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  1. With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding...

    Authors: Barbara L Hass-Jacobus, Montona Futrell-Griggs, Brian Abernathy, Rick Westerman, Jose-Luis Goicoechea, Joshua Stein, Patricia Klein, Bonnie Hurwitz, Bin Zhou, Fariborz Rakhshan, Abhijit Sanyal, Navdeep Gill, Jer-Young Lin, Jason G Walling, Mei Zhong Luo, Jetty Siva S Ammiraju…
    Citation: BMC Genomics 2006 7:199
    Content type: Research article Published on:

  3. Mucins are large glycoproteins that cover epithelial surfaces of the body. All mucins contain at least one PTS domain, a region rich in proline, threonine and serine. Mucins are also characterized by von Wille...

    Authors: Tiange Lang, Gunnar C Hansson and Tore Samuelsson
    Citation: BMC Genomics 2006 7:197
    Content type: Research article Published on:

  5. The major royal jelly proteins/yellow (MRJP/YELLOW) family possesses several physiological and chemical functions in the development of Apis mellifera and Drosophila melanogaster. Each protein of the family has a...

    Authors: Ai-Hua Xia, Qing-Xiang Zhou, Lin-Lin Yu, Wei-Guo Li, Yong-Zhu Yi, Yao-Zhou Zhang and Zhi-Fang Zhang
    Citation: BMC Genomics 2006 7:195
    Content type: Research article Published on:

  6. Comparative mapping provides new insights into the evolutionary history of genomes. In particular, recent studies in mammals have suggested a role for segmental duplication in genome evolution. In some species...

    Authors: Laurent Schibler, Anne Roig, Marie-Françoise Mahe, Pascal Laurent, Hélène Hayes, François Rodolphe and Edmond P Cribiu
    Citation: BMC Genomics 2006 7:194
    Content type: Research article Published on:

  7. The filamentous fungus Trichoderma harzianum is used as biological control agent of several plant-pathogenic fungi. In order to study the genome of this fungus, a functional genomics project called "TrichoEST" wa...

    Authors: Juan Antonio Vizcaíno, Francisco Javier González, M Belén Suárez, José Redondo, Julian Heinrich, Jesús Delgado-Jarana, Rosa Hermosa, Santiago Gutiérrez, Enrique Monte, Antonio Llobell and Manuel Rey
    Citation: BMC Genomics 2006 7:193
    Content type: Research article Published on:

  8. Single nucleotide polymorphisms (SNPs) represent the most abundant type of DNA variation in the vertebrate genome, and their applications as genetic markers in numerous studies of molecular ecology and conserv...

    Authors: Heikki J Ryynänen and Craig R Primmer
    Citation: BMC Genomics 2006 7:192
    Content type: Methodology article Published on:

  9. Helicobacter pylori is presumed to be co-evolved with its human host and is a highly diverse gastric pathogen at genetic levels. Ancient origins of H. pylori in the New World are still debatable. It is not clear ...

    Authors: S Manjulata Devi, Irshad Ahmed, Aleem A Khan, Syed Asad Rahman, Ayesha Alvi, Leonardo A Sechi and Niyaz Ahmed
    Citation: BMC Genomics 2006 7:191
    Content type: Research article Published on:

  10. Although microscopic diagnosis has been playing the decisive role in cancer diagnostics, there have been cases in which it does not satisfy the clinical need. Differential diagnosis of malignant and benign thy...

    Authors: Naoto Yukinawa, Shigeyuki Oba, Kikuya Kato, Kazuya Taniguchi, Kyoko Iwao-Koizumi, Yasuhiro Tamaki, Shinzaburo Noguchi and Shin Ishii
    Citation: BMC Genomics 2006 7:190
    Content type: Methodology article Published on:

  11. Alternative polyadenylation is a widespread mechanism contributing to transcript diversity in eukaryotes. Over half of mammalian genes are alternatively polyadenylated. Our understanding of poly(A) site evolut...

    Authors: Takeshi Ara, Fabrice Lopez, William Ritchie, Philippe Benech and Daniel Gautheret
    Citation: BMC Genomics 2006 7:189
    Content type: Research article Published on:

  12. Doublecortin (DCX) domains serve as protein-interaction platforms. Mutations in members of this protein superfamily are linked to several genetic diseases. Mutations in the human DCX gene result in abnormal neuro...

    Authors: Orly Reiner, Frédéric M Coquelle, Bastian Peter, Talia Levy, Anna Kaplan, Tamar Sapir, Irit Orr, Naama Barkai, Gregor Eichele and Sven Bergmann
    Citation: BMC Genomics 2006 7:188
    Content type: Research article Published on:

  13. Accurate evaluation of the quality of genomic or proteomic data and computational methods is vital to our ability to use them for formulating novel biological hypotheses and directing further experiments. Ther...

    Authors: Chad L Myers, Daniel R Barrett, Matthew A Hibbs, Curtis Huttenhower and Olga G Troyanskaya
    Citation: BMC Genomics 2006 7:187
    Content type: Research article Published on:

  14. Nanoarchaeum equitans, the only known hyperthermophilic archaeon exhibiting parasitic life style, has raised some new questions about the evolution of the Archaea and provided a model of choice to study the genom...

    Authors: Sabyasachi Das, Sandip Paul, Sumit K Bag and Chitra Dutta
    Citation: BMC Genomics 2006 7:186
    Content type: Research article Published on:

  15. Nuclear mitochondrial pseudogenes (numts) are a potential source of contamination during mitochondrial DNA PCR amplification. This possibility warrants careful experimental design and cautious interpretation o...

    Authors: Ryan L Parr, Jennifer Maki, Brian Reguly, Gabriel D Dakubo, Andrea Aguirre, Roy Wittock, Kerry Robinson, John P Jakupciak and Robert E Thayer
    Citation: BMC Genomics 2006 7:185
    Content type: Research article Published on:

  16. In the recent years a strong resemblance has been observed between the insect immune system and the mammalian innate immune mechanisms suggesting their common origin. Among the insects, only the dipterans (Drosop...

    Authors: Archana S Gandhe, K P Arunkumar, Serene H John and J Nagaraju
    Citation: BMC Genomics 2006 7:184
    Content type: Research article Published on:

  19. DNA methylation and histone deacetylation are epigenetic mechanisms that play major roles in eukaryotic gene regulation. We hypothesize that many genes in the human hepatoma cell line HepG2 are regulated by DN...

    Authors: Luke O Dannenberg and Howard J Edenberg
    Citation: BMC Genomics 2006 7:181
    Content type: Research article Published on:

  22. Currently most pastoral farmers rely on anthelmintic drenches to control gastrointestinal parasitic nematodes in sheep. Resistance to anthelmintics is rapidly increasing in nematode populations such that on so...

    Authors: Allan M Crawford, Korena A Paterson, Ken G Dodds, Cristina Diez Tascon, Penny A Williamson, Meredith Roberts Thomson, Stewart A Bisset, Anne E Beattie, Gordon J Greer, Richard S Green, Roger Wheeler, Richard J Shaw, Kevin Knowler and John C McEwan
    Citation: BMC Genomics 2006 7:178
    Content type: Research article Published on:

  24. Cleavage of messenger RNA (mRNA) precursors is an essential step in mRNA maturation. The signal recognized by the cleavage enzyme complex has been characterized as an A rich region upstream of the cleavage sit...

    Authors: Dorota Retelska, Christian Iseli, Philipp Bucher, C Victor Jongeneel and Felix Naef
    Citation: BMC Genomics 2006 7:176
    Content type: Research article Published on:

  25. Transcriptomic techniques are now being applied in ecotoxicology and toxicology to measure the impact of stressors and develop understanding of mechanisms of toxicity. Microarray technology in particular offer...

    Authors: Lars-Henrik Heckmann, Richard Connon, Thomas H Hutchinson, Steve J Maund, Richard M Sibly and Amanda Callaghan
    Citation: BMC Genomics 2006 7:175
    Content type: Research article Published on:

  26. High-throughput genotyping technologies represent a highly efficient way to accelerate genetic mapping and enable association studies. As a first step toward this goal, we aimed to develop a resource of candid...

    Authors: Nathalie Pavy, Lee S Parsons, Charles Paule, John MacKay and Jean Bousquet
    Citation: BMC Genomics 2006 7:174
    Content type: Research article Published on:

  27. Shigella bacteria cause dysentery, which remains a significant threat to public health. Shigella flexneri is the most common species in both developing and developed countries. Five Shigella genomes have been seq...

    Authors: Huan Nie, Fan Yang, Xiaobing Zhang, Jian Yang, Lihong Chen, Jing Wang, Zhaohui Xiong, Junping Peng, Lilian Sun, Jie Dong, Ying Xue, Xingye Xu, Shuxia Chen, Zhijian Yao, Yan Shen and Qi Jin
    Citation: BMC Genomics 2006 7:173
    Content type: Research article Published on:

  28. The sheep is an important model animal for testing novel fracture treatments and other medical applications. Despite these medical uses and the well known economic and cultural importance of the sheep, relativ...

    Authors: Jochen Hecht, Heiner Kuhl, Stefan A Haas, Sebastian Bauer, Albert J Poustka, Jasmin Lienau, Hanna Schell, Asita C Stiege, Volkhard Seitz, Richard Reinhardt, Georg N Duda, Stefan Mundlos and Peter N Robinson
    Citation: BMC Genomics 2006 7:172
    Content type: Research article Published on:

  29. Mature saturated brine (crystallizers) communities are largely dominated (>80% of cells) by the square halophilic archaeon "Haloquadratum walsbyi". The recent cultivation of the strain HBSQ001 and thesequencing o...

    Authors: Boris A Legault, Arantxa Lopez-Lopez, Jose Carlos Alba-Casado, W Ford Doolittle, Henk Bolhuis, Francisco Rodriguez-Valera and R Thane Papke
    Citation: BMC Genomics 2006 7:171
    Content type: Research article Published on:

  30. Prediction of secondary structures in the expressed sequences of bacterial genomes allows to investigate spontaneous folding of the corresponding RNA. This is particularly relevant in untranslated mRNA regions...

    Authors: Mauro Petrillo, Giustina Silvestro, Pier Paolo Di Nocera, Angelo Boccia and Giovanni Paolella
    Citation: BMC Genomics 2006 7:170
    Content type: Research article Published on:

  31. The square halophilic archaeon Haloquadratum walsbyi dominates NaCl-saturated and MgCl2 enriched aquatic ecosystems, which imposes a serious desiccation stress, caused by the extremely low water activity. The gen...

    Authors: Henk Bolhuis, Peter Palm, Andy Wende, Michaela Falb, Markus Rampp, Francisco Rodriguez-Valera, Friedhelm Pfeiffer and Dieter Oesterhelt
    Citation: BMC Genomics 2006 7:169
    Content type: Research article Published on:

  32. Pollen of the European white birch (Betula pendula, syn. B. verrucosa) is an important cause of hay fever. The main allergen is Bet v 1, member of the pathogenesis-related class 10 (PR-10) multigene family. To es...

    Authors: Martijn F Schenk, Ludovicus JWJ Gilissen, Gerhard D Esselink and Marinus JM Smulders
    Citation: BMC Genomics 2006 7:168
    Content type: Research article Published on:

  34. NCI60 cell lines are derived from cancers of 9 tissue origins and have been invaluable in vitro models for cancer research and anti-cancer drug screen. Although extensive studies have been carried out to assess t...

    Authors: Huixia Wang, Shuguang Huang, Jianyong Shou, Eric W Su, Jude E Onyia, Birong Liao and Shuyu Li
    Citation: BMC Genomics 2006 7:166
    Content type: Research article Published on:

  38. Pseudomonas aeruginosa is a genetically complex bacterium which can adopt and switch between a free-living or biofilm lifestyle, a versatility that enables it to thrive in many different environments and contribu...

    Authors: Richard D Waite, Alberto Paccanaro, Anastasia Papakonstantinopoulou, Jacob M Hurst, Mansoor Saqi, Eddie Littler and Michael A Curtis
    Citation: BMC Genomics 2006 7:162
    Content type: Research article Published on:

  40. Genomic approaches provide unique opportunities to study interactions of insects with their pathogens. We developed a cDNA microarray to analyze the gene transcription profile of the lepidopteran pest Spodoptera ...

    Authors: M Barat-Houari, F Hilliou, F-X Jousset, L Sofer, E Deleury, J Rocher, M Ravallec, L Galibert, P Delobel, R Feyereisen, P Fournier and A-N Volkoff
    Citation: BMC Genomics 2006 7:160
    Content type: Research article Published on:

  41. The purpose of this work was to study the gene expression of transient receptor potential (TRP) channels in the mouse. The application of a standardized and quantitative technique, TaqMan RT-PCR, should give i...

    Authors: Christiane Kunert-Keil, Frederike Bisping, Jana Krüger and Heinrich Brinkmeier
    Citation: BMC Genomics 2006 7:159
    Content type: Research article Published on:

  42. The maize INDETERMINATE1 gene, ID1, is a key regulator of the transition to flowering and the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finge...

    Authors: Joseph Colasanti, Reynald Tremblay, Ada YM Wong, Viktoriya Coneva, Akiko Kozaki and Barbara K Mable
    Citation: BMC Genomics 2006 7:158
    Content type: Research article Published on:

  43. The nematode Strongyloides ratti has two adult phases in its lifecycle: one obligate, female and parasitic and one facultative, dioecious and free-living. The molecular control of the development of this free-liv...

    Authors: Fiona J Thompson, Gary LA Barker, Louise Hughes, Clare P Wilkes, Jane Coghill and Mark E Viney
    Citation: BMC Genomics 2006 7:157
    Content type: Research article Published on:

  45. Trisomy of human chromosome 21 (Chr21) results in Down's syndrome, a complex developmental and neurodegenerative disease. Molecular analysis of Down's syndrome, however, poses a particular challenge, because t...

    Authors: Yu-Hui Hu, Hans-Jörg Warnatz, Dominique Vanhecke, Florian Wagner, Andrea Fiebitz, Sabine Thamm, Pascal Kahlem, Hans Lehrach, Marie-Laure Yaspo and Michal Janitz
    Citation: BMC Genomics 2006 7:155
    Content type: Research article Published on:

  46. Biologists are becoming increasingly aware that the interaction of animals, including humans, with their coevolved bacterial partners is essential for health. This growing awareness has been a driving force fo...

    Authors: Carlene K Chun, Todd E Scheetz, Maria de Fatima Bonaldo, Bartley Brown, Anik Clemens, Wendy J Crookes-Goodson, Keith Crouch, Tad DeMartini, Mari Eyestone, Michael S Goodson, Bernadette Janssens, Jennifer L Kimbell, Tanya A Koropatnick, Tamara Kucaba, Christina Smith, Jennifer J Stewart…
    Citation: BMC Genomics 2006 7:154
    Content type: Research article Published on:

  47. There are many potential sources of variability in a microarray experiment. Variation can arise from many aspects of the collection and processing of samples for gene expression analysis. Oligonucleotide-based...

    Authors: LanMin Zhang, Sean J Yoder and Steven A Enkemann
    Citation: BMC Genomics 2006 7:153
    Content type: Research article Published on:

  48. The snake venom gland is a specialized organ, which synthesizes and secretes the complex and abundant toxin proteins. Though gene expression in the snake venom gland has been extensively studied, the focus has...

    Authors: Bing Zhang, Qinghua Liu, Wei Yin, Xiaowei Zhang, Yijun Huang, Yingfeng Luo, Pengxin Qiu, Xingwen Su, Jun Yu, Songnian Hu and Guangmei Yan
    Citation: BMC Genomics 2006 7:152
    Content type: Research article Published on:

  49. Macrohaplogroups 'M' and 'N' have evolved almost in parallel from a founder haplogroup L3. Macrohaplogroup N in India has already been defined in previous studies and recently the macrohaplogroup M among the I...

    Authors: Kumarasamy Thangaraj, Gyaneshwer Chaubey, Vijay Kumar Singh, Ayyasamy Vanniarajan, Ismail Thanseem, Alla G Reddy and Lalji Singh
    Citation: BMC Genomics 2006 7:151
    Content type: Research article Published on:

  50. Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severel...

    Authors: Vasily Tcherepanov, Angelika Ehlers and Chris Upton
    Citation: BMC Genomics 2006 7:150
    Content type: Software Published on:

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