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  1. Burkholderia cenocepacia belongs to a group of closely related organisms called the B. cepacia complex (Bcc) which are important opportunistic human pathogens. B. cenocepacia utilizes a mechanism of cell-cell com...

    Authors: Eoin P O'Grady, Duber F Viteri, Rebecca J Malott and Pamela A Sokol
    Citation: BMC Genomics 2009 10:441
  2. Peptidase family A1, to which pepsin belongs, had been assumed to be restricted to eukaryotes. The tertiary structure of pepsin shows two lobes with similar folds and it has been suggested that the gene has ar...

    Authors: Neil D Rawlings and Alex Bateman
    Citation: BMC Genomics 2009 10:437
  3. 'Systems-wide' approaches such as microarray RNA-profiling are ideally suited to the study of the complex overlapping responses of plants to biotic and abiotic stresses. However, commercial microarrays are onl...

    Authors: Mark W Davey, Neil S Graham, Bartel Vanholme, Rony Swennen, Sean T May and Johan Keulemans
    Citation: BMC Genomics 2009 10:436
  4. The Senegalese sole (Solea senegalensis) is a marine flatfish of increasing commercial interest. However, the reproduction of this species in captivity is not yet controlled mainly because of the poor knowledge o...

    Authors: Angèle Tingaud-Sequeira, François Chauvigné, Juanjo Lozano, María J Agulleiro, Esther Asensio and Joan Cerdà
    Citation: BMC Genomics 2009 10:434
  5. Photorhabdus and Xenorhabdus are Gram-negative, phylogenetically related, enterobacteria, forming mutualism with the entomopathogenic nematodes Heterorhabditis and Steinernema, respectively. The mutualistic bacte...

    Authors: Ruisheng An, Srinand Sreevatsan and Parwinder S Grewal
    Citation: BMC Genomics 2009 10:433
  6. In view of the immense value of Brassica rapa in the fields of agriculture and molecular biology, the multinational Brassica rapa Genome Sequencing Project (BrGSP) was launched in 2003 by five countries. The deve...

    Authors: HyeRan Kim, Su Ryun Choi, Jina Bae, Chang Pyo Hong, Seo Yeon Lee, Md Jamil Hossain, Dan Van Nguyen, Mina Jin, Beom-Seok Park, Jea-Wook Bang, Ian Bancroft and Yong Pyo Lim
    Citation: BMC Genomics 2009 10:432
  7. Difference in adaptability responses to stress has been observed amongst bird species, strains, and individuals. Components of the HPA axis, one of the internal systems involved in homeostasis re-establishment...

    Authors: Clara Bureau, Christelle Hennequet-Antier, Michel Couty and Daniel Guémené
    Citation: BMC Genomics 2009 10:430
  8. Understanding how pathogens respond to antimicrobial peptides, and how this compares to currently available antibiotics, is crucial for optimizing antimicrobial therapy. Staphylococcus aureus has several known re...

    Authors: Milla Pietiäinen, Patrice François, Hanne-Leena Hyyryläinen, Manuela Tangomo, Vera Sass, Hans-Georg Sahl, Jacques Schrenzel and Vesa P Kontinen
    Citation: BMC Genomics 2009 10:429
  9. Interpretation of ever-increasing raw sequence information generated by modern genome sequencing technologies faces multiple challenges, such as gene function analysis and genome annotation. Indeed, nearly 40%...

    Authors: M Carmen Marques, Hugo Alonso-Cantabrana, Javier Forment, Raquel Arribas, Santiago Alamar, Vicente Conejero and Miguel A Perez-Amador
    Citation: BMC Genomics 2009 10:428
  10. Trypanosomes undergo extensive developmental changes during their complex life cycle. Crucial among these is the transition between slender and stumpy bloodstream forms and, thereafter, the differentiation fro...

    Authors: Sarah Kabani, Katelyn Fenn, Alan Ross, Al Ivens, Terry K Smith, Peter Ghazal and Keith Matthews
    Citation: BMC Genomics 2009 10:427
  11. The use of microarray technology for describing changes in mRNA expression to address ecological and evolutionary questions is becoming increasingly popular. Since three-spine stickleback are an important ecol...

    Authors: Erica H Leder, Juha Merilä and Craig R Primmer
    Citation: BMC Genomics 2009 10:426
  12. Lactobacillus plantarum is a normal, potentially probiotic, inhabitant of the human gastrointestinal (GI) tract. The bacterium has great potential as food-grade cell factory and for in situ delivery of biomolecul...

    Authors: Geir Mathiesen, Anita Sveen, May Bente Brurberg, Lasse Fredriksen, Lars Axelsson and Vincent GH Eijsink
    Citation: BMC Genomics 2009 10:425
  13. Proliferation and tumor differentiation captured by the genomic grade index (GGI) are important prognostic indicators in breast cancer (BC) especially for the estrogen receptor positive (ER+) disease. The aims...

    Authors: Jérôme Toussaint, Anieta M Sieuwerts, Benjamin Haibe-Kains, Christine Desmedt, Ghizlane Rouas, Adrian L Harris, Denis Larsimont, Martine Piccart, John A Foekens, Virginie Durbecq and Christos Sotiriou
    Citation: BMC Genomics 2009 10:424
  14. Cold storage is used to inhibit peach fruit ripening during shipment to distant markets. However, this cold storage can negatively affect the quality of the fruit when it is ripened, resulting in disorders suc...

    Authors: Paula Vizoso, Lee A Meisel, Andrés Tittarelli, Mariano Latorre, Juan Saba, Rodrigo Caroca, Jonathan Maldonado, Veronica Cambiazo, Reinaldo Campos-Vargas, Mauricio Gonzalez, Ariel Orellana and Herman Silva
    Citation: BMC Genomics 2009 10:423
  15. Allele-specific expression (ASE) assays can be used to identify cis, trans, and cis-by-trans regulatory variation. Understanding the source of expression variation has important implications for disease susceptib...

    Authors: Bradley J Main, Ryan D Bickel, Lauren M McIntyre, Rita M Graze, Peter P Calabrese and Sergey V Nuzhdin
    Citation: BMC Genomics 2009 10:422
  16. Information on the occurrence of zinc finger protein motifs in genomes is crucial to the developing field of molecular genome engineering. The knowledge of their target DNA-binding sequences is vital to develo...

    Authors: Mannu Jayakanthan, Jayaraman Muthukumaran, Sanniyasi Chandrasekar, Konika Chawla, Ankita Punetha and Durai Sundar
    Citation: BMC Genomics 2009 10:421
  17. Alterations in brain-derived neurotrophic factor (BDNF) gene expression contribute to serious pathologies such as depression, epilepsy, cancer, Alzheimer's, Huntington and Parkinson's disease. Therefore, explorin...

    Authors: Tamara Aid-Pavlidis, Pavlos Pavlidis and Tõnis Timmusk
    Citation: BMC Genomics 2009 10:420
  18. Tol2, a member of the hAT family of transposons, has become a useful tool for genetic manipulation of model animals, but information about its interactions with vertebrate genomes is still limited. Furthermore, p...

    Authors: Igor Kondrychyn, Marta Garcia-Lecea, Alexander Emelyanov, Sergey Parinov and Vladimir Korzh
    Citation: BMC Genomics 2009 10:418
  19. The general population is constantly exposed to low levels of radiation through natural, occupational or medical irradiation. Even if the biological effects of low-level radiation have been intensely debated a...

    Authors: Florian Bonin, Manuella Molina, Claude Malet, Chantal Ginestet, Odile Berthier-Vergnes, Michèle T Martin and Jérôme Lamartine
    Citation: BMC Genomics 2009 10:417
  20. WNT4 is a critical signalling molecule in embryogenesis and homeostasis, but the elements that control its transcriptional regulation are largely unknown. This study uses comparative cross species sequence and...

    Authors: Hongshi Yu, Andrew J Pask, Geoffrey Shaw and Marilyn B Renfree
    Citation: BMC Genomics 2009 10:416
  21. The ultimate phenome of any organism is modulated by regulated transcription of many genes. Characterization of genetic makeup is thus crucial for understanding the molecular basis of phenotypic diversity, evo...

    Authors: Nasheeman Ashraf, Deepali Ghai, Pranjan Barman, Swaraj Basu, Nagaraju Gangisetty, Mihir K Mandal, Niranjan Chakraborty, Asis Datta and Subhra Chakraborty
    Citation: BMC Genomics 2009 10:415
  22. Telomeric and subtelomeric regions are essential for genome stability and regular chromosome replication. In this work, we have characterized the wheat BAC (bacterial artificial chromosome) clones containing S...

    Authors: Elena A Salina, Ekaterina M Sergeeva, Irina G Adonina, Andrey B Shcherban, Dmitry A Afonnikov, Harry Belcram, Cecile Huneau and Boulos Chalhoub
    Citation: BMC Genomics 2009 10:414
  23. During microRNA (miRNA) maturation in humans and flies, Drosha and Dicer cut the precursor transcript, thereby producing a short RNA duplex. One strand of this duplex becomes a functional component of the RNA-...

    Authors: Hai Yang Hu, Zheng Yan, Ying Xu, Hao Hu, Corinna Menzel, Yan Hong Zhou, Wei Chen and Philipp Khaitovich
    Citation: BMC Genomics 2009 10:413
  24. Mapping DNaseI hypersensitive sites is commonly used to identify regulatory regions in the genome. However, currently available methods are either time consuming and laborious, expensive or require large numbe...

    Authors: Thomas Ohnesorg, Stefanie Eggers, Wouter N Leonhard, Andrew H Sinclair and Stefan J White
    Citation: BMC Genomics 2009 10:412
  25. DNA microarray technology provides us with a first step toward the goal of uncovering gene functions on a genomic scale. In recent years, vast amounts of gene expression data have been collected, much of which...

    Authors: Chunlai Feng, Michihiro Araki, Ryo Kunimoto, Akiko Tamon, Hiroki Makiguchi, Satoshi Niijima, Gozoh Tsujimoto and Yasushi Okuno
    Citation: BMC Genomics 2009 10:411
  26. The marine model organism Rhodopirellula baltica SH1T was the first Planctomycete to have its genome completely sequenced. The genome analysis predicted a complex lifestyle and a variety of genetic opportunities ...

    Authors: Patricia Wecker, Christine Klockow, Andreas Ellrott, Christian Quast, Philipp Langhammer, Jens Harder and Frank Oliver Glöckner
    Citation: BMC Genomics 2009 10:410
  27. Microarray analysis still is a powerful tool to identify new components of the transcriptosome. It helps to increase the knowledge of targets triggered by stress conditions such as hypoxia and nitric oxide. Ho...

    Authors: Emeka I Igwe, Silke Essler, Natalie Al-Furoukh, Nathalie Dehne and Bernhard Brüne
    Citation: BMC Genomics 2009 10:408
  28. MicroRNAs (miRNAs) have critical functions in various biological processes. MiRNA profiling is an important tool for the identification of differentially expressed miRNAs in normal cellular and disease process...

    Authors: Yongxin Chen, Jonathan AL Gelfond, Linda M McManus and Paula K Shireman
    Citation: BMC Genomics 2009 10:407
  29. Sodium tungstate is known to be an effective anti-diabetic agent, able to increase beta cell mass in animal models of diabetes, although the molecular mechanisms of this treatment and the genes that control pa...

    Authors: Jordi Altirriba, Albert Barbera, Héctor Del Zotto, Belen Nadal, Sandra Piquer, Alex Sánchez-Pla, Juan J Gagliardino and Ramon Gomis
    Citation: BMC Genomics 2009 10:406
  30. Amyotrophic Lateral Sclerosis (ALS) is a lethal disorder characterized by progressive degeneration of motor neurons in the brain and spinal cord. Diagnosis is mainly based on clinical symptoms, and there is cu...

    Authors: Christiaan GJ Saris, Steve Horvath, Paul WJ van Vught, Michael A van Es, Hylke M Blauw, Tova F Fuller, Peter Langfelder, Joseph DeYoung, John HJ Wokke, Jan H Veldink, Leonard H van den Berg and Roel A Ophoff
    Citation: BMC Genomics 2009 10:405
  31. We employed DNA microarray technology to investigate the host response to Streptococcus pneumoniae in a mouse model of asymptomatic carriage. Over a period of six weeks, we profiled transcript abundance and compl...

    Authors: Elizabeth A Joyce, Stephen J Popper and Stanley Falkow
    Citation: BMC Genomics 2009 10:404
  32. Human peripheral blood monocytes (Mo) consist of subsets distinguished by expression of CD16 (FCγRIII) and chemokine receptors. Classical CD16- Mo express CCR2 and migrate in response to CCL2, while a minor CD16+

    Authors: Petronela Ancuta, Kuang-Yu Liu, Vikas Misra, Vanessa Sue Wacleche, Annie Gosselin, Xiaobo Zhou and Dana Gabuzda
    Citation: BMC Genomics 2009 10:403
  33. Porcine enteropathogenic Escherichia coli (PEPEC) strains of serogroup O45 cause post-weaning diarrhea and produce characteristic attaching and effacing (A/E) lesions. Most O45 PEPEC strains possess the locus of ...

    Authors: Guillaume Bruant, Yongxiang Zhang, Philippe Garneau, Justin Wong, Chad Laing, John M Fairbrother, Victor PJ Gannon and Josée Harel
    Citation: BMC Genomics 2009 10:402
  34. Array comparative genomic hybridization (aCGH) is a popular technique for detection of genomic copy number imbalances. These play a critical role in the onset of various types of cancer. In the analysis of aCG...

    Authors: Bart PP van Houte, Thomas W Binsl, Hannes Hettling, Walter Pirovano and Jaap Heringa
    Citation: BMC Genomics 2009 10:401
  35. New sequencing technologies are rapidly emerging. Many laboratories are simultaneously working with the traditional Sanger ESTs and experimenting with ESTs generated by the 454 Life Science sequencers. Though ...

    Authors: Carol Soderlund, Eric Johnson, Matthew Bomhoff and Anne Descour
    Citation: BMC Genomics 2009 10:400
  36. Despite its primary economic importance, genomic information on olive tree is still lacking. 454 pyrosequencing was used to enrich the very few sequence data currently available for the Olea europaea species and ...

    Authors: Fiammetta Alagna, Nunzio D'Agostino, Laura Torchia, Maurizio Servili, Rosa Rao, Marco Pietrella, Giovanni Giuliano, Maria Luisa Chiusano, Luciana Baldoni and Gaetano Perrotta
    Citation: BMC Genomics 2009 10:399
  37. Rice and barley are both members of Poaceae (grass family) but have a marked difference in salt tolerance. The molecular mechanism underlying this difference was previously unexplored. This study employs a compar...

    Authors: Harkamal Walia, Clyde Wilson, Abdelbagi M Ismail, Timothy J Close and Xinping Cui
    Citation: BMC Genomics 2009 10:398
  38. The Mycobacterium leprae genome has less than 50% coding capacity and 1,133 pseudogenes. Preliminary evidence suggests that some pseudogenes are expressed. Therefore, defining pseudogene transcriptional and trans...

    Authors: Diana L Williams, Richard A Slayden, Amol Amin, Alejandra N Martinez, Tana L Pittman, Alex Mira, Anirban Mitra, Valakunja Nagaraja, Norman E Morrison, Milton Moraes and Thomas P Gillis
    Citation: BMC Genomics 2009 10:397
  39. Cyanobacteria often produce several different oligopeptides, with unknown biological functions, by nonribosomal peptide synthetases (NRPS). Although some cyanobacterial NRPS gene cluster types are well describ...

    Authors: Trine B Rounge, Thomas Rohrlack, Alexander J Nederbragt, Tom Kristensen and Kjetill S Jakobsen
    Citation: BMC Genomics 2009 10:396
  40. Pseudomonas syringae is a widespread bacterial pathogen that causes disease on a broad range of economically important plant species. Pathogenicity of P. syringae strains is dependent on the type III secretion sy...

    Authors: David J Studholme, Selena Gimenez Ibanez, Daniel MacLean, Jeffery L Dangl, Jeff H Chang and John P Rathjen
    Citation: BMC Genomics 2009 10:395
  41. Acidithiobacillus ferrooxidans gains energy from the oxidation of ferrous iron and various reduced inorganic sulfur compounds at very acidic pH. Although an initial model for the electron pathways involved in iro...

    Authors: Raquel Quatrini, Corinne Appia-Ayme, Yann Denis, Eugenia Jedlicki, David S Holmes and Violaine Bonnefoy
    Citation: BMC Genomics 2009 10:394
  42. Recent transcriptomic analyses in mammals have uncovered the widespread occurrence of endogenous antisense transcripts, termed natural antisense transcripts (NATs). NATs are transcribed from the opposite stran...

    Authors: Koji Numata, Yuko Osada, Yuki Okada, Rintaro Saito, Noriko Hiraiwa, Hajime Nakaoka, Naoyuki Yamamoto, Kazufumi Watanabe, Kazue Okubo, Chihiro Kohama, Akio Kanai, Kuniya Abe and Hidenori Kiyosawa
    Citation: BMC Genomics 2009 10:392
  43. During evolution selection forces such as changing environments shape the architecture of genomes. The distribution of genes along chromosomes and the length of intragenic regions are basic genomic features kn...

    Authors: Tamir Tuller, Eytan Ruppin and Martin Kupiec
    Citation: BMC Genomics 2009 10:391
  44. Chronic renal disease (CKD) is characterized by complex changes in cell metabolism leading to an increased production of oxygen radicals, that, in turn has been suggested to play a key role in numerous clinica...

    Authors: Simona Granata, Gianluigi Zaza, Simona Simone, Gaetano Villani, Dominga Latorre, Paola Pontrelli, Massimo Carella, Francesco Paolo Schena, Giuseppe Grandaliano and Giovanni Pertosa
    Citation: BMC Genomics 2009 10:388

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