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  1. The current study focused on the extent genetic diversity within a species (Mus musculus) affects gene co-expression network structure. To examine this issue, we have created a new mouse resource, a heterogeneous...

    Authors: Ovidiu D Iancu, Priscila Darakjian, Nicole AR Walter, Barry Malmanger, Denesa Oberbeck, John Belknap, Shannon McWeeney and Robert Hitzemann
    Citation: BMC Genomics 2010 11:585
    Content type: Research article Published on:

  2. The ecological niche occupied by a fungal species, its pathogenicity and its usefulness as a microbial cell factory to a large degree depends on its secretome. Protein secretion usually requires the presence o...

    Authors: Machtelt Braaksma, Elena S Martens-Uzunova, Peter J Punt and Peter J Schaap
    Citation: BMC Genomics 2010 11:584
    Content type: Research article Published on:

  3. Two year cancer bioassays conducted by the National Toxicology Program have shown chronic exposure to dioxin-like compounds (DLCs) to lead to the development of both neoplastic and non-neoplastic lesions in th...

    Authors: Bladimir J Ovando, Corie A Ellison, Chad M Vezina and James R Olson
    Citation: BMC Genomics 2010 11:583
    Content type: Research article Published on:

  4. All crustaceans periodically moult to renew their exoskeleton. In krill this involves partial digestion and resorption of the old exoskeleton and synthesis of new cuticle. Molecular events that underlie the mo...

    Authors: Paul J Seear, Geraint A Tarling, Gavin Burns, William P Goodall-Copestake, Edward Gaten, Özge Özkaya and Ezio Rosato
    Citation: BMC Genomics 2010 11:582
    Content type: Research article Published on:

  5. How the transcription factor binding sites (TFBSs) are distributed in the promoter region have implications for gene regulation. Previous studies used the translation start codon as the reference point to infe...

    Authors: Zhenguo Lin, Wei-Sheng Wu, Han Liang, Yong Woo and Wen-Hsiung Li
    Citation: BMC Genomics 2010 11:581
    Content type: Research article Published on:

  6. Understanding ethanol tolerance in microorganisms is important for the improvement of bioethanol production. Hence, we performed parallel-evolution experiments using Escherichia coli cells under ethanol stress to...

    Authors: Takaaki Horinouchi, Kuniyasu Tamaoka, Chikara Furusawa, Naoaki Ono, Shingo Suzuki, Takashi Hirasawa, Tetsuya Yomo and Hiroshi Shimizu
    Citation: BMC Genomics 2010 11:579
    Content type: Research article Published on:

  7. The onset of antibiotics production in Streptomyces species is co-ordinated with differentiation events. An understanding of the genetic circuits that regulate these coupled biological phenomena is essential to d...

    Authors: Marlene Castro-Melchor, Salim Charaniya, George Karypis, Eriko Takano and Wei-Shou Hu
    Citation: BMC Genomics 2010 11:578
    Content type: Research article Published on:

  8. Elevated parasite biomass in the human red blood cells can lead to increased malaria morbidity. The genes and mechanisms regulating growth and development of Plasmodium falciparum through its erythrocytic cycle a...

    Authors: Heather B Reilly Ayala, Mark A Wacker, Geoffrey Siwo and Michael T Ferdig
    Citation: BMC Genomics 2010 11:577
    Content type: Research article Published on:

  9. Genomic instability plays an important role in human cancers. We previously characterized genomic instability in esophageal squamous cell carcinomas (ESCC) in terms of loss of heterozygosity (LOH) and copy num...

    Authors: Nan Hu, Robert J Clifford, Howard H Yang, Chaoyu Wang, Alisa M Goldstein, Ti Ding, Philip R Taylor and Maxwell P Lee
    Citation: BMC Genomics 2010 11:576
    Content type: Research article Published on:

  10. The immune system of the purple sea urchin, Strongylocentrotus purpuratus, is complex and sophisticated. An important component of sea urchin immunity is the Sp185/333 gene family, which is significantly upregula...

    Authors: Chase A Miller, Katherine M Buckley, Rebecca L Easley and L Courtney Smith
    Citation: BMC Genomics 2010 11:575
    Content type: Research article Published on:

  11. Analysis of microarray experiments often involves testing for the overrepresentation of pre-defined sets of genes among lists of genes deemed individually significant. Most popular gene set testing methods ass...

    Authors: Daniel M Gatti, William T Barry, Andrew B Nobel, Ivan Rusyn and Fred A Wright
    Citation: BMC Genomics 2010 11:574
    Content type: Research article Published on:

  12. The human pathogen Listeria monocytogenes resides and proliferates within the cytoplasm of epithelial cells. While the virulence factors essentially contributing to this step of the infection cycle are well chara...

    Authors: Kristina Schauer, Gernot Geginat, Chunguang Liang, Werner Goebel, Thomas Dandekar and Thilo M Fuchs
    Citation: BMC Genomics 2010 11:573
    Content type: Research article Published on:

  13. Genetic analysis of transcriptional profiles is a promising approach for identifying and dissecting the genetics of complex traits like meat performance. Accordingly, expression levels obtained by microarray a...

    Authors: Siriluck Ponsuksili, Eduard Murani, Manfred Schwerin, Karl Schellander and Klaus Wimmers
    Citation: BMC Genomics 2010 11:572
    Content type: Research article Published on:

  14. Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is...

    Authors: Sujai Kumar and Mark L Blaxter
    Citation: BMC Genomics 2010 11:571
    Content type: Research article Published on:

  15. Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea prov...

    Authors: Jérôme Durand, Catherine Bodénès, Emilie Chancerel, Jean-Marc Frigerio, Giovanni Vendramin, Federico Sebastiani, Anna Buonamici, Oliver Gailing, Hans-Peter Koelewijn, Fiorella Villani, Claudia Mattioni, Marcello Cherubini, Pablo G Goicoechea, Ana Herrán, Ziortza Ikaran, Cyril Cabané…
    Citation: BMC Genomics 2010 11:570
    Content type: Research article Published on:

  16. Cucumber, Cucumis sativus L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucum...

    Authors: Pablo F Cavagnaro, Douglas A Senalik, Luming Yang, Philipp W Simon, Timothy T Harkins, Chinnappa D Kodira, Sanwen Huang and Yiqun Weng
    Citation: BMC Genomics 2010 11:569
    Content type: Research article Published on:

  17. Flexible genomes facilitate bacterial evolution and are classically organized into polymorphic strain-specific segments called regions of genomic plasticity (RGPs). Using a new web tool, RGPFinder, we investigate...

    Authors: Jean-Claude Ogier, Alexandra Calteau, Steve Forst, Heidi Goodrich-Blair, David Roche, Zoé Rouy, Garret Suen, Robert Zumbihl, Alain Givaudan, Patrick Tailliez, Claudine Médigue and Sophie Gaudriault
    Citation: BMC Genomics 2010 11:568
    Content type: Research article Published on:

  19. The Anopheles gambiae salivary glands play a major role in malaria transmission and express a variety of bioactive components that facilitate blood-feeding by preventing platelet aggregation, blood clotting, vaso...

    Authors: Suchismita Das, Andrea Radtke, Young-Jun Choi, Antonio M Mendes, Jesus G Valenzuela and George Dimopoulos
    Citation: BMC Genomics 2010 11:566
    Content type: Research article Published on:

  20. In addition to acting as an RNA quality control pathway, nonsense-mediated mRNA decay (NMD) plays roles in regulating normal gene expression. In particular, the extent to which alternative splicing is coupled ...

    Authors: Nicholas J McGlincy, Lit-Yeen Tan, Nicodeme Paul, Mihaela Zavolan, Kathryn S Lilley and Christopher WJ Smith
    Citation: BMC Genomics 2010 11:565
    Content type: Research article Published on:

  21. Rainbow trout are important fish for aquaculture and recreational fisheries and serves as a model species for research investigations associated with carcinogenesis, comparative immunology, toxicology and evol...

    Authors: Mohamed Salem, Caird E Rexroad III, Jiannan Wang, Gary H Thorgaard and Jianbo Yao
    Citation: BMC Genomics 2010 11:564
    Content type: Research article Published on:

  23. Flavonoid 3',5'-hydroxylases (F3'5'Hs) and flavonoid 3'-hydroxylases (F3'Hs) competitively control the synthesis of delphinidin and cyanidin, the precursors of blue and red anthocyanins. In most plants, F3'5'H ge...

    Authors: Luigi Falginella, Simone D Castellarin, Raffaele Testolin, Gregory A Gambetta, Michele Morgante and Gabriele Di Gaspero
    Citation: BMC Genomics 2010 11:562
    Content type: Research article Published on:

  24. Mycobacterium avium subsp. paratuberculosis (MAP) persistently infects intestines and mesenteric lymph nodes leading to a prolonged subclinical disease. The MAP genome sequence was published in 2005, yet its tran...

    Authors: Harish K Janagama, Elise A Lamont, Sajan George, John P Bannantine, Wayne W Xu, Zheng J Tu, Scott J Wells, Jeremy Schefers and Srinand Sreevatsan
    Citation: BMC Genomics 2010 11:561
    Content type: Research article Published on:

  25. Microsatellites are markers of choice in population genetics and genomics, as they provide useful insight into patterns and processes as diverse as genome evolutionary dynamics and demographic processes. The a...

    Authors: Jean-Francois Martin, Nicolas Pech, Emese Meglécz, Stéphanie Ferreira, Caroline Costedoat, Vincent Dubut, Thibaut Malausa and André Gilles
    Citation: BMC Genomics 2010 11:560
    Content type: Research article Published on:

  26. Bathymodiolus azoricus is a deep-sea hydrothermal vent mussel found in association with large faunal communities living in chemosynthetic environments at the bottom of the sea floor near the Azores Islands. Inves...

    Authors: Raul Bettencourt, Miguel Pinheiro, Conceição Egas, Paula Gomes, Mafalda Afonso, Timothy Shank and Ricardo Serrão Santos
    Citation: BMC Genomics 2010 11:559
    Content type: Research article Published on:

  28. Physiological left ventricular hypertrophy (LVH) involves complex cardiac remodeling that occurs as an adaptive response to chronic exercise. A stark clinical contrast exists between physiological LVH and path...

    Authors: Ignat Drozdov, Sophia Tsoka, Christos A Ouzounis and Ajay M Shah
    Citation: BMC Genomics 2010 11:557
    Content type: Research article Published on:

  29. Streptococcus suis serotype 2 (SS2), a major swine pathogen and an emerging zoonotic agent, has greatly challenged global public health. Systematical information about host immune response to the infection is imp...

    Authors: Ran Li, Anding Zhang, Bo Chen, Liu Teng, Ya Wang, Huanchun Chen and Meilin Jin
    Citation: BMC Genomics 2010 11:556
    Content type: Research article Published on:

  30. Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded as a...

    Authors: Nuria Fonknechten, Sébastien Chaussonnerie, Sabine Tricot, Aurélie Lajus, Jan R Andreesen, Nadia Perchat, Eric Pelletier, Michel Gouyvenoux, Valérie Barbe, Marcel Salanoubat, Denis Le Paslier, Jean Weissenbach, Georges N Cohen and Annett Kreimeyer
    Citation: BMC Genomics 2010 11:555
    Content type: Research article Published on:

  31. Japanese flounder (Paralichthys olivaceus) is one of the most economically important marine species in Northeast Asia. Information on genetic markers associated with quantitative trait loci (QTL) can be used in b...

    Authors: Cecilia Castaño-Sánchez, Kanako Fuji, Akiyuki Ozaki, Osamu Hasegawa, Takashi Sakamoto, Kagayaki Morishima, Ichiro Nakayama, Atsushi Fujiwara, Tetsuji Masaoka, Hiroyuki Okamoto, Kengo Hayashida, Michihira Tagami, Jun Kawai, Yoshihide Hayashizaki and Nobuaki Okamoto
    Citation: BMC Genomics 2010 11:554
    Content type: Research article Published on:

  32. Dietary zinc supplementation may help to promote growth, boost the immune system, protect against diabetes, and aid recovery from diarrhoea. We exploited the zebrafish (Danio rerio) gill as a unique vertebrate io...

    Authors: Dongling Zheng, Peter Kille, Graham P Feeney, Phil Cunningham, Richard D Handy and Christer Hogstrand
    Citation: BMC Genomics 2010 11:553
    Content type: Research article Published on:

  33. Thoroughbred horses have been selected for traits contributing to speed and stamina for centuries. It is widely recognized that inherited variation in physical and physiological characteristics is responsible ...

    Authors: Emmeline W Hill, Beatrice A McGivney, Jingjing Gu, Ronan Whiston and David E MacHugh
    Citation: BMC Genomics 2010 11:552
    Content type: Research article Published on:

  34. Despite a high genetic similarity to peach, almonds (Prunus dulcis) have a fleshless fruit and edible kernel, produced as a crop for human consumption. While the release of peach genome v1.0 provides an excellent...

    Authors: Iraj Tavassolian, Gholmereza Rabiei, Davina Gregory, Mourad Mnejja, Michelle G Wirthensohn, Peter W Hunt, John P Gibson, Christopher M Ford, Margaret Sedgley and Shu-Biao Wu
    Citation: BMC Genomics 2010 11:551
    Content type: Research article Published on:

  35. Neighboring gene pairs in the genome of Saccharomyces cerevisiae have a tendency to be expressed at the same time. The distribution of histone modifications along chromatin fibers is suggested to be an important ...

    Authors: Yangyang Deng, Xianhua Dai, Qian Xiang, Zhiming Dai, Caisheng He, Jiang Wang and Jihua Feng
    Citation: BMC Genomics 2010 11:550
    Content type: Research article Published on:

  36. Insect innate immunity can be affected by juvenile hormone (JH) and 20-hydroxyecdysone (20E), but how innate immunity is developmentally regulated by these two hormones in insects has not yet been elucidated. ...

    Authors: Ling Tian, Enen Guo, Yupu Diao, Shun Zhou, Qin Peng, Yang Cao, Erjun Ling and Sheng Li
    Citation: BMC Genomics 2010 11:549
    Content type: Research article Published on:

  37. Zinc deficiency is detrimental to organisms, highlighting its role as an essential micronutrient contributing to numerous biological processes. To investigate the underlying molecular events invoked by zinc de...

    Authors: Dongling Zheng, Peter Kille, Graham P Feeney, Phil Cunningham, Richard D Handy and Christer Hogstrand
    Citation: BMC Genomics 2010 11:548
    Content type: Research article Published on:

  38. The genome of Paramecium tetraurelia, a unicellular model that belongs to the ciliate phylum, has been shaped by at least 3 successive whole genome duplications (WGD). These dramatic events, which have also been ...

    Authors: Olivier Arnaiz, Jean-François Goût, Mireille Bétermier, Khaled Bouhouche, Jean Cohen, Laurent Duret, Aurélie Kapusta, Eric Meyer and Linda Sperling
    Citation: BMC Genomics 2010 11:547
    Content type: Research article Published on:

  39. The pivotal role of stress in the precipitation of psychiatric diseases such as depression is generally accepted. This study aims at the identification of genes that are directly or indirectly responding to st...

    Authors: Amalia Tsolakidou, Ludwig Czibere, Benno Pütz, Dietrich Trümbach, Markus Panhuysen, Jan M Deussing, Wolfgang Wurst, Inge Sillaber, Rainer Landgraf, Florian Holsboer and Theo Rein
    Citation: BMC Genomics 2010 11:546
    Content type: Research article Published on:

  40. Macrophages play essential roles in both innate and adaptive immune responses. Bacteria require endotoxin, a complex lipopolysaccharide, for outer membrane permeability and the host interprets endotoxin as a s...

    Authors: Ceren Ciraci, Christopher K Tuggle, Michael J Wannemuehler, Dan Nettleton and Susan J Lamont
    Citation: BMC Genomics 2010 11:545
    Content type: Research article Published on:

  41. There was a large scale outbreak of the highly pathogenic porcine reproductive and respiratory syndrome (PRRS) in China and Vietnam during 2006 and 2007 that resulted in unusually high morbidity and mortality ...

    Authors: Shuqi Xiao, Delin Mo, Qiwei Wang, Jianyu Jia, Limei Qin, Xiangchun Yu, Yuna Niu, Xiao Zhao, Xiaohong Liu and Yaosheng Chen
    Citation: BMC Genomics 2010 11:544
    Content type: Research article Published on:

  42. Giardia intestinalis is a protozoan parasite that causes diarrhea in a wide range of mammalian species. To further understand the genetic diversity between the Giardia intestinalis species, we have performed geno...

    Authors: Jon Jerlström-Hultqvist, Oscar Franzén, Johan Ankarklev, Feifei Xu, Eva Nohýnková, Jan O Andersson, Staffan G Svärd and Björn Andersson
    Citation: BMC Genomics 2010 11:543
    Content type: Research article Published on:

  43. Validation of microarrays data by quantitative real-time PCR (qPCR) is often limited by the low amount of available RNA. This raised the possibility to perform validation experiments on the amplified amino all...

    Authors: Céline Jeanty, Dan Longrois, Paul-Michel Mertes, Daniel R Wagner and Yvan Devaux
    Citation: BMC Genomics 2010 11:542
    Content type: Methodology article Published on:

  44. Drosophila melanogaster females show changes in behavior and physiology after mating that are thought to maximize the number of progeny resulting from the most recent copulation. Sperm and seminal fluid proteins ...

    Authors: Justin E Dalton, Tanvi S Kacheria, Simon RV Knott, Matthew S Lebo, Allison Nishitani, Laura E Sanders, Emma J Stirling, Ari Winbush and Michelle N Arbeitman
    Citation: BMC Genomics 2010 11:541
    Content type: Research article Published on:

  45. The demands of microarray expression technologies for quantities of RNA place a limit on the questions they can address. As a consequence, the RNA requirements have reduced over time as technologies have impro...

    Authors: Andy G Lynch, James Hadfield, Mark J Dunning, Michelle Osborne, Natalie P Thorne and Simon Tavaré
    Citation: BMC Genomics 2010 11:540
    Content type: Research article Published on:

  46. The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent ...

    Authors: Nicole L Quinn, Keith A Boroevich, Krzysztof P Lubieniecki, William Chow, Evelyn A Davidson, Ruth B Phillips, Ben F Koop and William S Davidson
    Citation: BMC Genomics 2010 11:539
    Content type: Research article Published on:

  47. As genome sequences are determined for increasing numbers of model organisms, demand has grown for better tools to facilitate unified genome annotation efforts by communities of biologists. Typically this proc...

    Authors: Felix Kokocinski, Jennifer Harrow and Tim Hubbard
    Citation: BMC Genomics 2010 11:538
    Content type: Software Published on:

  48. In the past, molecular mechanisms that drive the initiation of an inflammatory response have been studied intensively. However, corresponding mechanisms that sustain the expression of inflammatory response gen...

    Authors: Astrid Riehl, Tobias Bauer, Benedikt Brors, Hauke Busch, Regina Mark, Julia Németh, Christoffer Gebhardt, Angelika Bierhaus, Peter Nawroth, Roland Eils, Rainer König, Peter Angel and Jochen Hess
    Citation: BMC Genomics 2010 11:537
    Content type: Research article Published on:

  49. Grosmannia clavigera is a bark beetle-vectored fungal pathogen of pines that causes wood discoloration and may kill trees by disrupting nutrient and water transport. Trees respond to attacks from beetles and asso...

    Authors: Uljana Hesse-Orce, Scott DiGuistini, Christopher I Keeling, Ye Wang, Maria Li, Hannah Henderson, T Roderick Docking, Nancy Y Liao, Gordon Robertson, Robert A Holt, Steven JM Jones, Jörg Bohlmann and Colette Breuil
    Citation: BMC Genomics 2010 11:536
    Content type: Research article Published on:

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BMC Genomics

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