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  1. Neoplasia can be driven by mutations resulting in dysregulation of transcription. In the mesenchymal neoplasm, aggressive fibromatosis, subtractive hybridization identified sterile alpha motif domain 9 (SAMD9) as...

    Authors: Catherine F Li, Jeffrey R MacDonald, Robert Y Wei, Jocelyn Ray, Kimberly Lau, Christopher Kandel, Rachel Koffman, Sherilyn Bell, Stephen W Scherer and Benjamin A Alman

    Citation: BMC Genomics 2007 8:92

    Content type: Research article

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  2. In vitro models are indispensable study objects in the fields of cell and molecular biology, with advantages such as accessibility, homogeneity of the cell population, reproducibility, and growth rate. The Caco-2...

    Authors: Kaatje Lenaerts, Freek G Bouwman, Wouter H Lamers, Johan Renes and Edwin C Mariman

    Citation: BMC Genomics 2007 8:91

    Content type: Research article

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  3. LTR retrotransposons are a class of mobile genetic elements containing two similar long terminal repeats (LTRs). Currently, LTR retrotransposons are annotated in eukaryotic genomes mainly through the conventio...

    Authors: Mina Rho, Jeong-Hyeon Choi, Sun Kim, Michael Lynch and Haixu Tang

    Citation: BMC Genomics 2007 8:90

    Content type: Methodology article

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  4. Gene expression profiles of non-model mammals may provide valuable data for biomedical and evolutionary studies. However, due to lack of sequence information of other species, DNA microarrays are currently res...

    Authors: Manuel Nieto-Díaz, Wolfgang Pita-Thomas and Manuel Nieto-Sampedro

    Citation: BMC Genomics 2007 8:89

    Content type: Research article

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  5. Microarrays provide a means to simultaneously examine the gene expression of the entire transcriptome in a single sample. Many studies have highlighted the need for novel software and statistical approaches to...

    Authors: Walter D Park and Mark D Stegall

    Citation: BMC Genomics 2007 8:88

    Content type: Research article

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  6. Golden Promise is a salt-tolerant spring barley closely related to Maythorpe. Salt tolerance in Golden Promise has been attributed to a single mutation at the Ari-e locus (on 5H) resulting from irradiation of May...

    Authors: Harkamal Walia, Clyde Wilson, Pascal Condamine, Abdelbagi M Ismail, Jin Xu, Xinping Cui and Timothy J Close

    Citation: BMC Genomics 2007 8:87

    Content type: Research article

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  7. Little is known about the genes that drive embryonic stem cell differentiation. However, such knowledge is necessary if we are to exploit the therapeutic potential of stem cells. To uncover the genetic determi...

    Authors: Kagnew Hailesellasse Sene, Christopher J Porter, Gareth Palidwor, Carolina Perez-Iratxeta, Enrique M Muro, Pearl A Campbell, Michael A Rudnicki and Miguel A Andrade-Navarro

    Citation: BMC Genomics 2007 8:85

    Content type: Research article

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  8. Currently, two main technologies are used for screening of DNA copy number; the BAC (Bacterial Artificial Chromosome) and the recently developed oligonucleotide-based CGH (Chromosomal Comparative Genomic Hybri...

    Authors: Nicolas Wicker, Annaïck Carles, Ian G Mills, Maija Wolf, Abhi Veerakumarasivam, Henrik Edgren, Fabrice Boileau, Bohdan Wasylyk, Jack A Schalken, David E Neal, Olli Kallioniemi and Olivier Poch

    Citation: BMC Genomics 2007 8:84

    Content type: Methodology article

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  9. ATP binding cassette (ABC) systems are responsible for the import and export of a wide variety of molecules across cell membranes and comprise one of largest protein superfamilies found in prokarya, eukarya an...

    Authors: David N Harland, Elie Dassa, Richard W Titball, Katherine A Brown and Helen S Atkins

    Citation: BMC Genomics 2007 8:83

    Content type: Research article

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  10. A Paramecium tetraurelia pilot genome project, the subsequent sequencing of a Megabase chromosome as well as the Paramecium genome project aimed at gaining insight into the genome of Paramecium. These cells displ...

    Authors: Ivonne M Sehring, Jörg Mansfeld, Christoph Reiner, Erika Wagner, Helmut Plattner and Roland Kissmehl

    Citation: BMC Genomics 2007 8:82

    Content type: Research article

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  11. Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these ...

    Authors: Joshua A Udall, Lex E Flagel, Foo Cheung, Andrew W Woodward, Ran Hovav, Ryan A Rapp, Jordan M Swanson, Jinsuk J Lee, Alan R Gingle, Dan Nettleton, Christopher D Town, Z Jeffrey Chen and Jonathan F Wendel

    Citation: BMC Genomics 2007 8:81

    Content type: Methodology article

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  12. Aging has been associated with widespread changes at the gene expression level in multiple mammalian tissues. We have used high density oligonucleotide arrays and novel statistical methods to identify specific...

    Authors: Michael G Edwards, Rozalyn M Anderson, Ming Yuan, Christina M Kendziorski, Richard Weindruch and Tomas A Prolla

    Citation: BMC Genomics 2007 8:80

    Content type: Research article

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  13. Human muscular dystrophies are a heterogeneous group of genetic disorders which cause decreased muscle strength and often result in premature death. There is no known cure for muscular dystrophy, nor have all ...

    Authors: Leta S Steffen, Jeffrey R Guyon, Emily D Vogel, Rosanna Beltre, Timothy J Pusack, Yi Zhou, Leonard I Zon and Louis M Kunkel

    Citation: BMC Genomics 2007 8:79

    Content type: Research article

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  14. Genotyping technologies for whole genome association studies are now available. To perform such studies to an affordable price, pooled DNA can be used. Recent studies have shown that GeneChip Human Mapping 10 ...

    Authors: Stefan Wilkening, Bowang Chen, Michael Wirtenberger, Barbara Burwinkel, Asta Försti, Kari Hemminki and Federico Canzian

    Citation: BMC Genomics 2007 8:77

    Content type: Methodology article

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  15. The mouse C57BL/6 (C57) and DBA/2J (DBA) inbred strains differ substantially in many aspects of their response to drugs of abuse. The development of microarray analyses represents a genome-wide method for meas...

    Authors: Dorothy E Grice, Ilkka Reenilä, Pekka T Männistö, Andrew I Brooks, George G Smith, Greg T Golden, Joseph D Buxbaum and Wade H Berrettini

    Citation: BMC Genomics 2007 8:76

    Content type: Research article

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  16. Cattle and other ruminants have evolved the ability to derive most of their metabolic energy requirement from otherwise indigestible plant matter through a symbiotic relationship with plant fibre degrading mic...

    Authors: Thomas T Wheeler, Kylie A Hood, Nauman J Maqbool, John C McEwan, Colin D Bingle and Shaying Zhao

    Citation: BMC Genomics 2007 8:75

    Content type: Research article

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  17. Mutations in the PTEN induced putative kinase 1 (PINK1) are implicated in early-onset Parkinson's disease. PINK1 is expressed abundantly in mitochondria rich tissues, such as skeletal muscle, where it plays a cri...

    Authors: Camilla Scheele, Natasa Petrovic, Mohammad A Faghihi, Timo Lassmann, Katarina Fredriksson, Olav Rooyackers, Claes Wahlestedt, Liam Good and James A Timmons

    Citation: BMC Genomics 2007 8:74

    Content type: Research article

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  18. Soft tissue sarcoma (STS) diagnosis is challenging because of a multitude of histopathological subtypes, different genetic characteristics, and frequent intratumoral pleomorphism. One-third of STS metastasize ...

    Authors: Princy Francis, Heidi Maria Namløs, Christoph Müller, Patrik Edén, Josefin Fernebro, Jeanne-Marie Berner, Bodil Bjerkehagen, Måns Åkerman, Pär-Ola Bendahl, Anna Isinger, Anders Rydholm, Ola Myklebost and Mef Nilbert

    Citation: BMC Genomics 2007 8:73

    Content type: Research article

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  19. To better understand effects of iron restriction on Actinobacillus pleuropneumoniae and to identify new potential vaccine targets, we conducted transcript profiling studies using a DNA microarray containing all 2...

    Authors: Vincent Deslandes, John HE Nash, Josée Harel, James W Coulton and Mario Jacques

    Citation: BMC Genomics 2007 8:72

    Content type: Research article

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  20. Sugarcane is an increasingly economically and environmentally important C4 grass, used for the production of sugar and bioethanol, a low-carbon emission fuel. Sugarcane originated from crosses of Saccharum specie...

    Authors: Flávia R Rocha, Flávia S Papini-Terzi, Milton Y Nishiyama Jr, Ricardo ZN Vêncio, Renato Vicentini, Rodrigo DC Duarte, Vicente E de Rosa Jr, Fabiano Vinagre, Carla Barsalobres, Ane H Medeiros, Fabiana A Rodrigues, Eugênio C Ulian, Sônia M Zingaretti, João A Galbiatti, Raul S Almeida, Antonio VO Figueira…

    Citation: BMC Genomics 2007 8:71

    Content type: Research article

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  21. Human mesenchymal stem cells (MSC) with the capacity to differentiate into osteoblasts provide potential for the development of novel treatment strategies, such as improved healing of large bone defects. Howev...

    Authors: Birgit Kulterer, Gerald Friedl, Anita Jandrositz, Fatima Sanchez-Cabo, Andreas Prokesch, Christine Paar, Marcel Scheideler, Reinhard Windhager, Karl-Heinz Preisegger and Zlatko Trajanoski

    Citation: BMC Genomics 2007 8:70

    Content type: Research article

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  22. Genetical genomics is a very powerful tool to elucidate the basis of complex traits and disease susceptibility. Despite its relevance, however, statistical modeling of expression quantitative trait loci (eQTL)...

    Authors: Miguel Pérez-Enciso, José R Quevedo and Antonio Bahamonde

    Citation: BMC Genomics 2007 8:69

    Content type: Research article

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  23. Recent studies have shown that when individuals are grouped on the basis of genetic similarity, group membership corresponds closely to continental origin. There has been considerable debate about the implicat...

    Authors: Dominic J Allocco, Qing Song, Gary H Gibbons, Marco F Ramoni and Isaac S Kohane

    Citation: BMC Genomics 2007 8:68

    Content type: Research article

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  24. Plant promoter architecture is important for understanding regulation and evolution of the promoters, but our current knowledge about plant promoter structure, especially with respect to the core promoter, is ...

    Authors: Yoshiharu Y Yamamoto, Hiroyuki Ichida, Minami Matsui, Junichi Obokata, Tetsuya Sakurai, Masakazu Satou, Motoaki Seki, Kazuo Shinozaki and Tomoko Abe

    Citation: BMC Genomics 2007 8:67

    Content type: Research article

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  25. The hematopoietic stem cells (HSCs) niche of the bone marrow is comprised of HSCs, osteoblasts, endothelial cells and a stromal component of non-hematopoietic multipotent cells of mesenchymal origin named "mes...

    Authors: Enrico Pedemonte, Federica Benvenuto, Simona Casazza, Gianluigi Mancardi, Jorge R Oksenberg, Antonio Uccelli and Sergio E Baranzini

    Citation: BMC Genomics 2007 8:65

    Content type: Research article

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  26. For expression profiling to have a practical impact in the management of immune-related disease it is essential that it can be applied to peripheral blood cells. Early studies have used total peripheral blood ...

    Authors: Paul A Lyons, Maria Koukoulaki, Alexander Hatton, Karen Doggett, Hayley B Woffendin, Afzal N Chaudhry and Kenneth GC Smith

    Citation: BMC Genomics 2007 8:64

    Content type: Research article

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  27. Myostatin, a muscle-specific member of the Transforming Growth Factor beta family, negatively regulates muscle development. Double-muscled (DM) cattle have a loss-of-function mutation in their myostatin gene r...

    Authors: Isabelle Cassar-Malek, Florent Passelaigue, Carine Bernard, Jean Léger and Jean-François Hocquette

    Citation: BMC Genomics 2007 8:63

    Content type: Research article

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  28. Asbestos has been shown to cause chromosomal damage and DNA aberrations. Exposure to asbestos causes many lung diseases e.g. asbestosis, malignant mesothelioma, and lung cancer, but the disease-related process...

    Authors: Penny Nymark, Pamela M Lindholm, Mikko V Korpela, Leo Lahti, Salla Ruosaari, Samuel Kaski, Jaakko Hollmén, Sisko Anttila, Vuokko L Kinnula and Sakari Knuutila

    Citation: BMC Genomics 2007 8:62

    Content type: Research article

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  29. The non-human primate (NHP) research community has been intensely interested in obtaining whole-genome expression arrays for their work. Recently, novel approaches were used to generate the DNA sequence inform...

    Authors: Fenghai Duan, Eliot R Spindel, Yu-Hua Li and Robert B Norgren Jr

    Citation: BMC Genomics 2007 8:61

    Content type: Research article

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  30. The genome of Mycobacterium tuberculosis harbors four copies of a cluster of genes termed mce operons. Despite extensive research that has demonstrated the importance of these operons on infection outcome, their ...

    Authors: Nicola Casali and Lee W Riley

    Citation: BMC Genomics 2007 8:60

    Content type: Research article

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  31. One of the least common types of alternative splicing is the complete retention of an intron in a mature transcript. Intron retention (IR) is believed to be the result of intron, rather than exon, definition a...

    Authors: Noboru Jo Sakabe and Sandro José de Souza

    Citation: BMC Genomics 2007 8:59

    Content type: Research article

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  32. Bacterial invasion during sepsis induces disregulated systemic responses that could lead to fatal lung failure. The purpose of this study was to relate the temporal dynamics of gene expression to the pathophys...

    Authors: Hua Zhu, Yuhong Tang, Lacramioara Ivanciu, Michael Centola, Cristina Lupu, Fletcher B Taylor Jr and Florea Lupu

    Citation: BMC Genomics 2007 8:58

    Content type: Research article

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  33. Trypanosomatids exhibit a unique gene organization into large directional gene clusters (DGCs) in opposite directions. The transcription "strand switch region" (SSR) separating the two large DGCs that constitu...

    Authors: Jacques Puechberty, Christine Blaineau, Sabrina Meghamla, Lucien Crobu, Michel Pagès and Patrick Bastien

    Citation: BMC Genomics 2007 8:57

    Content type: Research article

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  34. Allopolyploidy is a preeminent process in plant evolution that results from the merger of distinct genomes in a common nucleus via inter-specific hybridization. Allopolyploid formation is usually related to genom...

    Authors: Warren Albertin, Karine Alix, Thierry Balliau, Philippe Brabant, Marlène Davanture, Christian Malosse, Benoît Valot and Hervé Thiellement

    Citation: BMC Genomics 2007 8:56

    Content type: Research article

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  35. Gamma-proteobacteria, such as Escherichia coli, can use a variety of respiratory substrates employing numerous aerobic and anaerobic respiratory systems controlled by multiple transcription regulators. Thus, in E...

    Authors: Dmitry A Ravcheev, Anna V Gerasimova, Andrey A Mironov and Mikhail S Gelfand

    Citation: BMC Genomics 2007 8:54

    Content type: Research article

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  36. Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mC...

    Authors: Judith N Kloth, Jan Oosting, Tom van Wezel, Karoly Szuhai, Jeroen Knijnenburg, Arko Gorter, Gemma G Kenter, Gert Jan Fleuren and Ekaterina S Jordanova

    Citation: BMC Genomics 2007 8:53

    Content type: Research article

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  37. Passerines (perching birds) are widely studied across many biological disciplines including ecology, population biology, neurobiology, behavioural ecology and evolutionary biology. However, understanding the m...

    Authors: Jon Slate, Matthew C Hale and Timothy R Birkhead

    Citation: BMC Genomics 2007 8:52

    Content type: Research article

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  38. Comparative genomic studies of the mitochondrion-lacking protist group Diplomonadida (diplomonads) has been lacking, although Giardia lamblia has been intensively studied. We have performed a sequence survey proj...

    Authors: Jan O Andersson, Åsa M Sjögren, David S Horner, Colleen A Murphy, Patricia L Dyal, Staffan G Svärd, John M Logsdon Jr, Mark A Ragan, Robert P Hirt and Andrew J Roger

    Citation: BMC Genomics 2007 8:51

    Content type: Research article

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  39. Expressed sequence tags (ESTs) have been used for rapid gene discovery in a variety of organisms and provide a valuable resource for whole genome annotation. Although the genome of one marsupial, the opossum Mono...

    Authors: Michelle L Baker, Sandra Indiviglio, April M Nyberg, George H Rosenberg, Kerstin Lindblad-Toh, Robert D Miller and Anthony T Papenfuss

    Citation: BMC Genomics 2007 8:50

    Content type: Research article

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  40. Identification of coordinately regulated genes according to the level of their expression during the time course of a process allows for discovering functional relationships among genes involved in the process.

    Authors: Cuong C To and Jiri Vohradsky

    Citation: BMC Genomics 2007 8:49

    Content type: Research article

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  41. Operon structures play an important role in transcriptional regulation in prokaryotes. However, there have been fewer studies on complicated operon structures in which the transcriptional units vary with chang...

    Authors: Shujiro Okuda, Shuichi Kawashima, Kazuo Kobayashi, Naotake Ogasawara, Minoru Kanehisa and Susumu Goto

    Citation: BMC Genomics 2007 8:48

    Content type: Research article

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  42. Molecular markers serve three important functions in physical map assembly. First, they provide anchor points to genetic maps facilitating functional genomic studies. Second, they reduce the overlap required f...

    Authors: Young-Sun Yim, Patricia Moak, Hector Sanchez-Villeda, Theresa A Musket, Pamela Close, Patricia E Klein, John E Mullet, Michael D McMullen, Zheiwei Fang, Mary L Schaeffer, Jack M Gardiner, Edward H Coe Jr and Georgia L Davis

    Citation: BMC Genomics 2007 8:47

    Content type: Research article

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  43. Human stem cells are viewed as a possible source of neurons for a cell-based therapy of neurodegenerative disorders, such as Parkinson's disease. Several protocols that generate different types of neurons from...

    Authors: Sergey V Anisimov, Nicolaj S Christophersen, Ana S Correia, Jia-Yi Li and Patrik Brundin

    Citation: BMC Genomics 2007 8:46

    Content type: Methodology article

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  44. Comparative teleost studies are of great interest since they are important in aquaculture and in evolutionary issues. Comparing genomes of fully sequenced model fish species with those of farmed fish species t...

    Authors: Elena Sarropoulou, Rafaella Franch, Bruno Louro, Deborah M Power, Luca Bargelloni, Antonios Magoulas, Fabrice Senger, Matina Tsalavouta, Tomaso Patarnello, Francis Galibert, Georgios Kotoulas and Robert Geisler

    Citation: BMC Genomics 2007 8:44

    Content type: Research article

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  45. Rhesus macaques serve a critical role in the study of human biomedical research. While both Indian and Chinese rhesus macaques are commonly used, genetic differences between these two subspecies affect aspects...

    Authors: Betsy Ferguson, Summer L Street, Hollis Wright, Carlo Pearson, Yibing Jia, Shaun L Thompson, Patrick Allibone, Christopher J Dubay, Eliot Spindel and Robert B Norgren Jr

    Citation: BMC Genomics 2007 8:43

    Content type: Research article

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  46. Many lines of evidence suggest that poly(ADP-ribose) polymerase-1 (Parp-1) is involved in transcriptional regulation of various genes as a coactivator or a corepressor by modulating chromatin structure. Howeve...

    Authors: Hideki Ogino, Tadashige Nozaki, Akemi Gunji, Miho Maeda, Hiroshi Suzuki, Tsutomu Ohta, Yasufumi Murakami, Hitoshi Nakagama, Takashi Sugimura and Mitsuko Masutani

    Citation: BMC Genomics 2007 8:41

    Content type: Research article

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