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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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

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