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  1. We present evidence that a major aspect of the mechanism of acute signal transduction regulation by insulin-like growth factor-1 (IGF-1) in cultured murine myoblasts is associated with a broad perturbation of ...

    Authors: C Ramana Bhasker and Theodore Friedmann
    Citation: BMC Genomics 2008 9:535
    Content type: Research article Published on:

  2. Authors: Steven L Salzberg, Daniel D Sommer, Michael C Schatz, Adam M Phillippy, Pablo D Rabinowicz, Seiji Tsuge, Ayako Furutani, Hirokazu Ochiai, Arthur L Delcher, David Kelley, Ramana Madupu, Daniela Puiu, Diana Radune, Martin Shumway, Cole Trapnell, Gudlur Aparna…
    Citation: BMC Genomics 2008 9:534
    Content type: Erratum Published on:

    The original article was published in BMC Genomics 2008 9:204

  3. Tandemly Repeated DNA represents a large portion of the human genome, and accounts for a significant amount of copy number variation. Here we present a genome wide analysis of the largest tandem repeats found ...

    Authors: Peter E Warburton, Dan Hasson, Flavia Guillem, Chloe Lescale, Xiaoping Jin and Gyorgy Abrusan
    Citation: BMC Genomics 2008 9:533
    Content type: Research article Published on:

  4. Complete mitochondrial (mt) genomes and the gene rearrangements therein are increasingly used as molecular markers for investigating phylogenetic relationships, especially for elucidating deep splits. Contribu...

    Authors: Katja Domes, Mark Maraun, Stefan Scheu and Stephen L Cameron
    Citation: BMC Genomics 2008 9:532
    Content type: Research article Published on:

  5. This paper presents a retrospective statistical study on the newly-released data set by the Stanley Neuropathology Consortium on gene expression in bipolar disorder and schizophrenia. This data set contains ge...

    Authors: Jan Struyf, Seth Dobrin and David Page
    Citation: BMC Genomics 2008 9:531
    Content type: Research article Published on:

  6. 'Omics' tools provide novel opportunities for system-wide analysis of complex cellular functions. Secondary metabolism is an example of a complex network of biochemical pathways, which, although well mapped fr...

    Authors: Debra Rossouw, Tormod Næs and Florian F Bauer
    Citation: BMC Genomics 2008 9:530
    Content type: Research article Published on:

  7. Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are bec...

    Authors: Amandine Bemmo, David Benovoy, Tony Kwan, Daniel J Gaffney, Roderick V Jensen and Jacek Majewski
    Citation: BMC Genomics 2008 9:529
    Content type: Methodology article Published on:

  8. The contribution of individual organs to the whole-body adaptive response to fasting has not been established. Hence, gene-expression profiling, pathway, network and gene-set enrichment analysis and immunohist...

    Authors: Milka Sokolović, Aleksandar Sokolović, Diederik Wehkamp, Emiel Ver Loren van Themaat, Dirk R de Waart, Lisa A Gilhuijs-Pederson, Yuri Nikolsky, Antoine HC van Kampen, Theodorus BM Hakvoort and Wouter H Lamers
    Citation: BMC Genomics 2008 9:528
    Content type: Research article Published on:

  9. The goal of these studies was to characterize the transcriptional network regulating changes in gene expression in the remnant liver of the rat after 70% partial hepatectomy (PHx) during the early phase respon...

    Authors: Egle Juskeviciute, Rajanikanth Vadigepalli and Jan B Hoek
    Citation: BMC Genomics 2008 9:527
    Content type: Research article Published on:

  10. Salmonella enterica serovar Enteritidis (SE) is one of the most common food-borne pathogens that cause human salmonellosis and usually results from the consumption of contaminated poultry products. The mechanism ...

    Authors: Hsin-I Chiang, Christina L Swaggerty, Michael H Kogut, Scot E Dowd, Xianyao Li, Igal Y Pevzner and Huaijun Zhou
    Citation: BMC Genomics 2008 9:526
    Content type: Research article Published on:

  11. Nematode.net http://​www.​nematode.​net is a web-accessible resource for investigating gene sequences from parasitic and free-living nematode genomes. Beyond th...

    Authors: Todd Wylie, John Martin, Sahar Abubucker, Yong Yin, David Messina, Zhengyuan Wang, James P McCarter and Makedonka Mitreva
    Citation: BMC Genomics 2008 9:525
    Content type: Database Published on:

  12. Genome variability generates phenotypic heterogeneity and is of relevance for adaptation to environmental change, but the extent of such variability in natural populations is still poorly understood. For examp...

    Authors: Laura Carreto, Maria F Eiriz, Ana C Gomes, Patrícia M Pereira, Dorit Schuller and Manuel AS Santos
    Citation: BMC Genomics 2008 9:524
    Content type: Research article Published on:

  13. The ascomycete fungus Cercospora zeae-maydis is an aggressive foliar pathogen of maize that causes substantial losses annually throughout the Western Hemisphere. Despite its impact on maize production, little is ...

    Authors: Burton H Bluhm, Braham Dhillon, Erika A Lindquist, Gert HJ Kema, Stephen B Goodwin and Larry D Dunkle
    Citation: BMC Genomics 2008 9:523
    Content type: Research article Published on:

  14. Growth hormone (GH) is an important regulator of skeletal growth, as well as other adapted processes in salmonids. The GH gene (gh) in salmonids is represented by duplicated, non-allelic isoforms designated as gh...

    Authors: Kristian R von Schalburg, Ryosuke Yazawa, Johan de Boer, Krzysztof P Lubieniecki, Benjamin Goh, Christopher A Straub, Marianne R Beetz-Sargent, Adrienne Robb, William S Davidson, Robert H Devlin and Ben F Koop
    Citation: BMC Genomics 2008 9:522
    Content type: Research article Published on:

  15. Interactions between the gene products encoded by the mitochondrial and nuclear genomes play critical roles in eukaryotic cellular function. However, the effects mitochondrial DNA (mtDNA) levels have on the nu...

    Authors: Darren Magda, Philip Lecane, Julia Prescott, Patricia Thiemann, Xuan Ma, Patricia K Dranchak, Donna M Toleno, Krishna Ramaswamy, Kimberly D Siegmund and Joseph G Hacia
    Citation: BMC Genomics 2008 9:521
    Content type: Research article Published on:

  18. Barley has one of the largest and most complex genomes of all economically important food crops. The rise of new short read sequencing technologies such as Illumina/Solexa permits such large genomes to be effe...

    Authors: Thomas Wicker, Apurva Narechania, Francois Sabot, Joshua Stein, Giang TH Vu, Andreas Graner, Doreen Ware and Nils Stein
    Citation: BMC Genomics 2008 9:518
    Content type: Research article Published on:

  19. The challenges of accurate gene prediction and enumeration are further aggravated in large genomes that contain highly repetitive transposable elements (TEs). Yet TEs play a substantial role in genome evolutio...

    Authors: Stefan Kurtz, Apurva Narechania, Joshua C Stein and Doreen Ware
    Citation: BMC Genomics 2008 9:517
    Content type: Methodology article Published on:

  20. By assaying hundreds of thousands of single nucleotide polymorphisms, genome wide association studies (GWAS) allow for a powerful, unbiased review of the entire genome to localize common genetic variants that ...

    Authors: Priya Duggal, Elizabeth M Gillanders, Taura N Holmes and Joan E Bailey-Wilson
    Citation: BMC Genomics 2008 9:516
    Content type: Research article Published on:

  22. In sharp contrast to humans and great apes, the expanded Mhc-B region of rhesus and cynomolgus macaques is characterized by the presence of differential numbers and unique combinations of polymorphic class I B ge...

    Authors: Maxime Bonhomme, Gaby GM Doxiadis, Corrine MC Heijmans, Virginie Vervoort, Nel Otting, Ronald E Bontrop and Brigitte Crouau-Roy
    Citation: BMC Genomics 2008 9:514
    Content type: Research article Published on:

  23. In recent years, a major increase in the occurrence of drug resistant falciparum malaria has been reported. Choline analogs, such as the bisthiazolium T4, represent a novel class of compounds with strong poten...

    Authors: Karine G Le Roch, Jeffrey R Johnson, Hugues Ahiboh, Duk-Won D Chung, Jacques Prudhomme, David Plouffe, Kerstin Henson, Yingyao Zhou, William Witola, John R Yates, Choukri Ben Mamoun, Elizabeth A Winzeler and Henri Vial
    Citation: BMC Genomics 2008 9:513
    Content type: Research article Published on:

  24. Theobroma cacao L., is a tree originated from the tropical rainforest of South America. It is one of the major cash crops for many tropical countries. T. cacao is mainly produced on smallholdings, providing resou...

    Authors: Xavier Argout, Olivier Fouet, Patrick Wincker, Karina Gramacho, Thierry Legavre, Xavier Sabau, Ange Marie Risterucci, Corinne Da Silva, Julio Cascardo, Mathilde Allegre, David Kuhn, Joseph Verica, Brigitte Courtois, Gaston Loor, Regis Babin, Olivier Sounigo…
    Citation: BMC Genomics 2008 9:512
    Content type: Research article Published on:

  25. The Spemann/Mangold organizer is a transient tissue critical for patterning the gastrula stage vertebrate embryo and formation of the three germ layers. Despite its important role during development, there are...

    Authors: Owen J Tamplin, Doris Kinzel, Brian J Cox, Christine E Bell, Janet Rossant and Heiko Lickert
    Citation: BMC Genomics 2008 9:511
    Content type: Research article Published on:

  28. The Senegalese sole, Solea senegalensis, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered...

    Authors: Joan Cerdà, Jaume Mercadé, Juan José Lozano, Manuel Manchado, Angèle Tingaud-Sequeira, Antonio Astola, Carlos Infante, Silke Halm, Jordi Viñas, Barbara Castellana, Esther Asensio, Pedro Cañavate, Gonzalo Martínez-Rodríguez, Francesc Piferrer, Josep V Planas, Francesc Prat…
    Citation: BMC Genomics 2008 9:508
    Content type: Research article Published on:

  30. Growing interest is turned to fat storage levels and allocation within body compartments, due to their impact on human health and quality properties of farm animals. Energy intake and genetic background are ma...

    Authors: Catherine-Ines Kolditz, Gilles Paboeuf, Maïena Borthaire, Diane Esquerré, Magali SanCristobal, Florence Lefèvre and Françoise Médale
    Citation: BMC Genomics 2008 9:506
    Content type: Research article Published on:

  33. The information from multiple microarray experiments can be integrated in an objective manner via meta-analysis. However, multiple meta-analysis approaches are available and their relative strengths have not been...

    Authors: Heather A Adams, Bruce R Southey, Gene E Robinson and Sandra L Rodriguez-Zas
    Citation: BMC Genomics 2008 9:503
    Content type: Research article Published on:

  35. Curated databases of completely sequenced genomes have been designed independently at the NCBI (RefSeq) and EBI (Genome Reviews) to cope with non-standard annotation found in the version of the sequenced genom...

    Authors: Stéphane Descorps-Declère, Matthieu Barba and Bernard Labedan
    Citation: BMC Genomics 2008 9:501
    Content type: Research article Published on:

  36. Mutations of the superoxide dismutase 1 (SOD1) gene are linked to amyotrophic lateral sclerosis (ALS), an invariably fatal neurological condition involving cortico-spinal degeneration. Mechanical injury can also ...

    Authors: Andrea Malaspina, Natasa Jokic, Wenlong L Huang and John V Priestley
    Citation: BMC Genomics 2008 9:500
    Content type: Research article Published on:

  37. In fish, molecular mechanisms that control follicle-enclosed oocyte progression throughout oogenesis and oocyte developmental competence acquisition remain poorly understood. Existing data in mammals have indi...

    Authors: Julien Bobe, Thaovi Nguyen, Sophie Mahé and Philippe Monget
    Citation: BMC Genomics 2008 9:499
    Content type: Research article Published on:

  38. The salmon louse (SL) is an ectoparasitic caligid crustacean infecting salmonid fishes in the marine environment. SL represents one of the major challenges for farming of salmonids, and veterinary intervention...

    Authors: Stanko Skugor, Kevin Alan Glover, Frank Nilsen and Aleksei Krasnov
    Citation: BMC Genomics 2008 9:498
    Content type: Research article Published on:

  39. Microarray comparative genomic hybridization (CGH) is currently one of the most powerful techniques to measure DNA copy number in large genomes. In humans, microarray CGH is widely used to assess copy number v...

    Authors: Stephane Flibotte and Donald G Moerman
    Citation: BMC Genomics 2008 9:497
    Content type: Methodology article Published on:

  40. With multiple strains of various pathogens being sequenced, it is necessary to develop high-throughput methods that can simultaneously process multiple bacterial or viral genomes to find common fingerprints as...

    Authors: Ravi Vijaya Satya, Nela Zavaljevski, Kamal Kumar, Elizabeth Bode, Susana Padilla, Leonard Wasieloski, Jeanne Geyer and Jaques Reifman
    Citation: BMC Genomics 2008 9:496
    Content type: Methodology article Published on:

  41. Despite a plethora of functional genomic efforts, the function of many genes in sequenced genomes remains unknown. The increasing amount of microarray data for many species allows employing the guilt-by-associ...

    Authors: Evert Jan Blom, Rainer Breitling, Klaas Jan Hofstede, Jos BTM Roerdink, Sacha AFT van Hijum and Oscar P Kuipers
    Citation: BMC Genomics 2008 9:495
    Content type: Software Published on:

  42. Non-biological experimental error routinely occurs in microarray data collected in different batches. It is often impossible to compare groups of samples from independent experiments because batch effects conf...

    Authors: Wynn L Walker, Isaac H Liao, Donald L Gilbert, Brenda Wong, Katherine S Pollard, Charles E McCulloch, Lisa Lit and Frank R Sharp
    Citation: BMC Genomics 2008 9:494
    Content type: Methodology article Published on:

  43. Very little is known about the immunological responses of amphibians to pathogens that are causing global population declines. We used a custom microarray gene chip to characterize gene expression responses of...

    Authors: Jennifer D Cotter, Andrew Storfer, Robert B Page, Christopher K Beachy and S Randal Voss
    Citation: BMC Genomics 2008 9:493
    Content type: Research article Published on:

  44. Copy number variations (CNVs) are deletions, insertions, duplications, and more complex variations ranging from 1 kb to sub-microscopic sizes. Recent advances in array technologies have enabled researchers to ...

    Authors: Tae-Wook Kang, Yeo-Jin Jeon, Eunsu Jang, Hee-Jin Kim, Jeong-Hwan Kim, Jong-Lyul Park, Siwoo Lee, Yong Sung Kim, Jong Yeol Kim and Seon-Young Kim
    Citation: BMC Genomics 2008 9:492
    Content type: Research article Published on:

  46. Trinitrobenzenesulphonic acid (TNBS) induced rat colitis is one of the most widely used models of inflammatory bowel disease (IBD), a condition whose aetiology and pathophysiology are incompletely understood. ...

    Authors: Olga Martínez-Augustin, Manel Merlos, Antonio Zarzuelo, María Dolores Suárez and Fermín Sánchez de Medina
    Citation: BMC Genomics 2008 9:490
    Content type: Research article Published on:

  47. Genomic hybridization platforms, including BAC-CGH and genotyping arrays, have been used to estimate chromosome copy number (CN) in tumor samples by detecting the relative strength of genomic signal. The metho...

    Authors: Paul J Gardina, Ken C Lo, Walter Lee, John K Cowell and Yaron Turpaz
    Citation: BMC Genomics 2008 9:489
    Content type: Research article Published on:

  48. In many genomics projects, numerous lists containing biological identifiers are produced. Often it is useful to see the overlap between different lists, enabling researchers to quickly observe similarities and...

    Authors: Tim Hulsen, Jacob de Vlieg and Wynand Alkema
    Citation: BMC Genomics 2008 9:488
    Content type: Software Published on:

  49. Dichlorodiphenyltrichloroethane (DDT) is a persistent estrogenic organochlorine pesticide that is a rodent hepatic tumor promoter, with inconclusive carcinogenicity in humans. We have previously reported that o,

    Authors: Naoki Kiyosawa, Joshua C Kwekel, Lyle D Burgoon, Edward Dere, Kurt J Williams, Colleen Tashiro, Brock Chittim and Timothy R Zacharewski
    Citation: BMC Genomics 2008 9:487
    Content type: Research article Published on:

  50. Rice (Oryza sativa L.) germplasm represents an extraordinary source of genes that control traits of agronomic importance such as drought tolerance. This diversity is the basis for the development of new cultivars...

    Authors: Aline R Rabello, Cléber M Guimarães, Paulo HN Rangel, Felipe R da Silva, Daniela Seixas, Emanuel de Souza, Ana CM Brasileiro, Carlos R Spehar, Márcio E Ferreira and Ângela Mehta
    Citation: BMC Genomics 2008 9:485
    Content type: Research article Published on:

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