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  1. Post-segregational killing systems are present in a large variety of microorganisms. When found on plasmids, they are described as addiction systems that act to maintain the plasmid during the partitioning of ...

    Authors: Sarah Fico and Jacques Mahillon
    Citation: BMC Genomics 2006 7:259
  2. The ability to rapidly characterize an unknown microorganism is critical in both responding to infectious disease and biodefense. To do this, we need some way of anticipating an organism's phenotype based on t...

    Authors: Chern-Sing Goh, Tara A Gianoulis, Yang Liu, Jianrong Li, Alberto Paccanaro, Yves A Lussier and Mark Gerstein
    Citation: BMC Genomics 2006 7:257
  3. Dermatophytes are the primary causative agent of dermatophytoses, a disease that affects billions of individuals worldwide. Trichophyton rubrum is the most common of the superficial fungi. Although T. rubrum is a...

    Authors: Lingling Wang, Li Ma, Wenchuan Leng, Tao Liu, Lu Yu, Jian Yang, Li Yang, Wenliang Zhang, Qian Zhang, Jie Dong, Ying Xue, Yafang Zhu, Xingye Xu, Zhe Wan, Guohui Ding, Fudong Yu…
    Citation: BMC Genomics 2006 7:255
  4. Cross-species primers have been used with moderate success to address a variety of questions concerning genome structure, evolution, and gene function. However, the factors affecting their success have never b...

    Authors: Donna JE Housley, Zachary A Zalewski, Stephanie E Beckett and Patrick J Venta
    Citation: BMC Genomics 2006 7:253
  5. RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but may distort the true abundanc...

    Authors: Ilhem Diboun, Lorenz Wernisch, Christine Anne Orengo and Martin Koltzenburg
    Citation: BMC Genomics 2006 7:252
  6. Allergy is a common debilitating and occasionally life threatening condition. The fungal kingdom contains a number of species that produce a wide range of well defined protein allergens although the vast major...

    Authors: Paul Bowyer, Marcin Fraczek and David W Denning
    Citation: BMC Genomics 2006 7:251
  7. Leishmania major is a protozoan parasite with a highly polarised cell shape that depends upon endocytosis and exocytosis from a single area of the plasma membrane, the flagellar pocket. SNAREs (soluble N-ethylmal...

    Authors: Sébastien Besteiro, Graham H Coombs and Jeremy C Mottram
    Citation: BMC Genomics 2006 7:250
  8. Pigment epithelium derived factor (PEDF), a member of the serpin family, regulates cell proliferation, promotes survival of neurons, and blocks growth of new blood vessels in mammals. Defining the molecular ph...

    Authors: Xuming Xu, Samuel Shao-Min Zhang, Colin J Barnstable and Joyce Tombran-Tink
    Citation: BMC Genomics 2006 7:248
  9. Chemostat cultures are commonly used in production of cellular material for systems-wide biological studies. We have used the novel TRAC (transcript analysis with aid of affinity capture) method to study expre...

    Authors: Jari J Rautio, Bart A Smit, Marilyn Wiebe, Merja Penttilä and Markku Saloheimo
    Citation: BMC Genomics 2006 7:247
  10. High throughput sequencing-by-synthesis is an emerging technology that allows the rapid production of millions of bases of data. Although the sequence reads are short, they can readily be used for re-sequencin...

    Authors: Matthew N Bainbridge, René L Warren, Martin Hirst, Tammy Romanuik, Thomas Zeng, Anne Go, Allen Delaney, Malachi Griffith, Matthew Hickenbotham, Vincent Magrini, Elaine R Mardis, Marianne D Sadar, Asim S Siddiqui, Marco A Marra and Steven JM Jones
    Citation: BMC Genomics 2006 7:246
  11. Members of the genus Phytophthora are notorious pathogens with world-wide distribution. The most devastating species include P. infestans, P. ramorum and P. sojae. In order to develop molecular methods for routin...

    Authors: Diana P Garnica, Andrés M Pinzón, Lina M Quesada-Ocampo, Adriana J Bernal, Emiliano Barreto, Niklaus J Grünwald and Silvia Restrepo
    Citation: BMC Genomics 2006 7:245
  12. Abnormalities of pre-mRNA splicing are increasingly recognized as an important mechanism through which gene mutations cause disease. However, apart from the mutations in the donor and acceptor sites, the effec...

    Authors: Patrizia Lastella, Nicoletta Concetta Surdo, Nicoletta Resta, Ginevra Guanti and Alessandro Stella
    Citation: BMC Genomics 2006 7:243
  13. Mitochondrial DNA-derived sequences have become popular markers for evolutionary studies, as their comparison may yield significant insights into the evolution of both the organisms and their genomes. From the...

    Authors: Gen Hua Yue, Woei Chang Liew and Laszlo Orban
    Citation: BMC Genomics 2006 7:242
  14. Sequence data and other characters from mitochondrial genomes (gene translocations, secondary structure of RNA molecules) are useful in phylogenetic studies among metazoan animals from population to phylum lev...

    Authors: Fabian Kilpert and Lars Podsiadlowski
    Citation: BMC Genomics 2006 7:241
  15. High throughput gene expression profiling (GEP) is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying ...

    Authors: Paul Honoré, Samuel Granjeaud, Rebecca Tagett, Stéphane Deraco, Emmanuel Beaudoing, Jacques Rougemont, Stéphane Debono and Pascal Hingamp
    Citation: BMC Genomics 2006 7:240
  16. Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA bind...

    Authors: Shalev Itzkovitz, Tsvi Tlusty and Uri Alon
    Citation: BMC Genomics 2006 7:239
  17. The recent advancement in human genome sequencing and genotyping has revealed millions of single nucleotide polymorphisms (SNP) which determine the variation among human beings. One of the particular important...

    Authors: Erwin Tantoso, Yuchen Yang and Kuo-Bin Li
    Citation: BMC Genomics 2006 7:238
  18. Genome-wide profiling has allowed the regulatory interaction networks of many organisms to be visualised and the pattern of connections between genes to be studied. These networks are non-random, following a p...

    Authors: Tim F Cooper, Andrew P Morby, Annabel Gunn and Dominique Schneider
    Citation: BMC Genomics 2006 7:237
  19. Gene knockouts in a model organism such as mouse provide a valuable resource for the study of basic biology and human disease. Determining which gene has been inactivated by an untargeted gene trapping event p...

    Authors: Courtney A Harper, Conrad C Huang, Doug Stryke, Michiko Kawamoto, Thomas E Ferrin and Patricia C Babbitt
    Citation: BMC Genomics 2006 7:236
  20. Changes in gene expression are known to be responsible for phenotypic variation and susceptibility to diseases. Identification and annotation of the genomic sequence variants that cause gene expression changes...

    Authors: Debraj GuhaThakurta, Tao Xie, Manish Anand, Stephen W Edwards, Guoya Li, Susanna S Wang and Eric E Schadt
    Citation: BMC Genomics 2006 7:235
  21. 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
  22. 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
  23. 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

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

  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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

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