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  1. The evolutionary diversification of gene families through gene creation (and loss) is a dynamic process believed to be critical to the evolution of functional novelty. Previous identification of a closely rela...

    Authors: Steve Dorus, Elaine C Wilkin and Timothy L Karr
    Citation: BMC Genomics 2011 12:177
    Content type: Research article Published on:

  2. MicroRNAs (miRNAs) are small non-coding RNAs that can exert multilevel inhibition/repression at a post-transcriptional or protein synthesis level during disease or development. Characterisation of miRNAs in ad...

    Authors: King-Hwa Ling, Peter J Brautigan, Christopher N Hahn, Tasman Daish, John R Rayner, Pike-See Cheah, Joy M Raison, Sandra Piltz, Jeffrey R Mann, Deidre M Mattiske, Paul Q Thomas, David L Adelson and Hamish S Scott
    Citation: BMC Genomics 2011 12:176
    Content type: Research article Published on:

  3. GlnR is an atypical response regulator found in actinomycetes that modulates the transcription of genes in response to changes in nitrogen availability. We applied a global in vivo approach to identify the GlnR r...

    Authors: Steven T Pullan, Govind Chandra, Mervyn J Bibb and Mike Merrick
    Citation: BMC Genomics 2011 12:175
    Content type: Research article Published on:

  4. High density linkage maps are essential for comparative analysis of synteny, fine mapping of quantitative trait loci (QTL), searching for candidate genes and facilitating genome sequence assembly. However, in ...

    Authors: Chun Ming Wang, Zhi Yi Bai, Xiao Ping He, Grace Lin, Jun Hong Xia, Fei Sun, Loong Chueng Lo, Felicia Feng, Ze Yuan Zhu and Gen Hua Yue
    Citation: BMC Genomics 2011 12:174
    Content type: Research article Published on:

  5. Exposure to the toxic metals arsenic and cadmium is associated with detrimental health effects including cancers of various organs. While arsenic and cadmium are well known to cause adverse health effects at h...

    Authors: Margaret Ann Benton, Julia E Rager, Lisa Smeester and Rebecca C Fry
    Citation: BMC Genomics 2011 12:173
    Content type: Research article Published on:

  7. Hibernation is an adaptive strategy to survive in highly seasonal or unpredictable environments. The molecular and genetic basis of hibernation physiology in mammals has only recently been studied using large ...

    Authors: Vadim B Fedorov, Anna V Goropashnaya, Øivind Tøien, Nathan C Stewart, Celia Chang, Haifang Wang, Jun Yan, Louise C Showe, Michael K Showe and Brian M Barnes
    Citation: BMC Genomics 2011 12:171
    Content type: Research article Published on:

  8. The Ahringer C. elegans RNAi feeding library prepared by cloning genomic DNA fragments has been widely used in genome-wide analysis of gene function. However, the library has not been thoroughly validated by dire...

    Authors: Wubin Qu, Changhong Ren, Yuan Li, Jinping Shi, Jiye Zhang, Xiaolei Wang, Xingyi Hang, Yiming Lu, Dongsheng Zhao and Chenggang Zhang
    Citation: BMC Genomics 2011 12:170
    Content type: Methodology article Published on:

  9. Foraminiferan protists, which are significant players in most marine ecosystems, are also genetic innovators, harboring unique modifications to proteins that make up the basic eukaryotic cell machinery. Despit...

    Authors: Andrea Habura, Yubo Hou, Andrew A Reilly and Samuel S Bowser
    Citation: BMC Genomics 2011 12:169
    Content type: Research article Published on:

  10. Yersinia enterocolitica strains responsible for mild gastroenteritis in humans are very diverse with respect to their metabolic and virulence properties. Strain W22703 (biotype 2, serotype O:9) was recently ident...

    Authors: Thilo M Fuchs, Katharina Brandt, Mandy Starke and Thomas Rattei
    Citation: BMC Genomics 2011 12:168
    Content type: Research article Published on:

  11. Transcripts can exhibit significant variation in tissue samples from inbred laboratory mice. We have designed and carried out a microarray experiment to examine transcript variation across samples from adipose...

    Authors: Peter T Vedell, Karen L Svenson and Gary A Churchill
    Citation: BMC Genomics 2011 12:167
    Content type: Research article Published on:

  12. The typical objective of Genome-wide association (GWA) studies is to identify single-nucleotide polymorphisms (SNPs) and corresponding genes with the strongest evidence of association (the 'most-significant SN...

    Authors: Annarita D'Addabbo, Orazio Palmieri, Anna Latiano, Vito Annese, Sayan Mukherjee and Nicola Ancona
    Citation: BMC Genomics 2011 12:166
    Content type: Software Published on:

  13. The concurrent release of rice genome sequences for two subspecies (Oryza sativa L. ssp. japonica and Oryza sativa L. ssp. indica) facilitates rice studies at the whole genome level. Since the advent of high-thro...

    Authors: Jun Wang, Lei Kong, Shuqi Zhao, He Zhang, Liang Tang, Zhe Li, Xiaocheng Gu, Jingchu Luo and Ge Gao
    Citation: BMC Genomics 2011 12:165
    Content type: Database Published on:

  15. Plant mitochondria, semiautonomous organelles that function as manufacturers of cellular ATP, have their own genome that has a slow rate of evolution and rapid rearrangement. Cytoplasmic male sterility (CMS), ...

    Authors: Huitao Liu, Peng Cui, Kehui Zhan, Qiang Lin, Guoyin Zhuo, Xiaoli Guo, Feng Ding, Wenlong Yang, Dongcheng Liu, Songnian Hu, Jun Yu and Aimin Zhang
    Citation: BMC Genomics 2011 12:163
    Content type: Research article Published on:

  16. High-throughput RNAi screening is widely applied in biological research, but remains expensive, infrastructure-intensive and conversion of many assays to HTS applications in microplate format is not feasible.

    Authors: Juha K Rantala, Rami Mäkelä, Anna-Riina Aaltola, Petra Laasola, John-Patrick Mpindi, Matthias Nees, Petri Saviranta and Olli Kallioniemi
    Citation: BMC Genomics 2011 12:162
    Content type: Methodology article Published on:

  17. Rust fungi are biotrophic basidiomycete plant pathogens that cause major diseases on plants and trees world-wide, affecting agriculture and forestry. Their biotrophic nature precludes many established molecula...

    Authors: Junhuan Xu, Rob Linning, John Fellers, Matthew Dickinson, Wenhan Zhu, Ivan Antonov, David L Joly, Michael E Donaldson, Tamar Eilam, Yehoshua Anikster, Travis Banks, Sarah Munro, Michael Mayo, Brian Wynhoven, Johar Ali, Richard Moore…
    Citation: BMC Genomics 2011 12:161
    Content type: Research article Published on:

  18. The β-amyloid precursor protein (APP) and the related β-amyloid precursor-like proteins (APLPs) undergo complex proteolytic processing giving rise to several fragments. Whereas it is well established that Aβ a...

    Authors: Dorothee Aydin, Mikhail A Filippov, Jakob-Andreas Tschäpe, Norbert Gretz, Marco Prinz, Roland Eils, Benedikt Brors and Ulrike C Müller
    Citation: BMC Genomics 2011 12:160
    Content type: Research article Published on:

  20. The sheep is an important model organism for many types of medically relevant research, but molecular genetic experiments in the sheep have been limited by the lack of knowledge about ovine gene sequences.

    Authors: Marten Jäger, Claus-Eric Ott, Johannes Grünhagen, Jochen Hecht, Hanna Schell, Stefan Mundlos, Georg N Duda, Peter N Robinson and Jasmin Lienau
    Citation: BMC Genomics 2011 12:158
    Content type: Research article Published on:

  21. Alu elements are the most abundant retrotransposable elements comprising ~11% of the human genome. Many studies have highlighted the role that Alu elements have in genetic instability and how their contribution t...

    Authors: Wensheng Zhang, Andrea Edwards, Wei Fan, Prescott Deininger and Kun Zhang
    Citation: BMC Genomics 2011 12:157
    Content type: Research article Published on:

  22. RT-qPCR is a sensitive and increasingly used method for gene expression quantification. To normalize RT-qPCR measurements between samples, most laboratories use endogenous reference genes as internal controls....

    Authors: Tomas Hruz, Markus Wyss, Mylene Docquier, Michael W Pfaffl, Sabine Masanetz, Lorenzo Borghi, Phebe Verbrugghe, Luba Kalaydjieva, Stefan Bleuler, Oliver Laule, Patrick Descombes, Wilhelm Gruissem and Philip Zimmermann
    Citation: BMC Genomics 2011 12:156
    Content type: Methodology article Published on:

  23. The genome of a number of species of malaria parasites (Plasmodium spp.) has been sequenced in the hope of identifying new drug and vaccine targets. However, almost one-half of predicted Plasmodium genes are anno...

    Authors: Jannik Fonager, Blandine MD Franke-Fayard, John H Adams, Jai Ramesar, Onny Klop, Shahid M Khan, Chris J Janse and Andrew P Waters
    Citation: BMC Genomics 2011 12:155
    Content type: Research article Published on:

  25. Aedes aegypti is arguably the most studied of all mosquito species in the laboratory and is the primary vector of both Dengue and Yellow Fever flaviviruses in the field. A large number of transcriptional studies ...

    Authors: Andrey A Ptitsyn, Guadalupe Reyes-Solis, Karla Saavedra-Rodriguez, Jonathan Betz, Erica L Suchman, Jonathan O Carlson and William C Black IV
    Citation: BMC Genomics 2011 12:153
    Content type: Research article Published on:

  26. The transcription factors peroxisome proliferator activated receptor γ (PPARγ) and CCAAT/enhancer binding protein α (C/EBPα) are key transcriptional regulators of adipocyte differentiation and function. We and...

    Authors: Søren F Schmidt, Mette Jørgensen, Yun Chen, Ronni Nielsen, Albin Sandelin and Susanne Mandrup
    Citation: BMC Genomics 2011 12:152
    Content type: Research article Published on:

  27. Without intensive selection, the majority of bovine oocytes submitted to in vitro embryo production (IVP) fail to develop to the blastocyst stage. This is attributed partly to their maturation status and competen...

    Authors: Solomon Mamo, Fiona Carter, Patrick Lonergan, Cláudia LV Leal, Abdullah Al Naib, Paul McGettigan, Jai P Mehta, Alexander CO Evans and Trudee Fair
    Citation: BMC Genomics 2011 12:151
    Content type: Research article Published on:

  28. Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomi...

    Authors: Robert HS Kraus, Hindrik HD Kerstens, Pim Van Hooft, Richard PMA Crooijmans, Jan J Van Der Poel, Johan Elmberg, Alain Vignal, Yinhua Huang, Ning Li, Herbert HT Prins and Martien AM Groenen
    Citation: BMC Genomics 2011 12:150
    Content type: Research article Published on:

  29. Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molec...

    Authors: Di Wang, Yajiao Pan, Xiuqin Zhao, Linghua Zhu, Binying Fu and Zhikang Li
    Citation: BMC Genomics 2011 12:149
    Content type: Research article Published on:

  30. Biodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofue...

    Authors: Hamid Rismani-Yazdi, Berat Z Haznedaroglu, Kyle Bibby and Jordan Peccia
    Citation: BMC Genomics 2011 12:148
    Content type: Research article Published on:

  32. Bacterial spot of tomato and pepper is caused by four Xanthomonas species and is a major plant disease in warm humid climates. The four species are distinct from each other based on physiological and molecular ch...

    Authors: Neha Potnis, Ksenia Krasileva, Virginia Chow, Nalvo F Almeida, Prabhu B Patil, Robert P Ryan, Molly Sharlach, Franklin Behlau, J Max Dow, MT Momol, Frank F White, James F Preston, Boris A Vinatzer, Ralf Koebnik, João C Setubal, David J Norman…
    Citation: BMC Genomics 2011 12:146
    Content type: Research article Published on:

  33. The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be ...

    Authors: Betty Pelgas, Jean Bousquet, Patrick G Meirmans, Kermit Ritland and Nathalie Isabel
    Citation: BMC Genomics 2011 12:145
    Content type: Research article Published on:

  34. MicroRNAs (miRNAs) represent a growing class of small non-coding RNAs that are important regulators of gene expression in both plants and animals. Studies have shown that miRNAs play a critical role in human c...

    Authors: Jin Sung Jang, Vernadette A Simon, Rod M Feddersen, Fariborz Rakhshan, Debra A Schultz, Michael A Zschunke, Wilma L Lingle, Christopher P Kolbert and Jin Jen
    Citation: BMC Genomics 2011 12:144
    Content type: Methodology article Published on:

  35. Skeletal muscle growth and development from embryo to adult consists of a series of carefully regulated changes in gene expression. Understanding these developmental changes in agriculturally important species...

    Authors: Kelly RB Sporer, Robert J Tempelman, Catherine W Ernst, Kent M Reed, Sandra G Velleman and Gale M Strasburg
    Citation: BMC Genomics 2011 12:143
    Content type: Research article Published on:

  36. Extensive DNA rearrangement of genic colinearity, as revealed by comparison of orthologous genomic regions, has been shown to be a general concept describing evolutionary dynamics of plant genomes. However, th...

    Authors: Zhixi Tian, Yanjun Yu, Feng Lin, Yeisoo Yu, Phillip J SanMiguel, Rod A Wing, Susan R McCouch, Jianxin Ma and Scott A Jackson
    Citation: BMC Genomics 2011 12:142
    Content type: Research article Published on:

  37. The salmon louse (Lepeophtheirus salmonis Krøyer), an ectoparasitic copepod with a complex life cycle causes significant losses in salmon aquaculture. Pesticide treatments against the parasite raise environmental...

    Authors: Tariku Markos Tadiso, Aleksei Krasnov, Stanko Skugor, Sergey Afanasyev, Ivar Hordvik and Frank Nilsen
    Citation: BMC Genomics 2011 12:141
    Content type: Research article Published on:

  38. Mucins are large glycoproteins implicated in protection of all mucosal surfaces. In humans and rodents, the mucin gene family has been well described and previous studies have investigated the distribution and...

    Authors: Prisca R Hoorens, Manuela Rinaldi, Robert W Li, Bruno Goddeeris, Edwin Claerebout, Jozef Vercruysse and Peter Geldhof
    Citation: BMC Genomics 2011 12:140
    Content type: Research article Published on:

  39. Trypanosoma cruzi is a protozoan parasite and the etiologic agent of Chagas disease, an important public health problem in Latin America. T. cruzi is diploid, almost exclusively asexual, and displays an extraordi...

    Authors: Todd A Minning, D Brent Weatherly, Stephane Flibotte and Rick L Tarleton
    Citation: BMC Genomics 2011 12:139
    Content type: Research article Published on:

  40. MicroRNAs (miRNAs) are post-transcriptional regulators of mRNA expression and are involved in numerous cellular processes. Consequently, miRNAs are an important component of gene regulatory networks and an imp...

    Authors: Vivek Jayaswal, Mark Lutherborrow, David DF Ma and Yee H Yang
    Citation: BMC Genomics 2011 12:138
    Content type: Methodology article Published on:

  41. Eucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding pr...

    Authors: Jorge AP Paiva, Elisa Prat, Sonia Vautrin, Mauro D Santos, Hélène San-Clemente, Sérgio Brommonschenkel, Paulo GS Fonseca, Dario Grattapaglia, Xiang Song, Jetty SS Ammiraju, David Kudrna, Rod A Wing, Ana T Freitas, Hélène Bergès and Jacqueline Grima-Pettenati
    Citation: BMC Genomics 2011 12:137
    Content type: Research article Published on:

  42. Ticks--vectors of medical and veterinary importance--are themselves also significant pests. Tick salivary proteins are the result of adaptation to blood feeding and contain inhibitors of blood clotting, platel...

    Authors: José MC Ribeiro, Jennifer M Anderson, Nicholas C Manoukis, Zhaojing Meng and Ivo MB Francischetti
    Citation: BMC Genomics 2011 12:136
    Content type: Research article Published on:

  43. Surface proteins are a key to a deeper understanding of the behaviour of Gram-positive bacteria interacting with the human gastro-intestinal tract. Such proteins contribute to cell wall synthesis and maintenan...

    Authors: Liv Anette Bøhle, Tahira Riaz, Wolfgang Egge-Jacobsen, Morten Skaugen, Øyvind L Busk, Vincent GH Eijsink and Geir Mathiesen
    Citation: BMC Genomics 2011 12:135
    Content type: Research article Published on:

  44. Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription fac...

    Authors: Joshua WK Ho, Eric Bishop, Peter V Karchenko, Nicolas Nègre, Kevin P White and Peter J Park
    Citation: BMC Genomics 2011 12:134
    Content type: Research article Published on:

  45. In recent years, planaria have emerged as an important model system for research into stem cells and regeneration. Attention is focused on their unique stem cells, the neoblasts, which can differentiate into a...

    Authors: Enrique Fernández-Taboada, Gustavo Rodríguez-Esteban, Emili Saló and Josep F Abril
    Citation: BMC Genomics 2011 12:133
    Content type: Research article Published on:

  46. Describing the patterns of gene expression during embryonic development has broadened our understanding of the processes and patterns that define morphogenesis. Yet gene expression patterns have not been descr...

    Authors: Goran Bozinovic, Tim L Sit, David E Hinton and Marjorie F Oleksiak
    Citation: BMC Genomics 2011 12:132
    Content type: Research article Published on:

  47. Tea is one of the most popular non-alcoholic beverages worldwide. However, the tea plant, Camellia sinensis, is difficult to culture in vitro, to transform, and has a large genome, rendering little genomic inform...

    Authors: Cheng-Ying Shi, Hua Yang, Chao-Ling Wei, Oliver Yu, Zheng-Zhu Zhang, Chang-Jun Jiang, Jun Sun, Ye-Yun Li, Qi Chen, Tao Xia and Xiao-Chun Wan
    Citation: BMC Genomics 2011 12:131
    Content type: Research article Published on:

  48. Bovine mastitis is one of the most costly and prevalent diseases affecting dairy cows worldwide. In order to develop new strategies to prevent Escherichia coli-induced mastitis, a detailed understanding of the mo...

    Authors: Bart Buitenhuis, Christine M Røntved, Stefan M Edwards, Klaus L Ingvartsen and Peter Sørensen
    Citation: BMC Genomics 2011 12:130
    Content type: Research article Published on:

  49. MicroRNAs are important components of the regulatory network of biological systems and thousands have been discovered in both animals and plants. Systematic investigations performed in species with sequenced g...

    Authors: Andreas W Schreiber, Bu-Jun Shi, Chun-Yuan Huang, Peter Langridge and Ute Baumann
    Citation: BMC Genomics 2011 12:129
    Content type: Research article Published on:

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