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  1. A semiparametric approach was used to identify groups of cDNAs and genes with distinct expression profiles across time and overcome the limitations of clustering to identify groups. The semiparametric approach...

    Authors: Sandra L Rodriguez-Zas, Bruce R Southey, Charles W Whitfield and Gene E Robinson

    Citation: BMC Genomics 2006 7:233

    Content type: Research article

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  2. Factor analysis (FA) has been widely applied in microarray studies as a data-reduction-tool without any a-priori assumption regarding associations between observed data and latent structure (Exploratory Factor...

    Authors: Anne PG Crijns, Frans Gerbens, A Edo D Plantinga, Gert Jan Meersma, Steven de Jong, Robert MW Hofstra, Elisabeth GE de Vries, Ate GJ van der Zee, Geertruida H de Bock and Gerard J te Meerman

    Citation: BMC Genomics 2006 7:232

    Content type: Methodology article

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  3. Previous studies demonstrated breast cancer tumor tissue samples could be classified into different subtypes based upon DNA microarray profiles. The most recent study presented evidence for the existence of fi...

    Authors: Amy V Kapp, Stefanie S Jeffrey, Anita Langerød, Anne-Lise Børresen-Dale, Wonshik Han, Dong-Young Noh, Ida RK Bukholm, Monica Nicolau, Patrick O Brown and Robert Tibshirani

    Citation: BMC Genomics 2006 7:231

    Content type: Research article

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    The Erratum to this article has been published in BMC Genomics 2007 8:101

  4. The stringent response is the initial reaction of microorganisms to nutritional stress. During stringent response the small nucleotides (p)ppGpp act as global regulators and reprogram bacterial transcription. ...

    Authors: Olaf Brockmann-Gretza and Jörn Kalinowski

    Citation: BMC Genomics 2006 7:230

    Content type: Research article

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  5. Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreov...

    Authors: Fiona M McCarthy, Nan Wang, G Bryce Magee, Bindu Nanduri, Mark L Lawrence, Evelyn B Camon, Daniel G Barrell, David P Hill, Mary E Dolan, W Paul Williams, Dawn S Luthe, Susan M Bridges and Shane C Burgess

    Citation: BMC Genomics 2006 7:229

    Content type: Database

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  6. More than 12,000 simple sequence repeats (SSRs) have been identified in the genome of Burkholderia mallei ATCC 23344. As a demonstrated mechanism of phase variation in other pathogenic bacteria, these may functio...

    Authors: Claudia M Romero, David DeShazer, Tamara Feldblyum, Jacques Ravel, Donald Woods, H Stanley Kim, Yan Yu, Catherine M Ronning and William C Nierman

    Citation: BMC Genomics 2006 7:228

    Content type: Research article

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  7. The cattle UL16-binding protein 1 (ULBP1) and ULBP2 genes encode members of the MHC Class I superfamily that have homology to the human ULBP genes. Human ULBP1 and ULBP2 interact with the NKG2D receptor to activa...

    Authors: Joshua H Larson, Brandy M Marron, Jonathan E Beever, Bruce A Roe and Harris A Lewin

    Citation: BMC Genomics 2006 7:227

    Content type: Research article

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  8. Salivary proteins from sandflies are potential targets for exploitation as vaccines to control Leishmania infection; in this work we tested the hypothesis that salivary proteins from geographically distant Phlebo...

    Authors: Hirotomo Kato, Jennifer M Anderson, Shaden Kamhawi, Fabiano Oliveira, Phillip G Lawyer, Van My Pham, Constance Souko Sangare, Sibiry Samake, Ibrahim Sissoko, Mark Garfield, Lucie Sigutova, Petr Volf, Seydou Doumbia and Jesus G Valenzuela

    Citation: BMC Genomics 2006 7:226

    Content type: Research article

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  9. The Gram-negative, xylem-limited phytopathogenic bacterium Xylella fastidiosa is responsible for causing economically important diseases in grapevine, citrus and many other plant species. Despite its economic imp...

    Authors: Harshavardhan Doddapaneni, Jiqiang Yao, Hong Lin, M Andrew Walker and Edwin L Civerolo

    Citation: BMC Genomics 2006 7:225

    Content type: Research article

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  10. The response of macrophages to danger signals is an important early stage in the immune response. Our understanding of this complex event has been furthered by microarray analysis, which allows the simultaneou...

    Authors: Kirsty Jensen, Richard Talbot, Edith Paxton, David Waddington and Elizabeth J Glass

    Citation: BMC Genomics 2006 7:224

    Content type: Research article

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  11. As in other eukaryotes, plant mitogen-activated protein kinase (MAPK) cascades are composed of three classes of hierarchically organized protein kinases, namely MAPKKKs, MAPKKs, and MAPKs. These modules rapidl...

    Authors: Marie-Claude Nicole, Louis-Philippe Hamel, Marie-Josée Morency, Nathalie Beaudoin, Brian E Ellis and Armand Séguin

    Citation: BMC Genomics 2006 7:223

    Content type: Research article

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  12. Carrot (Daucus carota) is a major food crop in the US and worldwide. Its capacity for storage and its lifecycle as a biennial make it an attractive species for the introduction of foreign genes, especially for or...

    Authors: Tracey Ruhlman, Seung-Bum Lee, Robert K Jansen, Jessica B Hostetler, Luke J Tallon, Christopher D Town and Henry Daniell

    Citation: BMC Genomics 2006 7:222

    Content type: Research article

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  13. Germ cells are the only cell type that can penetrate from one generation to next generation. At the early embryonic developmental stages, germ cells originally stem from primordial germ cells, and finally diff...

    Authors: Jae Yong Han, Tae Sub Park, Jin Nam Kim, Mi A Kim, Dajeong Lim, Jeong Mook Lim and Heebal Kim

    Citation: BMC Genomics 2006 7:220

    Content type: Research article

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  14. Compelling evidence indicates that Shigella species, the etiologic agents of bacillary dysentery, as well as enteroinvasive Escherichia coli, are derived from multiple origins of Escherichia coli and form a singl...

    Authors: Junping Peng, Xiaobing Zhang, Jian Yang, Jing Wang, E Yang, Wen Bin, Candong Wei, Meisheng Sun and Qi Jin

    Citation: BMC Genomics 2006 7:218

    Content type: Research article

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  15. Aroclor 1254 is a well-known hepatotoxin and consists of a complex mixture of polychlorinated biphenyls (PCBs), some of which have the ability to activate the aryl hydrocarbon receptor (AhR) and other transcri...

    Authors: Susanne Reymann and Jürgen Borlak

    Citation: BMC Genomics 2006 7:217

    Content type: Research article

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  16. Whole genome amplification is an increasingly common technique through which minute amounts of DNA can be multiplied to generate quantities suitable for genetic testing and analysis. Questions of amplification...

    Authors: Robert Pinard, Alex de Winter, Gary J Sarkis, Mark B Gerstein, Karrie R Tartaro, Ramona N Plant, Michael Egholm, Jonathan M Rothberg and John H Leamon

    Citation: BMC Genomics 2006 7:216

    Content type: Research article

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  17. Effects on gene expression due to environmental or genetic changes can be easily measured using microarrays. However, indirect effects on expression can be substantial. The indirect effects of a perturbation n...

    Authors: Lin Tang, Xiao Liu and Neil D Clarke

    Citation: BMC Genomics 2006 7:215

    Content type: Research article

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  18. Complementary single-nucleotide polymorphisms (SNPs) may not be distributed equally between two DNA strands if the strands are functionally distinct, such as in transcribed genes. In introns, an excess of A↔G ...

    Authors: Hui-Qi Qu, Steve G Lawrence, Fan Guo, Jacek Majewski and Constantin Polychronakos

    Citation: BMC Genomics 2006 7:213

    Content type: Research article

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  19. The rodent specific reproductive homeobox (Rhox) gene cluster on the X chromosome has been reported to contain twelve homeobox-containing genes, Rhox1-12.

    Authors: Melany Jackson, Alistair J Watt, Philippe Gautier, Derek Gilchrist, Johanna Driehaus, Gerard J Graham, Jon Keebler, Franck Prugnolle, Philip Awadalla and Lesley M Forrester

    Citation: BMC Genomics 2006 7:212

    Content type: Research article

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  20. At least three species of Borrelia burgdorferi sensu lato (Bbsl) cause tick-borne Lyme disease. Previous work including the genome analysis of B. burgdorferi B31 and B. garinii PBi suggested a highly variable pla...

    Authors: Gernot Glöckner, Ulrike Schulte-Spechtel, Markus Schilhabel, Marius Felder, Jürgen Sühnel, Bettina Wilske and Matthias Platzer

    Citation: BMC Genomics 2006 7:211

    Content type: Research article

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  21. Mast cells are well established effectors of IgE-triggered allergic reactions and immune responses to parasitic infections. Recent studies indicate that mast cells may play roles in adaptive and innate immunit...

    Authors: Manikandan Jayapal, Hwee Kee Tay, Renji Reghunathan, Liang Zhi, Kah Kiong Chow, Mary Rauff and Alirio J Melendez

    Citation: BMC Genomics 2006 7:210

    Content type: Research article

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  22. Killer Immunoglobulin-like Receptors (KIR) are essential immuno-surveillance molecules. They are expressed on natural killer and T cells, and interact with human leukocyte antigens. KIR genes are highly polymo...

    Authors: Jennifer G Sambrook, Arman Bashirova, Hanne Andersen, Mike Piatak, George S Vernikos, Penny Coggill, Jeff D Lifson, Mary Carrington and Stephan Beck

    Citation: BMC Genomics 2006 7:209

    Content type: Research article

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  23. Mycelium-to-yeast transition in the human host is essential for pathogenicity by the fungus Paracoccidioides brasiliensis and both cell types are therefore critical to the establishment of paracoccidioidomycosis ...

    Authors: Rosângela V Andrade, Hugo C Paes, André M Nicola, Maria José A de Carvalho, Ana Lúcia Fachin, Renato S Cardoso, Simoneide S Silva, Larissa Fernandes, Silvana P Silva, Eduardo A Donadi, Elza T Sakamoto-Hojo, Geraldo AS Passos, Célia MA Soares, Marcelo M Brígido and Maria Sueli S Felipe

    Citation: BMC Genomics 2006 7:208

    Content type: Research article

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  24. Complete or near-complete genomic sequence information is presently only available for a few plant species representing a large phylogenetic diversity among plants. In order to effectively transfer this inform...

    Authors: Jakob Fredslund, Lene H Madsen, Birgit K Hougaard, Anna Marie Nielsen, David Bertioli, Niels Sandal, Jens Stougaard and Leif Schauser

    Citation: BMC Genomics 2006 7:207

    Content type: Research article

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  25. Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology ...

    Authors: Peter Wenzl, Haobing Li, Jason Carling, Meixue Zhou, Harsh Raman, Edie Paul, Phillippa Hearnden, Christina Maier, Ling Xia, Vanessa Caig, Jaroslava Ovesná, Mehmet Cakir, David Poulsen, Junping Wang, Rosy Raman, Kevin P Smith…

    Citation: BMC Genomics 2006 7:206

    Content type: Research article

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  26. Corynebacterium glutamicum, a Gram-positive bacterium of the class Actinobacteria, is an industrially relevant producer of amino acids. Several methods for the targeted genetic manipulation of this organism and r...

    Authors: Sascha Mormann, Alexander Lömker, Christian Rückert, Lars Gaigalat, Andreas Tauch, Alfred Pühler and Jörn Kalinowski

    Citation: BMC Genomics 2006 7:205

    Content type: Research article

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  27. Uncoupling protein 2 (UCP2) belongs to the superfamily of mitochondrial anion carriers that dissociate the respiratory chain from ATP synthesis. It has been determined that UCP2 plays a role in several physiol...

    Authors: Issa Coulibaly, Scott A Gahr, Yniv Palti, Jianbo Yao and Caird E Rexroad III

    Citation: BMC Genomics 2006 7:203

    Content type: Research article

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  28. The Aβ-binding alcohol dehydrogenase/17β-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10) is an enzyme involved in pivotal metabolic processes and in the mitochondrial dysfunction seen in the Alzheimer's dise...

    Authors: Alexandra T Marques, Agostinho Antunes, Pedro A Fernandes and Maria J Ramos

    Citation: BMC Genomics 2006 7:202

    Content type: Research article

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  29. For holometabolous insects there has been an explosion of proteomic and peptidomic information thanks to large genome sequencing projects. Heterometabolous insects, although comprising many important species, ...

    Authors: Elke Clynen, Jurgen Huybrechts, Peter Verleyen, Arnold De Loof and Liliane Schoofs

    Citation: BMC Genomics 2006 7:201

    Content type: Research article

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  30. 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

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  31. 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

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  32. 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

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  33. 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

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  34. 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

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  35. 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

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  36. 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

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  37. 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

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  38. 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

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  39. 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

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  40. 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

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  41. 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

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  42. 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

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