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  1. Staphylococcus epidermidis, long regarded as an innocuous commensal bacterium of the human skin, is the most frequent cause of nosocomial infections associated with implanted medical devices. This conditional pat...

    Authors: Wu Wei, ZhiWei Cao, Yu-Li Zhu, XiaoJing Wang, GuoHui Ding, Hao Xu, PeiLin Jia, Di Qu, Antoine Danchin and YiXue Li
    Citation: BMC Genomics 2006 7:112
  2. One of the approaches for conducting genomics research in organisms without extant microarray platforms is to profile their expression patterns by using Cross-Species Hybridization (CSH). Several different stu...

    Authors: Carmiya Bar-Or, Meira Bar-Eyal, Tali Z Gal, Yoram Kapulnik, Henryk Czosnek and Hinanit Koltai
    Citation: BMC Genomics 2006 7:110
  3. Using microarrays by co-hybridizing two samples labeled with different dyes enables differential gene expression measurements and comparisons across slides while controlling for within-slide variability. Typic...

    Authors: Rishi L Khan, Gregory E Gonye, Guang Gao and James S Schwaber
    Citation: BMC Genomics 2006 7:109
  4. A number of publications have recently examined the occurrence and properties of the feed-forward motif in a variety of networks, including those that are of interest in genome biology, such as gene networks. ...

    Authors: Piers J Ingram, Michael PH Stumpf and Jaroslav Stark
    Citation: BMC Genomics 2006 7:108
  5. bZIPs are transcription factors that are found throughout the eukarya from fungi to flowering plants and mammals. They contain highly conserved basic region (BR) and leucine zipper (LZ) domains and often funct...

    Authors: Gregory D Amoutzias, Erich Bornberg-Bauer, Stephen G Oliver and David L Robertson
    Citation: BMC Genomics 2006 7:107
  6. Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to ...

    Authors: Meizhong Luo, HyeRan Kim, Dave Kudrna, Nicholas B Sisneros, So-Jeong Lee, Christopher Mueller, Kristi Collura, Andrea Zuccolo, E Bryan Buckingham, Suzanne M Grim, Kazuyo Yanagiya, Hidetoshi Inoko, Takashi Shiina, Martin F Flajnik, Rod A Wing and Yuko Ohta
    Citation: BMC Genomics 2006 7:106
  7. Fibroblast growth factors (FGFs) are multifunctional proteins that play important roles in cell communication, proliferation and differentiation. However, many aspects of their activities are not well defined....

    Authors: Cornel Popovici, Yael Berda, Fabien Conchonaud, Aurélie Harbis, Daniel Birnbaum and Régine Roubin
    Citation: BMC Genomics 2006 7:105
  8. Human embryonic stem (ES) cells hold great promise for medicine and science. The transcriptome of human ES cells has been studied in detail in recent years. However, no systematic analysis has yet addressed wh...

    Authors: Huai Li, Ying Liu, Soojung Shin, Yu Sun, Jeanne F Loring, Mark P Mattson, Mahendra S Rao and Ming Zhan 1
    Citation: BMC Genomics 2006 7:103
  9. By comparing the quail genome with that of chicken, chromosome rearrangements that have occurred in these two galliform species over 35 million years of evolution can be detected. From a more practical point o...

    Authors: Boniface B Kayang, Valérie Fillon, Miho Inoue-Murayama, Mitsuru Miwa, Sophie Leroux, Katia Fève, Jean-Louis Monvoisin, Frédérique Pitel, Matthieu Vignoles, Céline Mouilhayrat, Catherine Beaumont, Shin'ichi Ito, Francis Minvielle and Alain Vignal
    Citation: BMC Genomics 2006 7:101
  10. Chloroplasts descended from cyanobacteria and have a drastically reduced genome following an endosymbiotic event. Many genes of the ancestral cyanobacterial genome have been transferred to the plant nuclear ge...

    Authors: Zhuo Wang, Xin-Guang Zhu, Yazhu Chen, Yuanyuan Li, Jing Hou, Yixue Li and Lei Liu
    Citation: BMC Genomics 2006 7:100
  11. Nucleoplasmin is a nuclear chaperone protein that has been shown to participate in the remodeling of sperm chromatin immediately after fertilization by displacing highly specialized sperm nuclear basic protein...

    Authors: Lindsay J Frehlick, José María Eirín-López, Erin D Jeffery, Donald F Hunt and Juan Ausió
    Citation: BMC Genomics 2006 7:99
  12. The GIY-YIG domain was initially identified in homing endonucleases and later in other selfish mobile genetic elements (including restriction enzymes and non-LTR retrotransposons) and in enzymes involved in DN...

    Authors: Stanislaw Dunin-Horkawicz, Marcin Feder and Janusz M Bujnicki
    Citation: BMC Genomics 2006 7:98
  13. Gene expression profiling by microarray analysis of cells enriched by laser capture microdissection (LCM) faces several technical challenges. Frozen sections yield higher quality RNA than paraffin-imbedded sec...

    Authors: Hongyang Wang, James D Owens, Joanna H Shih, Ming-Chung Li, Robert F Bonner and J Frederic Mushinski
    Citation: BMC Genomics 2006 7:97
  14. Validation of a novel gene expression signature in independent data sets is a critical step in the development of a clinically useful test for cancer patient risk-stratification. However, validation is often u...

    Authors: Zhiyuan Hu, Cheng Fan, Daniel S Oh, JS Marron, Xiaping He, Bahjat F Qaqish, Chad Livasy, Lisa A Carey, Evangeline Reynolds, Lynn Dressler, Andrew Nobel, Joel Parker, Matthew G Ewend, Lynda R Sawyer, Junyuan Wu, Yudong Liu…
    Citation: BMC Genomics 2006 7:96
  15. Marrow-derived stromal cells (MSCs) maintain the capability of self-renewal and differentiation into multiple lineages in adult life. Age-related changes are recognized by a decline in the stemness potential t...

    Authors: Uri David Akavia, Irena Shur, Gideon Rechavi and Dafna Benayahu
    Citation: BMC Genomics 2006 7:95
  16. Owing to the explosion of information generated by human genomics, analysis of publicly available databases can help identify potential candidate genes relevant to the cancerous phenotype. The aim of this stud...

    Authors: Abdel Aouacheria, Vincent Navratil, Audrey Barthelaix, Dominique Mouchiroud and Christian Gautier
    Citation: BMC Genomics 2006 7:94
  17. The gene expression profiles of most human tissues have been studied by determining the transcriptome of whole tissue homogenates. Due to the solid composition of tissues it is difficult to study the transcrip...

    Authors: Asa J Oudes, Dave S Campbell, Carrie M Sorensen, Laura S Walashek, Lawrence D True and Alvin Y Liu
    Citation: BMC Genomics 2006 7:92
  18. Comparative genomic hybridization can rapidly identify chromosomal regions that vary between organisms and tissues. This technique has been applied to detecting differences between normal and cancerous tissues...

    Authors: Bradley D Anderson, Michael C Gilson, Abigail A Scott, Bryan S Biehl, Jeremy D Glasner, Gireesh Rajashekara, Gary A Splitter and Nicole T Perna
    Citation: BMC Genomics 2006 7:91
  19. Post-translational modification of histones resulting in chromatin remodelling plays a key role in the regulation of gene expression. Here we report characteristic patterns of expression of 12 members of 3 cla...

    Authors: Hilal Özdağ, Andrew E Teschendorff, Ahmed Ashour Ahmed, Sarah J Hyland, Cherie Blenkiron, Linda Bobrow, Abhi Veerakumarasivam, Glynn Burtt, Tanya Subkhankulova, Mark J Arends, V Peter Collins, David Bowtell, Tony Kouzarides, James D Brenton and Carlos Caldas
    Citation: BMC Genomics 2006 7:90
  20. The importance of a network motif (a recurring interconnected pattern of special topology which is over-represented in a biological network) lies in its position in the hierarchy between the protein molecule a...

    Authors: Wei-Po Lee, Bing-Chiang Jeng, Tun-Wen Pai, Chin-Pei Tsai, Chang-Yung Yu and Wen-Shyong Tzou
    Citation: BMC Genomics 2006 7:89
  21. Dinoflagellates are one of the most important classes of marine and freshwater algae, notable both for their functional diversity and ecological significance. They occur naturally as free-living cells, as endo...

    Authors: Deana L Erdner and Donald M Anderson
    Citation: BMC Genomics 2006 7:88
  22. The cynomolgus monkey (Macaca fascicularis) is one of the most widely used surrogate animal models for an increasing number of human diseases and vaccines, especially immune-system-related ones. Towards a better ...

    Authors: Wei-Hua Chen, Xue-Xia Wang, Wei Lin, Xiao-Wei He, Zhen-Qiang Wu, Ying Lin, Song-Nian Hu and Xiao-Ning Wang
    Citation: BMC Genomics 2006 7:82
  23. Due to the lack of availability of large genomic sequences for peach or other Prunus species, the degree of synteny conservation between the Prunus species and Arabidopsis has not been systematically assessed. Us...

    Authors: Sook Jung, Dorrie Main, Margaret Staton, Ilhyung Cho, Tatyana Zhebentyayeva, Pere Arús and Albert Abbott
    Citation: BMC Genomics 2006 7:81
  24. In vitro systems have inherent limitations in their ability to model whole organism gene responses, which must be identified and appropriately considered when developing predictive biomarkers of in vivo toxicity....

    Authors: Edward Dere, Darrell R Boverhof, Lyle D Burgoon and Timothy R Zacharewski
    Citation: BMC Genomics 2006 7:80
  25. The past three decades have witnessed a dramatic increase in interest in the whitefly Bemisia tabaci, owing to its nature as a taxonomically cryptic species, the damage it causes to a large number of herbaceous p...

    Authors: Dena Leshkowitz, Shirley Gazit, Eli Reuveni, Murad Ghanim, Henryk Czosnek, Cindy McKenzie, Robert L Shatters Jr and Judith K Brown
    Citation: BMC Genomics 2006 7:79
  26. Microsatellites are the tandem repeats of nucleotide motifs of size 1–6 bp observed in all known genomes. These repeats show length polymorphism characterized by either insertion or deletion (indels) of the re...

    Authors: Vattipally B Sreenu, Pankaj Kumar, Javaregowda Nagaraju and Hampapathalu A Nagarajaram
    Citation: BMC Genomics 2006 7:78
  27. Massively Parallel Signature Sequencing (MPSS) technology was recently developed as a high-throughput technology for measuring the concentration of mRNA transcripts in a sample. It has previously been observed...

    Authors: Junfeng Chen and Magnus Rattray
    Citation: BMC Genomics 2006 7:77
  28. Shewanella oneidensis MR-1 is a facultative, gram-negative bacterium capable of coupling the oxidation of organic carbon to a wide range of electron acceptors such as oxygen, nitrate and metals, and has potential...

    Authors: Weimin Gao, Yongqing Liu, Carol S Giometti, Sandra L Tollaksen, Tripti Khare, Liyou Wu, Dawn M Klingeman, Matthew W Fields and Jizhong Zhou
    Citation: BMC Genomics 2006 7:76
  29. Expression of the LIM-homeobox gene Lhx2 in murine hematopoietic cells allows for the generation of hematopoietic stem cell (HSC)-like cell lines. To address the molecular basis of Lhx2 function, we generated HSC...

    Authors: Karin Richter, Valtteri Wirta, Lina Dahl, Sara Bruce, Joakim Lundeberg, Leif Carlsson and Cecilia Williams
    Citation: BMC Genomics 2006 7:75
  30. Staphylococcus aureus or MRSA (Methicillin Resistant S. aureus), is an acquired pathogen and the primary cause of nosocomial infections worldwide. In S. aureus, teichoic acid is an essential component of the cell...

    Authors: Ziliang Qian, Yanbin Yin, Yong Zhang, Lingyi Lu, Yixue Li and Ying Jiang
    Citation: BMC Genomics 2006 7:74
  31. Cre-loxP recombination refers to the process of site-specific recombination mediated by two loxP sequences and the Cre recombinase protein. Transgenic experiments exploit integrative recombination, where a donor ...

    Authors: Perseus I Missirlis, Duane E Smailus and Robert A Holt
    Citation: BMC Genomics 2006 7:73
  32. DNA microarrays have proven powerful for functional genomics studies. Several technologies exist for the generation of whole-genome arrays. It is well documented that 25mer probes directed against different re...

    Authors: Danielle L Leiske, Anis Karimpour-Fard, Patrick S Hume, Benjamin D Fairbanks and Ryan T Gill
    Citation: BMC Genomics 2006 7:72
  33. The Stanley Medical Research Institute online genomics database (SMRIDB) is a comprehensive web-based system for understanding the genetic effects of human brain disease (i.e. bipolar, schizophrenia, and depre...

    Authors: Brandon W Higgs, Michael Elashoff, Sam Richman and Beata Barci
    Citation: BMC Genomics 2006 7:70
  34. During the last two decades progress in the genetics of aging in invertebrate models such as C. elegans and D. melanogaster has clearly demonstrated the existence of regulatory pathways that control the rate of a...

    Authors: Fabrice Girardot, Christelle Lasbleiz, Véronique Monnier and Hervé Tricoire
    Citation: BMC Genomics 2006 7:69
  35. Thymidylate synthase (TS) is a critical target for cancer chemotherapy and is one of the most extensively studied biomarkers for fluoropyrimidine-based chemotherapy. In addition to its critical role in enzyme ...

    Authors: Yaguang Xi, Go Nakajima, John C Schmitz, Edward Chu and Jingfang Ju
    Citation: BMC Genomics 2006 7:68
  36. Prostate cancer (CaP) is a disease with multifactorial etiology that includes both genetic and environmental components. The knowledge of the genetic basis of CaP has increased over the past years, mainly in t...

    Authors: Simon Hughes, Maisa Yoshimoto, Ben Beheshti, Richard S Houlston, Jeremy A Squire and Andrew Evans
    Citation: BMC Genomics 2006 7:65
  37. Transcriptome data from quantitative PCR (Q-PCR) and DNA microarrays are typically obtained from a fixed amount of RNA collected per sample. Therefore, variations in tissue cellularity and RNA yield across sam...

    Authors: Jun Kanno, Ken-ichi Aisaki, Katsuhide Igarashi, Noriyuki Nakatsu, Atsushi Ono, Yukio Kodama and Taku Nagao
    Citation: BMC Genomics 2006 7:64

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