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  1. Leakage of water and ions and soluble proteins from muscle cells occurs during prolonged exercise due to ischemia causing muscle damage. Also post mortem anoxia during conversion of muscle to meat is marked by lo...

    Authors: Siriluck Ponsuksili, Elisabeth Jonas, Eduard Murani, Chirawath Phatsara, Tiranun Srikanchai, Christina Walz, Manfred Schwerin, Karl Schellander and Klaus Wimmers
    Citation: BMC Genomics 2008 9:367
    Content type: Research article Published on:

  2. We previously described the first respiratory Saccharomyces cerevisiae strain, KOY.TM6*P, by integrating the gene encoding a chimeric hexose transporter, Tm6*, into the genome of an hxt null yeast. Subsequently w...

    Authors: Nicklas Bonander, Cecilia Ferndahl, Petter Mostad, Martin DB Wilks, Celia Chang, Louise Showe, Lena Gustafsson, Christer Larsson and Roslyn M Bill
    Citation: BMC Genomics 2008 9:365
    Content type: Research article Published on:

  3. The RUNX1 transcription factor gene is frequently mutated in sporadic myeloid and lymphoid leukemia through translocation, point mutation or amplification. It is also responsible for a familial platelet disorder ...

    Authors: Joëlle Michaud, Ken M Simpson, Robert Escher, Karine Buchet-Poyau, Tim Beissbarth, Catherine Carmichael, Matthew E Ritchie, Frédéric Schütz, Ping Cannon, Marjorie Liu, Xiaofeng Shen, Yoshiaki Ito, Wendy H Raskind, Marshall S Horwitz, Motomi Osato, David R Turner…
    Citation: BMC Genomics 2008 9:363
    Content type: Research article Published on:

  4. Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly ...

    Authors: Michael K Tran, Carolyn J Schultz and Ute Baumann
    Citation: BMC Genomics 2008 9:361
    Content type: Research article Published on:

  5. Human interfollicular epidermis is sustained by the proliferation of stem cells and their progeny, transient amplifying cells. Molecular characterization of these two cell populations is essential for better u...

    Authors: Salih S Koçer, Petar M Djurić, Mónica F Bugallo, Sanford R Simon and Maja Matic
    Citation: BMC Genomics 2008 9:359
    Content type: Research article Published on:

  7. Eggplant (Solanum melongena L.) is a member of the Solanaceae family. In spite of its widespread cultivation and nutritional and economic importance, its genome has not as yet been extensively investigated. Few a...

    Authors: Anikò Stàgel, Ezio Portis, Laura Toppino, Giuseppe Leonardo Rotino and Sergio Lanteri
    Citation: BMC Genomics 2008 9:357
    Content type: Research article Published on:

  8. Haplotype inference based on unphased SNP markers is an important task in population genetics. Although there are different approaches to the inference of haplotypes in diploid species, the existing software i...

    Authors: Jost Neigenfind, Gabor Gyetvai, Rico Basekow, Svenja Diehl, Ute Achenbach, Christiane Gebhardt, Joachim Selbig and Birgit Kersten
    Citation: BMC Genomics 2008 9:356
    Content type: Software Published on:

  9. Secondary structure interactions within introns have been shown to be essential for efficient splicing of several yeast genes. The nature of these base-pairing interactions and their effect on splicing efficie...

    Authors: Sanja Rogic, Ben Montpetit, Holger H Hoos, Alan K Mackworth, BF Francis Ouellette and Philip Hieter
    Citation: BMC Genomics 2008 9:355
    Content type: Research article Published on:

  10. A significant proportion of the human genome is comprised of human endogenous retroviruses (HERVs). HERV transcripts are found in every human tissue. Expression of proviruses of the HERV-K(HML-2) family has be...

    Authors: Aline Flockerzi, Alessia Ruggieri, Oliver Frank, Marlies Sauter, Esther Maldener, Bernd Kopper, Bernd Wullich, Wolfgang Seifarth, Nikolaus Müller-Lantzsch, Christine Leib-Mösch, Eckart Meese and Jens Mayer
    Citation: BMC Genomics 2008 9:354
    Content type: Research article Published on:

  11. Neuroblastoma is a very heterogeneous pediatric tumor of the sympathetic nervous system showing clinically significant patterns of genetic alterations. Favorable tumors usually have near-triploid karyotypes wi...

    Authors: Helena Carén, Jennie Erichsen, Linda Olsson, Charlotta Enerbäck, Rose-Marie Sjöberg, Jonas Abrahamsson, Per Kogner and Tommy Martinsson
    Citation: BMC Genomics 2008 9:353
    Content type: Research article Published on:

  12. The Prolactin (PRL) hormone gene family shows considerable variation among placental mammals. Whereas there is a single PRL gene in humans that is expressed by the pituitary, there are an additional 22 genes in m...

    Authors: David G Simmons, Saara Rawn, Alastair Davies, Martha Hughes and James C Cross
    Citation: BMC Genomics 2008 9:352
    Content type: Research article Published on:

  13. Kiwifruit (Actinidia spp.) are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer...

    Authors: Ross N Crowhurst, Andrew P Gleave, Elspeth A MacRae, Charles Ampomah-Dwamena, Ross G Atkinson, Lesley L Beuning, Sean M Bulley, David Chagne, Ken B Marsh, Adam J Matich, Mirco Montefiori, Richard D Newcomb, Robert J Schaffer, Björn Usadel, Andrew C Allan, Helen L Boldingh…
    Citation: BMC Genomics 2008 9:351
    Content type: Research article Published on:

  15. Independent lines of evidence suggested that a large fraction of human genes possess multiple promoters driving gene expression from distinct transcription start sites. Understanding which promoter is employed...

    Authors: Gregory AC Singer, Jiejun Wu, Pearlly Yan, Christoph Plass, Tim HM Huang and Ramana V Davuluri
    Citation: BMC Genomics 2008 9:349
    Content type: Research article Published on:

  16. The 70 kDa ribosomal protein S6 kinase (RPS6KB1), located at 17q23, is amplified and overexpressed in 10–30% of primary breast cancers and breast cancer cell lines. p70S6K is a serine/threonine kinase regulated b...

    Authors: Henna Heinonen, Anni Nieminen, Matti Saarela, Anne Kallioniemi, Juha Klefström, Sampsa Hautaniemi and Outi Monni
    Citation: BMC Genomics 2008 9:348
    Content type: Research article Published on:

  17. After 10-year-use of AFLP (Amplified Fragment Length Polymorphism) technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are available in public...

    Authors: Alessandro Botton, Giulio Galla, Ana Conesa, Christian Bachem, Angelo Ramina and Gianni Barcaccia
    Citation: BMC Genomics 2008 9:347
    Content type: Research article Published on:

  18. MicroRNAs play an important functional role in post-transcriptional gene regulation. One of the largest known microRNA clusters is located within the imprinted Dlk1/Gtl2 region on human chromosome 14 and mouse ch...

    Authors: Martin Kircher, Christoph Bock and Martina Paulsen
    Citation: BMC Genomics 2008 9:346
    Content type: Research article Published on:

  19. With over 20 parapatric races differing in their warningly colored wing patterns, the butterfly Heliconius erato provides a fascinating example of an adaptive radiation. Together with matching races of its co-mim...

    Authors: Riccardo Papa, Clayton M Morrison, James R Walters, Brian A Counterman, Rui Chen, Georg Halder, Laura Ferguson, Nicola Chamberlain, Richard ffrench-Constant, Durrell D Kapan, Chris D Jiggins, Robert D Reed and William O McMillan
    Citation: BMC Genomics 2008 9:345
    Content type: Research article Published on:

  20. The unicellular cyanobacterium Synechocystis sp. PCC 6803 is a model microbe for studying biochemistry, genetics and molecular biology of photobiological processes. Importance of this bacterium in basic and appli...

    Authors: Zhigang Zhang, Ninad D Pendse, Katherine N Phillips, James B Cotner and Arkady Khodursky
    Citation: BMC Genomics 2008 9:344
    Content type: Research article Published on:

  21. The development of transcriptomic tools has allowed exhaustive description of stress responses. These responses always superimpose a general response associated to growth rate decrease and a specific one corre...

    Authors: Clémentine Dressaire, Emma Redon, Helene Milhem, Philippe Besse, Pascal Loubière and Muriel Cocaign-Bousquet
    Citation: BMC Genomics 2008 9:343
    Content type: Research article Published on:

  22. The whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), and the viruses it transmits, are a major constraint to growing vegetable crops worldwide. Although the whitefly is often controlled using chemica...

    Authors: Assaf Mahadav, Dan Gerling, Yuval Gottlieb, Henryk Czosnek and Murad Ghanim
    Citation: BMC Genomics 2008 9:342
    Content type: Research article Published on:

  23. Characterization of cellular growth is central to understanding living systems. Here, we applied a three-factor design to study the relationship between specific growth rate and genome-wide gene expression in ...

    Authors: Alessandro Fazio, Michael C Jewett, Pascale Daran-Lapujade, Roberta Mustacchi, Renata Usaite, Jack T Pronk, Christopher T Workman and Jens Nielsen
    Citation: BMC Genomics 2008 9:341
    Content type: Research article Published on:

  24. A reciprocal relationship between bone and fat development in osteoporosis is clinically well established. Some of the key molecular regulators involved in this tissue replacement process have been identified....

    Authors: Marcel Scheideler, Christian Elabd, Laure-Emmanuelle Zaragosi, Chiara Chiellini, Hubert Hackl, Fatima Sanchez-Cabo, Sunaina Yadav, Kalina Duszka, Gerald Friedl, Christine Papak, Andreas Prokesch, Reinhard Windhager, Gerard Ailhaud, Christian Dani, Ez-Zoubir Amri and Zlatko Trajanoski
    Citation: BMC Genomics 2008 9:340
    Content type: Research article Published on:

  25. The Programmed Ribosomal Frameshift Database (PRFdb) provides an interface to help researchers identify potential programmed -1 ribosomal frameshift (-1 PRF) signals in eukaryotic genes or sequences of interest.

    Authors: Ashton T Belew, Nicholas L Hepler, Jonathan L Jacobs and Jonathan D Dinman
    Citation: BMC Genomics 2008 9:339
    Content type: Database Published on:

  26. Functional genomics has particular promise in silkworm biology for identifying genes involved in a variety of biological functions that include: synthesis and secretion of silk, sex determination pathways, ins...

    Authors: KP Arunkumar, Archana Tomar, Takaaki Daimon, Toru Shimada and J Nagaraju
    Citation: BMC Genomics 2008 9:338
    Content type: Database Published on:

  27. Gene expression analyses have led to a better understanding of growth control of prostate cancer cells. We and others have identified the presence of several zinc finger transcription factors in the neoplastic...

    Authors: Kurtis Eisermann, Sunpreet Tandon, Anton Bazarov, Adina Brett, Gail Fraizer and Helen Piontkivska
    Citation: BMC Genomics 2008 9:337
    Content type: Research article Published on:

  28. Protein kinases and phosphatases regulate protein phosphorylation, a critical means of modulating protein function, stability and localization. The identification of functional networks for protein phosphatase...

    Authors: Michael R Logan, Thao Nguyen, Nicolas Szapiel, James Knockleby, Hanting Por, Megan Zadworny, Michael Neszt, Paul Harrison, Howard Bussey, Craig A Mandato, Jackie Vogel and Guillaume Lesage
    Citation: BMC Genomics 2008 9:336
    Content type: Research article Published on:

  30. In contrast to the three mammalian p53 family members, p53, which is generally involved in DNA damage responses, and p63 and p73 which are primarily needed for developmental regulation, cep-1 encodes for the sing...

    Authors: Sebastian Greiss, Björn Schumacher, Kaj Grandien, Jonathan Rothblatt and Anton Gartner
    Citation: BMC Genomics 2008 9:334
    Content type: Research article Published on:

  31. Stress responses provide valuable models for deciphering the transcriptional networks controlling the adaptation of the cell to its environment. We analyzed the transcriptome response of yeast to toxic concent...

    Authors: Hélène Salin, Vivienne Fardeau, Eugenia Piccini, Gaelle Lelandais, Véronique Tanty, Sophie Lemoine, Claude Jacq and Frédéric Devaux
    Citation: BMC Genomics 2008 9:333
    Content type: Research article Published on:

  33. Knowledge of animal mitochondrial genomes is very important to understand their molecular evolution as well as for phylogenetic and population genetic studies. The Lepidoptera encompasses more than 160,000 des...

    Authors: Paola Salvato, Mauro Simonato, Andrea Battisti and Enrico Negrisolo
    Citation: BMC Genomics 2008 9:331
    Content type: Research article Published on:

  34. T-box anti-termination is an elegant and sensitive mechanism by which many bacteria maintain constant levels of amino acid-charged tRNAs. The amino acid specificity of the regulatory element is related to a so...

    Authors: Michiel Wels, Tom Groot Kormelink, Michiel Kleerebezem, Roland J Siezen and Christof Francke
    Citation: BMC Genomics 2008 9:330
    Content type: Research article Published on:

  35. Selenoprotein S (SelS) protects the functional integrity of the endoplasmic reticulum against the deleterious effects of metabolic stress. SEPS1/SelS polymorphisms have been involved in the increased release of p...

    Authors: Alfonso Martínez, Jose Luis Santiago, Jezabel Varadé, Ana Márquez, José Ramón Lamas, Juan Luis Mendoza, Hermenegildo de la Calle, Manuel Díaz-Rubio, Emilio G de la Concha, Benjamín Fernández-Gutiérrez and Elena Urcelay
    Citation: BMC Genomics 2008 9:329
    Content type: Research article Published on:

  36. The MicroArray Quality Control (MAQC) project evaluated the inter- and intra-platform reproducibility of seven microarray platforms and three quantitative gene expression assays in profiling the expression of ...

    Authors: Emi Arikawa, Yanyang Sun, Jie Wang, Qiong Zhou, Baitang Ning, Stacey L Dial, Lei Guo and Jingping Yang
    Citation: BMC Genomics 2008 9:328
    Content type: Research article Published on:

  37. The hypercellulolytic mutant Hypocrea jecorina (anamorph Trichoderma reesei) RUT C30 is the H. jecorina strain most frequently used for cellulase fermentations and has also often been employed for basic research ...

    Authors: Verena Seidl, Christian Gamauf, Irina S Druzhinina, Bernhard Seiboth, Lukas Hartl and Christian P Kubicek
    Citation: BMC Genomics 2008 9:327
    Content type: Research article Published on:

  38. Understanding the transcriptional regulation mechanisms in response to environmental challenges is of fundamental importance in biology. Transcription factors associated to response elements and the chromatin ...

    Authors: Jesus Hernandez-Romano, Francisco J Carlos-Rivera, Heladia Salgado, Hector Lamadrid-Figueroa, Veronica Valverde-Garduño, Mario H Rodriguez and Jesus Martinez-Barnetche
    Citation: BMC Genomics 2008 9:326
    Content type: Research article Published on:

  39. Virus infection induces the activation and suppression of global gene expression in the host. Profiling gene expression changes in the host may provide insights into the molecular mechanisms that underlie host...

    Authors: Mohan Babu, Jonathan S Griffiths, Tyng-Shyan Huang and Aiming Wang
    Citation: BMC Genomics 2008 9:325
    Content type: Research article Published on:

  41. Many of the world's most important food crops have either polyploid genomes or homeologous regions derived from segmental shuffling following polyploid formation. The soybean (Glycine max) genome has been shown t...

    Authors: Navinder Saini, Jeffry Shultz and David A Lightfoot
    Citation: BMC Genomics 2008 9:323
    Content type: Research article Published on:

  42. Epstein-Barr virus (EBV) presumably plays an important role in the pathogenesis of nasopharyngeal carcinoma (NPC), but the molecular mechanism of EBV-dependent neoplastic transformation is not well understood....

    Authors: Xia Chen, Shuang Liang, WenLing Zheng, ZhiJun Liao, Tao Shang and WenLi Ma
    Citation: BMC Genomics 2008 9:322
    Content type: Research article Published on:

  43. The bacterium Staphylococcus aureus causes significant morbidity and mortality in humans, primarily due to the emergence of strains that are resistant to antibiotics – notably methicillin-resistant S. aureus (MRS...

    Authors: Christina J Brandner, Richard H Maier, Daryl S Henderson, Helmut Hintner, Johann W Bauer and Kamil Önder
    Citation: BMC Genomics 2008 9:321
    Content type: Research article Published on:

  44. Type 2 Diabetes Mellitus (T2DM) is a non insulin dependent, complex trait disease that develops due to genetic predisposition and environmental factors. The advanced stage in type 2 diabetes mellitus leads to ...

    Authors: Shipra Agrawal, Nevenka Dimitrova, Prasanthi Nathan, K Udayakumar, S Sai Lakshmi, S Sriram, N Manjusha and Urmi Sengupta
    Citation: BMC Genomics 2008 9:320
    Content type: Software Published on:

  46. Understanding of genetic elements that contribute to key aspects of citrus biology will impact future improvements in this economically important crop. Global gene expression analysis demands microarray platfo...

    Authors: M Angeles Martinez-Godoy, Nuria Mauri, Jose Juarez, M Carmen Marques, Julia Santiago, Javier Forment and Jose Gadea
    Citation: BMC Genomics 2008 9:318
    Content type: Methodology article Published on:

  47. Microarrays are an important and widely used tool. Applications include capturing genomic DNA for high-throughput sequencing in addition to the traditional monitoring of gene expression and identifying DNA cop...

    Authors: Catriona Rennie, Harry A Noyes, Stephen J Kemp, Helen Hulme, Andy Brass and David C Hoyle
    Citation: BMC Genomics 2008 9:317
    Content type: Research article Published on:

  48. While the genomic annotations of diverse lineages of the Mycobacterium tuberculosis complex are available, divergences between gene prediction methods are still a challenge for unbiased protein dataset generation...

    Authors: Gustavo A de Souza, Hiwa Målen, Tina Søfteland, Gisle Sælensminde, Swati Prasad, Inge Jonassen and Harald G Wiker
    Citation: BMC Genomics 2008 9:316
    Content type: Research article Published on:

  49. Mitogenomics data, i.e. complete mitochondrial genome sequences, are popular molecular markers used for phylogenetic, phylogeographic and ecological studies in different animal lineages. Their comparative anal...

    Authors: Antonio Carapelli, Sara Comandi, Peter Convey, Francesco Nardi and Francesco Frati
    Citation: BMC Genomics 2008 9:315
    Content type: Research article Published on:

  50. Upland cotton has the highest yield, and accounts for > 95% of world cotton production. Decoding upland cotton genomes will undoubtedly provide the ultimate reference and resource for structural, functional, a...

    Authors: Wangzhen Guo, Caiping Cai, Changbiao Wang, Liang Zhao, Lei Wang and Tianzhen Zhang
    Citation: BMC Genomics 2008 9:314
    Content type: Research article Published on:

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BMC Genomics

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