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  1. Understanding of genetic elements that contribute to key aspects of citrus biology will impact future improvements in this economically important crop. Global gene expression analysis demands microarray platfo...

    Authors: M Angeles Martinez-Godoy, Nuria Mauri, Jose Juarez, M Carmen Marques, Julia Santiago, Javier Forment and Jose Gadea
    Citation: BMC Genomics 2008 9:318
  2. Microarrays are an important and widely used tool. Applications include capturing genomic DNA for high-throughput sequencing in addition to the traditional monitoring of gene expression and identifying DNA cop...

    Authors: Catriona Rennie, Harry A Noyes, Stephen J Kemp, Helen Hulme, Andy Brass and David C Hoyle
    Citation: BMC Genomics 2008 9:317
  3. While the genomic annotations of diverse lineages of the Mycobacterium tuberculosis complex are available, divergences between gene prediction methods are still a challenge for unbiased protein dataset generation...

    Authors: Gustavo A de Souza, Hiwa Målen, Tina Søfteland, Gisle Sælensminde, Swati Prasad, Inge Jonassen and Harald G Wiker
    Citation: BMC Genomics 2008 9:316
  4. Mitogenomics data, i.e. complete mitochondrial genome sequences, are popular molecular markers used for phylogenetic, phylogeographic and ecological studies in different animal lineages. Their comparative anal...

    Authors: Antonio Carapelli, Sara Comandi, Peter Convey, Francesco Nardi and Francesco Frati
    Citation: BMC Genomics 2008 9:315
  5. Upland cotton has the highest yield, and accounts for > 95% of world cotton production. Decoding upland cotton genomes will undoubtedly provide the ultimate reference and resource for structural, functional, a...

    Authors: Wangzhen Guo, Caiping Cai, Changbiao Wang, Liang Zhao, Lei Wang and Tianzhen Zhang
    Citation: BMC Genomics 2008 9:314
  6. Protein-protein interactions networks are most often generated from physical protein-protein interaction data. Co-conservation, also known as phylogenetic profiles, is an alternative source of information for ...

    Authors: Anis Karimpour-Fard, Sonia M Leach, Lawrence E Hunter and Ryan T Gill
    Citation: BMC Genomics 2008 9:313
  7. Benefits from high-throughput sequencing using 454 pyrosequencing technology may be most apparent for species with high societal or economic value but few genomic resources. Rapid means of gene sequence and SN...

    Authors: Evandro Novaes, Derek R Drost, William G Farmerie, Georgios J Pappas Jr, Dario Grattapaglia, Ronald R Sederoff and Matias Kirst
    Citation: BMC Genomics 2008 9:312
  8. Whooping cough caused by Bordetella pertussis in humans, is re-emerging in many countries despite vaccination. Several studies have shown that significant shifts have occurred in the B. pertussis population resul...

    Authors: Audrey J King, Tamara van Gorkom, Jeroen LA Pennings, Han GJ van der Heide, Qiushui He, Dimitri Diavatopoulos, Kees Heuvelman, Marjolein van Gent, Karin van Leeuwen and Frits R Mooi
    Citation: BMC Genomics 2008 9:311

    The Erratum to this article has been published in BMC Genomics 2010 11:196

  9. Hepatitis C virus (HCV) RNA synthesis and protein expression affect cell homeostasis by modulation of gene expression. The impact of HCV replication on global cell transcription has not been fully evaluated. T...

    Authors: Anna Rita Ciccaglione, Cinzia Marcantonio, Elena Tritarelli, Paola Tataseo, Alessandro Ferraris, Roberto Bruni, Bruno Dallapiccola, Germano Gerosolimo, Angela Costantino and Maria Rapicetta
    Citation: BMC Genomics 2008 9:309
  10. Polycomb group (PcG) proteins are a set of chromatin-modifying proteins that play a key role in epigenetic gene regulation. The PcG proteins form large multiprotein complexes with different activities. The two...

    Authors: Luis Sanchez-Pulido, Damien Devos, Zinmay R Sung and Myriam Calonje
    Citation: BMC Genomics 2008 9:308
  11. In a recent study it was demonstrated that a largely increased ovulation number is responsible for high prolificacy in two mouse lines selected for fertility performance. The objective of the present study was...

    Authors: Jens Vanselow, Gerd Nürnberg, Dirk Koczan, Martina Langhammer, Hans-Jürgen Thiesen and Norbert Reinsch
    Citation: BMC Genomics 2008 9:307
  12. Phytoplasmas are insect-transmitted, uncultivable bacterial plant pathogens that cause diseases in hundreds of economically important plants. They represent a monophyletic group within the class Mollicutes (trivi...

    Authors: Michael Kube, Bernd Schneider, Heiner Kuhl, Thomas Dandekar, Katja Heitmann, Alexander M Migdoll, Richard Reinhardt and Erich Seemüller
    Citation: BMC Genomics 2008 9:306
  13. Alu repetitive elements are the abundant sequences in human genome. Diversity of DNA sequences of these elements makes difficult the construction of theoretical patterns of Alu repeats cleavage by restriction ...

    Authors: Murat A Abdurashitov, Victor N Tomilov, Valery A Chernukhin and Sergey Kh Degtyarev
    Citation: BMC Genomics 2008 9:305
  14. Schistosoma japonicum is one of the three major blood fluke species, the etiological agents of schistosomiasis which remains a serious public health problem with an estimated 200 million people infected in 76 cou...

    Authors: Feng Liu, Ping Chen, Shu-Jian Cui, Zhi-Qin Wang and Ze-Guang Han
    Citation: BMC Genomics 2008 9:304
  15. Trichophyton rubrum is the most common dermatophyte causing fungal skin infections in humans. Asexual sporulation is an important means of propagation for T. rubrum, and conidia produced by this way are thought t...

    Authors: Wenchuan Leng, Tao Liu, Rui Li, Jian Yang, Candong Wei, Wenliang Zhang and Qi Jin
    Citation: BMC Genomics 2008 9:303
  16. In this study we assessed the respective ability of Affymetrix and Illumina microarray methodologies to answer a relevant biological question, namely the change in gene expression between resting monocytes and...

    Authors: Seraya Maouche, Odette Poirier, Tiphaine Godefroy, Robert Olaso, Ivo Gut, Jean-Phillipe Collet, Gilles Montalescot and François Cambien
    Citation: BMC Genomics 2008 9:302
  17. The parasitic mite, Varroa destructor, is the most serious pest of the western honey bee, Apis mellifera, and has caused the death of millions of colonies worldwide. This mite reproduces in brood cells and parasi...

    Authors: M Navajas, A Migeon, C Alaux, ML Martin-Magniette, GE Robinson, JD Evans, S Cros-Arteil, D Crauser and Y Le Conte
    Citation: BMC Genomics 2008 9:301
  18. Mice of the genus Peromyscus are found in nearly every habitat from Alaska to Central America and from the Atlantic to the Pacific. They provide an evolutionary outgroup to the Mus/Rattus lineage and serve as an ...

    Authors: Julie L Weston Glenn, Chin-Fu Chen, Adrienne Lewandowski, Chun-Huai Cheng, Clifton M Ramsdell, Rebecca Bullard-Dillard, Jianguo Chen, Michael J Dewey and Travis C Glenn
    Citation: BMC Genomics 2008 9:300
  19. There is an increasing drive to replace fish oil (FO) in finfish aquaculture diets with vegetable oils (VO), driven by the short supply of FO derived from wild fish stocks. However, little is known of the cons...

    Authors: Michael J Leaver, Laure AN Villeneuve, Alex Obach, Linda Jensen, James E Bron, Douglas R Tocher and John B Taggart
    Citation: BMC Genomics 2008 9:299
  20. Trypanosomatids utilise polycistronic transcription for production of the vast majority of protein-coding mRNAs, which operates in the absence of gene-specific promoters. Resolution of nascent transcripts by p...

    Authors: V Lila Koumandou, Senthil Kumar A Natesan, Tatiana Sergeenko and Mark C Field
    Citation: BMC Genomics 2008 9:298
  21. Ionizing-radiation-resistant bacteria (IRRB) show a surprising capacity for adaptation to ionizing radiation and desiccation. Positive Darwinian selection is expected to play an important role in this trait, b...

    Authors: Haïtham Sghaier, Kaïs Ghedira, Alia Benkahla and Insaf Barkallah
    Citation: BMC Genomics 2008 9:297
  22. Microsporidia are a group of parasites related to fungi that infect a wide variety of animals and have gained recognition from the medical community in the past 20 years due to their ability to infect immuno-c...

    Authors: Erin E Gill, James J Becnel and Naomi M Fast
    Citation: BMC Genomics 2008 9:296
  23. Flow cytometry facilitates sorting of single chromosomes and chromosome arms which can be used for targeted genome analysis. However, the recovery of microgram amounts of DNA needed for some assays requires so...

    Authors: Hana Šimková, Jan T Svensson, Pascal Condamine, Eva Hřibová, Pavla Suchánková, Prasanna R Bhat, Jan Bartoš, Jan Šafář, Timothy J Close and Jaroslav Doležel
    Citation: BMC Genomics 2008 9:294
  24. The jumonji C (JmjC) domain containing gene 6 (Jmjd6, previously known as phosphatidylserine receptor) has misleadingly been annotated to encode a transmembrane receptor for the engulfment of apoptotic cells. Giv...

    Authors: Phillip Hahn, Jens Böse, Stefanie Edler and Andreas Lengeling
    Citation: BMC Genomics 2008 9:293
  25. Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in humans. However, the factors that affect SNP density are poorly understood. The goal of this study was to estimate the re...

    Authors: Ivan P Gorlov, Olga Y Gorlova and Christopher I Amos
    Citation: BMC Genomics 2008 9:292
  26. Phagocytosis plays a major role in the defense of higher organisms against microbial infection and provides also the basis for antigen processing in the immune response. Cells of the model organism Dictyostelium ...

    Authors: Alessio Sillo, Gareth Bloomfield, Alessandra Balest, Alessandra Balbo, Barbara Pergolizzi, Barbara Peracino, Jason Skelton, Alasdair Ivens and Salvatore Bozzaro
    Citation: BMC Genomics 2008 9:291
  27. To gain insight into the branching order of the five main lineages currently recognized in the green algal class Chlorophyceae and to expand our understanding of chloroplast genome evolution, we have undertake...

    Authors: Jean-Simon Brouard, Christian Otis, Claude Lemieux and Monique Turmel
    Citation: BMC Genomics 2008 9:290
  28. Neurovirulent Venezuelan equine encephalitis virus (VEEV) causes lethal encephalitis in equines and is transmitted to humans by mosquitoes. VEEV is highly infectious when transmitted by aerosol and has been de...

    Authors: Anuj Sharma, Bhaskar Bhattacharya, Raj K Puri and Radha K Maheshwari
    Citation: BMC Genomics 2008 9:289
  29. Some of the biochemical events that lead to necrosis of the liver are well-known. However, the pathogenesis of necrosis of the liver from exposure to hepatotoxicants is a complex biological response to the inj...

    Authors: Lingkang Huang, Alexandra N Heinloth, Zhao-Bang Zeng, Richard S Paules and Pierre R Bushel
    Citation: BMC Genomics 2008 9:288
  30. During the last decade, numerous microsatellite markers were developed for genotyping and to identify closely related plant genotypes. In citrus, previously developed microsatellite markers were arisen from ge...

    Authors: François L Luro, Gilles Costantino, Javier Terol, Xavier Argout, Thierry Allario, Patrick Wincker, Manuel Talon, Patrick Ollitrault and Raphael Morillon
    Citation: BMC Genomics 2008 9:287
  31. The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum) which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in...

    Authors: Wei Zhu, Shu Ouyang, Marina Iovene, Kimberly O'Brien, Hue Vuong, Jiming Jiang and C Robin Buell
    Citation: BMC Genomics 2008 9:286
  32. The use of gene expression profiling in both clinical and laboratory settings would be enhanced by better characterization of variance due to individual, environmental, and technical factors. Meta-analysis of ...

    Authors: Michael J Boedigheimer, Russell D Wolfinger, Michael B Bass, Pierre R Bushel, Jeff W Chou, Matthew Cooper, J Christopher Corton, Jennifer Fostel, Susan Hester, Janice S Lee, Fenglong Liu, Jie Liu, Hui-Rong Qian, John Quackenbush, Syril Pettit and Karol L Thompson
    Citation: BMC Genomics 2008 9:285
  33. Genomes possess different levels of non-randomness, in particular, an inhomogeneity in their nucleotide composition. Inhomogeneity is manifest from the short-range where neighboring nucleotides influence the c...

    Authors: Jason M Bechtel, Thomas Wittenschlaeger, Trisha Dwyer, Jun Song, Sasi Arunachalam, Sadeesh K Ramakrishnan, Samuel Shepard and Alexei Fedorov
    Citation: BMC Genomics 2008 9:284
  34. A pig phenotype characterized by juvenile hairlessness, thin skin and age dependent lung emphysema has been discovered in a Danish pig herd. The trait shows autosomal co-dominant inheritance with all three gen...

    Authors: Camilla S Bruun, Claus B Jørgensen, Lene Bay, Susanna Cirera, Henrik E Jensen, Páll S Leifsson, Jens Nielsen, Knud Christensen and Merete Fredholm
    Citation: BMC Genomics 2008 9:283
  35. The lycophyte Selaginella moellendorffii is a vascular plant that diverged from the fern/seed plant lineage at least 400 million years ago. Although genomic information for S. moellendorffii is starting to be pro...

    Authors: Agnes P Chan, Admasu Melake-Berhan, Kimberly O'Brien, Stephanie Buckley, Hui Quan, Dan Chen, Matthew Lewis, Jo Ann Banks and Pablo D Rabinowicz
    Citation: BMC Genomics 2008 9:282
  36. In oviparous species, genes encoding proteins with functions in lipid remodeling, such as specialized lipases, may have evolved to facilitate the assembly and utilization of yolk lipids by the embryo. The mamm...

    Authors: Jani Saarela, Gerlinde Jung, Marcela Hermann, Johannes Nimpf and Wolfgang J Schneider
    Citation: BMC Genomics 2008 9:281
  37. The genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene fun...

    Authors: Jeong-Hwan Mun, Soo-Jin Kwon, Tae-Jin Yang, Hye-Sun Kim, Beom-Soon Choi, Seunghoon Baek, Jung Sun Kim, Mina Jin, Jin A Kim, Myung-Ho Lim, Soo In Lee, Ho-Il Kim, Hyungtae Kim, Yong Pyo Lim and Beom-Seok Park
    Citation: BMC Genomics 2008 9:280
  38. The bite of spiders belonging to the genus Loxosceles can induce a variety of clinical symptoms, including dermonecrosis, thrombosis, vascular leakage, haemolysis, and persistent inflammation. In order to examine...

    Authors: Matheus de F Fernandes-Pedrosa, Inácio de LM Junqueira-de-Azevedo, Rute M Gonçalves-de-Andrade, Leonardo S Kobashi, Diego D Almeida, Paulo L Ho and Denise V Tambourgi
    Citation: BMC Genomics 2008 9:279
  39. Short non-coding RNAs (ncRNAs) perform their cellular functions in ribonucleoprotein (RNP) complexes, which are also essential for maintaining the stability of the ncRNAs. Depletion of individual protein compo...

    Authors: Muhammad Nauman Aftab, Housheng He, Geir Skogerbø and Runsheng Chen
    Citation: BMC Genomics 2008 9:278
  40. The accurate detection of genes and the identification of functional regions is still an open issue in the annotation of genomic sequences. This problem affects new genomes but also those of very well studied ...

    Authors: Flavio Mignone, Anna Anselmo, Giacinto Donvito, Giorgio P Maggi, Giorgio Grillo and Graziano Pesole
    Citation: BMC Genomics 2008 9:277
  41. We describe the development of a novel matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)-based single nucleotide polymorphism (SNP) scoring strategy, termed Restriction Fragment Mass Polym...

    Authors: Sun Pyo Hong, Seung Il Ji, Hwanseok Rhee, Soo Kyeong Shin, Sun Young Hwang, Seung Hwan Lee, Soong Deok Lee, Heung-Bum Oh, Wangdon Yoo and Soo-Ok Kim
    Citation: BMC Genomics 2008 9:276
  42. Cultivated watermelon form large fruits that are highly variable in size, shape, color, and content, yet have extremely narrow genetic diversity. Whereas a plethora of genes involved in cell wall metabolism, e...

    Authors: W Patrick Wechter, Amnon Levi, Karen R Harris, Angela R Davis, Zhangjun Fei, Nurit Katzir, James J Giovannoni, Ayelet Salman-Minkov, Alvaro Hernandez, Jyothi Thimmapuram, Yaakov Tadmor, Vitaly Portnoy and Tova Trebitsh
    Citation: BMC Genomics 2008 9:275
  43. The colonial cyanobacterium Microcystis proliferates in a wide range of freshwater ecosystems and is exposed to changing environmental factors during its life cycle. Microcystis blooms are often toxic, potentiall...

    Authors: Lionel Frangeul, Philippe Quillardet, Anne-Marie Castets, Jean-François Humbert, Hans CP Matthijs, Diego Cortez, Andrew Tolonen, Cheng-Cai Zhang, Simonetta Gribaldo, Jan-Christoph Kehr, Yvonne Zilliges, Nadine Ziemert, Sven Becker, Emmanuel Talla, Amel Latifi, Alain Billault…
    Citation: BMC Genomics 2008 9:274
  44. Studies have shown that genetic and sex differences strongly influence gene expression in mice. Given the diversity and complexity of transcripts produced by alternative splicing, we sought to use microarrays ...

    Authors: Wan-Lin Su, Barmak Modrek, Debraj GuhaThakurta, Stephen Edwards, Jyoti K Shah, Amit V Kulkarni, Archie Russell, Eric E Schadt, Jason M Johnson and John C Castle
    Citation: BMC Genomics 2008 9:273
  45. In a traditional electrophoresis mobility shift assay (EMSA) a 32P-labeled double-stranded DNA oligonucleotide or a restriction fragment bound to a protein is separated from the unbound DNA by polyacrylamide gel ...

    Authors: Kristel Kaer, Kert Mätlik, Madis Metsis and Mart Speek
    Citation: BMC Genomics 2008 9:272
  46. Biological nitrogen fixation is a prokaryotic process that plays an essential role in the global nitrogen cycle. Azorhizobium caulinodans ORS571 has the dual capacity to fix nitrogen both as free-living organism ...

    Authors: Kyung-Bum Lee, Philippe De Backer, Toshihiro Aono, Chi-Te Liu, Shino Suzuki, Tadahiro Suzuki, Takakazu Kaneko, Manabu Yamada, Satoshi Tabata, Doris M Kupfer, Fares Z Najar, Graham B Wiley, Bruce Roe, Tim T Binnewies, David W Ussery, Wim D'Haeze…
    Citation: BMC Genomics 2008 9:271

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