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  1. Annotation of protein-coding genes is a key step in sequencing projects. Protein functions are mainly assigned on the basis of the amino acid sequence alone by searching of homologous proteins. However, fully ...

    Authors: Manuel J Rodríguez-Ortega, Inmaculada Luque, Carmen Tarradas and José A Bárcena
    Citation: BMC Genomics 2008 9:588
    Content type: Research article Published on:

  2. Nyctotherus ovalis is a single-celled eukaryote that has hydrogen-producing mitochondria and lives in the hindgut of cockroaches. Like all members of the ciliate taxon, it has two types of nuclei, a micronucleus ...

    Authors: Guénola Ricard, Rob M de Graaf, Bas E Dutilh, I Duarte, Theo A van Alen, Angela HAM van Hoek, Brigitte Boxma, Georg WM van der Staay, Seung Yeo Moon-van der Staay, Wei-Jen Chang, Laura F Landweber, Johannes HP Hackstein and Martijn A Huynen
    Citation: BMC Genomics 2008 9:587
    Content type: Research article Published on:

  3. Since the full genome sequences of Saccharomyces cerevisiae were released in 1996, genome sequences of over 90 fungal species have become publicly available. The heterogeneous formats of genome sequences archived...

    Authors: Kyongyong Jung, Jongsun Park, Jaeyoung Choi, Bongsoo Park, Seungill Kim, Kyohun Ahn, Jaehyuk Choi, Doil Choi, Seogchan Kang and Yong-Hwan Lee
    Citation: BMC Genomics 2008 9:586
    Content type: Database Published on:

  5. To maintain EU GMO regulations, producers of new GM crop varieties need to supply an event-specific method for the new variety. As a result methods are nowadays available for EU-authorised genetically modified...

    Authors: Theo W Prins, Jeroen P van Dijk, Henriek G Beenen, AM Angeline Van Hoef, Marleen M Voorhuijzen, Cor D Schoen, Henk JM Aarts and Esther J Kok
    Citation: BMC Genomics 2008 9:584
    Content type: Research article Published on:

  6. Functional genomics has received considerable attention in the post-genomic era, as it aims to identify function(s) for different genes. One way to study gene function is to investigate the alterations in the ...

    Authors: Md Alamgir, Veronika Eroukova, Matthew Jessulat, Jianhua Xu and Ashkan Golshani
    Citation: BMC Genomics 2008 9:583
    Content type: Research article Published on:

  8. Carbon and nitrogen fixation are essential pathways for autotrophic bacteria living in extreme environments. These bacteria can use carbon dioxide directly from the air as their sole carbon source and can use ...

    Authors: Gloria Levicán, Juan A Ugalde, Nicole Ehrenfeld, Alejandro Maass and Pilar Parada
    Citation: BMC Genomics 2008 9:581
    Content type: Research article Published on:

  9. Aquaculture represents the most sustainable alternative of seafood supply to substitute for the declining marine fisheries, but severe production bottlenecks remain to be solved. The application of genomic tec...

    Authors: Serena Ferraresso, Nicola Vitulo, Alba N Mininni, Chiara Romualdi, Barbara Cardazzo, Enrico Negrisolo, Richard Reinhardt, Adelino VM Canario, Tomaso Patarnello and Luca Bargelloni
    Citation: BMC Genomics 2008 9:580
    Content type: Research article Published on:

  10. The major facilitator superfamily (MFS) is one of the two largest superfamilies of membrane transporters present ubiquitously in bacteria, archaea, and eukarya and includes members that function as uniporters,...

    Authors: Manisha Gaur, Nidhi Puri, Raman Manoharlal, Versha Rai, Gauranga Mukhopadhayay, Devapriya Choudhury and Rajendra Prasad
    Citation: BMC Genomics 2008 9:579
    Content type: Research article Published on:

  11. Candida albicans is a diploid pathogenic fungus not yet amenable to routine genetic investigations. Understanding aspects of the regulation of its biological functions and the assembly of its protein complexes wo...

    Authors: Hugo Lavoie, Adnane Sellam, Christopher Askew, André Nantel and Malcolm Whiteway
    Citation: BMC Genomics 2008 9:578
    Content type: Methodology article Published on:

  12. Febrile respiratory illness (FRI) has a high impact on public health and global economics and poses a difficult challenge for differential diagnosis. A particular issue is the detection of genetically diverse ...

    Authors: Zheng Wang, Anthony P Malanoski, Baochuan Lin, Carolyn Kidd, Nina C Long, Kate M Blaney, Dzung C Thach, Clark Tibbetts and David A Stenger
    Citation: BMC Genomics 2008 9:577
    Content type: Research article Published on:

  13. Recent studies of 16S rRNA genes in the mammalian gut microbiota distinguished a higher Firmicutes/Bacteroidetes ratio in obese individuals compared to lean individuals. This ratio was estimated using a clonal Sa...

    Authors: Fabrice Armougom and Didier Raoult
    Citation: BMC Genomics 2008 9:576
    Content type: Research article Published on:

  15. An ideal format to describe transcriptome would be its composition measured on the scale of absolute numbers of individual mRNAs per cell. It would help not only to precisely grasp the structure of the transcr...

    Authors: Fumihito Miura, Noriko Kawaguchi, Mikio Yoshida, Chihiro Uematsu, Keiji Kito, Yoshiyuki Sakaki and Takashi Ito
    Citation: BMC Genomics 2008 9:574
    Content type: Methodology article Published on:

  16. The technological evolution of platforms for detecting genome-wide copy number imbalances has allowed the discovery of an unexpected amount of human sequence that is variable in copy number among individuals. ...

    Authors: Lorena Pantano, Lluís Armengol, Sergi Villatoro and Xavier Estivill
    Citation: BMC Genomics 2008 9:573
    Content type: Software Published on:

  17. The commonest pathogenic DMD changes are intragenic deletions/duplications which make up to 78% of all cases and point mutations (roughly 20%) detectable through direct sequencing. The remaining mutations (about ...

    Authors: Matteo Bovolenta, Marcella Neri, Sergio Fini, Marina Fabris, Cecilia Trabanelli, Anna Venturoli, Elena Martoni, Elena Bassi, Pietro Spitali, Simona Brioschi, Maria S Falzarano, Paola Rimessi, Roberto Ciccone, Emma Ashton, Joanne McCauley, Shu Yau…
    Citation: BMC Genomics 2008 9:572
    Content type: Research article Published on:

  19. Outbreak of V. parahaemolyticus infections occurred since 1996 was linked to a proposed clonal complex, the pandemic group. The whole genome sequence provides an unprecedented opportunity for dissecting genome pl...

    Authors: Haihong Han, Hin-chung Wong, Biao Kan, Zhaobiao Guo, Xiaotao Zeng, Shengjun Yin, Xiumei Liu, Ruifu Yang and Dongsheng Zhou
    Citation: BMC Genomics 2008 9:570
    Content type: Research article Published on:

  21. Avian pathogenic E. coli (APEC) are associated with extraintestinal diseases in poultry. The pstSCAB-phoU operon belongs to the Pho regulon and encodes the phosphate specific transport (Pst) system. A functional ...

    Authors: Sébastien Crépin, Martin G Lamarche, Philippe Garneau, Julie Séguin, Julie Proulx, Charles M Dozois and Josée Harel
    Citation: BMC Genomics 2008 9:568
    Content type: Research article Published on:

  23. Burkholderia pseudomallei is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of B. pseudomallei are predicted ...

    Authors: Apichai Tuanyok, Benjamin R Leadem, Raymond K Auerbach, Stephen M Beckstrom-Sternberg, James S Beckstrom-Sternberg, Mark Mayo, Vanaporn Wuthiekanun, Thomas S Brettin, William C Nierman, Sharon J Peacock, Bart J Currie, David M Wagner and Paul Keim
    Citation: BMC Genomics 2008 9:566
    Content type: Research article Published on:

  25. MicroRNAs (miRNAs) are important regulators of gene expression and have been implicated in development, differentiation and pathogenesis. Hundreds of miRNAs have been discovered in mammalian genomes. Approxima...

    Authors: Harpreet K Saini, Anton J Enright and Sam Griffiths-Jones
    Citation: BMC Genomics 2008 9:564
    Content type: Research article Published on:

  26. Glucosidation plays a major role in the inactivation and excretion of a great variety of both endogenous and exogenous compounds. A class of UDP-glycosyltransferases (UGTs) is involved in this process. Insect ...

    Authors: Fei-Fei Huang, Chun-Li Chai, Ze Zhang, Zeng-Hu Liu, Fang-Yin Dai, Cheng Lu and Zhong-Huai Xiang
    Citation: BMC Genomics 2008 9:563
    Content type: Research article Published on:

  27. Tetrahymena thermophila, a widely studied model for cellular and molecular biology, is a binucleated single-celled organism with a germline micronucleus (MIC) and somatic macronucleus (MAC). The recent draft MAC ...

    Authors: Robert S Coyne, Mathangi Thiagarajan, Kristie M Jones, Jennifer R Wortman, Luke J Tallon, Brian J Haas, Donna M Cassidy-Hanley, Emily A Wiley, Joshua J Smith, Kathleen Collins, Suzanne R Lee, Mary T Couvillion, Yifan Liu, Jyoti Garg, Ronald E Pearlman, Eileen P Hamilton…
    Citation: BMC Genomics 2008 9:562
    Content type: Research article Published on:

  28. The elucidation of transcriptional regulation in plant genes is important area of research for plant scientists, following the mapping of various plant genomes, such as A. thaliana, O. sativa and Z. mays. A varie...

    Authors: Wen-Chi Chang, Tzong-Yi Lee, Hsien-Da Huang, His-Yuan Huang and Rong-Long Pan
    Citation: BMC Genomics 2008 9:561
    Content type: Database Published on:

  29. Extraintestinal pathogenic Escherichia coli (ExPEC) strains represent a huge public health burden. Knowledge of their clonal diversity and of the association of clones with genomic content and clinical features i...

    Authors: Françoise Jaureguy, Luce Landraud, Virginie Passet, Laure Diancourt, Eric Frapy, Ghislaine Guigon, Etienne Carbonnelle, Olivier Lortholary, Olivier Clermont, Erick Denamur, Bertrand Picard, Xavier Nassif and Sylvain Brisse
    Citation: BMC Genomics 2008 9:560
    Content type: Research article Published on:

  30. Replication of bacterial chromosomes increases copy numbers of genes located near origins of replication relative to genes located near termini. Such differential gene dosage depends on replication rate, doubl...

    Authors: Rikard Dryselius, Kaori Izutsu, Takeshi Honda and Tetsuya Iida
    Citation: BMC Genomics 2008 9:559
    Content type: Research article Published on:

  31. Gene clusters, such as the Hox gene cluster, are known to have critical roles in development. In eukaryotes gene clusters arise primarily by tandem gene duplication and divergence. Genes within a cluster are ofte...

    Authors: Elizabeth J Duncan, Megan J Wilson, James M Smith and Peter K Dearden
    Citation: BMC Genomics 2008 9:558
    Content type: Research article Published on:

  32. Comparative genomic studies suggest that the modern day assemblage of ray-finned fishes have descended from an ancestral grouping of fishes that possessed 12–13 linkage groups. All jawed vertebrates are postul...

    Authors: Roy G Danzmann, Evelyn A Davidson, Moira M Ferguson, Karim Gharbi, Ben F Koop, Bjorn Hoyheim, Sigbjorn Lien, Krzysztof P Lubieniecki, Hooman K Moghadam, Jay Park, Ruth B Phillips and William S Davidson
    Citation: BMC Genomics 2008 9:557
    Content type: Research article Published on:

  34. Several studies suggested that the diploid ancestor of the B genome of tetraploid and hexaploid wheat species belongs to the Sitopsis section, having Aegilops speltoides (SS, 2n = 14) as the closest identified re...

    Authors: Jérome Salse, Véronique Chagué, Stéphanie Bolot, Ghislaine Magdelenat, Cécile Huneau, Caroline Pont, Harry Belcram, Arnaud Couloux, Soazic Gardais, Aurélie Evrard, Béatrice Segurens, Mathieu Charles, Catherine Ravel, Sylvie Samain, Gilles Charmet, Nathalie Boudet…
    Citation: BMC Genomics 2008 9:555
    Content type: Research article Published on:

  35. Genetic maps provide specific positions of genetic markers, which are required for performing genetic studies. Linkage analyses of Asian families have been performed with Caucasian genetic maps, since appropri...

    Authors: Young Seok Ju, Hansoo Park, Mi Kyeong Lee, Jong-Il Kim, Joohon Sung, Sung-Il Cho and Jeong-Sun Seo
    Citation: BMC Genomics 2008 9:554
    Content type: Research article Published on:

  36. Drought is the major constraint to increase yield in chickpea (Cicer arietinum). Improving drought tolerance is therefore of outmost importance for breeding. However, the complexity of the trait allowed only marg...

    Authors: Carlos Molina, Björn Rotter, Ralf Horres, Sripada M Udupa, Bert Besser, Luis Bellarmino, Michael Baum, Hideo Matsumura, Ryohei Terauchi, Günter Kahl and Peter Winter
    Citation: BMC Genomics 2008 9:553
    Content type: Research article Published on:

  37. Ticks are obligate blood feeders. The midgut is the first major region of the body where blood and microbes ingested with the blood meal come in contact with the tick's internal tissues. Little is known about ...

    Authors: Jennifer M Anderson, Daniel E Sonenshine and Jesus G Valenzuela
    Citation: BMC Genomics 2008 9:552
    Content type: Research article Published on:

  39. The protein phosphatase 2Cs (PP2Cs) from various organisms have been implicated to act as negative modulators of protein kinase pathways involved in diverse environmental stress responses and developmental pro...

    Authors: Tongtong Xue, Dong Wang, Shizhong Zhang, Juergen Ehlting, Fei Ni, Stephen Jakab, Chengchao Zheng and Yuan Zhong
    Citation: BMC Genomics 2008 9:550
    Content type: Research article Published on:

  40. Serine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life. While studies have established significant roles for many prokaryotic serine proteases in several ...

    Authors: Lokesh P Tripathi and R Sowdhamini
    Citation: BMC Genomics 2008 9:549
    Content type: Research article Published on:

  41. The basidiomycete fungus Moniliophthora perniciosa is the causal agent of Witches' Broom Disease (WBD) in cacao (Theobroma cacao). It is a hemibiotrophic pathogen that colonizes the apoplast of cacao's meristemat...

    Authors: Jorge MC Mondego, Marcelo F Carazzolle, Gustavo GL Costa, Eduardo F Formighieri, Lucas P Parizzi, Johana Rincones, Carolina Cotomacci, Dirce M Carraro, Anderson F Cunha, Helaine Carrer, Ramon O Vidal, Raíssa C Estrela, Odalys García, Daniela PT Thomazella, Bruno V de Oliveira, Acássia BL Pires…
    Citation: BMC Genomics 2008 9:548
    Content type: Research article Published on:

  42. Many microorganisms have a wide temperature growth range and versatility to tolerate large thermal fluctuations in diverse environments, however not many have been fully explored over their entire growth tempe...

    Authors: Debora F Rodrigues, Natalia Ivanova, Zhili He, Marianne Huebner, Jizhong Zhou and James M Tiedje
    Citation: BMC Genomics 2008 9:547
    Content type: Research article Published on:

  43. Pyrethroids are neurotoxic pesticides that interact with membrane bound ion channels in neurons and disrupt nerve function. The purpose of this study was to characterize and explore changes in gene expression ...

    Authors: Joshua A Harrill, Zhen Li, Fred A Wright, Nicholas M Radio, William R Mundy, Rogelio Tornero-Velez and Kevin M Crofton
    Citation: BMC Genomics 2008 9:546
    Content type: Research article Published on:

  44. Salmonids are of interest because of their relatively recent genome duplication, and their extensive use in wild fisheries and aquaculture. A comprehensive gene list and a comparison of genes in some of the di...

    Authors: Ben F Koop, Kristian R von Schalburg, Jong Leong, Neil Walker, Ryan Lieph, Glenn A Cooper, Adrienne Robb, Marianne Beetz-Sargent, Robert A Holt, Richard Moore, Sonal Brahmbhatt, Jamie Rosner, Caird E Rexroad III, Colin R McGowan and William S Davidson
    Citation: BMC Genomics 2008 9:545
    Content type: Research article Published on:

  45. Fluorescence of dyes bound to double-stranded PCR products has been utilized extensively in various real-time quantitative PCR applications, including post-amplification dissociation curve analysis, or differe...

    Authors: Kelli J Kochan, M Elisabete J Amaral, Richa Agarwala, Alejandro A Schäffer and Penny K Riggs
    Citation: BMC Genomics 2008 9:544
    Content type: Methodology article Published on:

  46. Fruits from several species of the Rosaceae family are reported to cause allergic reactions in certain populations. The allergens identified belong to mainly four protein families: pathogenesis related 10 prot...

    Authors: Lin Chen, Shuiming Zhang, Eudald Illa, Lijuan Song, Shandong Wu, Werner Howad, Pere Arús, Eric van de Weg, Kunsong Chen and Zhongshan Gao
    Citation: BMC Genomics 2008 9:543
    Content type: Research article Published on:

  47. Pythium species are an agriculturally important genus of plant pathogens, yet are not understood well at the molecular, genetic, or genomic level. They are closely related to other oomycete plant pathogens such a...

    Authors: Foo Cheung, Joe Win, Jillian M Lang, John Hamilton, Hue Vuong, Jan E Leach, Sophien Kamoun, C André Lévesque, Ned Tisserat and C Robin Buell
    Citation: BMC Genomics 2008 9:542
    Content type: Research article Published on:

  48. LC-MALDI-TOF/TOF analysis is a potent tool in biomarkers discovery characterized by its high sensitivity and high throughput capacity. However, methods based on MALDI-TOF/TOF for biomarkers discovery still nee...

    Authors: K Benkali, P Marquet, JP Rérolle, Y Le Meur and LN Gastinel
    Citation: BMC Genomics 2008 9:541
    Content type: Methodology article Published on:

  49. Anthozoan cnidarians are amongst the simplest animals at the tissue level of organization, but are surprisingly complex and vertebrate-like in terms of gene repertoire. As major components of tropical reef eco...

    Authors: Lauretta C Grasso, John Maindonald, Stephen Rudd, David C Hayward, Robert Saint, David J Miller and Eldon E Ball
    Citation: BMC Genomics 2008 9:540
    Content type: Research article Published on:

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BMC Genomics

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