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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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
    Content type: Research article Published on:

  24. 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
    Content type: Research article Published on:

  25. 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
    Content type: Research article Published on:

  26. 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
    Content type: Research article Published on:

  27. 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
    Content type: Research article Published on:

  28. 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
    Content type: Methodology article Published on:

  30. 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
    Content type: Database Published on:

  31. 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
    Content type: Research article Published on:

  32. 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
    Content type: Research article Published on:

  35. 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
    Content type: Research article Published on:

  36. 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
    Content type: Methodology article Published on:

  39. Cotton (Gossypium hirsutum) is the most important fiber crop grown in 90 countries. In 2004–2005, US farmers planted 79% of the 5.7-million hectares of nuclear transgenic cotton. Unfortunately, genetically modifi...

    Authors: Seung-Bum Lee, Charalambos Kaittanis, Robert K Jansen, Jessica B Hostetler, Luke J Tallon, Christopher D Town and Henry Daniell
    Citation: BMC Genomics 2006 7:61
    Content type: Research article Published on:

  40. The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA ...

    Authors: Scott J Westenberger, Gustavo C Cerqueira, Najib M El-Sayed, Bianca Zingales, David A Campbell and Nancy R Sturm
    Citation: BMC Genomics 2006 7:60
    Content type: Research article Published on:

  41. DNA microarrays are rapidly becoming a fundamental tool in discovery-based genomic and biomedical research. However, the reliability of the microarray results is being challenged due to the existence of differ...

    Authors: Yulei Wang, Catalin Barbacioru, Fiona Hyland, Wenming Xiao, Kathryn L Hunkapiller, Julie Blake, Frances Chan, Carolyn Gonzalez, Lu Zhang and Raymond R Samaha
    Citation: BMC Genomics 2006 7:59
    Content type: Research article Published on:

  43. Contrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and t...

    Authors: Robert A Edwards, Beltran Rodriguez-Brito, Linda Wegley, Matthew Haynes, Mya Breitbart, Dean M Peterson, Martin O Saar, Scott Alexander, E Calvin Alexander Jr and Forest Rohwer
    Citation: BMC Genomics 2006 7:57
    Content type: Research article Published on:

  44. We have studied alterations of gene expression associated with naturally-occurring early life stage mortality (M74) in Baltic salmon using a cDNA microarray and real time PCR. M74-affected fry have several typ...

    Authors: Kristiina AM Vuori, Heikki Koskinen, Aleksei Krasnov, Paula Koivumäki, Sergey Afanasyev, Pekka J Vuorinen and Mikko Nikinmaa
    Citation: BMC Genomics 2006 7:56
    Content type: Research article Published on:

  45. The Cleavage Stimulation Factor (CstF) is a required protein complex for eukaryotic mRNA 3'-processing. CstF interacts with 3'-processing downstream elements (DSEs) through its 64-kDa subunit, CstF-64; however...

    Authors: Jesse Salisbury, Keith W Hutchison and Joel H Graber
    Citation: BMC Genomics 2006 7:55
    Content type: Research article Published on:

  46. For many years gene mapping studies have been performed through linkage analyses based on pedigree data. Recently, linkage disequilibrium methods based on unrelated individuals have been advocated as powerful ...

    Authors: Simon Boitard, Jihad Abdallah, Hubert de Rochambeau, Christine Cierco-Ayrolles and Brigitte Mangin
    Citation: BMC Genomics 2006 7:54
    Content type: Methodology article Published on:

  47. A number of different quantitative trait loci (QTL) for various phenotypic traits, including milk production, functional, and conformation traits in dairy cattle as well as growth and body composition traits i...

    Authors: Rosemarie Weikard, Tom Goldammer, Pascal Laurent, James E Womack and Christa Kuehn
    Citation: BMC Genomics 2006 7:53
    Content type: Research article Published on:

  48. Immune responses to sandfly saliva have been shown to protect animals against Leishmania infection. Yet very little is known about the molecular characteristics of salivary proteins from different sandflies, part...

    Authors: Jennifer M Anderson, Fabiano Oliveira, Shaden Kamhawi, Ben J Mans, David Reynoso, Amy E Seitz, Phillip Lawyer, Mark Garfield, MyVan Pham and Jesus G Valenzuela
    Citation: BMC Genomics 2006 7:52
    Content type: Research article Published on:

  49. We compared the relative precision and accuracy of expression measurements obtained from three different state-of-the-art commercial short and long-oligonucleotide microarray platforms (Affymetrix GeneChip™, G...

    Authors: Aurélien de Reyniès, Daniela Geromin, Jean-Michel Cayuela, Fabien Petel, Philippe Dessen, François Sigaux and David S Rickman
    Citation: BMC Genomics 2006 7:51
    Content type: Research article Published on:

  50. The best studied insect-symbiont system is that of aphids and their primary bacterial endosymbiont Buchnera aphidicola. Buchnera inhabits specialized host cells called bacteriocytes, provides nutrients to the aph...

    Authors: Alex CC Wilson, Helen E Dunbar, Gregory K Davis, Wayne B Hunter, David L Stern and Nancy A Moran
    Citation: BMC Genomics 2006 7:50
    Content type: Research article Published on:

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