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  1. Integrating plant genomics and classical breeding is a challenge for both plant breeders and molecular biologists. Marker-assisted selection (MAS) is a tool that can be used to accelerate the development of no...

    Authors: David Chagné, Charmaine M Carlisle, Céline Blond, Richard K Volz, Claire J Whitworth, Nnadozie C Oraguzie, Ross N Crowhurst, Andrew C Allan, Richard V Espley, Roger P Hellens and Susan E Gardiner

    Citation: BMC Genomics 2007 8:212

    Content type: Research article

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  2. The recent discovery of widespread copy number variation in humans has forced a shift away from the assumption of two copies per locus per cell throughout the autosomal genome. In particular, a SNP site can no...

    Authors: Laura E MacConaill, Micheala A Aldred, Xincheng Lu and Thomas LaFramboise

    Citation: BMC Genomics 2007 8:211

    Content type: Research article

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  3. The pluripotency and self-renewal capabilities, which define the "stemness" state, of mouse embryonic stem (ES) cells, are usually investigated by functional assays or quantitative measurements of the expressi...

    Authors: Daniel YL Yap, David K Smith, Xue W Zhang and Jeffrey Hill

    Citation: BMC Genomics 2007 8:210

    Content type: Methodology article

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  4. To identify as many different transcripts/genes in the Atlantic salmon genome as possible, it is crucial to acquire good cDNA libraries from different tissues and developmental stages, their relevant sequences...

    Authors: Alexei A Adzhubei, Anna V Vlasova, Heidi Hagen-Larsen, Torgeir A Ruden, Jon K Laerdahl and Bjørn Høyheim

    Citation: BMC Genomics 2007 8:209

    Content type: Database

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  5. Osteoporosis is frequently observed among aging hens from egg-producing strains (layers) of domestic chicken. White Leghorn (WL) has been intensively selected for egg production and it manifests striking pheno...

    Authors: Carl-Johan Rubin, Johan Lindberg, Carolyn Fitzsimmons, Peter Savolainen, Per Jensen, Joakim Lundeberg, Leif Andersson and Andreas Kindmark

    Citation: BMC Genomics 2007 8:208

    Content type: Research article

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  6. The liver is the largest human internal organ – it is composed of multiple cell types and plays a vital role in fulfilling the body's metabolic needs and maintaining homeostasis. Of these cell types the hepato...

    Authors: Jian Huang, Pei Hao, Yun-Li Zhang, Fu-Xing Deng, Qing Deng, Yi Hong, Xiao-Wo Wang, Yun Wang, Ting-Ting Li, Xue-Gong Zhang, Yi-Xue Li, Peng-Yuan Yang, Hong-Yang Wang and Ze-Guang Han

    Citation: BMC Genomics 2007 8:207

    Content type: Research article

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  7. Changes in genomic copy number occur in many human diseases including cancer. Characterization of these changes is important for both basic understanding and diagnosis of these diseases. Microarrays have recen...

    Authors: Kyoko Iwao-Koizumi, Kazunori Maekawa, Yohko Nakamura, Sakae Saito, Shoko Kawamoto, Akira Nakagawara and Kikuya Kato

    Citation: BMC Genomics 2007 8:206

    Content type: Methodology article

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  8. Glucocorticoids (GCs) are widely used anti-inflammatory drugs. While useful in clinical practice, patients taking GCs often suffer from skeletal side effects including growth retardation in children and adoles...

    Authors: Claudine G James, Veronica Ulici, Jan Tuckermann, T Michael Underhill and Frank Beier

    Citation: BMC Genomics 2007 8:205

    Content type: Research article

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  9. Leptospirosis is a world-widely distributed zoonosis. Humans become infected via exposure to pathogenic Leptospira spp. from contaminated water or soil. The availability of genomic sequences of Leptospira interro...

    Authors: Ping He, Yue-Ying Sheng, Yao-Zhou Shi, Xiu-Gao Jiang, Jin-Hong Qin, Zhi-Ming Zhang, Guo-Ping Zhao and Xiao-Kui Guo

    Citation: BMC Genomics 2007 8:204

    Content type: Research article

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  10. Honey bees are known for several striking social behaviors, including a complex pattern of behavioral maturation that gives rise to an age-related colony division of labor and a symbolic dance language, by whi...

    Authors: Moushumi Sen Sarma, Charles W Whitfield and Gene E Robinson

    Citation: BMC Genomics 2007 8:202

    Content type: Research article

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  11. The Fox gene family comprises a large and functionally diverse group of forkhead-related transcriptional regulators, many of which are essential for metazoan embryogenesis and physiology. Defining conserved funct...

    Authors: Sergey Yaklichkin, Alexander Vekker, Steven Stayrook, Mitchell Lewis and Daniel S Kessler

    Citation: BMC Genomics 2007 8:201

    Content type: Research article

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  12. In the post-genomic era, comprehension of cellular processes and systems requires global and non-targeted approaches to handle vast amounts of biological information.

    Authors: Hirokazu Kobayashi, Joe Akitomi, Nobuyuki Fujii, Kazuo Kobayashi, Md Altaf-Ul-Amin, Ken Kurokawa, Naotake Ogasawara and Shigehiko Kanaya

    Citation: BMC Genomics 2007 8:197

    Content type: Research article

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  13. Bulked segregant analysis (BSA) identifies molecular markers associated with a phenotype by screening two DNA pools of phenotypically distinct plants for markers with skewed allele frequencies. In contrast to ...

    Authors: Peter Wenzl, Harsh Raman, Junping Wang, Meixue Zhou, Eric Huttner and Andrzej Kilian

    Citation: BMC Genomics 2007 8:196

    Content type: Methodology article

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  14. The zebrafish (Danio rerio) is an important vertebrate model organism system for biomedical research. The syntenic conservation between the zebrafish and human genome allows one to investigate the function of hum...

    Authors: Jennifer L Freeman, Adeola Adeniyi, Ruby Banerjee, Stephanie Dallaire, Sean F Maguire, Jianxiang Chi, Bee Ling Ng, Cinthya Zepeda, Carol E Scott, Sean Humphray, Jane Rogers, Yi Zhou, Leonard I Zon, Nigel P Carter, Fengtang Yang and Charles Lee

    Citation: BMC Genomics 2007 8:195

    Content type: Research article

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  15. Mammalian angiotensin converting enzyme (ACE) plays a key role in blood pressure regulation. Although multiple ACE-like proteins exist in non-mammalian organisms, to date only one other ACE homologue, ACE2, ha...

    Authors: Monika Rella, Joann L Elliot, Timothy J Revett, Jerry Lanfear, Anne Phelan, Richard M Jackson, Anthony J Turner and Nigel M Hooper

    Citation: BMC Genomics 2007 8:194

    Content type: Research article

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  16. Excessive accumulation of lipids in the adipose tissue is a major problem in the present-day broiler industry. However, few studies have analyzed the expression of adipose tissue genes that are involved in pat...

    Authors: Hong-Bao Wang, Hui Li, Qi-Gui Wang, Xin-Yu Zhang, Shou-Zhi Wang, Yu-Xiang Wang and Xiu-Ping Wang

    Citation: BMC Genomics 2007 8:193

    Content type: Research article

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  17. This study assesses the whole-genome gene expression changes in a panel of primary human cell lines in response to DNA damage mediated by decay of DNA-incorporated radioiodinated thymidine analog 5-[125I]iodo-2'-...

    Authors: Mykyta V Sokolov, Ronald D Neumann and Igor G Panyutin

    Citation: BMC Genomics 2007 8:192

    Content type: Research article

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  18. The carboxy termini of proteins are a frequent site of activity for a variety of biologically important functions, ranging from post-translational modification to protein targeting. Several short peptide motif...

    Authors: Ryan S Austin, Nicholas J Provart and Sean R Cutler

    Citation: BMC Genomics 2007 8:191

    Content type: Research article

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  19. The common marmoset monkey (Callithrix jacchus), a small non-endangered New World primate native to eastern Brazil, is becoming increasingly used as a non-human primate model in biomedical research, drug developm...

    Authors: Nicole A Datson, Maarten C Morsink, Srebrena Atanasova, Victor W Armstrong, Hans Zischler, Christina Schlumbohm, Bas E Dutilh, Martijn A Huynen, Brigitte Waegele, Andreas Ruepp, E Ronald de Kloet and Eberhard Fuchs

    Citation: BMC Genomics 2007 8:190

    Content type: Research article

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  20. Cholangiocarcinoma (CCA) – cancer of the bile ducts – is associated with chronic infection with the liver fluke, Opisthorchis viverrini. Despite being the only eukaryote that is designated as a 'class I carcinoge...

    Authors: Thewarach Laha, Porntip Pinlaor, Jason Mulvenna, Banchob Sripa, Manop Sripa, Michael J Smout, Robin B Gasser, Paul J Brindley and Alex Loukas

    Citation: BMC Genomics 2007 8:189

    Content type: Research article

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  21. Microarray gene expression (MAGE) signatures allow insights into the transcriptional processes of leukemias and may evolve as a molecular diagnostic test. Introduction of MAGE into clinical practice of leukemi...

    Authors: Marta Campo Dell'Orto, Andrea Zangrando, Luca Trentin, Rui Li, Wei-min Liu, Geertruy te Kronnie, Giuseppe Basso and Alexander Kohlmann

    Citation: BMC Genomics 2007 8:188

    Content type: Methodology article

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  22. Berries of grape (Vitis vinifera) contain three major tissue types (skin, pulp and seed) all of which contribute to the aroma, color, and flavor characters of wine. The pericarp, which is composed of the exocarp ...

    Authors: Jerome Grimplet, Laurent G Deluc, Richard L Tillett, Matthew D Wheatley, Karen A Schlauch, Grant R Cramer and John C Cushman

    Citation: BMC Genomics 2007 8:187

    Content type: Research article

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  23. Five species of the genus Schistosoma, a parasitic trematode flatworm, are causative agents of Schistosomiasis, a disease that is endemic in a large number of developing countries, affecting millions of patien...

    Authors: Elida PB Ojopi, Paulo SL Oliveira, Diana N Nunes, Apuã Paquola, Ricardo DeMarco, Sheila P Gregório, Karina A Aires, Carlos FM Menck, Luciana CC Leite, Sergio Verjovski-Almeida and Emmanuel Dias-Neto

    Citation: BMC Genomics 2007 8:186

    Content type: Research article

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  24. Cancer arises from the consecutive acquisition of genetic alterations. Increasing evidence suggests that as a consequence of these alterations, molecular interactions are reprogrammed in the context of highly ...

    Authors: Pilar Hernández, Jaime Huerta-Cepas, David Montaner, Fátima Al-Shahrour, Joan Valls, Laia Gómez, Gabriel Capellá, Joaquín Dopazo and Miguel Angel Pujana

    Citation: BMC Genomics 2007 8:185

    Content type: Research article

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  25. The human gastric pathogen Helicobacter pylori is co-evolved with its host and therefore, origins and expansion of multiple populations and sub populations of H. pylori mirror ancient human migrations. Ancestral ...

    Authors: S Manjulata Devi, Irshad Ahmed, Paolo Francalacci, M Abid Hussain, Yusuf Akhter, Ayesha Alvi, Leonardo A Sechi, Francis Mégraud and Niyaz Ahmed

    Citation: BMC Genomics 2007 8:184

    Content type: Research article

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  26. Many studies have found segregating quantitative trait loci (QTL) for milk production traits in different dairy cattle populations. However, even for relatively large effects with a saturated marker map the co...

    Authors: Micha Ron, Galit Israeli, Eyal Seroussi, Joel I Weller, Jeffrey P Gregg, Moshe Shani and Juan F Medrano

    Citation: BMC Genomics 2007 8:183

    Content type: Research article

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  27. The annotated genomes of two closely related strains of the intracellular bacterium Wolbachia pipientis have been reported without the identifications of the putative origin of replication (ori). Identifying the

    Authors: Panagiotis Ioannidis, Julie C Dunning Hotopp, Panagiotis Sapountzis, Stefanos Siozios, Georgios Tsiamis, Seth R Bordenstein, Laura Baldo, John H Werren and Kostas Bourtzis

    Citation: BMC Genomics 2007 8:182

    Content type: Research article

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  28. The parasitic trematode Schistosoma mansoni is one of the major causative agents of Schistosomiasis, a disease that affects approximately 200 million people, mostly in developing countries. Since much of the path...

    Authors: Michael Waisberg, Francisco P Lobo, Gustavo C Cerqueira, Liana KJ Passos, Omar S Carvalho, Glória R Franco and Najib M El-Sayed

    Citation: BMC Genomics 2007 8:181

    Content type: Research article

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  29. Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III)-oxides. Geobacter metal...

    Authors: Jessica E Butler, Qiang He, Kelly P Nevin, Zhili He, Jizhong Zhou and Derek R Lovley

    Citation: BMC Genomics 2007 8:180

    Content type: Research article

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  30. It has become evident that host cells react to recombinant protein production with a variety of metabolic and intrinsic stresses such as the unfolded protein response (UPR) pathway. Additionally, environmental...

    Authors: Brigitte Gasser, Michael Maurer, Jari Rautio, Michael Sauer, Anamitra Bhattacharyya, Markku Saloheimo, Merja Penttilä and Diethard Mattanovich

    Citation: BMC Genomics 2007 8:179

    Content type: Research article

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  31. Cotton, as an allopolyploid species, contains homoeologous A and D subgenomes. The study of the homoeologous (duplicated) segments or chromosomes can facilitate insight into the evolutionary process of polyplo...

    Authors: Kai Wang, Wangzhen Guo and Tianzhen Zhang

    Citation: BMC Genomics 2007 8:178

    Content type: Research article

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  32. EST sequencing is one of the most efficient means for gene discovery and molecular marker development, and can be additionally utilized in both comparative genome analysis and evaluation of gene duplications. ...

    Authors: Ping Li, Eric Peatman, Shaolin Wang, Jinian Feng, Chongbo He, Puttharat Baoprasertkul, Peng Xu, Huseyin Kucuktas, Samiran Nandi, Benjaporn Somridhivej, Jerry Serapion, Micah Simmons, Cemal Turan, Lei Liu, William Muir, Rex Dunham…

    Citation: BMC Genomics 2007 8:177

    Content type: Research article

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  33. The ciliate protozoan Ichthyophthirius multifiliis (Ich) is an important parasite of freshwater fish that causes 'white spot disease' leading to significant losses. A genomic resource for large-scale studies of t...

    Authors: Jason W Abernathy, Peng Xu, Ping Li, De-Hai Xu, Huseyin Kucuktas, Phillip Klesius, Covadonga Arias and Zhanjiang Liu

    Citation: BMC Genomics 2007 8:176

    Content type: Research article

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  34. Plants respond to low temperature through an intricately coordinated transcriptional network. The CBF/DREB-regulated network of genes has been shown to play a prominent role in freeze-tolerance of Arabidopsis thr...

    Authors: Chen Cheng, Kil-Young Yun, Habtom W Ressom, Bijayalaxmi Mohanty, Vladimir B Bajic, Yulin Jia, Song Joong Yun and Benildo G de los Reyes

    Citation: BMC Genomics 2007 8:175

    Content type: Research article

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  35. The number of completely sequenced plastid genomes available is growing rapidly. This array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is often useful t...

    Authors: Linda A Raubeson, Rhiannon Peery, Timothy W Chumley, Chris Dziubek, H Matthew Fourcade, Jeffrey L Boore and Robert K Jansen

    Citation: BMC Genomics 2007 8:174

    Content type: Research article

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  36. MicroRNAs (miRNAs) are a novel class of short double stranded RNA that mediate the post-transcriptional regulation of gene expression. Previous studies have implicated changes in miRNA expression in the regula...

    Authors: Andrew E Williams, Mark M Perry, Sterghios A Moschos and Mark A Lindsay

    Citation: BMC Genomics 2007 8:172

    Content type: Research article

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  37. Staphylococcus aureus, a leading cause of chronic or acute infections, is traditionally considered an extracellular pathogen despite repeated reports of S. aureus internalization by a variety of non-myeloid cells...

    Authors: Christian Garzoni, Patrice Francois, Antoine Huyghe, Sabine Couzinet, Caroline Tapparel, Yvan Charbonnier, Adriana Renzoni, Sacha Lucchini, Daniel P Lew, Pierre Vaudaux, William L Kelley and Jacques Schrenzel

    Citation: BMC Genomics 2007 8:171

    Content type: Research article

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  38. A number of studies have shown that peptidases and in particular cysteine peptidases constitute major pathogenicity factors in Entamoeba histolytica. Recent studies have suggested that a considerable number of ge...

    Authors: Manuela Tillack, Laura Biller, Henriette Irmer, Michelle Freitas, Maria A Gomes, Egbert Tannich and Iris Bruchhaus

    Citation: BMC Genomics 2007 8:170

    Content type: Research article

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  39. Currently, there is little data available regarding the role of gender-specific gene expression on synonymous codon usage (translational selection) in most organisms, and particularly plants. Using gender-spec...

    Authors: Carrie-Ann Whittle, Meghna R Malik and Joan E Krochko

    Citation: BMC Genomics 2007 8:169

    Content type: Research article

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  40. Genomic copy number variants (CNVs) involving >1 kb of DNA have recently been found to be widely distributed throughout the human genome. They represent a newly recognized form of DNA variation in normal popul...

    Authors: Ying Qiao, Xudong Liu, Chansonette Harvard, Sarah L Nolin, W Ted Brown, Maryam Koochek, Jeanette JA Holden, ME Suzanne Lewis and Evica Rajcan-Separovic

    Citation: BMC Genomics 2007 8:167

    Content type: Research article

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  41. Cartilage plays a fundamental role in the development of the human skeleton. Early in embryogenesis, mesenchymal cells condense and differentiate into chondrocytes to shape the early skeleton. Subsequently, th...

    Authors: Vincent A Funari, Allen Day, Deborah Krakow, Zachary A Cohn, Zugen Chen, Stanley F Nelson and Daniel H Cohn

    Citation: BMC Genomics 2007 8:165

    Content type: Research article

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  42. The distribution of isoelectric point (pI) of proteins in a proteome is universal for all organisms. It is bimodal dividing the proteome into two sets of acidic and basic proteins. Different species however ha...

    Authors: Joanna Kiraga, Pawel Mackiewicz, Dorota Mackiewicz, Maria Kowalczuk, Przemysław Biecek, Natalia Polak, Kamila Smolarczyk, Miroslaw R Dudek and Stanislaw Cebrat

    Citation: BMC Genomics 2007 8:163

    Content type: Research article

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  43. Campylobacter jejuni is the leading bacterial cause of human gastroenteritis in the developed world. To improve our understanding of this important human pathogen, the C. jejuni NCTC11168 genome was sequenced and...

    Authors: Ozan Gundogdu, Stephen D Bentley, Matt T Holden, Julian Parkhill, Nick Dorrell and Brendan W Wren

    Citation: BMC Genomics 2007 8:162

    Content type: Research article

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