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  1. Interpreting in vivo sampled microarray data is often complicated by changes in the cell population demographics. To put gene expression into its proper biological context, it is necessary to distinguish differen...

    Authors: Jason E Shoemaker, Tiago JS Lopes, Samik Ghosh, Yukiko Matsuoka, Yoshihiro Kawaoka and Hiroaki Kitano
    Citation: BMC Genomics 2012 13:460
    Content type: Software Published on:

  2. MicroRNAs (miRNAs) are a class of non-protein-coding genes that play a crucial regulatory role in mammalian development and disease. Whereas a large number of miRNAs have been annotated at the structural level...

    Authors: Agnieszka Podolska, Christian Anthon, Mads Bak, Niels Tommerup, Kerstin Skovgaard, Peter MH Heegaard, Jan Gorodkin, Susanna Cirera and Merete Fredholm
    Citation: BMC Genomics 2012 13:459
    Content type: Research article Published on:

  3. Most egg yolk precursors are synthesized by the liver, secreted into the blood and transferred into oocytes, to provide nutrients and bioactive molecules for the avian embryo. Three hundred and sixteen distinc...

    Authors: Marie Bourin, Joël Gautron, Magali Berges, Christelle Hennequet-Antier, Cédric Cabau, Yves Nys and Sophie Réhault-Godbert
    Citation: BMC Genomics 2012 13:457
    Content type: Research article Published on:

  4. To understand the genetic architecture of complex traits and bridge the genotype-phenotype gap, it is useful to study intermediate -omics data, e.g. the transcriptome. The present study introduces a method for...

    Authors: Alireza Ehsani, Peter Sørensen, Daniel Pomp, Mark Allan and Luc Janss
    Citation: BMC Genomics 2012 13:456
    Content type: Research article Published on:

  5. For many analytical methods the efficiency of DNA amplification varies across the genome and between samples. The most affected genome regions tend to correlate with high C + G content, however this relationsh...

    Authors: Colin D Veal, Peter J Freeman, Kevin Jacobs, Owen Lancaster, Stéphane Jamain, Marion Leboyer, Demetrius Albanes, Reshma R Vaghela, Ivo Gut, Stephen J Chanock and Anthony J Brookes
    Citation: BMC Genomics 2012 13:455
    Content type: Research article Published on:

  6. The anaerobic spirochaete Brachyspira pilosicoli causes enteric disease in avian, porcine and human hosts, amongst others. To date, the only available genome sequence of B. pilosicoli is that of strain 95/1000, a...

    Authors: Luke J Mappley, Michael L Black, Manal AbuOun, Alistair C Darby, Martin J Woodward, Julian Parkhill, A Keith Turner, Matthew I Bellgard, Tom La, Nyree D Phillips, Roberto M La Ragione and David J Hampson
    Citation: BMC Genomics 2012 13:454
    Content type: Research article Published on:

  7. Promyelocytic leukemia protein (PML) is a tumor suppressor that is highly expressed in endothelial cells nonetheless its role in endothelial cell biology remains elusive. Tumor necrosis factor alpha (TNFα) is an ...

    Authors: Xiwen Cheng and Hung-Ying Kao
    Citation: BMC Genomics 2012 13:453
    Content type: Research article Published on:

  8. There is increasing empirical evidence that whole-genome prediction (WGP) is a powerful tool for predicting line and hybrid performance in maize. However, there is a lack of knowledge about the sensitivity of ...

    Authors: Christian Riedelsheimer, Frank Technow and Albrecht E Melchinger
    Citation: BMC Genomics 2012 13:452
    Content type: Research article Published on:

  9. Non-coding DNA in and around the human Amyloid Precursor Protein (APP) gene that is central to Alzheimer’s disease (AD) shares little sequence similarity with that of appb in zebrafish. Identifying DNA domains re...

    Authors: Leighcraft A Shakes, Hansen Du, Hope M Wolf, Charles Hatcher, Derek C Norford, Patricia Precht, Ranjan Sen and Pradeep K Chatterjee
    Citation: BMC Genomics 2012 13:451
    Content type: Research article Published on:

  10. Visceral white adipose tissue (WAT) hypertrophy, adipokine production, inflammation and fibrosis are strongly associated with obesity, but the time-course of these changes in-vivo are not fully understood. Theref...

    Authors: Eun-Young Kwon, Su-Kyung Shin, Yun-Young Cho, Un Ju Jung, Eunjung Kim, Taesun Park, Jung Han Yoon Park, Jong Won Yun, Robin A McGregor, Yong Bok Park and Myung-Sook Choi
    Citation: BMC Genomics 2012 13:450
    Content type: Research article Published on:

  11. Most members of the serpin family of proteins are potent, irreversible inhibitors of specific serine or cysteine proteinases. Inhibitory serpins are distinguished from members of other families of proteinase i...

    Authors: Sheila E Francis, Renan A Ersoy, Joon-Woo Ahn, Brian J Atwell and Thomas H Roberts
    Citation: BMC Genomics 2012 13:449
    Content type: Research article Published on:

  12. Expansion of aquaculture requires alternative feeds and breeding strategies to reduce dependency on fish oil (FO) and better utilization of dietary vegetable oil (VO). Despite the central role of intestine in ...

    Authors: Sofia Morais, Tomé Silva, Odete Cordeiro, Pedro Rodrigues, Derrick R Guy, James E Bron, John B Taggart, J Gordon Bell and Douglas R Tocher
    Citation: BMC Genomics 2012 13:448
    Content type: Research article Published on:

  13. Endothelial progenitor cells (EPCs) play a fundamental role in post-natal vascular repair, yet EPCs from different anatomic locations possess unique biological properties. The underlying mechanisms are unclear.

    Authors: Cheng-Chung Cheng, Hung-Hao Lo, Tse-Shun Huang, Yi-Chieh Cheng, Shi-Ting Chang, Shing-Jyh Chang and Hsei-Wei Wang
    Citation: BMC Genomics 2012 13:447
    Content type: Research article Published on:

  14. The selenocysteine (Sec) containing proteins, selenoproteins, are an important group of proteins present throughout all 3 kingdoms of life. With the rapid progression of selenoprotein research in the post-geno...

    Authors: Liang Jiang, Jiazuan Ni and Qiong Liu
    Citation: BMC Genomics 2012 13:446
    Content type: Research article Published on:

  15. The expression of genes in Corynebacterium glutamicum, a Gram-positive non-pathogenic bacterium used mainly for the industrial production of amino acids, is regulated by seven different sigma factors of RNA polym...

    Authors: Tobias Busche, Radoslav Šilar, Martina Pičmanová, Miroslav Pátek and Jörn Kalinowski
    Citation: BMC Genomics 2012 13:445
    Content type: Research article Published on:

  16. Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has...

    Authors: Hitoshi Suzuki, Jacqueline MacDonald, Khajamohiddin Syed, Asaf Salamov, Chiaki Hori, Andrea Aerts, Bernard Henrissat, Ad Wiebenga, Patricia A vanKuyk, Kerrie Barry, Erika Lindquist, Kurt LaButti, Alla Lapidus, Susan Lucas, Pedro Coutinho, Yunchen Gong…
    Citation: BMC Genomics 2012 13:444
    Content type: Research article Published on:

  17. Zygotic transcription in fish embryos initiates around the time of gastrulation, and all prior development is initiated and controlled by maternally derived messenger RNAs. Atlantic cod egg and embryo viabilit...

    Authors: Lene Kleppe, Rolf B Edvardsen, Heiner Kuhl, Ketil Malde, Tomasz Furmanek, Øyvind Drivenes, Richard Reinhardt, Geir L Taranger and Anna Wargelius
    Citation: BMC Genomics 2012 13:443
    Content type: Research article Published on:

  18. The lavender phenotype in quail is a dilution of both eumelanin and phaeomelanin in feathers that produces a blue-grey colour on a wild-type feather pattern background. It has been previously demonstrated by inte...

    Authors: Bertrand Bed’hom, Mohsen Vaez, Jean-Luc Coville, David Gourichon, Olivier Chastel, Sarah Follett, Terry Burke and Francis Minvielle
    Citation: BMC Genomics 2012 13:442
    Content type: Research article Published on:

  19. Domestic broiler chickens rapidly accumulate adipose tissue due to intensive genetic selection for rapid growth and are naturally hyperglycemic and insulin resistant, making them an attractive addition to the ...

    Authors: Bo Ji, Ben Ernest, Jessica R Gooding, Suchita Das, Arnold M Saxton, Jean Simon, Joelle Dupont, Sonia Métayer-Coustard, Shawn R Campagna and Brynn H Voy
    Citation: BMC Genomics 2012 13:441
    Content type: Research article Published on:

  20. With over 1.3 billion people, India is estimated to contain three times more genetic diversity than does Europe. Next-generation sequencing technologies have facilitated the understanding of diversity by enabl...

    Authors: Ravi Gupta, Aakrosh Ratan, Changanamkandath Rajesh, Rong Chen, Hie Lim Kim, Richard Burhans, Webb Miller, Sam Santhosh, Ramana V Davuluri, Atul J Butte, Stephan C Schuster, Somasekar Seshagiri and George Thomas
    Citation: BMC Genomics 2012 13:440
    Content type: Research article Published on:

  21. The tuatara (Sphenodon punctatus) is a species of extraordinary zoological interest, being the only surviving member of an entire order of reptiles which diverged early in amniote evolution. In addition to their ...

    Authors: Hilary C Miller, Patrick J Biggs, Claudia Voelckel and Nicola J Nelson
    Citation: BMC Genomics 2012 13:439
    Content type: Research article Published on:

  22. A large number of genome-scale metabolic networks is now available for many organisms, mostly bacteria. Previous works on minimal gene sets, when analysing host-dependent bacteria, found small common sets of m...

    Authors: Cecilia Coimbra Klein, Ludovic Cottret, Janice Kielbassa, Hubert Charles, Christian Gautier, Ana Tereza Ribeiro de Vasconcelos, Vincent Lacroix and Marie-France Sagot
    Citation: BMC Genomics 2012 13:438
    Content type: Research article Published on:

  23. Current experimental evidence indicates that functionally related genes show coordinated expression in order to perform their cellular functions. In this way, the cell transcriptional machinery can respond opt...

    Authors: Mingzhu Zhu, Xin Deng, Trupti Joshi, Dong Xu, Gary Stacey and Jianlin Cheng
    Citation: BMC Genomics 2012 13:437
    Content type: Research article Published on:

  24. Chromatin organization has been increasingly studied in relation with its important influence on DNA-related metabolic processes such as replication or regulation of gene expression. Since its original design ...

    Authors: Axel Cournac, Hervé Marie-Nelly, Martial Marbouty, Romain Koszul and Julien Mozziconacci
    Citation: BMC Genomics 2012 13:436
    Content type: Methodology article Published on:

  25. Relationship between the level of repetitiveness in genomic sequence and genome size has been investigated by making use of complete prokaryotic and eukaryotic genomes, but relevant studies have been rarely ma...

    Authors: Xiangyan Zhao, Yonglei Tian, Ronghua Yang, Haiping Feng, Qingjian Ouyang, You Tian, Zhongyang Tan, Mingfu Li, Yile Niu, Jianhui Jiang, Guoli Shen and Ruqin Yu
    Citation: BMC Genomics 2012 13:435
    Content type: Research article Published on:

  26. Conifers have very large genomes (13 to 30 Gigabases) that are mostly uncharacterized although extensive cDNA resources have recently become available. This report presents a global overview of transcriptome v...

    Authors: Elie Raherison, Philippe Rigault, Sébastien Caron, Pier-Luc Poulin, Brian Boyle, Jukka-Pekka Verta, Isabelle Giguère, Claude Bomal, Jörg Bohlmann and John MacKay
    Citation: BMC Genomics 2012 13:434
    Content type: Research article Published on:

  27. Ribosomal protein genes (RPGs) are essential, tightly regulated, and highly expressed during embryonic development and cell growth. Even though their protein sequences are strongly conserved, their mechanism o...

    Authors: Monica C Sleumer, Guifeng Wei, Yunfei Wang, Hao Chang, Tao Xu, Runsheng Chen and Michael Q Zhang
    Citation: BMC Genomics 2012 13:433
    Content type: Research article Published on:

  28. Geographical isolation has generated a distinct difference between Atlantic salmon of European and North American Atlantic origin. The European Atlantic salmon generally has 29 pairs of chromosomes and 74 chro...

    Authors: Silje Brenna-Hansen, Jieying Li, Matthew P Kent, Elizabeth G Boulding, Sonja Dominik, William S Davidson and Sigbjørn Lien
    Citation: BMC Genomics 2012 13:432
    Content type: Research article Published on:

  29. Atlantic cod (Gadus morhua) reared in sea-cages can experience large variations in temperature, and these have been shown to affect their immune function. We used the new 20K Atlantic cod microarray to investigat...

    Authors: Tiago S Hori, A Kurt Gamperl, Marije Booman, Gordon W Nash and Matthew L Rise
    Citation: BMC Genomics 2012 13:431
    Content type: Research article Published on:

  30. Diversity Generating Retroelements (DGRs) are genetic cassettes that can introduce tremendous diversity into a short, defined region of the genome. They achieve hypermutation through replacement of the variabl...

    Authors: Thomas Schillinger, Mohamed Lisfi, Jingyun Chi, John Cullum and Nora Zingler
    Citation: BMC Genomics 2012 13:430
    Content type: Research article Published on:

  32. Phytophthora sojae is the primary pathogen of soybeans that are grown on poorly drained soils. Race-specific resistance to P. sojae in soybean is gene-for-gene, although in many areas of the US and worldwide ther...

    Authors: Hehe Wang, Asela Wijeratne, Saranga Wijeratne, Sungwoo Lee, Christopher G Taylor, Steven K St Martin, Leah McHale and Anne E Dorrance
    Citation: BMC Genomics 2012 13:428
    Content type: Research article Published on:

  33. At the core of the RNA interference (RNAi) pathway in Trypanosoma brucei is a single Argonaute protein, Tb AGO1, with an established role in controlling retroposon and repeat transcripts. Recent evidence from hig...

    Authors: Christian Tschudi, Huafang Shi, Joseph B Franklin and Elisabetta Ullu
    Citation: BMC Genomics 2012 13:427
    Content type: Research article Published on:

  34. Single nucleotide polymorphism (SNP) validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stres...

    Authors: Swarup K Parida, Mitali Mukerji, Ashok K Singh, Nagendra K Singh and Trilochan Mohapatra
    Citation: BMC Genomics 2012 13:426
    Content type: Research article Published on:

  35. Yellow lupin (Lupinus luteus L.) is a minor legume crop characterized by its high seed protein content. Although grown in several temperate countries, its orphan condition has limited the generation of genomic to...

    Authors: Lorena B Parra-González, Gabriela A Aravena-Abarzúa, Cristell S Navarro-Navarro, Joshua Udall, Jeff Maughan, Louis M Peterson, Haroldo E Salvo-Garrido and Iván J Maureira-Butler
    Citation: BMC Genomics 2012 13:425
    Content type: Research article Published on:

  36. Transcription regulation in pluripotent embryonic stem (ES) cells is a complex process that involves multitude of regulatory layers, one of which is post-translational modification of histones. Acetylation of ...

    Authors: Krishanpal Karmodiya, Arnaud R Krebs, Mustapha Oulad-Abdelghani, Hiroshi Kimura and Laszlo Tora
    Citation: BMC Genomics 2012 13:424
    Content type: Research article Published on:

  38. Francisella tularensis is an intracellular pathogen that causes tularemia in humans and the public health importance of this bacterium has been well documented in recent history. Francisella philomiragia, a dista...

    Authors: Shivakumara Siddaramappa, Jean F Challacombe, Jeannine M Petersen, Segaran Pillai and Cheryl R Kuske
    Citation: BMC Genomics 2012 13:422
    Content type: Research article Published on:

  39. MicroRNAs (miRNAs) are endogenous regulators of a broad range of physiological processes and act by either degrading mRNA or blocking its translation. Oilseed rape (Brassica napus) is one of the most important cr...

    Authors: Miao Y Xu, Yun Dong, Qiu X Zhang, Lan Zhang, Yan Z Luo, Jie Sun, Yun L Fan and Lei Wang
    Citation: BMC Genomics 2012 13:421
    Content type: Research article Published on:

  40. Quantitative trait locus (QTL) studies show that variation in salinity tolerance in Arctic charr and rainbow trout has a genetic basis, even though both these species have low to moderate salinity tolerance ca...

    Authors: Joseph D Norman, Mike Robinson, Brian Glebe, Moira M Ferguson and Roy G Danzmann
    Citation: BMC Genomics 2012 13:420
    Content type: Research article Published on:

  41. In recent years an increasing number of yeast infections in humans have been related to certain clinical isolates of Saccharomyces cerevisiae. Some clinical strains showed in vivo and in vitro virulence traits an...

    Authors: Silvia Llopis, Amparo Querol, Antje Heyken, Bernhard Hube, Lene Jespersen, M Teresa Fernández-Espinar and Roberto Pérez-Torrado
    Citation: BMC Genomics 2012 13:419
    Content type: Research article Published on:

  42. Acute lymphoblastic leukemia (ALL) cells treated with drugs can become drug-tolerant if co-cultured with protective stromal mouse embryonic fibroblasts (MEFs).

    Authors: Anna Arutyunyan, Sonia Stoddart, Sun-ju Yi, Fei Fei, Min Lim, Paula Groffen, Niklas Feldhahn, John Groffen and Nora Heisterkamp
    Citation: BMC Genomics 2012 13:418
    Content type: Research article Published on:

  43. Compared to classical genotyping, targeted next-generation sequencing (t NGS) can be custom-designed to interrogate entire genomic regions of interest, in order to detect novel as well as known variants. To bring...

    Authors: Abdou ElSharawy, Michael Forster, Nadine Schracke, Andreas Keller, Ingo Thomsen, Britt-Sabina Petersen, Björn Stade, Peer Stähler, Stefan Schreiber, Philip Rosenstiel and Andre Franke
    Citation: BMC Genomics 2012 13:417
    Content type: Research article Published on:

  46. Information on nucleotide diversity along completely sequenced human genomes has increased tremendously over the last few years. This makes it possible to reassess the diversity status of distinct receptor pro...

    Authors: Tsviya Olender, Sebastian M Waszak, Maya Viavant, Miriam Khen, Edna Ben-Asher, Alejandro Reyes, Noam Nativ, Charles J Wysocki, Dongliang Ge and Doron Lancet
    Citation: BMC Genomics 2012 13:414
    Content type: Research article Published on:

  47. MicroRNAs (miRNAs) exist pervasively across viruses, plants and animals and play important roles in the post-transcriptional regulation of genes. In the common carp, miRNA targets have not been investigated. I...

    Authors: Ya-Ping Zhu, Wei Xue, Jin-Tu Wang, Yu-Mei Wan, Shao-Lin Wang, Peng Xu, Yan Zhang, Jiong-Tang Li and Xiao-Wen Sun
    Citation: BMC Genomics 2012 13:413
    Content type: Research article Published on:

  48. Ribosomal proteins (RPs) have about 2000 pseudogenes in the human genome. While anecdotal reports for RP pseudogene transcription exists, it is unclear to what extent these pseudogenes are transcribed. The RP ...

    Authors: Peter Tonner, Vinodh Srinivasasainagendra, Shaojie Zhang and Degui Zhi
    Citation: BMC Genomics 2012 13:412
    Content type: Research article Published on:

  49. There is strong but mostly circumstantial evidence that genetic factors modulate the severity of influenza infection in humans. Using genetically diverse but fully inbred strains of mice it has been shown that...

    Authors: Tatiana Nedelko, Heike Kollmus, Frank Klawonn, Sabine Spijker, Lu Lu, Manuela Heßman, Rudi Alberts, Robert W Williams and Klaus Schughart
    Citation: BMC Genomics 2012 13:411
    Content type: Research article Published on:

  50. Interspecific hybrids between S. cerevisiae × S. kudriavzevii have frequently been detected in wine and beer fermentations. Significant physiological differences among parental and hybrid strains under different ...

    Authors: David Peris, Christian A Lopes, Carmela Belloch, Amparo Querol and Eladio Barrio
    Citation: BMC Genomics 2012 13:407
    Content type: Research article Published on:

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BMC Genomics

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