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  1. 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:

  2. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  35. Copy number variation (CNV) represents another important source of genetic variation complementary to single nucleotide polymorphism (SNP). High-density SNP array data have been routinely used to detect human ...

    Authors: Yali Hou, George E Liu, Derek M Bickhart, Maria Francesca Cardone, Kai Wang, Eui-soo Kim, Lakshmi K Matukumalli, Mario Ventura, Jiuzhou Song, Paul M VanRaden, Tad S Sonstegard and Curt P Van Tassell
    Citation: BMC Genomics 2011 12:127
    Content type: Research article Published on:

  36. Iron acquisition systems are important virulence factors in pathogenic bacteria. To identify these systems in Acinetobacter baumannii, the transcriptomic response of the completely sequenced strain ATCC 17978 und...

    Authors: Bart A Eijkelkamp, Karl A Hassan, Ian T Paulsen and Melissa H Brown
    Citation: BMC Genomics 2011 12:126
    Content type: Research article Published on:

  37. Evolutionary divergence in the position of the translational start site among orthologous genes can have significant functional impacts. Divergence can alter the translation rate, degradation rate, subcellular...

    Authors: John Dunbar, Judith D Cohn and Michael E Wall
    Citation: BMC Genomics 2011 12:125
    Content type: Research article Published on:

  38. We have previously demonstrated that alcohol exposure at early neurulation induces growth retardation, neural tube abnormalities, and alteration of DNA methylation. To explore the global gene expression change...

    Authors: Feng C Zhou, Qianqian Zhao, Yunlong Liu, Charles R Goodlett, Tiebing Liang, Jeanette N McClintick, Howard J Edenberg and Lang Li
    Citation: BMC Genomics 2011 12:124
    Content type: Research article Published on:

  39. Mucosal infections elicit inflammatory responses via regulated signaling pathways. Infection outcome depends strongly on early events occurring immediately when bacteria start interacting with cells in the muc...

    Authors: Jorrit Boekel, Örjan Källskog, Monica Rydén-Aulin, Mikael Rhen and Agneta Richter-Dahlfors
    Citation: BMC Genomics 2011 12:123
    Content type: Research article Published on:

  40. Fusarium oxysporum f. sp. melonis Snyd. & Hans. (FOM) causes Fusarium wilt, the most important infectious disease of melon (Cucumis melo L.). The four known races of this pathogen can be distinguished only by inf...

    Authors: Sara Sestili, Annalisa Polverari, Laura Luongo, Alberto Ferrarini, Michele Scotton, Jamshaid Hussain, Massimo Delledonne, Nadia Ficcadenti and Alessandra Belisario
    Citation: BMC Genomics 2011 12:122
    Content type: Research article Published on:

  41. Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene ...

    Authors: Luca Lenzi, Federica Facchin, Francesco Piva, Matteo Giulietti, Maria Chiara Pelleri, Flavia Frabetti, Lorenza Vitale, Raffaella Casadei, Silvia Canaider, Stefania Bortoluzzi, Alessandro Coppe, Gian Antonio Danieli, Giovanni Principato, Sergio Ferrari and Pierluigi Strippoli
    Citation: BMC Genomics 2011 12:121
    Content type: Research article Published on:

  42. Small interspersed repeats are commonly found in many bacterial chromosomes. Two families of repeats (BOX and RUP) have previously been identified in the genome of Streptococcus pneumoniae, a nasopharyngeal comme...

    Authors: Nicholas J Croucher, Georgios S Vernikos, Julian Parkhill and Stephen D Bentley
    Citation: BMC Genomics 2011 12:120
    Content type: Research article Published on:

  43. Many parasites use multicopy protein families to avoid their host's immune system through a strategy called antigenic variation. RIFIN and STEVOR proteins are variable surface antigens uniquely found in the ma...

    Authors: Nicolas Joannin, Yvonne Kallberg, Mats Wahlgren and Bengt Persson
    Citation: BMC Genomics 2011 12:119
    Content type: Methodology article Published on:

  45. Chickpea (Cicer arietinum L.) is an economically important cool season grain legume crop that is valued for its nutritive seeds having high protein content. However, several biotic and abiotic stresses and the lo...

    Authors: Rashmi Gaur, Niroj K Sethy, Shalu Choudhary, Bhumika Shokeen, Varsha Gupta and Sabhyata Bhatia
    Citation: BMC Genomics 2011 12:117
    Content type: Research article Published on:

  46. Knowledge of the origins, distribution, and inheritance of variation in the malaria parasite (Plasmodium falciparum) genome is crucial for understanding its evolution; however the 81% (A+T) genome poses challenge...

    Authors: Upeka Samarakoon, Allison Regier, Asako Tan, Brian A Desany, Brendan Collins, John C Tan, Scott J Emrich and Michael T Ferdig
    Citation: BMC Genomics 2011 12:116
    Content type: Methodology article Published on:

  47. The Mycoplasma mycoides cluster consists of five species or subspecies that are ruminant pathogens. One subspecies, Mycoplasma mycoides subspecies mycoides Small Colony (MmmSC), is the causative agent of contagio...

    Authors: Francois Thiaucourt, Lucia Manso-Silvan, Woubit Salah, Valérie Barbe, Benoit Vacherie, Daniel Jacob, Marc Breton, Virginie Dupuy, Anne Marie Lomenech, Alain Blanchard and Pascal Sirand-Pugnet
    Citation: BMC Genomics 2011 12:114
    Content type: Research article Published on:

  48. The processing ability of poultry meat is highly related to its ultimate pH, the latter being mainly determined by the amount of glycogen in the muscle at death. The genetic determinism of glycogen and related...

    Authors: Vonick Sibut, Christelle Hennequet-Antier, Elisabeth Le Bihan-Duval, Sylvain Marthey, Michel J Duclos and Cécile Berri
    Citation: BMC Genomics 2011 12:112
    Content type: Research article Published on:

  49. C57BL/6J mice possess a single intelectin (Itln) gene on chromosome 1. The function of intelectins is not well understood, but roles have been postulated in insulin sensitivity, bacterial recognition, intestinal ...

    Authors: Zen H Lu, Alex di Domenico, Steven H Wright, Pamela A Knight, C Bruce A Whitelaw and Alan D Pemberton
    Citation: BMC Genomics 2011 12:110
    Content type: Research article Published on:

  50. Several tools are available to identify miRNAs from deep-sequencing data, however, only a few of them, like miRDeep, can identify novel miRNAs and are also available as a standalone application. Given the diff...

    Authors: Vivek Thakur, Samart Wanchana, Mercedes Xu, Richard Bruskiewich, William Paul Quick, Axel Mosig and Xin-Guang Zhu
    Citation: BMC Genomics 2011 12:108
    Content type: Methodology article Published on:

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BMC Genomics

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