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  1. Insects provide tractable models for enhancing our understanding of the physiological and cellular processes that enable survival at extreme low temperatures. They possess three main strategies to survive the ...

    Authors: Melody S Clark, Michael AS Thorne, Jelena Purać, Gavin Burns, Guy Hillyard, Željko D Popović, Gordana Grubor-Lajšić and M Roger Worland
    Citation: BMC Genomics 2009 10:328
    Content type: Research article Published on:

  2. Recent work has revealed that a core group of transcription factors (TFs) regulates the key characteristics of embryonic stem (ES) cells: pluripotency and self-renewal. Current efforts focus on identifying gen...

    Authors: Mike J Mason, Guoping Fan, Kathrin Plath, Qing Zhou and Steve Horvath
    Citation: BMC Genomics 2009 10:327
    Content type: Research article Published on:

  3. Gene expression profiling of small numbers of cells requires high-fidelity amplification of sub-nanogram amounts of RNA. Several methods for RNA amplification are available; however, there has been little cons...

    Authors: Julie E Lang, Mark Jesus M Magbanua, Janet H Scott, G Mike Makrigiorgos, Gang Wang, Scot Federman, Laura J Esserman, John W Park and Christopher M Haqq
    Citation: BMC Genomics 2009 10:326
    Content type: Research article Published on:

  4. The free-living nematode Caenorhabditis elegans makes a developmental decision based on environmental conditions: larvae either arrest as dauer larva, or continue development into reproductive adults. There is na...

    Authors: Simon C Harvey, Gary LA Barker, Alison Shorto and Mark E Viney
    Citation: BMC Genomics 2009 10:325
    Content type: Research article Published on:

  5. More than 20% of human transcripts have naturally occurring antisense products (or natural antisense transcripts – NATs), some of which may play a key role in a range of human diseases. To date, several databa...

    Authors: Anita Grigoriadis, Gavin R Oliver, Austin Tanney, Howard Kendrick, Matt J Smalley, Parmjit Jat and A Munro Neville
    Citation: BMC Genomics 2009 10:324
    Content type: Research article Published on:

  6. The B cell antigen receptor (BCR) is a signaling complex that mediates the differentiation of stage-specific cell fate decisions in B lymphocytes. While several studies have shown differences in signal transdu...

    Authors: Jernej Murn, Irena Mlinaric-Rascan, Pierre Vaigot, Olivier Alibert, Vincent Frouin and Xavier Gidrol
    Citation: BMC Genomics 2009 10:323
    Content type: Research article Published on:

  7. Patterns of mouse DNA hydrolysis with restriction enzymes are coincided with calculated diagrams of genomic DNA digestion in silico, except presence of additional bright bands, which correspond to monomer and dim...

    Authors: Murat A Abdurashitov, Valery A Chernukhin, Danila A Gonchar and Sergey Kh Degtyarev
    Citation: BMC Genomics 2009 10:322
    Content type: Research article Published on:

  8. About 45% of the human genome is comprised of mobile transposable elements or "junk DNA". The exaptation or co-option of these elements to provide important cellular functions is hypothesized to have played a ...

    Authors: Adrian F Gombart, Tsuyako Saito and H Phillip Koeffler
    Citation: BMC Genomics 2009 10:321
    Content type: Research article Published on:

  9. Association mapping approaches are dependent upon discovery and validation of single nucleotide polymorphisms (SNPs). To further association studies in Anopheles gambiae we conducted a major resequencing programm...

    Authors: Craig S Wilding, David Weetman, Keith Steen and Martin J Donnelly
    Citation: BMC Genomics 2009 10:320
    Content type: Research article Published on:

  11. As the amount of genome sequencing data grows, so does the problem of computational gene identification, and in particular, the splicing signals that flank exon borders. Traditional methods for identifying spl...

    Authors: Katherine M Buckley, Liliana D Florea and L Courtney Smith
    Citation: BMC Genomics 2009 10:318
    Content type: Research article Published on:

  13. Magnaporthe oryzae, rice blast fungus, is the most devastating pathogen of rice. It has emerged as a model phytopathogen for the study of host-pathogen interactions. A large body of data has been generated on dif...

    Authors: Shalabh Thakur, Sanjay Jha, Subhankar Roy-Barman and Bharat Chattoo
    Citation: BMC Genomics 2009 10:316
    Content type: Database Published on:

  14. With the escalation of high throughput prokaryotic genome sequencing, there is an ever-increasing need for databases that characterise, catalogue and present data relating to particular gene sets and genomes/m...

    Authors: Mohamed Barakat, Philippe Ortet, Cécile Jourlin-Castelli, Mireille Ansaldi, Vincent Méjean and David E Whitworth
    Citation: BMC Genomics 2009 10:315
    Content type: Database Published on:

  15. The transcription factor OCT4 is highly expressed in pluripotent embryonic stem cells which are derived from the inner cell mass of mammalian blastocysts. Pluripotency and self renewal are controlled by a tran...

    Authors: Lukas Chavez, Abha S Bais, Martin Vingron, Hans Lehrach, James Adjaye and Ralf Herwig
    Citation: BMC Genomics 2009 10:314
    Content type: Research article Published on:

  16. NOD26-like intrinsic proteins (NIPs) that belong to the aquaporin superfamily are plant-specific and exhibit a similar three-dimensional structure. Experimental evidences however revealed that functional diver...

    Authors: Qingpo Liu, Huasen Wang, Zhonghua Zhang, Jiasheng Wu, Ying Feng and Zhujun Zhu
    Citation: BMC Genomics 2009 10:313
    Content type: Research article Published on:

  17. Apicomplexan parasites are causative agents of various diseases including malaria and have been targets of extensive genomic sequencing. We generated 5'-EST collections for six apicomplexa parasites using our ...

    Authors: Hiroyuki Wakaguri, Yutaka Suzuki, Masahide Sasaki, Sumio Sugano and Junichi Watanabe
    Citation: BMC Genomics 2009 10:312
    Content type: Research article Published on:

  18. Human T-cell leukemia virus type 1 (HTLV-I) is a human retrovirus that is etiologically linked to adult T-cell leukemia (ATL), an aggressive and fatal lymphoproliferative disease. The viral transactivator, Tax...

    Authors: John M Taylor, Sofiane Ghorbel and Christophe Nicot
    Citation: BMC Genomics 2009 10:311
    Content type: Research article Published on:

  19. MHC class I antigens are encoded by a rapidly evolving gene family comprising classical and non-classical genes that are found in all vertebrates and involved in diverse immune functions. However, there is a f...

    Authors: Hannah V Siddle, Janine E Deakin, Penny Coggill, Elizabeth Hart, Yuanyuan Cheng, Emily SW Wong, Jennifer Harrow, Stephan Beck and Katherine Belov
    Citation: BMC Genomics 2009 10:310
    Content type: Research article Published on:

  20. Genomic studies in non-domestic avian models, such as the California condor and white-throated sparrow, can lead to more comprehensive conservation plans and provide clues for understanding mechanisms affectin...

    Authors: Michael N Romanov, Elaina M Tuttle, Marlys L Houck, William S Modi, Leona G Chemnick, Marisa L Korody, Emily M Stremel Mork, Christie A Otten, Tanya Renner, Kenneth C Jones, Sugandha Dandekar, Jeanette C Papp, Yang Da, Eric D Green, Vincent Magrini, Matthew T Hickenbotham…
    Citation: BMC Genomics 2009 10(Suppl 2):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  21. Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group th...

    Authors: Xueyan Shan, David A Ray, John A Bunge and Daniel G Peterson
    Citation: BMC Genomics 2009 10(Suppl 2):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  22. With the publication of the draft chicken genome and the recent production of several BAC clone libraries from non-avian reptiles and birds, it is now possible to undertake more detailed comparative genomic st...

    Authors: Charles Chapus and Scott V Edwards
    Citation: BMC Genomics 2009 10(Suppl 2):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  23. Proteins that selectively transport water across the membranes of cells are recognized as important in the normal functioning of the body systems of vertebrates. There are 13 known mammalian aquaporins (AQP0 t...

    Authors: Raphael D Isokpehi, Rajendram V Rajnarayanan, Cynthia D Jeffries, Tolulola O Oyeleye and Hari HP Cohly
    Citation: BMC Genomics 2009 10(Suppl 2):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  24. Systems Biology research tools, such as Cytoscape, have greatly extended the reach of genomic research. By providing platforms to integrate data with molecular interaction networks, researchers can more rapidl...

    Authors: Jay H Konieczka, Kevin Drew, Alex Pine, Kevin Belasco, Sean Davey, Tatiana A Yatskievych, Richard Bonneau and Parker B Antin
    Citation: BMC Genomics 2009 10(Suppl 2):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  25. Comparative genomics is an essential component of the post-genomic era. The chicken genome is the first avian genome to be sequenced and it will serve as a model for other avian species. Moreover, due to its u...

    Authors: David W Burt, Wilfrid Carrë, Mark Fell, Andy S Law, Parker B Antin, Donna R Maglott, Janet A Weber, Carl J Schmidt, Shane C Burgess and Fiona M McCarthy
    Citation: BMC Genomics 2009 10(Suppl 2):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  26. Pasteurella multocida is a gram-negative bacterial pathogen that has a broad host range. One of the diseases it causes is fowl cholera in poultry. The availability of the genome sequence of avian P. multocida iso...

    Authors: Bindu Nanduri, Leslie A Shack, Shane C Burgess and Mark L Lawrence
    Citation: BMC Genomics 2009 10(Suppl 2):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  27. With the threat of emerging infectious diseases such as avian influenza, whose natural hosts are thought to be a variety of wild water birds including duck, we are armed with very few genomic resources to inve...

    Authors: Tamsyn M Crowley, Volker R Haring, Simon Burggraaf and Robert J Moore
    Citation: BMC Genomics 2009 10(Suppl 2):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  28. The genome sequence and a high-density SNP map are now available for the chicken and can be used to identify genetic markers for use in marker-assisted selection (MAS). Effective MAS requires high linkage dise...

    Authors: Behnam Abasht, Erin Sandford, Jesus Arango, Petek Settar, Janet E Fulton, Neil P O'Sullivan, Abebe Hassen, David Habier, Rohan L Fernando, Jack CM Dekkers and Susan J Lamont
    Citation: BMC Genomics 2009 10(Suppl 2):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  30. The Avian Genomics Conference and Gene Ontology Annotation Workshop brought together researchers and students from around the world to present their latest research addressing the delivery of value from the bi...

    Authors: Susan M Bridges, Shane C Burgess and Fiona M McCarthy
    Citation: BMC Genomics 2009 10(Suppl 2):I1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  32. Aquatic organisms are continuously exposed to complex mixtures of chemicals, many of which can interfere with their endocrine system, resulting in impaired reproduction, development or survival, among others. ...

    Authors: Natàlia Garcia-Reyero, Kevin J Kroll, Li Liu, Edward F Orlando, Karen H Watanabe, María S Sepúlveda, Daniel L Villeneuve, Edward J Perkins, Gerald T Ankley and Nancy D Denslow
    Citation: BMC Genomics 2009 10:308
    Content type: Research article Published on:

  33. Hormones are signaling molecules that play vital roles in various life processes, like growth and differentiation, physiology, and reproduction. These molecules are mostly secreted by endocrine glands, and tra...

    Authors: Mamoon Rashid, Deepak Singla, Arun Sharma, Manish Kumar and Gajendra PS Raghava
    Citation: BMC Genomics 2009 10:307
    Content type: Database Published on:

  34. The thermotolerance of Aspergillus fumigatus plays a critical role in mammalian and avian infections. Thus, the identification of its adaptation mechanism to higher temperature is very important for an efficient ...

    Authors: Jin Hwan Do, Rui Yamaguchi and Satoru Miyano
    Citation: BMC Genomics 2009 10:306
    Content type: Research article Published on:

  35. Skeletal muscle growth and maintenance are essential for human health. One of the muscle regulatory genes, namely myostatin, a member of transforming growth factor-β, plays a dominant role in the genetic contr...

    Authors: Baoping Zhao, Eileena J Li, Robert J Wall and Jinzeng Yang
    Citation: BMC Genomics 2009 10:305
    Content type: Research article Published on:

  36. ATP-dependent chromatin remodeling and the covalent modification of histones play central roles in determining chromatin structure and function. Although several specific interactions between these two activit...

    Authors: Zhiming Dai, Xianhua Dai, Qian Xiang, Jihua Feng, Jiang Wang, Yangyang Deng and Caisheng He
    Citation: BMC Genomics 2009 10:304
    Content type: Research article Published on:

  37. The Gram-negative bacterium Photorhabdus asymbiotica (Pa) has been recovered from human infections in both North America and Australia. Recently, Pa has been shown to have a nematode vector that can also infect i...

    Authors: Paul Wilkinson, Nicholas R Waterfield, Lisa Crossman, Craig Corton, Maria Sanchez-Contreras, Isabella Vlisidou, Andrew Barron, Alexandra Bignell, Louise Clark, Douglas Ormond, Matthew Mayho, Nathalie Bason, Frances Smith, Mark Simmonds, Carol Churcher, David Harris…
    Citation: BMC Genomics 2009 10:302
    Content type: Research article Published on:

  38. Affymetrix GeneChip® high-density oligonucleotide arrays are widely used in biological and medical research because of production reproducibility, which facilitates the comparison of results between experiment ru...

    Authors: Zhongxue Chen, Monnie McGee, Qingzhong Liu, Megan Kong, Youping Deng and Richard H Scheuermann
    Citation: BMC Genomics 2009 10(Suppl 1):S19
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  39. In this study, we formulate a computational reaction model following a chemical kinetic theory approach to predict the binding rate constant for the siRNA-RISC complex formation reaction. The model allowed us ...

    Authors: Preetam Ghosh, Robert Dullea, James E Fischer, Tom G Turi, Ronald W Sarver, Chaoyang Zhang, Kalyan Basu, Sajal K Das and Bradley W Poland
    Citation: BMC Genomics 2009 10(Suppl 1):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  40. Inferring a gene regulatory network (GRN) from high throughput biological data is often an under-determined problem and is a challenging task due to the following reasons: (1) thousands of genes are involved i...

    Authors: Yuji Zhang, Jianhua Xuan, Benildo G de los Reyes, Robert Clarke and Habtom W Ressom
    Citation: BMC Genomics 2009 10(Suppl 1):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  41. How gene duplication has influenced the evolution of gene networks is one of the core problems in evolution. Current duplication-divergence theories generally suggested that genes on the periphery of the netwo...

    Authors: Yong Huang, Ying Zheng, Zhixi Su and Xun Gu
    Citation: BMC Genomics 2009 10(Suppl 1):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  42. Knowledge of protein-DNA interactions at the structural-level can provide insights into the mechanisms of protein-DNA recognition and gene regulation. Although over 1400 protein-DNA complex structures have bee...

    Authors: RyangGuk Kim and Jun-tao Guo
    Citation: BMC Genomics 2009 10(Suppl 1):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  43. The steadily increasing number of prokaryotic genomes has accelerated the study of genome evolution; in particular, the availability of sets of genomes from closely related bacteria has facilitated the explora...

    Authors: Jianying Gu, Jennifer Neary, Hong Cai, Audrey Moshfeghian, Stephen A Rodriguez, Timothy G Lilburn and Yufeng Wang
    Citation: BMC Genomics 2009 10(Suppl 1):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  45. The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases.

    Authors: John D Osborne, Jared Flatow, Michelle Holko, Simon M Lin, Warren A Kibbe, Lihua (Julie) Zhu, Maria I Danila, Gang Feng and Rex L Chisholm
    Citation: BMC Genomics 2009 10(Suppl 1):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  46. Alternative transcript diversity manifests itself as a prime cause of complexity in higher eukaryotes. Recently, transcript diversity studies have suggested that 60–80% of human genes are alternatively spliced...

    Authors: Elsa Chacko and Shoba Ranganathan
    Citation: BMC Genomics 2009 10(Suppl 1):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  47. In the classification of Mass Spectrometry (MS) proteomics data, peak detection, feature selection, and learning classifiers are critical to classification accuracy. To better understand which methods are more...

    Authors: Qingzhong Liu, Andrew H Sung, Mengyu Qiao, Zhongxue Chen, Jack Y Yang, Mary Qu Yang, Xudong Huang and Youping Deng
    Citation: BMC Genomics 2009 10(Suppl 1):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  48. Gene expression time series array data has become a useful resource for investigating gene functions and the interactions between genes. However, the gene expression arrays are always mixed with noise, and man...

    Authors: Yadong Wang, Guohua Wang, Bo Yang, Haijun Tao, Jack Y Yang, Youping Deng and Yunlong Liu
    Citation: BMC Genomics 2009 10(Suppl 1):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  49. Protein-DNA interactions are involved in many biological processes essential for cellular function. To understand the molecular mechanism of protein-DNA recognition, it is necessary to identify the DNA-binding...

    Authors: Liangjiang Wang, Mary Qu Yang and Jack Y Yang
    Citation: BMC Genomics 2009 10(Suppl 1):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  50. The advent of high-throughput next generation sequencing technologies have fostered enormous potential applications of supercomputing techniques in genome sequencing, epi-genetics, metagenomics, personalized m...

    Authors: Mary Qu Yang, Brian D Athey, Hamid R Arabnia, Andrew H Sung, Qingzhong Liu, Jack Y Yang, Jinghe Mao and Youping Deng
    Citation: BMC Genomics 2009 10(Suppl 1):I1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

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