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  1. Gene expression profiling has been used to define molecular phenotypes of complex diseases such as breast cancer. The luminal A and basal-like subtypes have been repeatedly identified and validated as the two ...

    Authors: Therese Sørlie, Yulei Wang, Chunlin Xiao, Hilde Johnsen, Bjørn Naume, Raymond R Samaha and Anne-Lise Børresen-Dale
    Citation: BMC Genomics 2006 7:127
    Content type: Research article Published on:

  2. Genomes of gram-positive bacteria encode many putative cell-surface proteins, of which the majority has no known function. From the rapidly increasing number of available genome sequences it has become apparen...

    Authors: Roland Siezen, Jos Boekhorst, Lidia Muscariello, Douwe Molenaar, Bernadet Renckens and Michiel Kleerebezem
    Citation: BMC Genomics 2006 7:126
    Content type: Research article Published on:

  5. The Fragile Histidine Triad gene (FHIT) is an oncosuppressor implicated in many human cancers, including vesical tumors. FHIT is frequently hit by deletions caused by fragility at FRA3B, the most active of human ...

    Authors: Cristina Uboldi, Elena Guidi, Sante Roperto, Valeria Russo, Franco Roperto, Giulia Pia Di Meo, Leopoldo Iannuzzi, Sandrine Floriot, Mekki Boussaha, André Eggen and Luca Ferretti
    Citation: BMC Genomics 2006 7:123
    Content type: Research article Published on:

  7. Olfactory receptors (ORs) are the largest gene family in the human genome. Although they are expected to be expressed specifically in olfactory tissues, some ectopic expression has been reported, with special ...

    Authors: Ester Feldmesser, Tsviya Olender, Miriam Khen, Itai Yanai, Ron Ophir and Doron Lancet
    Citation: BMC Genomics 2006 7:121
    Content type: Research article Published on:

  8. The majority of introns in gene transcripts are found within the coding sequences (CDSs). A small but significant fraction of introns are also found to reside within the untranslated regions (5'UTRs and 3'UTRs...

    Authors: Betty YW Chung, Cas Simons, Andrew E Firth, Chris M Brown and Roger P Hellens
    Citation: BMC Genomics 2006 7:120
    Content type: Research article Published on:

  9. Large scale sequencing of cDNA libraries can provide profiles of genes expressed in an organism under defined biological and environmental circumstances. We have analyzed sequences of 4541 Expressed Sequence T...

    Authors: Ali N Dana, Maureen E Hillenmeyer, Neil F Lobo, Marcia K Kern, Patricia A Romans and Frank H Collins
    Citation: BMC Genomics 2006 7:119
    Content type: Research article Published on:

  10. The autism spectrum encompasses a set of complex multigenic developmental disorders that severely impact the development of language, non-verbal communication, and social skills, and are associated with odd, s...

    Authors: Valerie W Hu, Bryan C Frank, Shannon Heine, Norman H Lee and John Quackenbush
    Citation: BMC Genomics 2006 7:118
    Content type: Research article Published on:

  11. The evolution of viral quasispecies can influence viral pathogenesis and the response to antiviral treatments. Mutant clouds in infected organisms represent the first stage in the genetic and antigenic diversi...

    Authors: Verónica Martín, Celia Perales, David Abia, Angel R Ortíz, Esteban Domingo and Carlos Briones
    Citation: BMC Genomics 2006 7:117
    Content type: Methodology article Published on:

  12. The completed sequence of the Anopheles gambiae genome has enabled genome-wide analyses of gene expression and regulation in this principal vector of human malaria. These investigations have created a demand for ...

    Authors: Sumudu N Dissanayake, Osvaldo Marinotti, Jose Marcos C Ribeiro and Anthony A James
    Citation: BMC Genomics 2006 7:116
    Content type: Database Published on:

  14. Transmissible spongiform encephalopathies (TSEs) or prion diseases are fatal neurodegenerative disorders which occur in humans and various animal species. Examples include Creutzfeldt-Jakob disease (CJD) in hu...

    Authors: Pamela J Skinner, Hayet Abbassi, Bruce Chesebro, Richard E Race, Cavan Reilly and Ashley T Haase
    Citation: BMC Genomics 2006 7:114
    Content type: Research article Published on:

  15. Comparative genomic analysis using cDNA microarray is a new approach and a useful tool to identify important genetic sequences or genes that are conserved throughout evolution. Identification of these conserve...

    Authors: Maud Vallée, Claude Robert, Steve Méthot, Marie-France Palin and Marc-André Sirard
    Citation: BMC Genomics 2006 7:113
    Content type: Research article Published on:

  16. 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
    Content type: Research article Published on:

  17. The MRP 1 gene encodes the 190 kDa multidrug resistance-associated protein 1 (MRP1/ABCC1) and effluxes diverse drugs and xenobiotics. Sequence variations within this gene might account for differences in drug res...

    Authors: Zihua Wang, Pui-Hoon Sew, Helen Ambrose, Stephen Ryan, Samuel S Chong, Edmund JD Lee and Caroline GL Lee
    Citation: BMC Genomics 2006 7:111
    Content type: Research article Published on:

  18. 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
    Content type: Methodology article Published on:

  19. 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
    Content type: Methodology article Published on:

  20. 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
    Content type: Research article Published on:

  21. 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
    Content type: Research article Published on:

  22. 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
    Content type: Research article Published on:

  23. 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
    Content type: Research article Published on:

  25. 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
    Content type: Research article Published on:

  27. 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
    Content type: Research article Published on:

  28. 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
    Content type: Research article Published on:

  29. 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
    Content type: Research article Published on:

  30. 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
    Content type: Research article Published on:

  31. 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
    Content type: Research article Published on:

  32. 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
    Content type: Research article Published on:

  33. 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
    Content type: Research article Published on:

  34. 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
    Content type: Research article Published on:

  36. 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
    Content type: Research article Published on:

  37. 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
    Content type: Software Published on:

  38. 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
    Content type: Research article Published on:

  39. 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
    Content type: Research article Published on:

  40. 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
    Content type: Research article Published on:

  46. 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
    Content type: Research article Published on:

  47. 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
    Content type: Research article Published on:

  48. 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
    Content type: Research article Published on:

  49. 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
    Content type: Research article Published on:

  50. 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
    Content type: Research article Published on:

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