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  1. The multi-step process of carcinogenesis can be more fully understood by characterizing gene expression changes induced in cells by carcinogens. In this study, expression microarrays were used to monitor the a...

    Authors: Sarah L Hockley, Volker M Arlt, Daniel Brewer, Ian Giddings and David H Phillips
    Citation: BMC Genomics 2006 7:260
    Content type: Research article Published on:

  2. 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
    Content type: Research article Published on:

  3. Quantitative variation in gene expression has been proposed to underlie phenotypic variation among human individuals. A facilitating step towards understanding the basis for gene expression variability is asso...

    Authors: Vineet K Sharma, Anu Sharma, Naveen Kumar, Mamta Khandelwal, Kiran Kumar Mandapati, Shirley Horn-Saban, Liora Strichman-Almashanu, Doron Lancet, Samir K Brahmachari and Srinivasan Ramachandran
    Citation: BMC Genomics 2006 7:258
    Content type: Database Published on:

  4. 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
    Content type: Methodology article Published on:

  6. 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
    Content type: Research article Published on:

  8. 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
    Content type: Research article Published on:

  9. 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
    Content type: Research article Published on:

  10. 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
    Content type: Research article Published on:

  11. 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
    Content type: Research article Published on:

  13. 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
    Content type: Research article Published on:

  14. 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
    Content type: Research article Published on:

  15. 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
    Content type: Methodology article Published on:

  16. 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
    Content type: Research article Published on:

  18. 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
    Content type: Research article Published on:

  19. 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
    Content type: Research article Published on:

  20. 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
    Content type: Research article Published on:

  21. 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
    Content type: Software Published on:

  22. 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
    Content type: Research article Published on:

  23. 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
    Content type: Research article Published on:

  24. 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
    Content type: Research article Published on:

  25. 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
    Content type: Research article Published on:

  26. 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
    Content type: Research article Published on:

  28. 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 Published on:

  29. 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 Published on:

  30. 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 Published on:

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

  31. 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 Published on:

  32. 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 Published on:

  33. 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 Published on:

  34. 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 Published on:

  35. 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 Published on:

  36. 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 Published on:

  37. 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 Published on:

  38. 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 Published on:

  39. 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 Published on:

  41. 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 Published on:

  43. 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 Published on:

  44. 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 Published on:

  45. 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 Published on:

  46. 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 Published on:

  48. 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 Published on:

  49. 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 Published on:

  50. 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 Published on:

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BMC Genomics

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