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  1. Neurodegenerative diseases are progressive and irreversible and they can be initiated by mutations in specific genes. Spalt-like genes (Sall) encode transcription factors expressed in the central nervous system. ...

    Authors: María José Ferreiro, Naiara Rodríguez-Ezpeleta, Coralia Pérez, Michael Hackenberg, Ana María Aransay, Rosa Barrio and Rafael Cantera
    Citation: BMC Genomics 2012 13:483
    Content type: Research article Published on:

  2. The analysis of gene promoters is essential to understand the mechanisms of transcriptional regulation required under the effects of physiological processes, nutritional intake or pathologies. In higher eukary...

    Authors: Pierre-Yves Dupont, Audrey Guttin, Jean-Paul Issartel and Georges Stepien
    Citation: BMC Genomics 2012 13:482
    Content type: Research article Published on:

  3. MicroRNAs (miRNAs) are small RNAs (sRNAs) approximately 21 nucleotides in length that negatively control gene expression by cleaving or inhibiting the translation of target gene transcripts. Within this contex...

    Authors: Abdelali Barakat, Aditya Sriram, Joseph Park, Tetyana Zhebentyayeva, Dorrie Main and Albert Abbott
    Citation: BMC Genomics 2012 13:481
    Content type: Research article Published on:

  4. Gene bodies are the most evolutionarily conserved targets of DNA methylation in eukaryotes. However, the regulatory functions of gene body DNA methylation remain largely unknown. DNA methylation in insects app...

    Authors: Kevin Flores, Florian Wolschin, Jason J Corneveaux, April N Allen, Matthew J Huentelman and Gro V Amdam
    Citation: BMC Genomics 2012 13:480
    Content type: Research article Published on:

  5. Environmental stresses and inhibitors encountered by Saccharomyces cerevisiae strains are the main limiting factors in bioethanol fermentation. Strains with different genetic backgrounds usually show diverse stre...

    Authors: Dao-Qiong Zheng, Pin-Mei Wang, Jie Chen, Ke Zhang, Tian-Zhe Liu, Xue-Chang Wu, Yu-Dong Li and Yu-Hua Zhao
    Citation: BMC Genomics 2012 13:479
    Content type: Research article Published on:

  6. While multiple replication origins have been observed in archaea, considerably less is known about their evolutionary processes. Here, we performed a comparative analysis of the predicted (proved in part) orc/cdc...

    Authors: Zhenfang Wu, Hailong Liu, Jingfang Liu, Xiaoqing Liu and Hua Xiang
    Citation: BMC Genomics 2012 13:478
    Content type: Research article Published on:

  7. A detailed analysis of whole genomes can be now achieved with next generation sequencing. Epstein Barr Virus (EBV) transformation is a widely used strategy in clinical research to obtain an unlimited source of...

    Authors: Dorothee Nickles, Lohith Madireddy, Shan Yang, Pouya Khankhanian, Steve Lincoln, Stephen L Hauser, Jorge R Oksenberg and Sergio E Baranzini
    Citation: BMC Genomics 2012 13:477
    Content type: Research article Published on:

  8. miRNAs are short single-stranded non-coding RNAs involved in post-transcriptional gene regulation that play a major role in normal biological functions and diseases. Little is currently known about how express...

    Authors: Michael J Parsons, Christina Grimm, Jose L Paya-Cano, Cathy Fernandes, Lin Liu, Vivek M Philip, Elissa J Chesler, Wilfried Nietfeld, Hans Lehrach and Leonard C Schalkwyk
    Citation: BMC Genomics 2012 13:476
    Content type: Research article Published on:

  9. Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consen...

    Authors: Xiao Yang, Patrick Charlebois, Sante Gnerre, Matthew G Coole, Niall J Lennon, Joshua Z Levin, James Qu, Elizabeth M Ryan, Michael C Zody and Matthew R Henn
    Citation: BMC Genomics 2012 13:475
    Content type: Methodology article Published on:

  10. The release of oil resulting from the blowout of the Deepwater Horizon (DH) drilling platform was one of the largest in history discharging more than 189 million gallons of oil and subject to widespread applic...

    Authors: Tzintzuni I Garcia, Yingjia Shen, Douglas Crawford, Marjorie F Oleksiak, Andrew Whitehead and Ronald B Walter
    Citation: BMC Genomics 2012 13:474
    Content type: Research article Published on:

  11. Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is av...

    Authors: Kyung-Do Park, Jongsun Park, Junsu Ko, Byung Chul Kim, Heui-Soo Kim, Kung Ahn, Kyoung-Tag Do, Hansol Choi, Hak-Min Kim, Sanghoon Song, Sunghoon Lee, Sungwoong Jho, Hong-Sik Kong, Young Mok Yang, Byung-Hak Jhun, Chulhong Kim…
    Citation: BMC Genomics 2012 13:473
    Content type: Research article Published on:

  12. Psoriasis is an immune-mediated disease characterised by chronically elevated pro-inflammatory cytokine levels, leading to aberrant keratinocyte proliferation and differentiation. Although certain clinical phe...

    Authors: Chrysanthi Ainali, Najl Valeyev, Gayathri Perera, Andrew Williams, Johann E Gudjonsson, Christos A Ouzounis, Frank O Nestle and Sophia Tsoka
    Citation: BMC Genomics 2012 13:472
    Content type: Research article Published on:

  13. A new strain of Geobacter sulfurreducens, strain KN400, produces more electrical current in microbial fuel cells and reduces insoluble Fe(III) oxides much faster than the wildtype strain, PCA. The genome of KN400...

    Authors: Jessica E Butler, Nelson D Young, Muktak Aklujkar and Derek R Lovley
    Citation: BMC Genomics 2012 13:471
    Content type: Research article Published on:

  14. Studies conducted with gilthead sea bream (Sparus aurata L.) have determined the maximum dietary replacement of fish meal and oil without compromising growth or product quality. The present study aimed to analyze...

    Authors: Josep A Calduch-Giner, Ariadna Sitjà-Bobadilla, Grace C Davey, Michael T Cairns, Sadasivam Kaushik and Jaume Pérez-Sánchez
    Citation: BMC Genomics 2012 13:470
    Content type: Research article Published on:

  15. Cultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (...

    Authors: Ervin D Nagy, Yufang Guo, Shunxue Tang, John E Bowers, Rebecca A Okashah, Christopher A Taylor, Dong Zhang, Sameer Khanal, Adam F Heesacker, Nelly Khalilian, Andrew D Farmer, Noelia Carrasquilla-Garcia, R Varma Penmetsa, Douglas Cook, H Thomas Stalker, Niels Nielsen…
    Citation: BMC Genomics 2012 13:469
    Content type: Research article Published on:

  16. Whole-genome sequencing is an important tool for understanding microbial evolution and identifying the emergence of functionally important variants over the course of epidemics. In October 2010, a severe chole...

    Authors: Rachel Sealfon, Stephen Gire, Crystal Ellis, Stephen Calderwood, Firdausi Qadri, Lisa Hensley, Manolis Kellis, Edward T Ryan, Regina C LaRocque, Jason B Harris and Pardis C Sabeti
    Citation: BMC Genomics 2012 13:468
    Content type: Research article Published on:

  17. Yersinia enterocolitica is a gastrointestinal foodborne pathogen found worldwide and which especially affects infants and young children. While different bioserotypes have been associated with varying pathogenici...

    Authors: Debora Garzetti, Hicham Bouabe, Juergen Heesemann and Alexander Rakin
    Citation: BMC Genomics 2012 13:467
    Content type: Research article Published on:

  18. Animals co-evolve with their gut microbiota; the latter can perform complex metabolic reactions that cannot be done independently by the host. Although the importance of gut microbiota has been well demonstrat...

    Authors: Hsiao-Pei Lu, Yu-bin Wang, Shiao-Wei Huang, Chung-Yen Lin, Martin Wu, Chih-hao Hsieh and Hon-Tsen Yu
    Citation: BMC Genomics 2012 13:466
    Content type: Research article Published on:

  19. The genus Saccharothrix is a representative of the family Pseudonocardiaceae, known to include producer strains of a wide variety of potent antibiotics. Saccharothrix espanaensis produces both saccharomicins A an...

    Authors: Tina Strobel, Arwa Al-Dilaimi, Jochen Blom, Arne Gessner, Jörn Kalinowski, Marta Luzhetska, Alfred Pühler, Rafael Szczepanowski, Andreas Bechthold and Christian Rückert
    Citation: BMC Genomics 2012 13:465
    Content type: Research article Published on:

  20. The Azadirachta indica (neem) tree is a source of a wide number of natural products, including the potent biopesticide azadirachtin. In spite of its widespread applications in agriculture and medicine, the molecu...

    Authors: Neeraja M Krishnan, Swetansu Pattnaik, Prachi Jain, Prakhar Gaur, Rakshit Choudhary, Srividya Vaidyanathan, Sa Deepak, Arun K Hariharan, PG Bharath Krishna, Jayalakshmi Nair, Linu Varghese, Naveen K Valivarthi, Kunal Dhas, Krishna Ramaswamy and Binay Panda
    Citation: BMC Genomics 2012 13:464
    Content type: Research article Published on:

  21. The availability of a large number of recently sequenced vertebrate genomes opens new avenues to integrate cytogenetics and genomics in comparative and evolutionary studies. Cytogenetic mapping can offer alter...

    Authors: Juliana Mazzuchelli, Thomas David Kocher, Fengtang Yang and Cesar Martins
    Citation: BMC Genomics 2012 13:463
    Content type: Research article Published on:

  22. Next generation sequencing platforms are now well implanted in sequencing centres and some laboratories. Upcoming smaller scale machines such as the 454 junior from Roche or the MiSeq from Illumina will increa...

    Authors: Jérôme Mariette, Frédéric Escudié, Nicolas Allias, Gérald Salin, Céline Noirot, Sylvain Thomas and Christophe Klopp
    Citation: BMC Genomics 2012 13:462
    Content type: Software Published on:

  23. Rice in tropical and sub-tropical areas is often subjected to cold stress at the seedling stage, resulting in poor growth and yield loss. Although japonica rice is generally more cold tolerant (CT) than indica ri...

    Authors: Fan Zhang, Liyu Huang, Wensheng Wang, Xiuqin Zhao, Linghua Zhu, Binying Fu and Zhikang Li
    Citation: BMC Genomics 2012 13:461
    Content type: Research article Published on:

  24. 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:

  25. 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:

  26. Chromosome 17q21.31 contains a common inversion polymorphism of approximately 900 kb in populations with European ancestry. Two divergent MAPT haplotypes, H1 and H2 are described with distinct linkage disequilibr...

    Authors: Simone de Jong, Iouri Chepelev, Esther Janson, Eric Strengman, Leonard H van den Berg, Jan H Veldink and Roel A Ophoff
    Citation: BMC Genomics 2012 13:458
    Content type: Research article Published on:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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:

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BMC Genomics

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