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  1. Massive parallel sequencing has the potential to replace microarrays as the method for transcriptome profiling. Currently there are two protocols: full-length RNA sequencing (RNA-SEQ) and 3'-tag digital gene e...

    Authors: Yan W Asmann, Eric W Klee, E Aubrey Thompson, Edith A Perez, Sumit Middha, Ann L Oberg, Terry M Therneau, David I Smith, Gregory A Poland, Eric D Wieben and Jean-Pierre A Kocher
    Citation: BMC Genomics 2009 10:531
    Content type: Research article Published on:

  2. The understanding of the biological function, regulation, and cellular interactions of the yeast genome and proteome, along with the high conservation in gene function found between yeast genes and their human...

    Authors: Adriana Arita, Xue Zhou, Thomas P Ellen, Xin Liu, Jingxiang Bai, John P Rooney, Adrienne Kurtz, Catherine B Klein, Wei Dai, Thomas J Begley and Max Costa
    Citation: BMC Genomics 2009 10:524
    Content type: Research article Published on:

  3. Chickpea (Cicer arietinum L.), an important grain legume crop of the world is seriously challenged by terminal drought and salinity stresses. However, very limited number of molecular markers and candidate genes ...

    Authors: Rajeev K Varshney, Pavana J Hiremath, Pazhamala Lekha, Junichi Kashiwagi, Jayashree Balaji, Amit A Deokar, Vincent Vadez, Yongli Xiao, Ramamurthy Srinivasan, Pooran M Gaur, Kadambot HM Siddique, Christopher D Town and David A Hoisington
    Citation: BMC Genomics 2009 10:523
    Content type: Research article Published on:

  4. Microarray-based Comparative Genomic Hybridisation (CGH) has been used to assess genetic variability between bacterial strains. Crucial for interpretation of microarray data is the availability of a reference ...

    Authors: Neeltje Carpaij, Ad C Fluit, Jodi A Lindsay, Marc JM Bonten and Rob JL Willems
    Citation: BMC Genomics 2009 10:522
    Content type: Methodology article Published on:

  5. With the completion of the whole genome sequence for many organisms, investigations into genomic structure have revealed that gene distribution is variable, and that genes with similar function or expression a...

    Authors: Simon C Lovell, Xiting Li, Nimmi R Weerasinghe and Kathryn E Hentges
    Citation: BMC Genomics 2009 10:521
    Content type: Research article Published on:

  7. The emergence of isoform-sensitive microarrays has helped fuel in-depth studies of the human transcriptome. The Affymetrix GeneChip Human Exon 1.0 ST Array (Exon Array) has been previously shown to be effectiv...

    Authors: Kevin CH Ha, Jasmin Coulombe-Huntington and Jacek Majewski
    Citation: BMC Genomics 2009 10:519
    Content type: Methodology article Published on:

  8. Alternative polyadenylation sites within a gene can lead to alternative transcript variants. Although bioinformatic analysis has been conducted to detect polyadenylation sites using nucleic acid sequences (EST...

    Authors: Pingzhang Wang, Peng Yu, Peng Gao, Taiping Shi and Dalong Ma
    Citation: BMC Genomics 2009 10:518
    Content type: Research article Published on:

  10. Gene expression microarrays and real-time PCR are common methods used to measure mRNA levels. Each method has a fundamentally different approach of normalization between samples. Relative quantification of gen...

    Authors: Lasse Folkersen, Sanela Kurtovic, Anton Razuvaev, Hanna E Agardh, Anders Gabrielsen and Gabrielle Paulsson-Berne
    Citation: BMC Genomics 2009 10:516
    Content type: Research article Published on:

  11. SnoRNAs represent an excellent model for studying the structural and functional evolution of small non-coding RNAs involved in the post-transcriptional modification machinery for rRNAs and snRNAs in eukaryotic...

    Authors: Na Liu, Zhen-Dong Xiao, Chun-Hong Yu, Peng Shao, Yin-Tong Liang, Dao-Gang Guan, Jian-Hua Yang, Chun-Long Chen, Liang-Hu Qu and Hui Zhou
    Citation: BMC Genomics 2009 10:515
    Content type: Research article Published on:

  12. There are thousands of very diverse ciliate species from which only a handful mitochondrial genomes have been studied so far. These genomes are rather similar because the ciliates analysed (Tetrahymena spp. and P...

    Authors: Rob M de Graaf, Theo A van Alen, Bas E Dutilh, Jan WP Kuiper, Hanneke JAA van Zoggel, Minh Bao Huynh, Hans-Dieter Görtz, Martijn A Huynen and Johannes HP Hackstein
    Citation: BMC Genomics 2009 10:514
    Content type: Research article Published on:

  13. Mid-range inhomogeneity or MRI is the significant enrichment of particular nucleotides in genomic sequences extending from 30 up to several thousands of nucleotides. The best-known manifestation of MRI is CpG ...

    Authors: Ashwin Prakash, Samuel S Shepard, Jie He, Benjamin Hart, Miao Chen, Surya P Amarachintha, Olga Mileyeva-Biebesheimer, Jason Bechtel and Alexei Fedorov
    Citation: BMC Genomics 2009 10:513
    Content type: Research article Published on:

  14. MicroRNAs (miRNAs) play critical roles in a wide spectrum of biological processes and have been shown to be important effectors in the intricate host-pathogen interaction networks. Avian influenza virus (AIV) ...

    Authors: Ying Wang, Vinayak Brahmakshatriya, Huifeng Zhu, Blanca Lupiani, Sanjay M Reddy, Byung-Jun Yoon, Preethi H Gunaratne, Jong Hwan Kim, Rui Chen, Junjun Wang and Huaijun Zhou
    Citation: BMC Genomics 2009 10:512
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2010 11:373

  15. Somatic cell nuclear transfer (scNT)-derived piglets have high rates of mortality, including stillbirth and postnatal death. Here, we examined severe malformed umbilical cords (MUC), as well as other organs, f...

    Authors: Jong-Yi Park, Jae-Hwan Kim, Yun-Jung Choi, Kyu-Chan Hwang, Seong-Keun Cho, Ho-Hyun Park, Seung-Sam Paik, Teoan Kim, ChanKyu Park, Hoon Taek Lee, Han Geuk Seo, Soo-Bong Park, Seongsoo Hwang and Jin-Hoi Kim
    Citation: BMC Genomics 2009 10:511
    Content type: Research article Published on:

  16. Subcellular trafficking is a hallmark of eukaryotic cells. Because of their pivotal role in the process, a great deal of attention has been paid to the SNARE proteins. Most R-SNAREs, or "longins", however, als...

    Authors: Marco Vedovato, Valeria Rossi, Joel B Dacks and Francesco Filippini
    Citation: BMC Genomics 2009 10:510
    Content type: Research article Published on:

  17. The purpose of this research was to develop a novel information theoretic method and an efficient algorithm for analyzing the gene-gene (GGI) and gene-environmental interactions (GEI) associated with quantitat...

    Authors: Pritam Chanda, Lara Sucheston, Song Liu, Aidong Zhang and Murali Ramanathan
    Citation: BMC Genomics 2009 10:509
    Content type: Methodology article Published on:

  19. Emerging evidences suggest that enteric glial cells (EGC), a major constituent of the enteric nervous system (ENS), are key regulators of intestinal epithelial barrier (IEB) functions. Indeed EGC inhibit intes...

    Authors: Laurianne Van Landeghem, Maxime M Mahé, Raluca Teusan, Jean Léger, Isabelle Guisle, Rémi Houlgatte and Michel Neunlist
    Citation: BMC Genomics 2009 10:507
    Content type: Research article Published on:

  20. The mechanisms that shape the host plant range of herbivorous insect are to date not well understood but knowledge of these mechanisms and the selective forces that influence them can expand our understanding ...

    Authors: Hanna M Heidel-Fischer, Dalial Freitak, Niklas Janz, Lina Söderlind, Heiko Vogel and Sören Nylin
    Citation: BMC Genomics 2009 10:506
    Content type: Research article Published on:

  21. Plant growth is a complex process involving cell division and elongation. Arabidopsis thaliana hypocotyls undergo a 100-fold length increase mainly by cell elongation. Cell enlargement implicates significant chan...

    Authors: Elisabeth Jamet, David Roujol, Hélène San-Clemente, Muhammad Irshad, Ludivine Soubigou-Taconnat, Jean-Pierre Renou and Rafael Pont-Lezica
    Citation: BMC Genomics 2009 10:505
    Content type: Research article Published on:

  22. The origin of novel traits and their subsequent diversification represent central themes in evo-devo and evolutionary ecology. Here we explore the genetic and genomic basis of a class of traits that is both no...

    Authors: Teiya Kijimoto, James Costello, Zuojian Tang, Armin P Moczek and Justen Andrews
    Citation: BMC Genomics 2009 10:504
    Content type: Research article Published on:

  23. Furunculosis, a disease caused with gram negative bacteria Aeromonas salmonicida produces heavy losses in aquaculture. Vaccination against furunculosis reduces mortality of Atlantic salmon but fails to eradicate ...

    Authors: Stanko Škugor, Sven Martin Jørgensen, Bjarne Gjerde and Aleksei Krasnov
    Citation: BMC Genomics 2009 10:503
    Content type: Research article Published on:

  24. Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs) are an important tool for correct annotation and clusteri...

    Authors: Rune Andreassen, Sigbjørn Lunner and Bjørn Høyheim
    Citation: BMC Genomics 2009 10:502
    Content type: Research article Published on:

  25. New and improved antimicrobial countermeasures are urgently needed to counteract increased resistance to existing antimicrobial treatments and to combat currently untreatable or new emerging infectious disease...

    Authors: Chris J Stubben, Melanie L Duffield, Ian A Cooper, Donna C Ford, Jason D Gans, Andrey V Karlyshev, Bryan Lingard, Petra CF Oyston, Anna de Rochefort, Jian Song, Brendan W Wren, Rick W Titball and Murray Wolinsky
    Citation: BMC Genomics 2009 10:501
    Content type: Research article Published on:

  26. The nuclear receptor superfamily currently consists of seven gene subfamilies that encompass over 80 distinct receptor proteins. These transcription factors typically share a common five-domain structure with ...

    Authors: Susanne A Thomson, William S Baldwin, Ying H Wang, Gwijun Kwon and Gerald A LeBlanc
    Citation: BMC Genomics 2009 10:500
    Content type: Research article Published on:

  27. The active form of Vitamin D, 1,25-dihydroxyvitamin D3 (1,25D), has strong anti-proliferative effects, yet the molecular mechanisms underneath this effect remain unclear. In contrast, the molecular mechanism of 1...

    Authors: José L Costa, Paul P Eijk, Mark A van de Wiel, Derk ten Berge, Fernando Schmitt, Carmen J Narvaez, JoEllen Welsh and Bauke Ylstra
    Citation: BMC Genomics 2009 10:499
    Content type: Research article Published on:

  28. Many mammalian genes are arranged in a bidirectional manner, sharing a common promoter and regulatory elements. This is especially true for promoters containing a CpG island, usually unmethylated and associate...

    Authors: Paul Kalitsis and Richard Saffery
    Citation: BMC Genomics 2009 10:498
    Content type: Research article Published on:

  29. Regulation of gene expression is essential for normal development and cellular growth. Transcriptional events are tightly controlled both spatially and temporally by specific DNA-protein interactions. In this ...

    Authors: Danette D Hartzell, Nathan D Trinklein, Jacqui Mendez, Nancy Murphy, Shelley F Aldred, Keith Wood and Marjeta Urh
    Citation: BMC Genomics 2009 10:497
    Content type: Research article Published on:

  30. Brachypodium distachyon (Brachypodium) has been recognized as a new model species for comparative and functional genomics of cereal and bioenergy crops because it possesses many biological attributes desirable in...

    Authors: Yong Q Gu, Yaqin Ma, Naxin Huo, John P Vogel, Frank M You, Gerard R Lazo, William M Nelson, Carol Soderlund, Jan Dvorak, Olin D Anderson and Ming-Cheng Luo
    Citation: BMC Genomics 2009 10:496
    Content type: Research article Published on:

  31. Trypanosome gene expression is regulated almost exclusively at the post-transcriptional level, with mRNA degradation playing a decisive role. When trypanosomes are transferred from the blood of a mammal to the...

    Authors: Rafael Queiroz, Corinna Benz, Kurt Fellenberg, Jörg D Hoheisel and Christine Clayton
    Citation: BMC Genomics 2009 10:495
    Content type: Research article Published on:

  32. The yellow fever mosquito Aedes aegypti is a major vector of dengue and hemorrhagic fevers, causing up to 100 million dengue infections every year. As there is still no medicine and efficient vaccine available, v...

    Authors: Sébastien Marcombe, Rodolphe Poupardin, Frederic Darriet, Stéphane Reynaud, Julien Bonnet, Clare Strode, Cecile Brengues, André Yébakima, Hilary Ranson, Vincent Corbel and Jean-Philippe David
    Citation: BMC Genomics 2009 10:494
    Content type: Research article Published on:

  33. Microarray technology provides a powerful tool for defining gene expression profiles of airway epithelium that lend insight into the pathogenesis of human airway disorders. The focus of this study was to estab...

    Authors: Tina Raman, Timothy P O'Connor, Neil R Hackett, Wei Wang, Ben-Gary Harvey, Marc A Attiyeh, David T Dang, Matthew Teater and Ronald G Crystal
    Citation: BMC Genomics 2009 10:493
    Content type: Research article Published on:

  34. Trichuris muris in the mouse is an invaluable model for infection of man with the gastrointestinal nematode Trichuris trichiura. Three T. muris isolates have been studied, the Edinburgh (E), the Japan (J) and the...

    Authors: Riccardo D'Elia, Matthew L deSchoolmeester, Leo AH Zeef, Steven H Wright, Alan D Pemberton and Kathryn J Else
    Citation: BMC Genomics 2009 10:492
    Content type: Research article Published on:

  35. Pseudorabies virus (PRV), a neurotropic herpesvirus of pigs, serves as an excellent model system with which to investigate the herpesvirus life cycle both in cultured cells and in vivo. Real-time RT-PCR is a very...

    Authors: Dóra Tombácz, Judit S Tóth, Pál Petrovszki and Zsolt Boldogkői
    Citation: BMC Genomics 2009 10:491
    Content type: Research article Published on:

  36. Physiological processes occur in many species for which there is yet no sequenced genome and for which we would like to identify the genetic basis. For example, some species increase their vascular network to ...

    Authors: John MJ Herbert, Francesca M Buffa, Henrik Vorschmitt, Stuart Egginton and Roy Bicknell
    Citation: BMC Genomics 2009 10:490
    Content type: Methodology article Published on:

  37. The Drosophila melanogaster genome contains 29 serpin genes, 12 as single transcripts and 17 within 6 gene clusters. Many of these serpins have a conserved "hinge" motif characteristic of active proteinase inhibi...

    Authors: Matthew Garrett, Ane Fullaondo, Laurent Troxler, Gos Micklem and David Gubb
    Citation: BMC Genomics 2009 10:489
    Content type: Research article Published on:

  38. New chemotherapeutic agents against Schistosoma mansoni, an etiological agent of human schistosomiasis, are a priority due to the emerging drug resistance and the inability of current drug treatments to prevent r...

    Authors: David H Bos, Chris Mayfield and Dennis J Minchella
    Citation: BMC Genomics 2009 10:488
    Content type: Research article Published on:

  40. The silkworm, Bombyx mori, is one of the most economically important insects in many developing countries owing to its large-scale cultivation for silk production. With the development of genomic and biotechnolog...

    Authors: Michihiko Shimomura, Hiroshi Minami, Yoshitaka Suetsugu, Hajime Ohyanagi, Chikatada Satoh, Baltazar Antonio, Yoshiaki Nagamura, Keiko Kadono-Okuda, Hideyuki Kajiwara, Hideki Sezutsu, Javaregowda Nagaraju, Marian R Goldsmith, Qingyou Xia, Kimiko Yamamoto and Kazuei Mita
    Citation: BMC Genomics 2009 10:486
    Content type: Database Published on:

  41. Rare population variants are known to have important biomedical implications, but their systematic discovery has only recently been enabled by advances in DNA sequencing. The design process of a discovery proj...

    Authors: Michael C Wendl and Richard K Wilson
    Citation: BMC Genomics 2009 10:485
    Content type: Research article Published on:

  42. How photosynthetic organelles, or plastids, were acquired by diverse eukaryotes is among the most hotly debated topics in broad scale eukaryotic evolution. The history of plastid endosymbioses commonly is inte...

    Authors: John W Stiller, Jinling Huang, Qin Ding, Jing Tian and Carol Goodwillie
    Citation: BMC Genomics 2009 10:484
    Content type: Research article Published on:

  43. Several global transcriptomic and proteomic approaches have been applied in order to obtain new molecular insights on skeletal myogenesis, but none has generated any specific data on glycogenome expression, an...

    Authors: Mathilde Janot, Aymeric Audfray, Céline Loriol, Agnès Germot, Abderrahman Maftah and Fabrice Dupuy
    Citation: BMC Genomics 2009 10:483
    Content type: Research article Published on:

  44. Trypanosoma brucei, the causative agent of African sleeping sickness, undergoes a complex developmental cycle that takes place in mammalian and insect hosts and is accompanied by changes in metabolism and cellula...

    Authors: Bryan C Jensen, Dhileep Sivam, Charles T Kifer, Peter J Myler and Marilyn Parsons
    Citation: BMC Genomics 2009 10:482
    Content type: Research article Published on:

  45. During gut colonization, the enteric pathogen Campylobacter jejuni must surmount the toxic effects of reactive oxygen species produced by its own metabolism, the host immune system, and intestinal microflora. Elu...

    Authors: Kiran Palyada, Yi-Qian Sun, Annika Flint, James Butcher, Hemant Naikare and Alain Stintzi
    Citation: BMC Genomics 2009 10:481
    Content type: Research article Published on:

  46. Pseudogenes provide a record of the molecular evolution of genes. As glycolysis is such a highly conserved and fundamental metabolic pathway, the pseudogenes of glycolytic enzymes comprise a standardized genom...

    Authors: Yuen-Jong Liu, Deyou Zheng, Suganthi Balasubramanian, Nicholas Carriero, Ekta Khurana, Rebecca Robilotto and Mark B Gerstein
    Citation: BMC Genomics 2009 10:480
    Content type: Research article Published on:

  47. The development of second generation sequencing methods has enabled large scale DNA variation studies at moderate cost. For the high throughput discovery of single nucleotide polymorphisms (SNPs) in species la...

    Authors: Hindrik HD Kerstens, Richard PMA Crooijmans, Albertine Veenendaal, Bert W Dibbits, Thomas FC Chin-A-Woeng, Johan T den Dunnen and Martien AM Groenen
    Citation: BMC Genomics 2009 10:479
    Content type: Methodology article Published on:

  48. miRNAs play important roles in the regulation of gene functions. Maternal dietary modifications during pregnancy and gestation have long-term effects on the offspring, but it is not known whether a maternal hi...

    Authors: Junlong Zhang, Fang Zhang, Xavier Didelot, Kimberley D Bruce, Felino R Cagampang, Manu Vatish, Mark Hanson, Hendrik Lehnert, Antonio Ceriello and Christopher D Byrne
    Citation: BMC Genomics 2009 10:478
    Content type: Research article Published on:

  49. Bacterial artificial chromosomes (BACs) are among the most widely used tools for studies of gene regulation and function in model vertebrates, yet methods for predictable delivery of BAC transgenes to the geno...

    Authors: Maximiliano L Suster, Kenta Sumiyama and Koichi Kawakami
    Citation: BMC Genomics 2009 10:477
    Content type: Methodology article Published on:

  50. The development and maintenance of the prostate is dependent on androgens and the androgen receptor. The androgen pathway continues to be important in prostate cancer. Here, we evaluated the transcriptome of p...

    Authors: Tammy L Romanuik, Gang Wang, Robert A Holt, Steven JM Jones, Marco A Marra and Marianne D Sadar
    Citation: BMC Genomics 2009 10:476
    Content type: Research article Published on:

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