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Articles

690 result(s) within Volume 9 of BMC Genomics

Page 1 of 14

  1. Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS) and cellular antioxidant defence. To defend ...

    Authors: David Thybert, Stéphane Avner, Céline Lucchetti-Miganeh, Angélique Chéron and Frédérique Barloy-Hubler
    Citation: BMC Genomics 2008 9:637
    Content type: Database Published on:

  3. Mismatched oligonucleotides are widely used on microarrays to differentiate specific from nonspecific hybridization. While many experiments rely on such oligos, the hybridization behavior of various degrees of...

    Authors: Michael Seringhaus, Joel Rozowsky, Thomas Royce, Ugrappa Nagalakshmi, Justin Jee, Michael Snyder and Mark Gerstein
    Citation: BMC Genomics 2008 9:635
    Content type: Methodology article Published on:

  4. Biomphalaria glabrata is an intermediate snail host for Schistosoma mansoni, one of the important schistosomes infecting man. B. glabrata/S. mansoni provides a useful model system for investigating the intimate i...

    Authors: Anne E Lockyer, Jenny Spinks, Richard A Kane, Karl F Hoffmann, Jennifer M Fitzpatrick, David Rollinson, Leslie R Noble and Catherine S Jones
    Citation: BMC Genomics 2008 9:634
    Content type: Research article Published on:

  5. Quantitative polymerase chain reaction (QPCR) is a widely applied analytical method for the accurate determination of transcript abundance. Primers for QPCR have been designed on a genomic scale but non-specif...

    Authors: Athanasia Spandidos, Xiaowei Wang, Huajun Wang, Stefan Dragnev, Tara Thurber and Brian Seed
    Citation: BMC Genomics 2008 9:633
    Content type: Research article Published on:

  6. One of the most striking features of mammalian and birds chromosomes is the variation in the guanine-cytosine (GC) content that occurs over scales of hundreds of kilobases to megabases; this is known as the "i...

    Authors: Christelle Melodelima and Christian Gautier
    Citation: BMC Genomics 2008 9:632
    Content type: Research article Published on:

  7. The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparat...

    Authors: M Elisabete J Amaral, Jason R Grant, Penny K Riggs, Nedenia B Stafuzza, Edson A Rodrigues Filho, Tom Goldammer, Rosemarie Weikard, Ronald M Brunner, Kelli J Kochan, Anthony J Greco, Jooha Jeong, Zhipeng Cai, Guohui Lin, Aparna Prasad, Satish Kumar, G Pardha Saradhi…
    Citation: BMC Genomics 2008 9:631
    Content type: Research article Published on:

  8. Skeletal muscle mass can be markedly reduced through a process called atrophy, as a consequence of many diseases or critical physiological and environmental situations. Atrophy is characterised by loss of cont...

    Authors: Enrica Calura, Stefano Cagnin, Anna Raffaello, Paolo Laveder, Gerolamo Lanfranchi and Chiara Romualdi
    Citation: BMC Genomics 2008 9:630
    Content type: Research article Published on:

  9. We have recently released a comprehensive, manually curated database of mammalian protein complexes called CORUM. Combining CORUM with other resources, we assembled a dataset of over 2700 mammalian complexes. ...

    Authors: Philip Wong, Sonja Althammer, Andrea Hildebrand, Andreas Kirschner, Philipp Pagel, Bernd Geissler, Pawel Smialowski, Florian Blöchl, Matthias Oesterheld, Thorsten Schmidt, Normann Strack, Fabian J Theis, Andreas Ruepp and Dmitrij Frishman
    Citation: BMC Genomics 2008 9:629
    Content type: Research article Published on:

  11. Acute changes in environmental parameters (e.g., O2, pH, UV, osmolarity, nutrients, etc.) evoke a common transcriptomic response in yeast referred to as the "environmental stress response" (ESR) or "common enviro...

    Authors: Liang-Chuan Lai, Matthew T Kissinger, Patricia V Burke and Kurt E Kwast
    Citation: BMC Genomics 2008 9:627
    Content type: Research article Published on:

  12. Mus spretus diverged from Mus musculus over one million years ago. These mice are genetically and phenotypically divergent. Despite the value of utilizing M. musculus and M. spretus for quantitative trait locus (...

    Authors: Kimberly L Mahler, Jessica L Fleming, Amy M Dworkin, Nicholas Gladman, Hee-Yeon Cho, Jian-Hua Mao, Allan Balmain and Amanda Ewart Toland
    Citation: BMC Genomics 2008 9:626
    Content type: Research article Published on:

  13. Phosphorylation by protein kinases is a common event in many cellular processes. Further, many kinases perform specialized roles and are regulated by non-kinase domains tethered to kinase domain. Perturbation ...

    Authors: Krishanpal Anamika, Juliette Martin and Narayanaswamy Srinivasan
    Citation: BMC Genomics 2008 9:625
    Content type: Research article Published on:

  14. MicroRNAs (miRNAs) play key roles in mammalian gene expression and several cellular processes, including differentiation, development, apoptosis and cancer pathomechanisms. Recently the biological importance o...

    Authors: Priyanka Pandey, Benedikt Brors, Prashant K Srivastava, Andrea Bott, Susanne NE Boehn, Herrmann-Josef Groene and Norbert Gretz
    Citation: BMC Genomics 2008 9:624
    Content type: Research article Published on:

  15. Increasing evidence shows that whole genomes of eukaryotes are almost entirely transcribed into both protein coding genes and an enormous number of non-protein-coding RNAs (ncRNAs). Therefore, revealing the un...

    Authors: Lin Wan, Dayong Li, Donglei Zhang, Xue Liu, Wenjiang J Fu, Lihuang Zhu, Minghua Deng, Fengzhu Sun and Minping Qian
    Citation: BMC Genomics 2008 9:623
    Content type: Research article Published on:

  16. Sodium channels are heteromultimeric, integral membrane proteins that belong to a superfamily of ion channels. The mutations in genes encoding for sodium channel proteins have been linked with several inherite...

    Authors: Sunil Sagar, Mandeep Kaur, Adam Dawe, Sundararajan Vijayaraghava Seshadri, Alan Christoffels, Ulf Schaefer, Aleksandar Radovanovic and Vladimir B Bajic
    Citation: BMC Genomics 2008 9:622
    Content type: Database Published on:

  17. Many plant genomes are resistant to whole-genome assembly due to an abundance of repetitive sequence, leading to the development of gene-rich sequencing techniques. Two such techniques are hypomethylated parti...

    Authors: William Nelson, Meizhong Luo, Jianxin Ma, Matt Estep, James Estill, Ruifeng He, Jayson Talag, Nicholas Sisneros, David Kudrna, HyeRan Kim, Jetty SS Ammiraju, Kristi Collura, Arvind K Bharti, Joachim Messing, Rod A Wing, Phillip SanMiguel…
    Citation: BMC Genomics 2008 9:621
    Content type: Research article Published on:

  19. Seed oil accumulates primarily as triacylglycerol (TAG). While the biochemical pathway for TAG biosynthesis is known, its regulation remains unclear. Previous research identified microsomal diacylglycerol acyl...

    Authors: Nirmala Sharma, Maureen Anderson, Arvind Kumar, Yan Zhang, E Michael Giblin, Suzanne R Abrams, L Irina Zaharia, David C Taylor and Pierre R Fobert
    Citation: BMC Genomics 2008 9:619
    Content type: Research article Published on:

  20. The Tephritidae family of insects includes the most important agricultural pests of fruits and vegetables, belonging mainly to four genera (Bactrocera, Ceratitis, Anastrepha and Rhagoletis). The olive fruit fly,

    Authors: Antonios A Augustinos, Elias E Stratikopoulos, Eleni Drosopoulou, Evdoxia G Kakani, Penelope Mavragani-Tsipidou, Antigone Zacharopoulou and Kostas D Mathiopoulos
    Citation: BMC Genomics 2008 9:618
    Content type: Research article Published on:

  21. The bacterial cell wall is the target of many antibiotics and cell envelope constituents are critical to host-pathogen interactions. To combat resistance development and virulence, a detailed knowledge of the ...

    Authors: Judith Hübscher, Lucas Lüthy, Brigitte Berger-Bächi and Patricia Stutzmann Meier
    Citation: BMC Genomics 2008 9:617
    Content type: Research article Published on:

  22. The fish pathogen Aliivibrio salmonicida is the causative agent of cold-water vibriosis in marine aquaculture. The Gram-negative bacterium causes tissue degradation, hemolysis and sepsis in vivo.

    Authors: Erik Hjerde, Marit Sjo Lorentzen, Matthew TG Holden, Kathy Seeger, Steinar Paulsen, Nathalie Bason, Carol Churcher, David Harris, Halina Norbertczak, Michael A Quail, Suzanne Sanders, Scott Thurston, Julian Parkhill, Nils Peder Willassen and Nicholas R Thomson
    Citation: BMC Genomics 2008 9:616
    Content type: Research article Published on:

  23. The Burkholderia cepacia complex (BCC) is a versatile group of Gram negative organisms that can be found throughout the environment in sources such as soil, water, and plants. While BCC bacteria can be involved i...

    Authors: Amanda D Goudie, Karlene H Lynch, Kimberley D Seed, Paul Stothard, Savita Shrivastava, David S Wishart and Jonathan J Dennis
    Citation: BMC Genomics 2008 9:615
    Content type: Research article Published on:

  26. Compound microsatellites are a special variation of microsatellites in which two or more individual microsatellites are found directly adjacent to each other. Until now, such composite microsatellites have not...

    Authors: Robert Kofler, Christian Schlötterer, Evita Luschützky and Tamas Lelley
    Citation: BMC Genomics 2008 9:612
    Content type: Research article Published on:

  27. Starvation triggers a complex array of adaptative metabolic responses including energy-metabolic responses, a process which must imply tissue specific alterations in gene expression and in which the liver play...

    Authors: Colette Désert, Michel J Duclos, Pierre Blavy, Frédéric Lecerf, François Moreews, Christophe Klopp, Marc Aubry, Frédéric Herault, Pascale Le Roy, Cécile Berri, Madeleine Douaire, Christian Diot and Sandrine Lagarrigue
    Citation: BMC Genomics 2008 9:611
    Content type: Research article Published on:

  28. Nucleotide sequences and the gene arrangements of mitochondrial genomes are effective tools for resolving phylogenetic problems. Hemipteroid insects are known to possess highly reorganized mitochondrial genome...

    Authors: Jimeng Hua, Ming Li, Pengzhi Dong, Ying Cui, Qiang Xie and Wenjun Bu
    Citation: BMC Genomics 2008 9:610
    Content type: Research article Published on:

  30. Lipopolysaccharide (LPS) is a cell wall component of Gram-negative bacteria with proved role in pathogenesis of sepsis. Brain injury was observed with both patients dead from sepsis and animal septic models. H...

    Authors: Gang Yue, Guanfang Shi, Marco A Azaro, Qifeng Yang, Guohong Hu, Minjie Luo, Kingsley Yin, Robert G Nagele, Daniel H Fine, Jin-Ming Yang and Honghua Li
    Citation: BMC Genomics 2008 9:608
    Content type: Research article Published on:

  31. Streptococcus agalactiae (group B Streptococcus; GBS) is a significant bacterial pathogen of neonates and an emerging pathogen of adults. Though transcriptional regulators are abundantly encoded on the GBS genome...

    Authors: Joshua D Bryan, Roxanne Liles, Urska Cvek, Marjan Trutschl and Daniel Shelver
    Citation: BMC Genomics 2008 9:607
    Content type: Research article Published on:

  32. Lymphotoxin signaling via the lymphotoxin-β receptor (LTβR) has been implicated in biological processes ranging from development of secondary lymphoid organs, maintenance of spleen architecture, host defense a...

    Authors: Agnes Lovas, Dörte Radke, Daniela Albrecht, Z Buket Yilmaz, Ulrich Möller, Andreas JR Habenicht and Falk Weih
    Citation: BMC Genomics 2008 9:606
    Content type: Research article Published on:

  34. Environmental signals usually enhance secondary metabolite production in Streptomycetes by initiating complex signal transduction system. It is known that different sigma factors respond to different types of str...

    Authors: Yoon Jung Kim, Myung Hee Moon, Jae Yang Song, Colin P Smith, Soon-Kwang Hong and Yong Keun Chang
    Citation: BMC Genomics 2008 9:604
    Content type: Research article Published on:

  35. Massively parallel DNA sequencing instruments are enabling the decoding of whole genomes at significantly lower cost and higher throughput than classical Sanger technology. Each of these technologies have been...

    Authors: Jean-Marc Aury, Corinne Cruaud, Valérie Barbe, Odile Rogier, Sophie Mangenot, Gaelle Samson, Julie Poulain, Véronique Anthouard, Claude Scarpelli, François Artiguenave and Patrick Wincker
    Citation: BMC Genomics 2008 9:603
    Content type: Research article Published on:

  37. Expression of a large number of yeast genes is repressed by glucose. The zinc finger protein Mig1 is the main effector in glucose repression, but yeast also has two related proteins: Mig2 and Mig3. We have use...

    Authors: Jakub Orzechowski Westholm, Niklas Nordberg, Eva Murén, Adam Ameur, Jan Komorowski and Hans Ronne
    Citation: BMC Genomics 2008 9:601
    Content type: Research article Published on:

  38. Members of the genus Rhodococcus are frequently found in soil and other natural environments and are highly resistant to stresses common in those environments. The accumulation of storage compounds permits cells ...

    Authors: Martín A Hernández, William W Mohn, Eliana Martínez, Enrique Rost, Adrián F Alvarez and Héctor M Alvarez
    Citation: BMC Genomics 2008 9:600
    Content type: Research article Published on:

  39. The small leucine-rich repeat proteins and proteoglycans (SLRPs) form an important family of regulatory molecules that participate in many essential functions. They typically control the correct assembly of co...

    Authors: Hosil Park, Julie Huxley-Jones, Ray P Boot-Handford, Paul N Bishop, Teresa K Attwood and Jordi Bella
    Citation: BMC Genomics 2008 9:599
    Content type: Research article Published on:

  40. The study of genome-wide DNA methylation changes has become more accessible with the development of various array-based technologies though when studying species other than human the choice of applications are...

    Authors: Kathy Boon, John K Tomfohr, Nathaniel W Bailey, Stavros Garantziotis, Zhuowei Li, David M Brass, Shuichiro Maruoka, John W Hollingsworth and David A Schwartz
    Citation: BMC Genomics 2008 9:598
    Content type: Methodology article Published on:

  41. Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, γ-proteobacterium using ene...

    Authors: Jorge Valdés, Inti Pedroso, Raquel Quatrini, Robert J Dodson, Herve Tettelin, Robert Blake II, Jonathan A Eisen and David S Holmes
    Citation: BMC Genomics 2008 9:597
    Content type: Research article Published on:

  43. Identification and mapping of repetitive elements is a key step for accurate gene prediction and overall structural annotation of genomes. During the assembly and annotation of three highly repetitive amoeba g...

    Authors: Hernan Lorenzi, Mathangi Thiagarajan, Brian Haas, Jennifer Wortman, Neil Hall and Elisabet Caler
    Citation: BMC Genomics 2008 9:595
    Content type: Research article Published on:

  44. Bodo saltans is a free-living kinetoplastid and among the closest relatives of the trypanosomatid parasites, which cause such human diseases as African sleeping sickness, leishmaniasis and Chagas disease. A B. sa...

    Authors: Andrew P Jackson, Michael A Quail and Matthew Berriman
    Citation: BMC Genomics 2008 9:594
    Content type: Research article Published on:

  45. High-throughput sequencing technology is capable to identify novel short RNAs in plant species. We used Solexa sequencing to find new microRNAs in one of the model legume species, barrel medic (Medicago truncatul...

    Authors: Gyorgy Szittya, Simon Moxon, Dulce M Santos, Runchun Jing, Manuel PS Fevereiro, Vincent Moulton and Tamas Dalmay
    Citation: BMC Genomics 2008 9:593
    Content type: Research article Published on:

  47. Understanding the molecular control of cell lineages and fate determination in complex tissues is key to not only understanding the developmental biology and cellular homeostasis of such tissues but also for o...

    Authors: Howard Kendrick, Joseph L Regan, Fiona-Ann Magnay, Anita Grigoriadis, Costas Mitsopoulos, Marketa Zvelebil and Matthew J Smalley
    Citation: BMC Genomics 2008 9:591
    Content type: Research article Published on:

  48. In bacteriology, the ability to grow in selective media and to form colonies on nutrient agar plates is routinely used as a retrospective criterion for the detection of living bacteria. However, the utilizatio...

    Authors: Remco Kort, Bart J Keijser, Martien PM Caspers, Frank H Schuren and Roy Montijn
    Citation: BMC Genomics 2008 9:590
    Content type: Research article Published on:

  49. We have made use of publicly available gene expression data to identify transcription factors and transcriptional modules (regulons) associated with leaf development in Populus. Different tissue types were compar...

    Authors: Nathaniel Robert Street, Andreas Sjödin, Max Bylesjö, Petter Gustafsson, Johan Trygg and Stefan Jansson
    Citation: BMC Genomics 2008 9:589
    Content type: Research article Published on:

  50. 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:

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BMC Genomics

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