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  1. Fish under intensive culture conditions are exposed to a variety of acute and chronic stressors, including high rearing densities, sub-optimal water quality, and severe thermal fluctuations. Such stressors are...

    Authors: Cecilia C Sánchez, Gregory M Weber, Guangtu Gao, Beth M Cleveland, Jianbo Yao and Caird E Rexroad III
    Citation: BMC Genomics 2011 12:626
    Content type: Research article Published on:

  2. Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) are related human tumor viruses that cause primary effusion lymphomas (PEL) and Burkitt's lymphomas (BL), respectively. Viral genes e...

    Authors: Lindsay R Dresang, Jeremy R Teuton, Huichen Feng, Jon M Jacobs, David G Camp II, Samuel O Purvine, Marina A Gritsenko, Zhihua Li, Richard D Smith, Bill Sugden, Patrick S Moore and Yuan Chang
    Citation: BMC Genomics 2011 12:625
    Content type: Research article Published on:

  3. Bioinformatic analyses of expression control sequences in promoters of co-expressed or functionally related genes enable the discovery of common regulatory sequence motifs that might be involved in co-ordinate...

    Authors: Stefan Roepcke, Silke Stahlberg, Holger Klein, Marcel H Schulz, Lars Theobald, Sabrina Gohlke, Martin Vingron and Diego J Walther
    Citation: BMC Genomics 2011 12:624
    Content type: Research article Published on:

  4. Understanding polyphenism, the ability of a single genome to express multiple morphologically and behaviourally distinct phenotypes, is an important goal for evolutionary and developmental biology. Polyphenism...

    Authors: Thomas J Colgan, James C Carolan, Stephen J Bridgett, Seirian Sumner, Mark L Blaxter and Mark JF Brown
    Citation: BMC Genomics 2011 12:623
    Content type: Research article Published on:

  5. Admixture mapping is a powerful gene mapping approach for an admixed population formed from ancestral populations with different allele frequencies. The power of this method relies on the ability of ancestry i...

    Authors: Lili Ding, Howard Wiener, Tilahun Abebe, Mekbib Altaye, Rodney CP Go, Carolyn Kercsmar, Greg Grabowski, Lisa J Martin, Gurjit K Khurana Hershey, Ranajit Chakorborty and Tesfaye M Baye
    Citation: BMC Genomics 2011 12:622
    Content type: Research article Published on:

  6. DIRS1-like elements compose one superfamily of tyrosine recombinase-encoding retrotransposons. They have been previously reported in only a few diverse eukaryote species, describing a patchy distribution, and ...

    Authors: Mathieu Piednoël, Isabelle R Gonçalves, Dominique Higuet and Eric Bonnivard
    Citation: BMC Genomics 2011 12:621
    Content type: Research article Published on:

  7. Quantitative transcriptome data for the malaria-transmitting mosquito Anopheles gambiae covers a broad range of biological and experimental conditions, including development, blood feeding and infection. Web-base...

    Authors: Robert M MacCallum, Seth N Redmond and George K Christophides
    Citation: BMC Genomics 2011 12:620
    Content type: Research article Published on:

  8. Many temperate insects survive the harsh conditions of winter by undergoing photoperiodic diapause, a pre-programmed developmental arrest initiated by short day lengths. Despite the well-established ecological...

    Authors: Monica F Poelchau, Julie A Reynolds, David L Denlinger, Christine G Elsik and Peter A Armbruster
    Citation: BMC Genomics 2011 12:619
    Content type: Research article Published on:

  9. Subtilisin/kexin-like proprotein convertase (PCSK) enzymes have important regulatory function in a wide variety of biological processes. PCSKs proteolytically process at a target sequence that contains basic a...

    Authors: Hannu Turpeinen, Sampo Kukkurainen, Kati Pulkkinen, Timo Kauppila, Kalle Ojala, Vesa P Hytönen and Marko Pesu
    Citation: BMC Genomics 2011 12:618
    Content type: Research article Published on:

  10. De novo retrotransposition of Alu elements has been recognized as a major driver for insertion polymorphisms in human populations. In this study, we exploited Alu-anchored bisulfite PCR libraries to identify evol...

    Authors: Alexandre de Andrade, Min Wang, Maria F Bonaldo, Hehuang Xie and Marcelo B Soares
    Citation: BMC Genomics 2011 12:617
    Content type: Research article Published on:

  11. Growth rate is a major determinant of intracellular function. However its effects can only be properly dissected with technically demanding chemostat cultivations in which it can be controlled. Recent work on Sac...

    Authors: Mikko Arvas, Tiina Pakula, Bart Smit, Jari Rautio, Heini Koivistoinen, Paula Jouhten, Erno Lindfors, Marilyn Wiebe, Merja Penttilä and Markku Saloheimo
    Citation: BMC Genomics 2011 12:616
    Content type: Research article Published on:

  12. The Atlantic salmon genome is in the process of returning to a diploid state after undergoing a whole genome duplication (WGD) event between 25 and100 million years ago. Existing data on the proportion of para...

    Authors: Sigbjørn Lien, Lars Gidskehaug, Thomas Moen, Ben J Hayes, Paul R Berg, William S Davidson, Stig W Omholt and Matthew P Kent
    Citation: BMC Genomics 2011 12:615
    Content type: Research article Published on:

  13. Protein phosphorylation modulates protein function in organisms at all levels of complexity. Parasites of the Leishmania genus undergo various developmental transitions in their life cycle triggered by changes in...

    Authors: Antonio Palmeri, Pier Federico Gherardini, Polina Tsigankov, Gabriele Ausiello, Gerald F Späth, Dan Zilberstein and Manuela Helmer-Citterich
    Citation: BMC Genomics 2011 12:614
    Content type: Research article Published on:

  14. In the biotechnological workhorse Trichoderma reesei (Hypocrea jecorina) transcription of cellulase genes as well as efficiency of the secreted cellulase mixture are modulated by light. Components of the heterotr...

    Authors: Doris Tisch, Christian P Kubicek and Monika Schmoll
    Citation: BMC Genomics 2011 12:613
    Content type: Research article Published on:

  15. Little is known about the composition and function of the saliva in black flies such as Simulium guianense, the main vector of river blindness disease in Brazil. The complex salivary potion of hematophagous arthr...

    Authors: Andrezza C Chagas, Eric Calvo, Paulo FP Pimenta and José MC Ribeiro
    Citation: BMC Genomics 2011 12:612
    Content type: Research article Published on:

  16. Mycobacterium bovis is the causative agent of bovine tuberculosis (BTB), a pathological infection with significant economic impact. Recent studies have highlighted the role of functional genomics to better unders...

    Authors: Kate E Killick, John A Browne, Stephen DE Park, David A Magee, Irene Martin, Kieran G Meade, Stephen V Gordon, Eamonn Gormley, Cliona O'Farrelly, Karsten Hokamp and David E MacHugh
    Citation: BMC Genomics 2011 12:611
    Content type: Research article Published on:

  17. Regulatory T cells (Tregs) play an essential role in the control of the immune response. Treg cells represent important targets for therapeutic interventions of the immune system. Therefore, it will be very im...

    Authors: Rudi Alberts, Hairong Chen, Claudia Pommerenke, August B Smit, Sabine Spijker, Robert W Williams, Robert Geffers, Dunja Bruder and Klaus Schughart
    Citation: BMC Genomics 2011 12:610
    Content type: Research article Published on:

  18. As a newly identified category of DNA transposon, helitrons have been found in a large number of eukaryotes genomes. Helitrons have contributed significantly to the intra-specific genome diversity in maize. Altho...

    Authors: Yongbin Dong, Xiaomin Lu, Weibin Song, Lei Shi, Mei Zhang, Hainan Zhao, Yinping Jiao and Jinsheng Lai
    Citation: BMC Genomics 2011 12:609
    Content type: Research article Published on:

  19. In trees, a substantial amount of carbon is directed towards production of phenolics for development and defense. This metabolic pathway is also a major factor in resistance to insect pathogens in spruce. In s...

    Authors: Ilga Porth, Björn Hamberger, Richard White and Kermit Ritland
    Citation: BMC Genomics 2011 12:608
    Content type: Research article Published on:

  20. In livestock populations the genetic contribution to muscling is intensively monitored in the progeny of industry sires and used as a tool in selective breeding programs. The genes and pathways conferring this...

    Authors: Lisette JA Kogelman, Keren Byrne, Tony Vuocolo, Nathan S Watson-Haigh, Haja N Kadarmideen, James W Kijas, Hutton V Oddy, Graham E Gardner, Cedric Gondro and Ross L Tellam
    Citation: BMC Genomics 2011 12:607
    Content type: Research article Published on:

  21. The piRNA pathway has been shown in model organisms to be involved in silencing of transposons thereby providing genome stability. In D. melanogaster the majority of piRNAs map to these sequences. The medically i...

    Authors: Peter Arensburger, Robert H Hice, Jennifer A Wright, Nancy L Craig and Peter W Atkinson
    Citation: BMC Genomics 2011 12:606
    Content type: Research article Published on:

  22. MicroRNAs (miRNAs) play important roles in regulating the expression of protein-coding genes by directing the degradation and/or repression of the translation of gene transcripts. Growing evidence shows that m...

    Authors: Ruolin Yang, Zhonghua Dai, Shue Chen and Liangbiao Chen
    Citation: BMC Genomics 2011 12:605
    Content type: Research article Published on:

  23. Driven essentially by random genetic drift, subfunctionalization has been identified as a possible non-adaptive mechanism for the retention of duplicate genes in small-population species, where widespread dele...

    Authors: Ariel Fernández, Yun-Huei Tzeng and Sze-Bi Hsu
    Citation: BMC Genomics 2011 12:604
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2013 14:260

  24. Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor. The Gene Wiki makes use of Wikiped...

    Authors: Benjamin M Good, Douglas G Howe, Simon M Lin, Warren A Kibbe and Andrew I Su
    Citation: BMC Genomics 2011 12:603
    Content type: Research article Published on:

  25. Acute quadriplegic myopathy (AQM) or critical illness myopathy (CIM) is frequently observed in intensive care unit (ICU) patients. To elucidate duration-dependent effects of the ICU intervention on molecular a...

    Authors: Monica Llano-Diez, Ann-Marie Gustafson, Carl Olsson, Hanna Goransson and Lars Larsson
    Citation: BMC Genomics 2011 12:602
    Content type: Research article Published on:

  26. Despite extensive efforts to discover transcription factors and their binding sites in the human malaria parasite Plasmodium falciparum, only a few transcription factor binding motifs have been experimentally val...

    Authors: Elena Y Harris, Nadia Ponts, Karine G Le Roch and Stefano Lonardi
    Citation: BMC Genomics 2011 12:601
    Content type: Methodology article Published on:

  27. Euphorbia fischeriana is an important medicinal plant found in Northeast China. The plant roots contain many medicinal compounds including 12-deoxyphorbol-13-acetate, commonly known as prostratin that is a phorbo...

    Authors: Roberto A Barrero, Brett Chapman, Yanfang Yang, Paula Moolhuijzen, Gabriel Keeble-Gagnère, Nan Zhang, Qi Tang, Matthew I Bellgard and Deyou Qiu
    Citation: BMC Genomics 2011 12:600
    Content type: Research article Published on:

  28. Gene duplication is an important biological phenomenon associated with genomic redundancy, degeneration, specialization, innovation, and speciation. After duplication, both copies continue functioning when nat...

    Authors: Frédéric JJ Chain, Jonathan Dushoff and Ben J Evans
    Citation: BMC Genomics 2011 12:599
    Content type: Research article Published on:

  29. Sequencing-by-ligation (SBL) is one of several next-generation sequencing methods that has been developed for massive sequencing of DNA immobilized on arrayed beads (or other clonal amplicons). SBL has the adv...

    Authors: Antoine Ho, Maurice Murphy, Susan Wilson, Susan R Atlas and Jeremy S Edwards
    Citation: BMC Genomics 2011 12:598
    Content type: Methodology article Published on:

  30. DNA methylation plays important roles in gene regulation during both normal developmental and disease states. In the past decade, a number of methods have been developed and applied to characterize the genome-...

    Authors: Junwen Wang, Hui Jiang, Guanyu Ji, Fei Gao, Mingzhi Wu, Jihua Sun, Huijuan Luo, Jinghua Wu, Renhua Wu and Xiuqing Zhang
    Citation: BMC Genomics 2011 12:597
    Content type: Methodology article Published on:

  31. G protein-coupled receptors (GPCRs) constitute one of the largest groupings of eukaryotic proteins, and represent a particularly lucrative set of pharmaceutical targets. They play an important role in eukaryot...

    Authors: Mostafa Zamanian, Michael J Kimber, Paul McVeigh, Steve A Carlson, Aaron G Maule and Tim A Day
    Citation: BMC Genomics 2011 12:596
    Content type: Research article Published on:

  32. Wolbachia are endosymbiotic bacteria that are frequently found in arthropods and nematodes. These maternally inherited bacteria manipulate host reproduction by several mechanisms including cytoplasmic incompatibi...

    Authors: Ya Zheng, Jia-Lin Wang, Chen Liu, Cui-Ping Wang, Thomas Walker and Yu-Feng Wang
    Citation: BMC Genomics 2011 12:595
    Content type: Research article Published on:

  33. Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development ...

    Authors: Jan M de Boer, Theo JA Borm, Taco Jesse, Bart Brugmans, Xiaomin Tang, Glenn J Bryan, Jaap Bakker, Herman J van Eck and Richard GF Visser
    Citation: BMC Genomics 2011 12:594
    Content type: Research article Published on:

  36. Male infertility is an increasing problem in all domestic species including man. Localization and identification of genes involved in defects causing male infertility provide valuable information of specific e...

    Authors: Anu Sironen, Pekka Uimari, Heli Venhoranta, Magnus Andersson and Johanna Vilkki
    Citation: BMC Genomics 2011 12:591
    Content type: Research article Published on:

  37. The complete and accurate human reference genome is important for functional genomics researches. Therefore, the incomplete reference genome and individual specific sequences have significant effects on variou...

    Authors: Geng Chen, Ruiyuan Li, Leming Shi, Junyi Qi, Pengzhan Hu, Jian Luo, Mingyao Liu and Tieliu Shi
    Citation: BMC Genomics 2011 12:590
    Content type: Research article Published on:

  38. Systematic processing noise, which includes batch effects, is very common in microarray experiments but is often ignored despite its potential to confound or compromise experimental results. Compromised result...

    Authors: Robert R Kitchen, Vicky S Sabine, Arthur A Simen, J Michael Dixon, John MS Bartlett and Andrew H Sims
    Citation: BMC Genomics 2011 12:589
    Content type: Research article Published on:

  39. The nonautonomous maize Ds transposons can only move in the presence of the autonomous element Ac. They comprise a heterogeneous group that share 11-bp terminal inverted repeats (TIRs) and some subterminal repeat...

    Authors: Chunguang Du, Andrew Hoffman, Limei He, Jason Caronna and Hugo K Dooner
    Citation: BMC Genomics 2011 12:588
    Content type: Research article Published on:

  40. Genome rearrangements are studied on the basis of genome-wide analysis of gene orders and important in the evolution of species. In the last two decades, a variety of rearrangement operations, such as reversal...

    Authors: Keng-Hsuan Huang, Kun-Tze Chen and Chin Lung Lu
    Citation: BMC Genomics 2011 12(Suppl 3):S26
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  41. Cardiovascular disease is the chief cause of death in Taiwan and many countries, of which myocardial infarction (MI) is the most serious condition. Hyperlipidemia appears to be a significant cause of myocardia...

    Authors: Wei-Chung Shia, Tien-Hsiung Ku, Yu-Ming Tsao, Chien-Hsun Hsia, Yung-Ming Chang, Ching-Hui Huang, Yeh-Ching Chung, Shih-Lan Hsu, Kae-Woei Liang and Fang-Rong Hsu
    Citation: BMC Genomics 2011 12(Suppl 3):S23
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  42. Many viruses contain genes that originate from their hosts. Some of these acquired genes give viruses the ability to interfere with host immune responses by various mechanisms. Genes of host origin that appear...

    Authors: Akira R Kinjo, Yutaro Kumagai, Huy Dinh, Osamu Takeuchi and Daron M Standley
    Citation: BMC Genomics 2011 12(Suppl 3):S21
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  43. Metagenomics is a rapidly growing field of research aimed at studying assemblages of uncultured organisms using various sequencing technologies, with the hope of understanding the true diversity of microbes, t...

    Authors: Suparna Mitra, Mario Stärk and Daniel H Huson
    Citation: BMC Genomics 2011 12(Suppl 3):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  44. Metagenomic studies, accelerated by the evolution of sequencing technologies and the rapid development of genomic analysis methods, can reveal genetic diversity and biodiversity in various samples including th...

    Authors: Atsushi Ogura, Mengjie Lin, Yuya Shigenobu, Atushi Fujiwara, Kazuho Ikeo and Satoshi Nagai
    Citation: BMC Genomics 2011 12(Suppl 3):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  45. Granzyme B is a serine protease which cleaves at unique tetrapeptide sequences. It is involved in several signaling cross-talks with caspases and functions as a pivotal mediator in a broad range of cellular pr...

    Authors: Lawrence JK Wee, Esmond PS Er, Lisa FP Ng and JC Tong
    Citation: BMC Genomics 2011 12(Suppl 3):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  46. The phylogenetic profile is widely used to characterize functional linkage and conservation between proteins without amino acid sequence similarity. To survey the conservative regulatory properties of rate-lim...

    Authors: Min Zhao and Hong Qu
    Citation: BMC Genomics 2011 12(Suppl 3):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  47. Over the recent years, a number of genomes have been successfully sequenced and this was followed by genome annotation projects to help understand the biological capabilities of newly sequenced genomes. To imp...

    Authors: Jamshaid Ali, Umadevi Paila and Akash Ranjan
    Citation: BMC Genomics 2011 12(Suppl 3):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  48. Taxonomic classification of metagenomic sequences is the first step in metagenomic analysis. Existing taxonomic classification approaches are of two types, similarity-based and composition-based. Similarity-ba...

    Authors: Monzoorul Haque Mohammed, Tarini Shankar Ghosh, Rachamalla Maheedhar Reddy, Chennareddy Venkata Siva Kumar Reddy, Nitin Kumar Singh and Sharmila S Mande
    Citation: BMC Genomics 2011 12(Suppl 3):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  49. Detoxification proteins are a class of proteins for degradation and/or elimination of endogenous and exogenous toxins or medicines, as well as reactive oxygen species (ROS) produced by these materials. Most of...

    Authors: Zhen Yang, Ying Yu, Lei Yao, Guangui Li, Lin Wang, Yiyao Hu, Haibin Wei, Li Wang, Riadh Hammami, Roxanne Razavi, Yang Zhong and Xufang Liang
    Citation: BMC Genomics 2011 12(Suppl 3):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  50. In 2009 the International Society for Computational Biology (ISCB) started to roll out regional bioinformatics conferences in Africa, Latin America and Asia. The open and competitive bid for the first meeting ...

    Authors: Christian Schönbach, Tin Wee Tan, Janet Kelso, Burkhard Rost, Sheila Nathan and Shoba Ranganathan
    Citation: BMC Genomics 2011 12(Suppl 3):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

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