaap and David Francis
    Citation: BMC Genomics 2007 8:465
  13. Sexual reproduction is a core biological function that is conserved throughout eukaryotic evolution, yet breeding systems are extremely variable. Genome-wide comparative studies can be effectively used to iden...

    Authors: Brian D Eads, John K Colbourne, Elizabeth Bohuski and Justen Andrews
    Citation: BMC Genomics 2007 8:464
  14. Armigeres subalbatus is a natural vector of the filarial worm Brugia pahangi, but it rapidly and proficiently kills Brugia malayi microfilariae by melanotic encapsulation. Because B. malayi and B. pahangi are mor...

    Authors: Matthew T Aliota, Jeremy F Fuchs, George F Mayhew, Cheng-Chen Chen and Bruce M Christensen
    Citation: BMC Genomics 2007 8:463
  15. The mosquito, Armigeres subalbatus, mounts a distinctively robust innate immune response when infected with the nematode Brugia malayi, a causative agent of lymphatic filariasis. In order to mine the transcriptom...

    Authors: George F Mayhew, Lyric C Bartholomay, Hang-Yen Kou, Thomas A Rocheleau, Jeremy F Fuchs, Matthew T Aliota, I-Yu Tsao, Chiung-Yen Huang, Tze-Tze Liu, Kwang-Jen Hsiao, Shih-Feng Tsai, Ueng-Cheng Yang, Nicole T Perna, Wen-Long Cho, Bruce M Christensen and Cheng-Chen Chen
    Citation: BMC Genomics 2007 8:462
  16. The biomedical literature is a rich source of associative information but too vast for complete manual review. We have developed an automated method of literature interrogation called "Literature Lab" that ide...

    Authors: Phillip G Febbo, Mike G Mulligan, David A Slonina, Kimberly Stegmaier, Dolores Di Vizio, Paul R Martinez, Massimo Loda and Stephen C Taylor
    Citation: BMC Genomics 2007 8:461
  17. Gene fusion detection – also known as the 'Rosetta Stone' method – involves the identification of fused composite genes in a set of reference genomes, which indicates potential interactions between its un-fuse...

    Authors: Atanas Kamburov, Leon Goldovsky, Shiri Freilich, Aliki Kapazoglou, Victor Kunin, Anton J Enright, Athanasios Tsaftaris and Christos A Ouzounis
    Citation: BMC Genomics 2007 8:460
  18. Craniosynostosis, the premature fusion of calvarial sutures, is a common craniofacial abnormality. Causative mutations in more than 10 genes have been identified, involving fibroblast growth factor, transformi...

    Authors: Anna K Coussens, Christopher R Wilkinson, Ian P Hughes, C Phillip Morris, Angela van Daal, Peter J Anderson and Barry C Powell
    Citation: BMC Genomics 2007 8:458
  19. The recent advances in human genetics have recently provided new insights into phenotypic variation and genome variability. Current forensic DNA techniques involve the search for genetic similarities and diffe...

    Authors: Emiliano Giardina, Ilenia Pietrangeli, Claudia Martone, Paola Asili, Irene Predazzi, Patrizio Marsala, Luciano Gabriele, Claudio Pipolo, Omero Ricci, Gianluca Solla, Luca Sineo, Aldo Spinella and Giuseppe Novelli
    Citation: BMC Genomics 2007 8:457
  20. The signal transducer and activator of transcription 3 (STAT3) mediates gene expression in response to numerous growth factors and cytokines, playing an important role in many cellular processes. To better und...

    Authors: Yan Xu, Machiko Ikegami, Yanhua Wang, Yohei Matsuzaki and Jeffrey A Whitsett
    Citation: BMC Genomics 2007 8:455
  21. Wild-type laboratory strains of model organisms are typically kept in isolation for many years, with the action of genetic drift and selection on mutational variation causing lineages to diverge with time. Nat...

    Authors: Dean A Baker, Lisa A Meadows, Jing Wang, Julian AT Dow and Steven Russell
    Citation: BMC Genomics 2007 8:454
  22. Phthalate esters like n-butyl benzyl phthalate (BBP) are widely used plasticizers. BBP has shown endocrine-disrupting properties, thus having a potential effect on hormone-sensitive tissues. The aim of this st...

    Authors: Raquel Moral, Richard Wang, Irma H Russo, Daniel A Mailo, Coral A Lamartiniere and Jose Russo
    Citation: BMC Genomics 2007 8:453
  23. Microarray analyses allow the identification and assessment of molecular signatures in whole tissues undergoing pathological processes. To better understand cerebral malaria pathogenesis, we investigated intra...

    Authors: Nicolas F Delahaye, Nicolas Coltel, Denis Puthier, Mathieu Barbier, Philippe Benech, Florence Joly, Fuad A Iraqi, Georges E Grau, Catherine Nguyen and Pascal Rihet
    Citation: BMC Genomics 2007 8:452
  24. Plasmodium infection has been shown to compromise the fitness of the mosquito vector, reducing its fecundity and longevity. However, from an evolutionary perspective, the impact of Plasmodium infection as a selec...

    Authors: Ruth Aguilar, Suchismita Das, Yuemei Dong and George Dimopoulos
    Citation: BMC Genomics 2007 8:451
  25. Soluble sugars, which play a central role in plant structure and metabolism, are also involved in the responses to a number of stresses, and act as metabolite signalling molecules that activate specific or hor...

    Authors: Fanny Ramel, Cécile Sulmon, Francisco Cabello-Hurtado, Ludivine Taconnat, Marie-Laure Martin-Magniette, Jean-Pierre Renou, Abdelhak El Amrani, Ivan Couée and Gwenola Gouesbet
    Citation: BMC Genomics 2007 8:450
  26. In fungi, light is primarily known to influence general morphogenesis and both sexual and asexual sporulation. In order to expand the knowledge on the effect of light in fungi and to determine the role of the ...

    Authors: Andrè Schuster, Christian P Kubicek, Martina A Friedl, Irina S Druzhinina and Monika Schmoll
    Citation: BMC Genomics 2007 8:449
  27. Populus is one of favorable model plants because of its small genome. Structural genomics of Populus has reached a breakpoint as nucleotides of the entire genome have been determined. Reaching the post genome era...

    Authors: Tokihiko Nanjo, Tetsuya Sakurai, Yasushi Totoki, Atsushi Toyoda, Mitsuru Nishiguchi, Tomoyuki Kado, Tomohiro Igasaki, Norihiro Futamura, Motoaki Seki, Yoshiyuki Sakaki, Kazuo Shinozaki and Kenji Shinohara
    Citation: BMC Genomics 2007 8:448
  28. Restriction landmark genomic scanning (RLGS) is one of the most successfully applied methods for the identification of aberrant CpG island hypermethylation in cancer, as well as the identification of tissue sp...

    Authors: Dominic J Smiraglia, Ramakrishnan Kazhiyur-Mannar, Christopher C Oakes, Yue-Zhong Wu, Ping Liang, Tahmina Ansari, Jian Su, Laura J Rush, Laura T Smith, Li Yu, Chunhui Liu, Zunyan Dai, Shih-Shih Chen, Shu-Huei Wang, Joseph Costello, Ilya Ioshikhes…
    Citation: BMC Genomics 2007 8:446
  29. This study reports the first collection of validated microRNA genes in the sea squirt, Ciona intestinalis. MicroRNAs are processed from hairpin precursors to ~22 nucleotide RNAs that base pair to target mRNAs and...

    Authors: Trina M Norden-Krichmar, Janette Holtz, Amy E Pasquinelli and Terry Gaasterland
    Citation: BMC Genomics 2007 8:445
  30. The evolutionary forces that determine the arrangement of synonymous codons within open reading frames and fine tune mRNA translation efficiency are not yet understood. In order to tackle this question we have...

    Authors: Gabriela R Moura, José P Lousado, Miguel Pinheiro, Laura Carreto, Raquel M Silva, José L Oliveira and Manuel AS Santos
    Citation: BMC Genomics 2007 8:444
  31. Aproximately 5–10% of cases of mental retardation in males are due to copy number variations (CNV) on the X chromosome. Novel technologies, such as array comparative genomic hybridization (aCGH), may help to u...

    Authors: I Madrigal, L Rodríguez-Revenga, L Armengol, E González, B Rodriguez, C Badenas, A Sánchez, F Martínez, M Guitart, I Fernández-Carvajal, JA Arranz, MI Tejada, LA Pérez-Jurado, X Estivill and M Milà
    Citation: BMC Genomics 2007 8:443
  32. Xp10 and OP1 are phages of Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial leaf blight in rice plants, which were isolated in 1967 in Taiwan and in 1954 in Japan, respectively. We recently i...

    Authors: Chia-Ni Lee, Rouh-Mei Hu, Teh-Yuan Chow, Juey-Wen Lin, Hui-Yi Chen, Yi-Hsiung Tseng and Shu-Fen Weng
    Citation: BMC Genomics 2007 8:442
  33. Transcription factors (TFs) regulate gene transcription and play pivotal roles in various biological processes such as development, cell cycle progression, cell differentiation and tumor suppression. Identifying

    Authors: Alison P Lee, Yuchen Yang, Sydney Brenner and Byrappa Venkatesh
    Citation: BMC Genomics 2007 8:441
  34. Previous studies have shown that burn-elicited stress signals alter expression of certain murine endogenous retroviruses (MuERVs) in distant organs of mice. These findings suggest that MuERVs may participate i...

    Authors: Young-Kwan Lee, Alex Chew, Lauren Fitzsimon, Rita Thomas, David Greenhalgh and Kiho Cho
    Citation: BMC Genomics 2007 8:440
  35. Pancreatic cancer is the 5th leading cause of cancer death in both males and females. In recent years, a wealth of gene and protein expression studies have been published broadening our understanding of pancre...

    Authors: Claude Chelala, Stephan A Hahn, Hannah J Whiteman, Sayka Barry, Deepak Hariharan, Tomasz P Radon, Nicholas R Lemoine and Tatjana Crnogorac-Jurcevic
    Citation: BMC Genomics 2007 8:439
  36. Recovery growth is a phase of rapid growth that is triggered by adequate refeeding of animals following a period of weight loss caused by starvation. In this study, to obtain more information on the system-wid...

    Authors: Pierre-Yves Rescan, Jerome Montfort, Cécile Rallière, Aurélie Le Cam, Diane Esquerré and Karine Hugot
    Citation: BMC Genomics 2007 8:438
  37. So far very limited knowledge exists on L-arginine catabolism in cyanobacteria, although six major L-arginine-degrading pathways have been described for prokaryotes. Thus, we have performed a bioinformatic ana...

    Authors: Sarah Schriek, Christian Rückert, Dorothee Staiger, Elfriede K Pistorius and Klaus-Peter Michel
    Citation: BMC Genomics 2007 8:437
  38. Secreted modular calcium binding protein-1 (Smoc-1) belongs to the BM-40 family which has been implicated with tissue remodeling, angiogenesis and bone mineralization. Besides its anticipated role in embryogenesi...

    Authors: Jyoti Srivastava, Sanjay Premi, Sudhir Kumar, Iqbal Parwez and Sher Ali
    Citation: BMC Genomics 2007 8:436
  39. Superoxide dismutases (SOD) are ubiquitous metalloenzymes that catalyze the disproportion of superoxide to peroxide and molecular oxygen through alternate oxidation and reduction of their metal ions. In genera...

    Authors: Balakrishnan Priya, Jagadeesan Premanandh, Raman T Dhanalakshmi, Thangaraj Seethalakshmi, Lakshmanan Uma, Dharmar Prabaharan and Gopalakrishnan Subramanian
    Citation: BMC Genomics 2007 8:435
  40. The genomes of the three parasitic protozoa Trypanosoma cruzi, Trypanosoma brucei and Leishmania major are the main subject of this study. These parasites are responsible for devastating human diseases known as C...

    Authors: Rachel Brenchley, Humera Tariq, Helen McElhinney, Balázs Szöőr, Julie Huxley-Jones, Robert Stevens, Keith Matthews and Lydia Tabernero
    Citation: BMC Genomics 2007 8:434
  41. Clenbuterol, a beta-agonist, can dramatically reduce pig adipose accumulation at high dosages. However, it has been banned in pig production because people who eat pig products treated with clenbuterol can be ...

    Authors: Jin Zhang, Qiang He, Qiu Y Liu, Wei Guo, Xue M Deng, Wei W Zhang, Xiao X Hu and Ning Li
    Citation: BMC Genomics 2007 8:433
  42. Despite the potential of the endoplasmic reticulum (ER) stress response to accommodate adaptive pathways, its integration with other environmental-induced responses is poorly understood in plants. We have prev...

    Authors: André ST Irsigler, Maximiller DL Costa, Ping Zhang, Pedro AB Reis, Ralph E Dewey, Rebecca S Boston and Elizabeth PB Fontes
    Citation: BMC Genomics 2007 8:431
  43. Wounds are increasingly important in our aging societies. Pathologies such as diabetes predispose patients to chronic wounds that can cause pain, infection, and amputation. The vacuum assisted closure device s...

    Authors: Vishal Saxena, Dennis Orgill and Isaac Kohane
    Citation: BMC Genomics 2007 8:430
  44. Grape berry development is a dynamic process that involves a complex series of molecular genetic and biochemical changes divided into three major phases. During initial berry growth (Phase I), berry size incre...

    Authors: Laurent G Deluc, Jérôme Grimplet, Matthew D Wheatley, Richard L Tillett, David R Quilici, Craig Osborne, David A Schooley, Karen A Schlauch, John C Cushman and Grant R Cramer
    Citation: BMC Genomics 2007 8:429
  45. Grapevine (Vitis species) is among the most important fruit crops in terms of cultivated area and economic impact. Despite this relevance, little is known about the transcriptional changes and the regulatory circ...

    Authors: Stefania Pilati, Michele Perazzolli, Andrea Malossini, Alessandro Cestaro, Lorenzo Demattè, Paolo Fontana, Antonio Dal Ri, Roberto Viola, Riccardo Velasco and Claudio Moser
    Citation: BMC Genomics 2007 8:428

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