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  1. MicroRNAs (miRNAs) are expressed by a wide range of eukaryotic organisms, and function in diverse biological processes. Numerous miRNAs have been identified in Bombyx mori, but the temporal expression profiles of...

    Authors: Shiping Liu, Liang Zhang, Qibin Li, Ping Zhao, Jun Duan, Daojun Cheng, Zhonghuai Xiang and Qingyou Xia
    Citation: BMC Genomics 2009 10:455
    Content type: Research article Published on:

    The Retraction Note to this article has been published in BMC Genomics 2011 12:284

  2. The globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its geneti...

    Authors: Davide Scaglione, Alberto Acquadro, Ezio Portis, Christopher A Taylor, Sergio Lanteri and Steven J Knapp
    Citation: BMC Genomics 2009 10:454
    Content type: Research article Published on:

  3. There is little information about the DNA sequence variation within and between closely related plant species. The combination of re-sequencing technologies, large-scale DNA pools and availability of reference...

    Authors: Carsten Külheim, Suat Hui Yeoh, Jens Maintz, William J Foley and Gavin F Moran
    Citation: BMC Genomics 2009 10:452
    Content type: Research article Published on:

  4. The freshwater snail Lymnaea stagnalis (L. stagnalis) has served as a successful model for studies in the field of Neuroscience. However, a serious drawback in the molecular analysis of the nervous system of L. s...

    Authors: Z-P Feng, Z Zhang, RE van Kesteren, VA Straub, P van Nierop, K Jin, N Nejatbakhsh, JI Goldberg, GE Spencer, MS Yeoman, W Wildering, JR Coorssen, RP Croll, LT Buck, NI Syed and AB Smit
    Citation: BMC Genomics 2009 10:451
    Content type: Research article Published on:

  5. Gluconacetobacter diazotrophicus Pal5 is an endophytic diazotrophic bacterium that lives in association with sugarcane plants. It has important biotechnological features such as nitrogen fixation, plant growth pr...

    Authors: Marcelo Bertalan, Rodolpho Albano, Vânia de Pádua, Luc Rouws, Cristian Rojas, Adriana Hemerly, Kátia Teixeira, Stefan Schwab, Jean Araujo, André Oliveira, Leonardo França, Viviane Magalhães, Sylvia Alquéres, Alexander Cardoso, Welington Almeida, Marcio Martins Loureiro…
    Citation: BMC Genomics 2009 10:450
    Content type: Research article Published on:

  6. MicroRNAs (miRNAs) are endogenous small RNAs having large-scale regulatory effects on plant development and stress responses. Extensive studies of miRNAs have only been performed in a few model plants. Althoug...

    Authors: Jingyu Zhang, Yunyuan Xu, Qing Huan and Kang Chong
    Citation: BMC Genomics 2009 10:449
    Content type: Research article Published on:

  7. Systemic administration of β-adrenoceptor (β-AR) agonists has been found to induce skeletal muscle hypertrophy and significant metabolic changes. In the context of energy homeostasis, the importance of β-AR si...

    Authors: Michael A Pearen, James G Ryall, Gordon S Lynch and George EO Muscat
    Citation: BMC Genomics 2009 10:448
    Content type: Research article Published on:

  8. Rhodoferax ferrireducens is a metabolically versatile, Fe(III)-reducing, subsurface microorganism that is likely to play an important role in the carbon and metal cycles in the subsurface. It also has the unique ...

    Authors: Carla Risso, Jun Sun, Kai Zhuang, Radhakrishnan Mahadevan, Robert DeBoy, Wael Ismail, Susmita Shrivastava, Heather Huot, Sagar Kothari, Sean Daugherty, Olivia Bui, Christophe H Schilling, Derek R Lovley and Barbara A Methé
    Citation: BMC Genomics 2009 10:447
    Content type: Research article Published on:

  9. The detection of odorants is mediated by olfactory receptors (ORs). ORs are G-protein coupled receptors that form a remarkably large protein superfamily in vertebrate genomes. We used data that became availabl...

    Authors: Silke S Steiger, Vladimir Y Kuryshev, Marcus C Stensmyr, Bart Kempenaers and Jakob C Mueller
    Citation: BMC Genomics 2009 10:446
    Content type: Research article Published on:

  10. Subtelomeric RIFIN genes constitute the most abundant multigene family in Plasmodium falciparum. RIFIN products are targets for the human immune response and contribute to the antigenic variability of the parasit...

    Authors: Emanuele Bultrini, Kevin Brick, Srayanta Mukherjee, Yang Zhang, Francesco Silvestrini, Pietro Alano and Elisabetta Pizzi
    Citation: BMC Genomics 2009 10:445
    Content type: Research article Published on:

  11. Mastitis is the most important disease in dairy cows and it causes significant lost of profit to producers. Identification of the genes, and their variants, involved in innate immune responses is essential for...

    Authors: Karin Alain, Niel A Karrow, Catherine Thibault, Jessika St-Pierre, Martin Lessard and Nathalie Bissonnette
    Citation: BMC Genomics 2009 10:444
    Content type: Research article Published on:

  12. MicroRNAs are the major class of gene-regulating molecules playing diverse roles through sequence complementarity to target mRNAs at post-transcriptional level. Tightly regulated expression and interaction of ...

    Authors: Md Munir Hossain, Nasser Ghanem, Michael Hoelker, Franca Rings, Chirawath Phatsara, Ernst Tholen, Karl Schellander and Dawit Tesfaye
    Citation: BMC Genomics 2009 10:443
    Content type: Research article Published on:

  13. Diamond-Blackfan anaemia (DBA) is a rare inherited red cell hypoplasia characterised by a defect in the maturation of erythroid progenitors and in some cases associated with malformations. Patients have an inc...

    Authors: Federica Avondo, Paola Roncaglia, Nicoletta Crescenzio, Helena Krmac, Emanuela Garelli, Marta Armiraglio, Carlotta Castagnoli, Maria Francesca Campagnoli, Ugo Ramenghi, Stefano Gustincich, Claudio Santoro and Irma Dianzani
    Citation: BMC Genomics 2009 10:442
    Content type: Research article Published on:

  14. 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
    Content type: Research article Published on:

  15. Many genes oscillate in their level of expression through the cell division cycle. Previous studies have identified such genes by applying Fourier analysis to cell cycle time course experiments. Typically, suc...

    Authors: Saumyadipta Pyne, Roee Gutman, Chang Sik Kim and Bruce Futcher
    Citation: BMC Genomics 2009 10:440
    Content type: Research article Published on:

  16. With the increasing number of expression profiling technologies, researchers today are confronted with choosing the technology that has sufficient power with minimal sample size, in order to reduce cost and ti...

    Authors: M van Iterson, PAC 't Hoen, P Pedotti, GJEJ Hooiveld, JT den Dunnen, GJB van Ommen, JM Boer and RX Menezes
    Citation: BMC Genomics 2009 10:439
    Content type: Methodology article Published on:

  17. Oceans cover more than 70% of the earth's surface and are critical for the homeostasis of the environment. Among the components of the ocean ecosystem, zooplankton play vital roles in energy and matter transfe...

    Authors: Ryuji J Machida, Yasuyuki Hashiguchi, Mutsumi Nishida and Shuhei Nishida
    Citation: BMC Genomics 2009 10:438
    Content type: Research article Published on:

  18. 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
    Content type: Research article Published on:

  19. '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
    Content type: Research article Published on:

  21. 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
    Content type: Research article Published on:

  22. 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
    Content type: Research article Published on:

  23. 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
    Content type: Research article Published on:

  25. 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
    Content type: Research article Published on:

  26. 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
    Content type: Research article Published on:

  27. 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
    Content type: Research article Published on:

  28. 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
    Content type: Research article Published on:

  29. 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
    Content type: Methodology article Published on:

  30. 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
    Content type: Research article Published on:

  31. 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
    Content type: Methodology article Published on:

  32. 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
    Content type: Research article Published on:

  33. 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
    Content type: Methodology article Published on:

  34. 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
    Content type: Database Published on:

  35. 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
    Content type: Research article Published on:

  37. 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
    Content type: Research article Published on:

  38. 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
    Content type: Research article Published on:

  39. 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
    Content type: Research article Published on:

  40. 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
    Content type: Research article Published on:

  41. 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
    Content type: Research article Published on:

  42. 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
    Content type: Research article Published on:

  43. 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
    Content type: Methodology article Published on:

  44. 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
    Content type: Software Published on:

  45. 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
    Content type: Research article Published on:

  47. 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
    Content type: Research article Published on:

  48. 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
    Content type: Methodology article Published on:

  49. 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
    Content type: Research article Published on:

  50. 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
    Content type: Research article Published on:

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BMC Genomics

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