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  1. Shewanella oneidensis MR-1 exhibits diverse metal ion-reducing capabilities and thus is of potential utility as a bioremediation agent. Knowledge of the molecular components and regulatory mechanisms dictating ce...

    Authors: Karuna Chourey, Wei Wei, Xiu-Feng Wan and Dorothea K Thompson
    Citation: BMC Genomics 2008 9:395
    Content type: Research article Published on:

  2. During the last years, several groups have identified prognostic gene expression signatures with apparently similar performances. However, signatures were never compared on an independent population of untreat...

    Authors: Benjamin Haibe-Kains, Christine Desmedt, Fanny Piette, Marc Buyse, Fatima Cardoso, Laura van't Veer, Martine Piccart, Gianluca Bontempi and Christos Sotiriou
    Citation: BMC Genomics 2008 9:394
    Content type: Research article Published on:

  3. Protein phosphatase 2A (PP2A) is a serine/threonine-specific phosphatase displaying vital functions in growth and development through its role in various signalling pathways. PP2A holoenzymes comprise a core d...

    Authors: Karen Zwaenepoel, Justin V Louis, Jozef Goris and Veerle Janssens
    Citation: BMC Genomics 2008 9:393
    Content type: Research article Published on:

  5. One of the loci responsible for feather development in chickens is K. The K allele is partially dominant to the k+ allele and causes a retard in the emergence of flight feathers at hatch. The K locus is sex li...

    Authors: Martin G Elferink, Amélie AA Vallée, Annemieke P Jungerius, Richard PMA Crooijmans and Martien AM Groenen
    Citation: BMC Genomics 2008 9:391
    Content type: Research article Published on:

  6. DNA Microarrays are regarded as a valuable tool for basic and applied research in microbiology. However, for many industrially important microorganisms the lack of commercially available microarrays still hamp...

    Authors: Alexandra Graf, Brigitte Gasser, Martin Dragosits, Michael Sauer, Germán G Leparc, Thomas Tüchler, David P Kreil and Diethard Mattanovich
    Citation: BMC Genomics 2008 9:390
    Content type: Research article Published on:

  8. Translation of the genome sequence of Plasmodium sp. into biologically relevant information relies on high through-put genomics technology which includes transcriptome analysis. However, few studies to date have ...

    Authors: Onguma Natalang, Emmanuel Bischoff, Guillaume Deplaine, Caroline Proux, Marie-Agnès Dillies, Odile Sismeiro, Ghislaine Guigon, Serge Bonnefoy, Jintana Patarapotikul, Odile Mercereau-Puijalon, Jean-Yves Coppée and Peter H David
    Citation: BMC Genomics 2008 9:388
    Content type: Research article Published on:

  10. Phenylobacterium zucineum is a recently identified facultative intracellular species isolated from the human leukemia cell line K562. Unlike the known intracellular pathogens, P. zucineum maintains a stable assoc...

    Authors: Yingfeng Luo, Xiaoli Xu, Zonghui Ding, Zhen Liu, Bing Zhang, Zhiyu Yan, Jie Sun, Songnian Hu and Xun Hu
    Citation: BMC Genomics 2008 9:386
    Content type: Research article Published on:

  11. African trypanosomes (including Trypanosoma brucei) are unicellular parasites which multiply in the mammalian bloodstream. T. brucei has about twenty telomeric bloodstream form Variant Surface Glycoprotein (VSG) ...

    Authors: Rosanna Young, Jesse E Taylor, Ayako Kurioka, Marion Becker, Edward J Louis and Gloria Rudenko
    Citation: BMC Genomics 2008 9:385
    Content type: Research article Published on:

  12. It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of lin...

    Authors: Tomàs Marques-Bonet, Ze Cheng, Xinwei She, Evan E Eichler and Arcadi Navarro
    Citation: BMC Genomics 2008 9:384
    Content type: Research article Published on:

  13. Cryptomeria japonica D. Don is one of the most commercially important conifers in Japan. However, the allergic disease caused by its pollen is a severe public health problem in Japan. Since large-scale analysis o...

    Authors: Norihiro Futamura, Yasushi Totoki, Atsushi Toyoda, Tomohiro Igasaki, Tokihiko Nanjo, Motoaki Seki, Yoshiyuki Sakaki, Adriano Mari, Kazuo Shinozaki and Kenji Shinohara
    Citation: BMC Genomics 2008 9:383
    Content type: Research article Published on:

  15. Many fruit-tree species, including relevant Citrus spp varieties exhibit a reproductive biology that impairs breeding and strongly constrains genetic improvements. In citrus, juvenility increases the generation t...

    Authors: Gabino Ríos, Miguel A Naranjo, Domingo J Iglesias, Omar Ruiz-Rivero, Marion Geraud, Antonio Usach and Manuel Talón
    Citation: BMC Genomics 2008 9:381
    Content type: Research article Published on:

  16. The development of genetic markers is complex and costly in species with little pre-existing genomic information. Faba bean possesses one of the largest and least studied genomes among cultivated crop plants a...

    Authors: Simon R Ellwood, Huyen TT Phan, Megan Jordan, James Hane, Anna M Torres, Carmen M Avila, Serafín Cruz-Izquierdo and Richard P Oliver
    Citation: BMC Genomics 2008 9:380
    Content type: Research article Published on:

  17. Microarray Comparative Genomic Hybridization (array CGH) provides a means to examine DNA copy number aberrations. Various platforms, brands and underlying technologies are available, facing the user with many ...

    Authors: LO Baumbusch, J Aarøe, FE Johansen, J Hicks, H Sun, L Bruhn, K Gunderson, B Naume, VN Kristensen, K Liestøl, A-L Børresen-Dale and OC Lingjærde
    Citation: BMC Genomics 2008 9:379
    Content type: Research article Published on:

  18. Grape ripening represents the third phase of the double sigmoidal curve of berry development and is characterized by deep changes in the organoleptic characteristics. In this process, the skin plays a central ...

    Authors: Alfredo S Negri, Bhakti Prinsi, Mara Rossoni, Osvaldo Failla, Attilio Scienza, Maurizio Cocucci and Luca Espen
    Citation: BMC Genomics 2008 9:378
    Content type: Research article Published on:

  19. Coeliac disease is a multifactorial inflammatory disorder of the intestine caused by ingestion of gluten in genetically susceptible individuals. Genes within the HLA-DQ locus are considered to contribute some ...

    Authors: Suzanne Bracken, Greg Byrne, Jacinta Kelly, John Jackson and Conleth Feighery
    Citation: BMC Genomics 2008 9:377
    Content type: Research article Published on:

  20. Although exposure to asbestos is now regulated, patients continue to be diagnosed with mesothelioma, asbestosis, fibrosis and lung carcinoma because of the long latent period between exposure and clinical dise...

    Authors: Joan M Hevel, Laura C Olson-Buelow, Balasubramanian Ganesan, John R Stevens, Jared P Hardman and Ann E Aust
    Citation: BMC Genomics 2008 9:376
    Content type: Research article Published on:

  21. Michiels et al. (Lancet 2005; 365: 488–92) employed a resampling strategy to show that the genes identified as predictors of prognosis from resamplings of a single gene expression dataset are highly variable. The...

    Authors: Martin H van Vliet, Fabien Reyal, Hugo M Horlings, Marc J van de Vijver, Marcel JT Reinders and Lodewyk FA Wessels
    Citation: BMC Genomics 2008 9:375
    Content type: Research article Published on:

  22. There is limited knowledge on the extent and dynamics of the mucosal response to commensal and probiotic species in the human intestinal lumen. This study aimed to identify the acute, time-dependent responses ...

    Authors: Freddy J Troost, Peter van Baarlen, Patrick Lindsey, Andrea Kodde, Willem M de Vos, Michiel Kleerebezem and Robert-Jan M Brummer
    Citation: BMC Genomics 2008 9:374
    Content type: Research article Published on:

  23. Variation in genomes among different closely-related organisms can be linked to phenotypic differences. A number of mechanisms, such as replication error, repeat expansion and contraction, recombination and tr...

    Authors: Anchal Vishnoi, Alok Srivastava, Rahul Roy and Alok Bhattacharya
    Citation: BMC Genomics 2008 9:373
    Content type: Database Published on:

  24. Subolesin is an evolutionary conserved protein that was discovered recently in Ixodes scapularis as a tick protective antigen and has a role in tick blood digestion, reproduction and development. In other organis...

    Authors: José de la Fuente, Christine Maritz-Olivier, Victoria Naranjo, Patricia Ayoubi, Ard M Nijhof, Consuelo Almazán, Mario Canales, José M Pérez de la Lastra, Ruth C Galindo, Edmour F Blouin, Christian Gortazar, Frans Jongejan and Katherine M Kocan
    Citation: BMC Genomics 2008 9:372
    Content type: Research article Published on:

  25. The presence of highly conserved sequences within cis-regulatory regions can serve as a valuable starting point for elucidating the basis of enhancer function. This study focuses on regulation of gene expression ...

    Authors: Thomas Brody, Wayne Rasband, Kevin Baler, Alexander Kuzin, Mukta Kundu and Ward F Odenwald
    Citation: BMC Genomics 2008 9:371
    Content type: Research article Published on:

  26. The Zap1 transcription factor is a central player in the response of yeast to changes in zinc status. We previously used transcriptome profiling with DNA microarrays to identify 46 potential Zap1 target genes ...

    Authors: Chang-Yi Wu, Amanda J Bird, Lisa M Chung, Michael A Newton, Dennis R Winge and David J Eide
    Citation: BMC Genomics 2008 9:370
    Content type: Research article Published on:

  27. Peripheral arterial disease (PAD), a major manifestation of atherosclerosis, is associated with significant cardiovascular morbidity, limb loss and death. However, mechanisms underlying the genesis and progres...

    Authors: Shijun Fu, Haiguang Zhao, Jiantao Shi, Arhat Abzhanov, Keith Crawford, Lucila Ohno-Machado, Jianqin Zhou, Yanzhi Du, Winston Patrick Kuo, Ji Zhang, Mier Jiang and Jason Gang Jin
    Citation: BMC Genomics 2008 9:369
    Content type: Research article Published on:

  28. Experiments using whole transcriptome microarrays produce massive amounts of data. To gain a comprehensive understanding of this gene expression data it needs to be integrated with other available information ...

    Authors: Kei Chin Christine Cheng and Martina V Strömvik
    Citation: BMC Genomics 2008 9:368
    Content type: Database Published on:

  29. 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:

  31. 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:

  32. Anaplasma phagocytophilum (Ap) is an obligate intracellular bacterium and the agent of human granulocytic anaplasmosis, an emerging tick-borne disease. Ap alternately infects ticks and mammals and a variety of ce...

    Authors: Curtis M Nelson, Michael J Herron, Roderick F Felsheim, Brian R Schloeder, Suzanne M Grindle, Adela Oliva Chavez, Timothy J Kurtti and Ulrike G Munderloh
    Citation: BMC Genomics 2008 9:364
    Content type: Research article Published on:

  33. 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:

  34. Previous research has demonstrated that increased milking frequency of dairy cattle during the first few weeks of lactation enhances milk yield, and that the effect persists throughout the entire lactation per...

    Authors: Erin E Connor, Stephen Siferd, Theodore H Elsasser, Christina M Evock-Clover, Curtis P Van Tassell, Tad S Sonstegard, Violet M Fernandes and Anthony V Capuco
    Citation: BMC Genomics 2008 9:362
    Content type: Research article Published on:

  35. 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:

  36. The difficulty in elucidating the genetic basis of complex diseases roots in the many factors that can affect the development of a disease. Some of these genetic effects may interact in complex ways, proving u...

    Authors: Javier Gayán, Antonio González-Pérez, Fernando Bermudo, María Eugenia Sáez, Jose Luis Royo, Antonio Quintas, Jose Jorge Galan, Francisco Jesús Morón, Reposo Ramirez-Lorca, Luis Miguel Real and Agustín Ruiz
    Citation: BMC Genomics 2008 9:360
    Content type: Methodology article Published on:

  37. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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:

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BMC Genomics

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