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  1. A complex network of signaling pathways and transcription factors regulates vertebrate mesoderm development. Zebrafish mutants provide a powerful tool for examining the roles of individual genes in such a netw...

    Authors: Rachel Lockridge Mueller, Cheng Huang and Robert K Ho
    Citation: BMC Genomics 2010 11:492
  2. Out-of-frame stop codons (OSCs) occur naturally in coding sequences of all organisms, providing a mechanism of early termination of translation in incorrect reading frame so that the metabolic cost associated ...

    Authors: Herman Tse, James J Cai, Hoi-Wah Tsoi, Esther PT Lam and Kwok-Yung Yuen
    Citation: BMC Genomics 2010 11:491
  3. Bacterial phenotype may be profoundly affected by the physical arrangement of their genes in the genome. The Gram-negative species Aggregatibacter actinomycetemcomitans is a major etiologic agent of human periodo...

    Authors: Weerayuth Kittichotirat, Roger Bumgarner and Casey Chen
    Citation: BMC Genomics 2010 11:489
  4. Bacterial vaginosis (BV) is an ecological disorder of the vaginal microbiota that affects millions of women annually, and is associated with numerous adverse health outcomes including pre-term birth and the ac...

    Authors: Zongxin Ling, Jianming Kong, Fang Liu, Haibin Zhu, Xiaoyi Chen, Yuezhu Wang, Lanjuan Li, Karen E Nelson, Yaxian Xia and Charlie Xiang
    Citation: BMC Genomics 2010 11:488
  5. Multifactorial diseases such as cancer and cardiovascular diseases are caused by the complex interplay between genes and environment. The detection of these interactions remains challenging due to computationa...

    Authors: Lara Sucheston, Pritam Chanda, Aidong Zhang, David Tritchler and Murali Ramanathan
    Citation: BMC Genomics 2010 11:487
  6. The Atlantic salmon (Salmo salar) immunoglobulin heavy chain (IgH) locus possesses two parallel IgH isoloci (IGH-A and IGH-B), that are related to the genomic duplication event in the family Salmonidae. These dup...

    Authors: Motoshige Yasuike, Johan de Boer, Kristian R von Schalburg, Glenn A Cooper, Linda McKinnel, Amber Messmer, Stacy So, William S Davidson and Ben F Koop
    Citation: BMC Genomics 2010 11:486
  7. Discontinuous genes have been observed in bacteria, archaea, and eukaryotic nuclei, mitochondria and chloroplasts. Gene discontinuity occurs in multiple forms: the two most frequent forms result from introns t...

    Authors: Coren A Milbury, Jung C Lee, Jamie J Cannone, Patrick M Gaffney and Robin R Gutell
    Citation: BMC Genomics 2010 11:485
  8. The relationships between parasitoids and their insect hosts have attracted attention at two levels. First, the basic biology of host-parasitoid interactions is of fundamental interest. Second, parasitoids are...

    Authors: Qi Fang, Lei Wang, Jiaying Zhu, Yanmin Li, Qisheng Song, David W Stanley, Zunnu-raen Akhtar and Gongyin Ye
    Citation: BMC Genomics 2010 11:484
  9. Mitochondria are semi-autonomous, semi-self-replicating organelles harboring their own DNA (mitochondrial DNA, mtDNA), and their dysregulation is involved in the development of various diseases. While mtDNA do...

    Authors: Masaki Takasugi, Shintaro Yagi, Keiji Hirabayashi and Kunio Shiota
    Citation: BMC Genomics 2010 11:481
  10. The locus Rk confers resistance against several species of root-knot nematodes (Meloidogyne spp., RKN) in cowpea (Vigna unguiculata). Based on histological and reactive oxygen species (ROS) profiles, Rk confers a...

    Authors: Sayan Das, Jeffrey D Ehlers, Timothy J Close and Philip A Roberts
    Citation: BMC Genomics 2010 11:480
  11. Mitochondrial (mt) gene arrangement has been highly conserved among vertebrates from jawless fishes to mammals for more than 500 million years. It remains unclear, however, whether such long-term persistence i...

    Authors: Takashi P Satoh, Yukuto Sato, Naoharu Masuyama, Masaki Miya and Mutsumi Nishida
    Citation: BMC Genomics 2010 11:479
  12. Regulation of meiosis and sporulation in Saccharomyces cerevisiae is a model for a highly regulated developmental process. Meiosis middle phase transcriptional regulation is governed by two transcription factors:...

    Authors: Michael Klutstein, Zahava Siegfried, Ariel Gispan, Shlomit Farkash-Amar, Guy Zinman, Ziv Bar-Joseph, Giora Simchen and Itamar Simon
    Citation: BMC Genomics 2010 11:478
  13. Complementary approaches to assaying global gene expression are needed to assess gene expression in regions that are poorly assayed by current methodologies. A key component of nearly all gene expression assay...

    Authors: Aleksandra B Adomas, Francesc Lopez-Giraldez, Travis A Clark, Zheng Wang and Jeffrey P Townsend
    Citation: BMC Genomics 2010 11:477
  14. Calcium ion is tightly regulated in body fluids and for euryhaline fish, which are exposed to rapid changes in environmental [Ca2+], homeostasis is especially challenging. The gill is the main organ of active cal...

    Authors: Patrícia IS Pinto, Hideo Matsumura, Michael AS Thorne, Deborah M Power, Ryohei Terauchi, Richard Reinhardt and Adelino VM Canário
    Citation: BMC Genomics 2010 11:476
  15. Next generation sequencing has significantly increased the speed at which single nucleotide polymorphisms (SNPs) can be discovered and subsequently used as molecular markers for research. Unfortunately, for sp...

    Authors: David L Hyten, Qijian Song, Edward W Fickus, Charles V Quigley, Jong-Sung Lim, Ik-Young Choi, Eun-Young Hwang, Marcial Pastor-Corrales and Perry B Cregan
    Citation: BMC Genomics 2010 11:475
  16. A large proportion of pregnancy losses occur during the pre-implantation period, when the developing embryo is elongating rapidly and signalling its presence to the maternal system. The molecular mechanisms th...

    Authors: Caroline G Walker, Susanne Meier, Mathew D Littlejohn, Klaus Lehnert, John R Roche and Murray D Mitchell
    Citation: BMC Genomics 2010 11:474
  17. Identifying associations between genotypes and gene expression levels using microarrays has enabled systematic interrogation of regulatory variation underlying complex phenotypes. This approach has vast potent...

    Authors: Tomas Babak, Philip Garrett-Engele, Christopher D Armour, Christopher K Raymond, Mark P Keller, Ronghua Chen, Carol A Rohl, Jason M Johnson, Alan D Attie, Hunter B Fraser and Eric E Schadt
    Citation: BMC Genomics 2010 11:473
  18. Systematic research on fish immunogenetics is indispensable in understanding the origin and evolution of immune systems. This has long been a challenging task because of the limited number of deep sequencing t...

    Authors: Li-xin Xiang, Ding He, Wei-ren Dong, Yi-wen Zhang and Jian-zhong Shao
    Citation: BMC Genomics 2010 11:472
  19. When compared to skin, oral mucosal wounds heal rapidly and with reduced scar formation. Recent studies suggest that intrinsic differences in inflammation, growth factor production, levels of stem cells, and c...

    Authors: Lin Chen, Zarema H Arbieva, Shujuan Guo, Phillip T Marucha, Thomas A Mustoe and Luisa A DiPietro
    Citation: BMC Genomics 2010 11:471
  20. Systems biology and functional genomics require genome-wide datasets and resources. Complete sets of cloned open reading frames (ORFs) have been made for about a dozen bacterial species and allow researchers t...

    Authors: Seesandra V Rajagopala, Natsuko Yamamoto, Adrienne E Zweifel, Tomoko Nakamichi, Hsi-Kuang Huang, Jorge David Mendez-Rios, Jonathan Franca-Koh, Meher Preethi Boorgula, Kazutoshi Fujita, Ken-ichirou Suzuki, James C Hu, Barry L Wanner, Hirotada Mori and Peter Uetz
    Citation: BMC Genomics 2010 11:470
  21. With the advance of new massively parallel genotyping technologies, quantitative trait loci (QTL) fine mapping and map-based cloning become more achievable in identifying genes for important and complex traits...

    Authors: Xiaolei Wu, Chengwei Ren, Trupti Joshi, Tri Vuong, Dong Xu and Henry T Nguyen
    Citation: BMC Genomics 2010 11:469
  22. Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs ...

    Authors: Chrystel Deulvot, Hélène Charrel, Amandine Marty, Françoise Jacquin, Cécile Donnadieu, Isabelle Lejeune-Hénaut, Judith Burstin and Grégoire Aubert
    Citation: BMC Genomics 2010 11:468
  23. In the recent years, there has been a rise in gene expression profiling reports. Unfortunately, it has not been possible to make maximum use of available gene expression data. Many databases and programs can b...

    Authors: Kshitish K Acharya, Darshan S Chandrashekar, Neelima Chitturi, Hardik Shah, Varun Malhotra, Sreelakshmi KS, Deepti H, Akhilesh Bajpai, Sravanthi Davuluri, Pranami Bora and Leena Rao
    Citation: BMC Genomics 2010 11:467
  24. The ovine Major Histocompatibility Complex (MHC) harbors clusters of genes involved in overall resistance/susceptibility of an animal to infectious pathogens. However, only a limited number of ovine MHC genes ...

    Authors: Jianfeng Gao, Ka Liu, Haibo Liu, Hugh T Blair, Gang Li, Chuangfu Chen, Pingping Tan and Runlin Z Ma
    Citation: BMC Genomics 2010 11:466
  25. Tissue differentiation is accompanied by genome-wide changes in the underlying chromatin structure and dynamics, or epigenome. By controlling when, where, and what regulatory factors have access to the underly...

    Authors: Ky Sha, Sam G Gu, Luiz C Pantalena-Filho, Amy Goh, Jamie Fleenor, Daniel Blanchard, Chaya Krishna and Andrew Fire
    Citation: BMC Genomics 2010 11:465
  26. Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, ...

    Authors: Jon Bohlin, Lars Snipen, Simon P Hardy, Anja B Kristoffersen, Karin Lagesen, Torunn Dønsvik, Eystein Skjerve and David W Ussery
    Citation: BMC Genomics 2010 11:464
  27. Termites (Isoptera) are eusocial insects whose colonies consist of morphologically and behaviorally specialized castes of sterile workers and soldiers, and reproductive alates. Previous studies on eusocial ins...

    Authors: Matthew M Steller, Srinivas Kambhampati and Doina Caragea
    Citation: BMC Genomics 2010 11:463
  28. To date, oil-rich plants are the main source of biodiesel products. Because concerns have been voiced about the impact of oil-crop cultivation on the price of food commodities, the interest in oil plants not u...

    Authors: Gustavo GL Costa, Kiara C Cardoso, Luiz EV Del Bem, Aline C Lima, Muciana AS Cunha, Luciana de Campos-Leite, Renato Vicentini, Fábio Papes, Raquel C Moreira, José A Yunes, Francisco AP Campos and Márcio J Da Silva
    Citation: BMC Genomics 2010 11:462
  29. Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pr...

    Authors: Manuel Stark, Simon A Berger, Alexandros Stamatakis and Christian von Mering
    Citation: BMC Genomics 2010 11:461
  30. Modern biomedical research depends on a complete and accurate proteome. With the widespread adoption of new sequencing technologies, genome sequences are generated at a near exponential rate, diminishing the t...

    Authors: Samuel H Payne, Shih-Ting Huang and Rembert Pieper
    Citation: BMC Genomics 2010 11:460
  31. Heterochromatin plays an important role in chromosome function and gene regulation. Despite the availability of polytene chromosomes and genome sequence, the heterochromatin of the major malaria vector Anopheles ...

    Authors: Maria V Sharakhova, Phillip George, Irina V Brusentsova, Scotland C Leman, Jeffrey A Bailey, Christopher D Smith and Igor V Sharakhov
    Citation: BMC Genomics 2010 11:459
  32. The advent of cheap high through-put sequencing methods has facilitated low coverage skims of a large number of organisms. To maximise the utility of the sequences, assembly into contigs and then ordering of t...

    Authors: Abhirami Ratnakumar, Sean McWilliam, Wesley Barris and Brian P Dalrymple
    Citation: BMC Genomics 2010 11:458
  33. Phosphoinositide metabolism is essential to membrane dynamics and impinges on many cellular processes, including phagocytosis. Modulation of phosphoinositide metabolism is important for pathogenicity and virul...

    Authors: Nicola J Beresford, Charis Saville, Hayley J Bennett, Ian S Roberts and Lydia Tabernero
    Citation: BMC Genomics 2010 11:457
  34. Human leukocyte antigen (HLA)-B27 is strongly associated with the development of reactive arthritis (ReA) in humans after salmonellosis. Human monocytic U937 cells transfected with HLA-B27 are less able to eli...

    Authors: Shichao Ge, Vittoria Danino, Qiushui He, Jay CD Hinton and Kaisa Granfors
    Citation: BMC Genomics 2010 11:456
  35. Haemophilus parasuis is the causative agent of Glässer's disease in pigs. Currently, little is known about the molecular mechanisms that contribute to disease susceptibility. This study used a porcine oligonucleo...

    Authors: Jamie M Wilkinson, Carole A Sargent, Lucina Galina-Pantoja and Alexander W Tucker
    Citation: BMC Genomics 2010 11:455
  36. Alu repeats in the human transcriptome undergo massive adenosine to inosine RNA editing. This process is selective, as editing efficiency varies greatly among different adenosines. Several studies have identif...

    Authors: Yoav Kleinberger and Eli Eisenberg
    Citation: BMC Genomics 2010 11:453
  37. Lychas mucronatus is one scorpion species widely distributed in Southeast Asia and southern China. Anything is hardly known about its venom components, despite the fact that it can often cause human accidents. In...

    Authors: Zhao Ruiming, Ma Yibao, He Yawen, Di Zhiyong, Wu Yingliang, Cao Zhijian and Li Wenxin
    Citation: BMC Genomics 2010 11:452
  38. Pulmonary surfactant is required for lung function at birth and throughout life. Lung lipid and surfactant homeostasis requires regulation among multi-tiered processes, coordinating the synthesis of surfactant...

    Authors: Yan Xu, Minlu Zhang, Yanhua Wang, Pooja Kadambi, Vrushank Dave, Long J Lu and Jeffrey A Whitsett
    Citation: BMC Genomics 2010 11:451
  39. Rhipicephalus sanguineus, known as the brown dog tick, is a common ectoparasite of domestic dogs and can be found worldwide. R. sanguineus is recognized as the primary vector of the etiological agent of canine mo...

    Authors: Elen Anatriello, José MC Ribeiro, Isabel KF de Miranda-Santos, Lucinda G Brandão, Jennifer M Anderson, Jesus G Valenzuela, Sandra R Maruyama, João S Silva and Beatriz R Ferreira
    Citation: BMC Genomics 2010 11:450
  40. Genome reduction is a common evolutionary process in symbiotic and pathogenic bacteria. This process has been extensively characterized in bacterial endosymbionts of insects, where primary mutualistic bacteria...

    Authors: Eugeni Belda, Andrés Moya, Stephen Bentley and Francisco J Silva
    Citation: BMC Genomics 2010 11:449
  41. The physiological function of the prion protein remains largely elusive while its key role in prion infection has been expansively documented. To potentially assess this conundrum, we performed a comparative t...

    Authors: Sead Chadi, Rachel Young, Sandrine Le Guillou, Gaëlle Tilly, Frédérique Bitton, Marie-Laure Martin-Magniette, Ludivine Soubigou-Taconnat, Sandrine Balzergue, Marthe Vilotte, Coralie Peyre, Bruno Passet, Vincent Béringue, Jean-Pierre Renou, Fabienne Le Provost, Hubert Laude and Jean-Luc Vilotte
    Citation: BMC Genomics 2010 11:448
  42. Mitochondrial genomes provide a rich source of molecular variation of proven and widespread utility in molecular ecology, population genetics and evolutionary biology. The tapeworm genus Taenia includes a diversi...

    Authors: Wan-Zhong Jia, Hong-Bin Yan, Ai-Jiang Guo, Xing-Quan Zhu, Yu-Chao Wang, Wan-Gui Shi, Hao-Tai Chen, Fang Zhan, Shao-Hua Zhang, Bao-Quan Fu, D Timothy J Littlewood and Xue-Peng Cai
    Citation: BMC Genomics 2010 11:447
  43. Brown and white adipose tissues (BAT and WAT) play critical roles in controlling energy homeostasis and in the development of obesity and diabetes. The mouse Fat-Specific protein 27 (FSP27), a member of the ce...

    Authors: De Li, Yinxin Zhang, Li Xu, Linkang Zhou, Yue Wang, Bofu Xue, Zilong Wen, Peng Li and Jianli Sang
    Citation: BMC Genomics 2010 11:446
  44. Infection by infectious laryngotracheitis virus (ILTV; gallid herpesvirus 1) causes acute respiratory diseases in chickens often with high mortality. To better understand host-ILTV interactions at the host transc...

    Authors: Jeong Yoon Lee, Joon Jin Song, Ann Wooming, Xianyao Li, Huaijun Zhou, Walter G Bottje and Byung-Whi Kong
    Citation: BMC Genomics 2010 11:445
  45. The rate of emergence of human pathogens is steadily increasing; most of these novel agents originate in wildlife. Bats, remarkably, are the natural reservoirs of many of the most pathogenic viruses in humans....

    Authors: Thomas B Kepler, Christopher Sample, Kathryn Hudak, Jeffrey Roach, Albert Haines, Allyson Walsh and Elizabeth A Ramsburg
    Citation: BMC Genomics 2010 11:444
  46. The DNA repair and recombination (DRR) proteins protect organisms against genetic damage, caused by environmental agents and other genotoxic agents, by removal of DNA lesions or helping to abide them.

    Authors: Sanjay K Singh, Sujit Roy, Swarup Roy Choudhury and Dibyendu N Sengupta
    Citation: BMC Genomics 2010 11:443
  47. Chlamydia pneumoniae is a widespread pathogen causing upper and lower respiratory tract infections in addition to a range of other diseases in humans and animals. Previous whole genome analyses have focused on fo...

    Authors: Candice M Mitchell, Kelley M Hovis, Patrik M Bavoil, Garry SA Myers, Jose A Carrasco and Peter Timms
    Citation: BMC Genomics 2010 11:442

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