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  1. Wood is a major renewable natural resource for the timber, fibre and bioenergy industry. Pinus radiata D. Don is the most important commercial plantation tree species in Australia and several other countries; how...

    Authors: Xinguo Li, Harry X Wu, Shannon K Dillon and Simon G Southerton
    Citation: BMC Genomics 2009 10:41
    Content type: Research article Published on:

  2. The native Australian fly Drosophila serrata belongs to the highly speciose montium subgroup of the melanogaster species group. It has recently emerged as an excellent model system with which to address a number ...

    Authors: Francesca D Frentiu, Marcin Adamski, Elizabeth A McGraw, Mark W Blows and Stephen F Chenoweth
    Citation: BMC Genomics 2009 10:40
    Content type: Research article Published on:

  3. Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using...

    Authors: Nicholas A Tinker, Andrzej Kilian, Charlene P Wight, Katarzyna Heller-Uszynska, Peter Wenzl, Howard W Rines, Åsmund Bjørnstad, Catherine J Howarth, Jean-Luc Jannink, Joseph M Anderson, Brian G Rossnagel, Deon D Stuthman, Mark E Sorrells, Eric W Jackson, Stine Tuvesson, Frederic L Kolb…
    Citation: BMC Genomics 2009 10:39
    Content type: Research article Published on:

  4. High throughput proteomics experiments are useful for analyzing the protein expression of an organism, identifying the correct gene structure of a genome, or locating possible post-translational modifications ...

    Authors: Carlos J Madrid-Aliste, Joseph M Dybas, Ruth Hogue Angeletti, Louis M Weiss, Kami Kim, Istvan Simon and Andras Fiser
    Citation: BMC Genomics 2009 10:38
    Content type: Database Published on:

  5. Short-read high-throughput DNA sequencing technologies provide new tools to answer biological questions. However, high cost and low throughput limit their widespread use, particularly in organisms with smaller...

    Authors: Philippe Lefrançois, Ghia M Euskirchen, Raymond K Auerbach, Joel Rozowsky, Theodore Gibson, Christopher M Yellman, Mark Gerstein and Michael Snyder
    Citation: BMC Genomics 2009 10:37
    Content type: Methodology article Published on:

  6. Of the > 2000 serovars of Salmonella enterica subspecies I, most cause self-limiting gastrointestinal disease in a wide range of mammalian hosts. However, S. enterica serovars Typhi and Paratyphi A are restricted...

    Authors: Kathryn E Holt, Nicholas R Thomson, John Wain, Gemma C Langridge, Rumina Hasan, Zulfiqar A Bhutta, Michael A Quail, Halina Norbertczak, Danielle Walker, Mark Simmonds, Brian White, Nathalie Bason, Karen Mungall, Gordon Dougan and Julian Parkhill
    Citation: BMC Genomics 2009 10:36
    Content type: Research article Published on:

  7. Mast cells (MCs) play pivotal roles in allergy and innate immunity and consist of heterogenous subclasses. However, the molecular basis determining the different characteristics of these multiple MC subclasses...

    Authors: Soken Tsuchiya, Yuki Tachida, Eri Segi-Nishida, Yasushi Okuno, Shigero Tamba, Gozoh Tsujimoto, Satoshi Tanaka and Yukihiko Sugimoto
    Citation: BMC Genomics 2009 10:35
    Content type: Research article Published on:

  8. Zymomonas mobilis ZM4 (ZM4) produces near theoretical yields of ethanol with high specific productivity and recombinant strains are able to ferment both C-5 and C-6 sugars. Z. mobilis performs best under anaerobi...

    Authors: Shihui Yang, Timothy J Tschaplinski, Nancy L Engle, Sue L Carroll, Stanton L Martin, Brian H Davison, Anthony V Palumbo, Miguel Rodriguez Jr and Steven D Brown
    Citation: BMC Genomics 2009 10:34
    Content type: Research article Published on:

  9. The evolutionary importance of horizontal gene transfer (HGT) from Wolbachia endosymbiotic bacteria to their eukaryotic hosts is a topic of considerable interest and debate. Recent transfers of genome fragments f...

    Authors: Lisa Klasson, Zakaria Kambris, Peter E Cook, Thomas Walker and Steven P Sinkins
    Citation: BMC Genomics 2009 10:33
    Content type: Research article Published on:

  10. Genomic analysis will greatly benefit from considering in a global way various sources of molecular data with the related biological knowledge. It is thus of great importance to provide useful integrative appr...

    Authors: Marie de Tayrac, Sébastien Lê, Marc Aubry, Jean Mosser and François Husson
    Citation: BMC Genomics 2009 10:32
    Content type: Methodology article Published on:

  11. Avian coccidiosis is a major parasitic disease of poultry, causing severe economical loss to poultry production by affecting growth and feed efficiency of infected birds. Current control strategies using mainl...

    Authors: Marie-Hélène Pinard-van der Laan, Bertrand Bed'hom, Jean-Luc Coville, Frédérique Pitel, Katia Feve, Sophie Leroux, Hélène Legros, Aurélie Thomas, David Gourichon, Jean-Michel Repérant and Paul Rault
    Citation: BMC Genomics 2009 10:31
    Content type: Research article Published on:

  12. The recent development within high-throughput technologies for expression profiling has allowed for parallel analysis of transcriptomes and proteomes in biological systems such as comparative analysis of trans...

    Authors: Henrik Hornshøj, Emøke Bendixen, Lene N Conley, Pernille K Andersen, Jakob Hedegaard, Frank Panitz and Christian Bendixen
    Citation: BMC Genomics 2009 10:30
    Content type: Research article Published on:

  13. Whole genome sequencing techniques have added a new dimension to studies on bacterial adaptation, evolution and diversity in chronic infections. By using this powerful approach it was demonstrated that Pseudomona...

    Authors: Andreas Dötsch, Claudia Pommerenke, Florian Bredenbruch, Robert Geffers and Susanne Häussler
    Citation: BMC Genomics 2009 10:29
    Content type: Methodology article Published on:

  14. Current techniques of screening bacterial artificial chromosome (BAC) libraries for molecular markers during the construction of physical maps are slow, laborious and often assign multiple BAC contigs to a sin...

    Authors: Ming-Cheng Luo, Kenong Xu, Yaqin Ma, Karin R Deal, Charles M Nicolet and Jan Dvorak
    Citation: BMC Genomics 2009 10:28
    Content type: Methodology article Published on:

  15. Mitochondrial genomes are a valuable source of data for analysing phylogenetic relationships. Besides sequence information, mitochondrial gene order may add phylogenetically useful information, too. Sipuncula ...

    Authors: Adina Mwinyi, Achim Meyer, Christoph Bleidorn, Bernhard Lieb, Thomas Bartolomaeus and Lars Podsiadlowski
    Citation: BMC Genomics 2009 10:27
    Content type: Research article Published on:

  16. Analyzing gene expression data by assessing the significance of pre-defined gene sets, rather than individual genes, has become a main approach in microarray data analysis and this has promisingly derive new b...

    Authors: Chien-Yi Tung, Chih-Hung Jen, Ming-Ta Hsu, Hsei-Wei Wang and Chi-Hung Lin
    Citation: BMC Genomics 2009 10:26
    Content type: Methodology article Published on:

  17. Infection of cattle with Mycobacterium avium subspecies paratuberculosis (M. ap) causes severe economic losses to the dairy industry in the USA and worldwide. In an effort to better examine diversity among M. ap ...

    Authors: Chia-wei Wu, Timothy M Schramm, Shiguo Zhou, David C Schwartz and Adel M Talaat
    Citation: BMC Genomics 2009 10:25
    Content type: Research article Published on:

  18. The dog is an important model organism and it is considered to be closer to humans than rodents regarding metabolism and responses to drugs. The close relationship between humans and dogs over many centuries h...

    Authors: Tatjana Haitina, Robert Fredriksson, Steven M Foord, Helgi B Schiöth and David E Gloriam
    Citation: BMC Genomics 2009 10:24
    Content type: Research article Published on:

  20. Biologists need to perform complex queries, often across a variety of databases. Typically, each data resource provides an advanced query interface, each of which must be learnt by the biologist before they ca...

    Authors: Damian Smedley, Syed Haider, Benoit Ballester, Richard Holland, Darin London, Gudmundur Thorisson and Arek Kasprzyk
    Citation: BMC Genomics 2009 10:22
    Content type: Software Published on:

  21. Evolution has resulted in large repertoires of olfactory receptor (OR) genes, forming the largest gene families in mammalian genomes. Knowledge of the genetic diversity of olfactory receptors is essential if w...

    Authors: Stéphanie Robin, Sandrine Tacher, Maud Rimbault, Amaury Vaysse, Stéphane Dréano, Catherine André, Christophe Hitte and Francis Galibert
    Citation: BMC Genomics 2009 10:21
    Content type: Research article Published on:

  22. Marek's disease (MD) is a T-cell lymphoma of chickens caused by the Marek's disease virus (MDV), an oncogenic avian herpesvirus. MD is a major cause of economic loss to the poultry industry and the most seriou...

    Authors: Eliyahu M Heifetz, Janet E Fulton, Neil P O'Sullivan, James A Arthur, Hans Cheng, Jing Wang, Morris Soller and Jack CM Dekkers
    Citation: BMC Genomics 2009 10:20
    Content type: Research article Published on:

  23. The basis of genome size variation remains an outstanding question because DNA sequence data are lacking for organisms with large genomes. Sixteen BAC clones from the Mexican axolotl (Ambystoma mexicanum: c-value...

    Authors: Jeramiah J Smith, Srikrishna Putta, Wei Zhu, Gerald M Pao, Inder M Verma, Tony Hunter, Susan V Bryant, David M Gardiner, Timothy T Harkins and S Randal Voss
    Citation: BMC Genomics 2009 10:19
    Content type: Research article Published on:

  24. Regulation of gene expression in Plasmodium falciparum (Pf) remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription...

    Authors: Prathima Iengar and NV Joshi
    Citation: BMC Genomics 2009 10:18
    Content type: Research article Published on:

  25. Large-scale comparison of metazoan genomes has revealed that a significant fraction of genes of the last common ancestor of Bilateria (Urbilateria) is lost in each animal lineage. This event could be one of th...

    Authors: Toshiaki Matsui, Toshiyuki Yamamoto, Stefan Wyder, Evgeny M Zdobnov and Tatsuhiko Kadowaki
    Citation: BMC Genomics 2009 10:17
    Content type: Research article Published on:

  26. With the recent completion of numerous sequenced bacterial genomes, notable advances have been made in understanding the level of conservation between various species. However, relatively little is known about...

    Authors: Michael J Dark, David R Herndon, Lowell S Kappmeyer, Mikel P Gonzales, Elizabeth Nordeen, Guy H Palmer, Donald P Knowles Jr and Kelly A Brayton
    Citation: BMC Genomics 2009 10:16
    Content type: Research article Published on:

  27. The nucleosome is the fundamental unit of eukaryotic genomes. Its positioning plays a central role in diverse cellular processes that rely on access to genomic DNA. Experimental evidence suggests that the geno...

    Authors: Zhiming Dai, Xianhua Dai, Qian Xiang, Jihua Feng, Jiang Wang, Yangyang Deng and Caisheng He
    Citation: BMC Genomics 2009 10:15
    Content type: Research article Published on:

  29. Atherosclerosis affects aorta, coronary, carotid, and iliac arteries most frequently than any other body vessel. There may be common molecular pathways sustaining this process. Plaque presence and diffusion is...

    Authors: Stefano Cagnin, Michele Biscuola, Cristina Patuzzo, Elisabetta Trabetti, Alessandra Pasquali, Paolo Laveder, Giuseppe Faggian, Mauro Iafrancesco, Alessandro Mazzucco, Pier Franco Pignatti and Gerolamo Lanfranchi
    Citation: BMC Genomics 2009 10:13
    Content type: Research article Published on:

  30. Plasmids are extrachromosomal elements that replicate autonomously, and many can be transmitted between bacterial cells through conjugation. Although the transcription pattern of genes on a plasmid can be alte...

    Authors: Masatoshi Miyakoshi, Hiromi Nishida, Masaki Shintani, Hisakazu Yamane and Hideaki Nojiri
    Citation: BMC Genomics 2009 10:12
    Content type: Research article Published on:

  31. Cold adapted or psychrophilic organisms grow at low temperatures, where most of other organisms cannot grow. This adaptation requires a vast array of sequence, structural and physiological adjustments. To unde...

    Authors: Raghu Prasad Rao Metpally and Boojala Vijay B Reddy
    Citation: BMC Genomics 2009 10:11
    Content type: Research article Published on:

  32. The first week of human pre-embryo development is characterized by the induction of totipotency and then pluripotency. The understanding of this delicate process will have far reaching implication for in vitro...

    Authors: Said Assou, Doris Cerecedo, Sylvie Tondeur, Véronique Pantesco, Outi Hovatta, Bernard Klein, Samir Hamamah and John De Vos
    Citation: BMC Genomics 2009 10:10
    Content type: Research article Published on:

  33. The promoter is a critical necessary transcriptional cis-regulatory element. In addition to its role as an assembly site for the basal transcriptional apparatus, the promoter plays a key part in mediating tempora...

    Authors: Qianqian Zhu and Marc S Halfon
    Citation: BMC Genomics 2009 10:9
    Content type: Research article Published on:

  34. Transcriptional regulatory elements are central to development and interspecific phenotypic variation. Current regulatory element prediction tools rely heavily upon conservation for prediction of putative elem...

    Authors: David M McGaughey, Zachary E Stine, Jimmy L Huynh, Ryan M Vinton and Andrew S McCallion
    Citation: BMC Genomics 2009 10:8
    Content type: Research article Published on:

  35. The control of gene expression in eukaryotic cells occurs both transcriptionally and post-transcriptionally. Although many genes are now known to be regulated at the translational level, in general, the mechan...

    Authors: Craig Lawless, Richard D Pearson, Julian N Selley, Julia B Smirnova, Christopher M Grant, Mark P Ashe, Graham D Pavitt and Simon J Hubbard
    Citation: BMC Genomics 2009 10:7
    Content type: Research article Published on:

  36. Haemophilus influenzae requires heme for aerobic growth and possesses multiple mechanisms to obtain this essential nutrient. Although an understanding of the heme acquisition mechanisms of H. influenzae is emergi...

    Authors: Paul W Whitby, Thomas W Seale, Timothy M VanWagoner, Daniel J Morton and Terrence L Stull
    Citation: BMC Genomics 2009 10:6
    Content type: Research article Published on:

  37. Fourmidable is an infrastructure to curate and share the emerging genetic, molecular, and functional genomic data and protocols for ants.

    Authors: Yannick Wurm, Paolo Uva, Frédéric Ricci, John Wang, Stephanie Jemielity, Christian Iseli, Laurent Falquet and Laurent Keller
    Citation: BMC Genomics 2009 10:5
    Content type: Database Published on:

  38. Single nucleotide polymorphisms (SNPs) are ideal genetic markers due to their high abundance and the highly automated way in which SNPs are detected and SNP assays are performed. The number of SNPs identified ...

    Authors: Hindrik HD Kerstens, Sonja Kollers, Arun Kommadath, Marisol del Rosario, Bert Dibbits, Sylvia M Kinders, Richard P Crooijmans and Martien AM Groenen
    Citation: BMC Genomics 2009 10:4
    Content type: Research article Published on:

  39. Persistent colonization of the human stomach by Helicobacter pylori is associated with asymptomatic gastric inflammation (gastritis) and an increased risk of duodenal ulceration, gastric ulceration, and non-cardi...

    Authors: Mark S McClain, Carrie L Shaffer, Dawn A Israel, Richard M Peek Jr and Timothy L Cover
    Citation: BMC Genomics 2009 10:3
    Content type: Research article Published on:

  40. Peripheral blood is an accessible and informative source of transcriptomal information for many human disease and pharmacogenomic studies. While there can be significant advantages to analyzing RNA isolated fr...

    Authors: Kristina Vartanian, Rachel Slottke, Timothy Johnstone, Amanda Casale, Stephen R Planck, Dongseok Choi, Justine R Smith, James T Rosenbaum and Christina A Harrington
    Citation: BMC Genomics 2009 10:2
    Content type: Methodology article Published on:

  41. Genomic resources for the majority of free-living vertebrates of ecological and evolutionary importance are scarce. Therefore, linkage maps with high-density genome coverage are needed for progress in genomics...

    Authors: Sonja Jaari, Meng-Hua Li and Juha Merilä
    Citation: BMC Genomics 2009 10:1
    Content type: Research article Published on:

  42. Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS) and cellular antioxidant defence. To defend ...

    Authors: David Thybert, Stéphane Avner, Céline Lucchetti-Miganeh, Angélique Chéron and Frédérique Barloy-Hubler
    Citation: BMC Genomics 2008 9:637
    Content type: Database Published on:

  44. Mismatched oligonucleotides are widely used on microarrays to differentiate specific from nonspecific hybridization. While many experiments rely on such oligos, the hybridization behavior of various degrees of...

    Authors: Michael Seringhaus, Joel Rozowsky, Thomas Royce, Ugrappa Nagalakshmi, Justin Jee, Michael Snyder and Mark Gerstein
    Citation: BMC Genomics 2008 9:635
    Content type: Methodology article Published on:

  45. Biomphalaria glabrata is an intermediate snail host for Schistosoma mansoni, one of the important schistosomes infecting man. B. glabrata/S. mansoni provides a useful model system for investigating the intimate i...

    Authors: Anne E Lockyer, Jenny Spinks, Richard A Kane, Karl F Hoffmann, Jennifer M Fitzpatrick, David Rollinson, Leslie R Noble and Catherine S Jones
    Citation: BMC Genomics 2008 9:634
    Content type: Research article Published on:

  46. Quantitative polymerase chain reaction (QPCR) is a widely applied analytical method for the accurate determination of transcript abundance. Primers for QPCR have been designed on a genomic scale but non-specif...

    Authors: Athanasia Spandidos, Xiaowei Wang, Huajun Wang, Stefan Dragnev, Tara Thurber and Brian Seed
    Citation: BMC Genomics 2008 9:633
    Content type: Research article Published on:

  47. One of the most striking features of mammalian and birds chromosomes is the variation in the guanine-cytosine (GC) content that occurs over scales of hundreds of kilobases to megabases; this is known as the "i...

    Authors: Christelle Melodelima and Christian Gautier
    Citation: BMC Genomics 2008 9:632
    Content type: Research article Published on:

  48. The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparat...

    Authors: M Elisabete J Amaral, Jason R Grant, Penny K Riggs, Nedenia B Stafuzza, Edson A Rodrigues Filho, Tom Goldammer, Rosemarie Weikard, Ronald M Brunner, Kelli J Kochan, Anthony J Greco, Jooha Jeong, Zhipeng Cai, Guohui Lin, Aparna Prasad, Satish Kumar, G Pardha Saradhi…
    Citation: BMC Genomics 2008 9:631
    Content type: Research article Published on:

  49. Acute changes in environmental parameters (e.g., O2, pH, UV, osmolarity, nutrients, etc.) evoke a common transcriptomic response in yeast referred to as the "environmental stress response" (ESR) or "common enviro...

    Authors: Liang-Chuan Lai, Matthew T Kissinger, Patricia V Burke and Kurt E Kwast
    Citation: BMC Genomics 2008 9:627
    Content type: Research article Published on:

  50. Phosphorylation by protein kinases is a common event in many cellular processes. Further, many kinases perform specialized roles and are regulated by non-kinase domains tethered to kinase domain. Perturbation ...

    Authors: Krishanpal Anamika, Juliette Martin and Narayanaswamy Srinivasan
    Citation: BMC Genomics 2008 9:625
    Content type: Research article Published on:

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BMC Genomics

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