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  1. Gene knockouts are a critical resource for functional genomics. In Arabidopsis, comprehensive knockout collections were generated by amplifying and sequencing genomic DNA flanking insertion mutants. These Flan...

    Authors: A Mark Settles, David R Holding, Bao Cai Tan, Susan P Latshaw, Juan Liu, Masaharu Suzuki, Li Li, Brent A O'Brien, Diego S Fajardo, Ewa Wroclawska, Chi-Wah Tseung, Jinsheng Lai, Charles T Hunter III, Wayne T Avigne, John Baier, Joachim Messing…

    Citation: BMC Genomics 2007 8:116

    Content type: Research article

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  2. Quantitative phenotypic variation of agronomic characters in crop plants is controlled by environmental and genetic factors (quantitative trait loci = QTL). To understand the molecular basis of such QTL, the i...

    Authors: Agim Ballvora, Anika Jöcker, Prisca Viehöver, Hirofumi Ishihara, Jürgen Paal, Khalid Meksem, Rémy Bruggmann, Heiko Schoof, Bernd Weisshaar and Christiane Gebhardt

    Citation: BMC Genomics 2007 8:112

    Content type: Research article

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  3. Array-based comparative genomic hybridization (aCGH) is a high-throughput method for measuring genome-wide DNA copy number changes. Current aCGH methods have limited resolution, sensitivity and reproducibility...

    Authors: Herbert Auer, David L Newsom, Norma J Nowak, Kirk M McHugh, Sunita Singh, Chack-Yung Yu, Yan Yang, Gail D Wenger, Julie M Gastier-Foster and Karl Kornacker

    Citation: BMC Genomics 2007 8:111

    Content type: Methodology article

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  4. Previous studies have sought to identify a link between the distribution of variable genes amongst isolates of Campylobacter jejuni and particular host preferences. The genomic sequence data available currently w...

    Authors: Philip J Hepworth, Howard Leatherbarrow, C Anthony Hart and Craig Winstanley

    Citation: BMC Genomics 2007 8:110

    Content type: Research article

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  5. As the developmental costs of genomic tools decline, genomic approaches to non-model systems are becoming more feasible. Many of these systems may lack advanced genetic tools but are extremely valuable models ...

    Authors: Patrick D Danley, Sean P Mullen, Fenglong Liu, Vishvanath Nene, John Quackenbush and Kerry L Shaw

    Citation: BMC Genomics 2007 8:109

    Content type: Research article

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  6. The Cation Diffusion Facilitator (CDF) family is a ubiquitous family of heavy metal transporters. Much interest in this family has focused on implications for human health and bioremediation. In this work a br...

    Authors: Barbara Montanini, Damien Blaudez, Sylvain Jeandroz, Dale Sanders and Michel Chalot

    Citation: BMC Genomics 2007 8:107

    Content type: Research article

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  7. We provide a re-analysis of the Golden Spike dataset, a first generation "spike-in" control microarray dataset. The original analysis of the Golden Spike dataset was presented in a manuscript by Choe et al. an...

    Authors: Daniel P Gaile and Jeffrey C Miecznikowski

    Citation: BMC Genomics 2007 8:105

    Content type: Research article

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  8. Comprehensive identification and classification of the transcription factors (TFs) in a given genome is an important aspect in understanding transcriptional regulatory networks of a specific organism. Cyanobac...

    Authors: Jinyu Wu, Fangqing Zhao, Shengqin Wang, Gang Deng, Junrong Wang, Jie Bai, Jianxin Lu, Jia Qu and Qiyu Bao

    Citation: BMC Genomics 2007 8:104

    Content type: Database

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  9. The number of completed eukaryotic genome sequences and cDNA projects has increased exponentially in the past few years although most of them have not been published yet. In addition, many microarray analyses ...

    Authors: Florian Odronitz, Marcel Hellkamp and Martin Kollmar

    Citation: BMC Genomics 2007 8:103

    Content type: Database

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  10. The salivary glands of hematophagous animals contain a complex cocktail that interferes with the host hemostasis and inflammation pathways, thus increasing feeding success. Fleas represent a relatively recent ...

    Authors: John F Andersen, B Joseph Hinnebusch, David A Lucas, Thomas P Conrads, Timothy D Veenstra, Van M Pham and José MC Ribeiro

    Citation: BMC Genomics 2007 8:102

    Content type: Research article

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  11. Following the publication of our recent article (Kapp et al., BMC Genomics 2006, 7:231), we (the authors) regrettably found several errors in the published Table 5. This correction article not only describes what...

    Authors: Amy V Kapp, Stefanie S Jeffrey, Anita Langerød, Anne-Lise Børresen-Dale, Wonshik Han, Dong-Young Noh, Ida RK Bukholm, Monica Nicolau, Patrick O Brown and Robert Tibshirani

    Citation: BMC Genomics 2007 8:101

    Content type: Erratum

    Published on:

    The original article was published in BMC Genomics 2006 7:231

  12. Conidia are considered to be the primary cause of infections by Trichophyton rubrum.

    Authors: Tao Liu, Qian Zhang, Lingling Wang, Lu Yu, Wenchuan Leng, Jian Yang, Lihong Chen, Junping Peng, Li Ma, Jie Dong, Xingye Xu, Ying Xue, Yafang Zhu, Wenliang Zhang, Li Yang, Weijun Li…

    Citation: BMC Genomics 2007 8:100

    Content type: Research article

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  13. Mammalian hepatic lipase (HL) genes are transcribed almost exclusively in hepatocytes. The basis for this liver-restricted expression is not completely understood. We hypothesized that the responsible cis-acti...

    Authors: Diederik van Deursen, Gert-Jan Botma, Hans Jansen and Adrie JM Verhoeven

    Citation: BMC Genomics 2007 8:99

    Content type: Research article

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  14. TGF-beta is one of the key cytokines implicated in various disease processes including cancer. TGF-beta inhibits growth and promotes apoptosis in normal epithelial cells and in contrast, acts as a pro-tumour c...

    Authors: Prathibha Ranganathan, Animesh Agrawal, Raghu Bhushan, Aravinda K Chavalmane, Ravi Kiran Reddy Kalathur, Takashi Takahashi and Paturu Kondaiah

    Citation: BMC Genomics 2007 8:98

    Content type: Research article

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  15. Mycotoxins are fungal secondary metabolites commonly present in feed and food, and are widely regarded as hazardous contaminants. Citrinin, one of the very well known mycotoxins that was first isolated from Penic...

    Authors: Hitoshi Iwahashi, Emiko Kitagawa, Yoshiteru Suzuki, Youji Ueda, Yo-hei Ishizawa, Hitoshi Nobumasa, Yoshihide Kuboki, Hiroshi Hosoda and Yumiko Iwahashi

    Citation: BMC Genomics 2007 8:95

    Content type: Research article

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  16. The mammalian brain is divided into distinct regions with structural and neurophysiological differences. As a result, gene expression is likely to vary between regions in relation to their cellular composition...

    Authors: Christine Stansberg, Audun Osland Vik-Mo, Rita Holdhus, Harald Breilid, Boleslaw Srebro, Kjell Petersen, Hugo A Jørgensen, Inge Jonassen and Vidar M Steen

    Citation: BMC Genomics 2007 8:94

    Content type: Research article

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  17. Insects constitute the vast majority of known species with their importance including biodiversity, agricultural, and human health concerns. It is likely that the successful adaptation of the Insecta clade dep...

    Authors: Guojie Zhang, Hongsheng Wang, Junjie Shi, Xiaoling Wang, Hongkun Zheng, Gane Ka-Shu Wong, Terry Clark, Wen Wang, Jun Wang and Le Kang

    Citation: BMC Genomics 2007 8:93

    Content type: Research article

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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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

    Published on:

  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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

    Published on:

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