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  1. About forty human diseases are caused by repeat instability mutations. A distinct subset of these diseases is the result of extreme expansions of polymorphic trinucleotide repeats; typically CAG repeats encodi...

    Authors: Vicki Whan, Matthew Hobbs, Sean McWilliam, David J Lynn, Ylva Strandberg Lutzow, Mehar Khatkar, William Barendse, Herman Raadsma and Ross L Tellam
    Citation: BMC Genomics 2010 11:654
    Content type: Research article Published on:

  2. Advanced cycle breeding utilizes crosses among elite lines and is a successful method to develop new inbreds. However, it results in a reduction in genetic diversity within the breeding population. The develop...

    Authors: María Muñoz-Amatriaín, Yanwen Xiong, Mark R Schmitt, Hatice Bilgic, Allen D Budde, Shiaoman Chao, Kevin P Smith and Gary J Muehlbauer
    Citation: BMC Genomics 2010 11:653
    Content type: Research article Published on:

  3. The genus Neisseria contains two important yet very different pathogens, N. meningitidis and N. gonorrhoeae, in addition to non-pathogenic species, of which N. lactamica is the best characterized. Genomic compari...

    Authors: Julia S Bennett, Stephen D Bentley, Georgios S Vernikos, Michael A Quail, Inna Cherevach, Brian White, Julian Parkhill and Martin CJ Maiden
    Citation: BMC Genomics 2010 11:652
    Content type: Research article Published on:

  4. In Lactic Acid Bacteria (LAB), the extracellular and surface-associated proteins can be involved in processes such as cell wall metabolism, degradation and uptake of nutrients, communication and binding to sub...

    Authors: Miaomiao Zhou, Daniel Theunissen, Michiel Wels and Roland J Siezen
    Citation: BMC Genomics 2010 11:651
    Content type: Research article Published on:

  5. The Fagaceae family comprises about 1,000 woody species worldwide. About half belong to the Quercus family. These oaks are often a source of raw material for biomass wood and fiber. Pedunculate and sessile oaks, ...

    Authors: Saneyoshi Ueno, Grégoire Le Provost, Valérie Léger, Christophe Klopp, Céline Noirot, Jean-Marc Frigerio, Franck Salin, Jérôme Salse, Michael Abrouk, Florent Murat, Oliver Brendel, Jérémy Derory, Pierre Abadie, Patrick Léger, Cyril Cabane, Aurélien Barré…
    Citation: BMC Genomics 2010 11:650
    Content type: Research article Published on:

  6. Genomic imprinting is an evolutionary conserved mechanism of epigenetic gene regulation in placental mammals that results in silencing of one of the parental alleles. In order to decipher interactions between ...

    Authors: Barbara Hutter, Matthias Bieg, Volkhard Helms and Martina Paulsen
    Citation: BMC Genomics 2010 11:649
    Content type: Research article Published on:

  7. Widespread use of chromium (Cr) contaminated fields due to careless and inappropriate management practices of effluent discharge, mostly from industries related to metallurgy, electroplating, production of pai...

    Authors: Sonali Dubey, Prashant Misra, Sanjay Dwivedi, Sandipan Chatterjee, Sumit K Bag, Shrikant Mantri, Mehar H Asif, Arti Rai, Smita Kumar, Manju Shri, Preeti Tripathi, Rudra D Tripathi, Prabodh K Trivedi, Debasis Chakrabarty and Rakesh Tuli
    Citation: BMC Genomics 2010 11:648
    Content type: Research article Published on:

  8. The turkey (Meleagris gallopavo) is an important agricultural species that is the second largest contributor to the world's poultry meat production. The genomic resources of turkey provide turkey breeders with to...

    Authors: Muhammad L Aslam, John WM Bastiaansen, Richard PMA Crooijmans, Addie Vereijken, Hendrik-Jan Megens and Martien AM Groenen
    Citation: BMC Genomics 2010 11:647
    Content type: Research article Published on:

  9. mRNA polyadenylation is an essential step of pre-mRNA processing in eukaryotes. Accurate prediction of the pre-mRNA 3'-end cleavage/polyadenylation sites is important for defining the gene boundaries and under...

    Authors: Malik Nadeem Akhtar, Syed Abbas Bukhari, Zeeshan Fazal, Raheel Qamar and Ilham A Shahmuradov
    Citation: BMC Genomics 2010 11:646
    Content type: Methodology article Published on:

  10. A goal of the Bovine Genome Database (BGD; http://​BovineGenome.​org) has been to support the Bovine Genome Sequencing and Analysis Consortium (BGSAC) in the annotation and analysis of the bovine genome. We were...

    Authors: Justin T Reese, Christopher P Childers, Jaideep P Sundaram, C Michael Dickens, Kevin L Childs, Donald C Vile and Christine G Elsik
    Citation: BMC Genomics 2010 11:645
    Content type: Database Published on:

  11. Hypocrea jecorina (anamorph Trichoderma reesei) is a filamentous ascomycete of industrial importance due to its hydrolases (e.g., xylanases and cellulases). The regulation of gene expression can influence the com...

    Authors: Astrid R Mach-Aigner, Karin Grosstessner-Hain, Marcio J Poças-Fonseca, Karl Mechtler and Robert L Mach
    Citation: BMC Genomics 2010 11:644
    Content type: Methodology article Published on:

  12. Increasing use of zebrafish in drug discovery and mechanistic toxicology demands knowledge of cytochrome P450 (CYP) gene regulation and function. CYP enzymes catalyze oxidative transformation leading to activa...

    Authors: Jared V Goldstone, Andrew G McArthur, Akira Kubota, Juliano Zanette, Thiago Parente, Maria E Jönsson, David R Nelson and John J Stegeman
    Citation: BMC Genomics 2010 11:643
    Content type: Research article Published on:

  13. Monocyte-derived macrophages and dendritic cells (DCs) are important in inflammatory processes and are often used for immunotherapeutic approaches. Blood monocytes can be differentiated into macrophages and DC...

    Authors: Liina Tserel, Raivo Kolde, Ana Rebane, Kai Kisand, Tõnis Org, Hedi Peterson, Jaak Vilo and Pärt Peterson
    Citation: BMC Genomics 2010 11:642
    Content type: Research article Published on:

  14. The primary goal of genetic linkage analysis is to identify genes affecting a phenotypic trait. After localisation of the linkage region, efficient genetic dissection of the disease linked loci requires that f...

    Authors: Nik Cummings, Rob King, Andre Rickers, Antony Kaspi, Sebastian Lunke, Izhak Haviv and Jeremy BM Jowett
    Citation: BMC Genomics 2010 11:641
    Content type: Methodology article Published on:

  15. The transcriptional cofactor, Hairless (HR), acts as one of the key regulators of hair follicle cycling; the loss of function mutations is the cause of the expression of the hairless phenotype in humans and mi...

    Authors: Bong-Kyu Kim, In-Cheol Baek, Hwa-Young Lee, Jeong-Ki Kim, Hae-Hiang Song and Sungjoo K Yoon
    Citation: BMC Genomics 2010 11:640
    Content type: Research article Published on:

  16. The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies...

    Authors: Luca Fontanesi, Pier Luigi Martelli, Francesca Beretti, Valentina Riggio, Stefania Dall'Olio, Michela Colombo, Rita Casadio, Vincenzo Russo and Baldassare Portolano
    Citation: BMC Genomics 2010 11:639
    Content type: Research article Published on:

  18. Phytophthora infestans is the most devastating pathogen of potato and a model organism for the oomycetes. It exhibits high evolutionary potential and rapidly adapts to host plants. The P. infestans genome experie...

    Authors: Sylvain Raffaele, Joe Win, Liliana M Cano and Sophien Kamoun
    Citation: BMC Genomics 2010 11:637
    Content type: Research article Published on:

  19. The Nile tilapia is the second most important fish in aquaculture. It is an excellent laboratory model, and is closely related to the African lake cichlids famous for their rapid rates of speciation. A suite o...

    Authors: Lucile Soler, Matthew A Conte, Takayuki Katagiri, Aimee E Howe, Bo-Young Lee, Chris Amemiya, Andrew Stuart, Carole Dossat, Julie Poulain, Jeremy Johnson, Federica Di Palma, Kerstin Lindblad-Toh, Jean-Francois Baroiller, Helena D'Cotta, Catherine Ozouf-Costaz and Thomas D Kocher
    Citation: BMC Genomics 2010 11:636
    Content type: Research article Published on:

  20. Once highly abundant, the European eel (Anguilla anguilla L.; Anguillidae; Teleostei) is considered to be critically endangered and on the verge of extinction, as the stock has declined by 90-99% since the 1980s....

    Authors: Alessandro Coppe, Jose Martin Pujolar, Gregory E Maes, Peter F Larsen, Michael M Hansen, Louis Bernatchez, Lorenzo Zane and Stefania Bortoluzzi
    Citation: BMC Genomics 2010 11:635
    Content type: Research article Published on:

  21. Alvinella pompejana is a representative of Annelids, a key phylum for evo-devo studies that is still poorly studied at the sequence level. A. pompejana inhabits deep-sea hydrothermal vents and is currently known ...

    Authors: Nicolas Gagnière, Didier Jollivet, Isabelle Boutet, Yann Brélivet, Didier Busso, Corinne Da Silva, Françoise Gaill, Dominique Higuet, Stéphane Hourdez, Bernard Knoops, François Lallier, Emmanuelle Leize-Wagner, Jean Mary, Dino Moras, Emmanuel Perrodou, Jean-François Rees…
    Citation: BMC Genomics 2010 11:634
    Content type: Research article Published on:

  22. Traumatic injuries can undermine neurological functions and act as risk factors for the development of irreversible and fatal neurodegenerative disorders like amyotrophic lateral sclerosis (ALS). In this study...

    Authors: Natasa Jokic, Ping K Yip, Adina Michael-Titus, John V Priestley and Andrea Malaspina
    Citation: BMC Genomics 2010 11:633
    Content type: Research article Published on:

  23. Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by...

    Authors: Deanna C Tremblay, Graham Alexander Jr, Shawn Moseley and Brian P Chadwick
    Citation: BMC Genomics 2010 11:632
    Content type: Research article Published on:

  24. The EcoTILLING technique allows polymorphisms in target genes of natural populations to be quickly analysed or identified and facilitates the screening of genebank collections for desired traits. We have devel...

    Authors: Vicente P Ibiza, Joaquín Cañizares and Fernando Nuez
    Citation: BMC Genomics 2010 11:631
    Content type: Research article Published on:

  25. Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-i...

    Authors: David Cohen, Marie-Béatrice Bogeat-Triboulot, Emilie Tisserant, Sandrine Balzergue, Marie-Laure Martin-Magniette, Gaëlle Lelandais, Nathalie Ningre, Jean-Pierre Renou, Jean-Philippe Tamby, Didier Le Thiec and Irène Hummel
    Citation: BMC Genomics 2010 11:630
    Content type: Research article Published on:

  26. The barley-Puccinia hordei (barley leaf rust) pathosystem is a model for investigating partial disease resistance in crop plants and genetic mapping of phenotypic resistance has identified several quantitative tr...

    Authors: Xinwei Chen, Rients E Niks, Peter E Hedley, Jenny Morris, Arnis Druka, Thierry C Marcel, Anton Vels and Robbie Waugh
    Citation: BMC Genomics 2010 11:629
    Content type: Research article Published on:

  27. A central tenet in biochemistry for over 50 years has held that microorganisms, plants and, more recently, certain apicomplexan parasites synthesize essential aromatic compounds via elaboration of a complete s...

    Authors: Jurica Zucko, Walter C Dunlap, J Malcolm Shick, John Cullum, François Cercelet, Bijal Amin, Lena Hammen, Timothy Lau, Jamal Williams, Daslav Hranueli and Paul F Long
    Citation: BMC Genomics 2010 11:628
    Content type: Research article Published on:

  28. Despite vaccination since the 1950s, pertussis has persisted and resurged. It remains a major cause of infant death worldwide and is the most prevalent vaccine-preventable disease in developed countries. The r...

    Authors: Marieke J Bart, Marjolein van Gent, Han GJ van der Heide, Jos Boekhorst, Peter Hermans, Julian Parkhill and Frits R Mooi
    Citation: BMC Genomics 2010 11:627
    Content type: Research article Published on:

  29. When selecting mates, many vertebrate species seek partners with major histocompatibility complex (MHC) genes different from their own, presumably in response to selective pressure against inbreeding and towar...

    Authors: Pouya Khankhanian, Pierre-Antoine Gourraud, Stacy J Caillier, Adam Santaniello, Stephen L Hauser, Sergio E Baranzini and Jorge R Oksenberg
    Citation: BMC Genomics 2010 11:626
    Content type: Research article Published on:

  30. Regulation of bacterial gene expression by small RNAs (sRNAs) have proved to be important for many biological processes. Francisella tularensis is a highly pathogenic Gram-negative bacterium that causes the disea...

    Authors: Guillaume Postic, Eric Frapy, Marion Dupuis, Iharilalao Dubail, Jonathan Livny, Alain Charbit and Karin L Meibom
    Citation: BMC Genomics 2010 11:625
    Content type: Research article Published on:

  31. Infestation of ovine skin with the ectoparasitic mite Psoroptes ovis results in a rapid cutaneous immune response, leading to the crusted skin lesions characteristic of sheep scab. Little is known regarding the m...

    Authors: Stewart TG Burgess, David Frew, Francesca Nunn, Craig A Watkins, Tom N McNeilly, Alasdair J Nisbet and John F Huntley
    Citation: BMC Genomics 2010 11:624
    Content type: Research article Published on:

  32. Marbling (intramuscular fat) is a valuable trait that impacts on meat quality and an important factor determining price of beef in the Korean beef market. Animals that are destined for this high marbling marke...

    Authors: Seung-Hwan Lee, Cedric Gondro, Julius van der Werf, Nam-Kuk Kim, Da-jeong Lim, Eung-Woo Park, Sung-Jong Oh, John P Gibson and John M Thompson
    Citation: BMC Genomics 2010 11:623
    Content type: Research article Published on:

  33. We evaluated (a) the feasibility of whole genome cDNA-mediated Annealing, Selection, extension and Ligation (DASL) assay on formalin-fixed paraffin-embedded (FFPE) tissue and (b) whether similar conclusions ca...

    Authors: Muhammad G Kibriya, Farzana Jasmine, Shantanu Roy, Rachelle M Paul-Brutus, Maria Argos and Habibul Ahsan
    Citation: BMC Genomics 2010 11:622
    Content type: Research article Published on:

  34. The genus Aquilegia, consisting of approximately 70 taxa, is a member of the basal eudicot lineage, Ranuculales, which is evolutionarily intermediate between monocots and core eudicots, and represents a relativel...

    Authors: Guang-Chen Fang, Barbara P Blackmon, David C Henry, Margaret E Staton, Christopher A Saski, Scott A Hodges, Jeff P Tomkins and Hong Luo
    Citation: BMC Genomics 2010 11:621
    Content type: Research article Published on:

  35. Germin and germin-like proteins constitute a ubiquitous family of plant proteins. A role of some family members in defense against pathogen attack had been proposed based on gene regulation studies and transge...

    Authors: Mo Lu, Ying-Peng Han, Ji-Guo Gao, Xiang-Jing Wang and Wen-Bin Li
    Citation: BMC Genomics 2010 11:620
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2011 12:16

  36. As the only truly flying mammals, bats use their unique wing - consisting of four elongated digits (digits II-V) connected by membranes - to power their flight. In addition to the elongated digits II-V, the fo...

    Authors: Zhe Wang, Dong Dong, Binghua Ru, Rebecca L Young, Naijian Han, Tingting Guo and Shuyi Zhang
    Citation: BMC Genomics 2010 11:619
    Content type: Research article Published on:

  37. Although melon (Cucumis melo L.) is an economically important fruit crop, no genome-wide sequence information is openly available at the current time. We therefore sequenced BAC-ends representing a total of 33,02...

    Authors: Víctor M González, Luis Rodríguez-Moreno, Emilio Centeno, Andrej Benjak, Jordi Garcia-Mas, Pere Puigdomènech and Miguel A Aranda
    Citation: BMC Genomics 2010 11:618
    Content type: Research article Published on:

  38. In many microbial genomes, a strong preference for a small number of codons can be observed in genes whose products are needed by the cell in large quantities. This codon usage bias (CUB) improves translationa...

    Authors: Conrad von Mandach and Rainer Merkl
    Citation: BMC Genomics 2010 11:617
    Content type: Research article Published on:

  39. The chicken karyotype is composed of 39 chromosome pairs, of which 9 still remain totally absent from the current genome sequence assembly, despite international efforts towards complete coverage. Some others ...

    Authors: Romain Solinhac, Sophie Leroux, Svetlana Galkina, Olympe Chazara, Katia Feve, Florence Vignoles, Mireille Morisson, Svetlana Derjusheva, Bertrand Bed'hom, Alain Vignal, Valérie Fillon and Frédérique Pitel
    Citation: BMC Genomics 2010 11:616
    Content type: Research article Published on:

  40. Recent studies have provided extensive evidence for multitudes of non-coding RNA (ncRNA) transcripts in a wide range of eukaryotic genomes. ncRNAs are emerging as key players in multiple layers of cellular reg...

    Authors: Tirza Doniger, Rodolfo Katz, Chaim Wachtel, Shulamit Michaeli and Ron Unger
    Citation: BMC Genomics 2010 11:615
    Content type: Research article Published on:

  41. Sexual dimorphism in brain gene expression has been recognized in several animal species. However, the relevant regulatory mechanisms remain poorly understood. To investigate whether sex-biased gene expression...

    Authors: Björn Reinius, Chengxi Shi, Liu Hengshuo, Kuljeet Singh Sandhu, Katarzyna J Radomska, Glenn D Rosen, Lu Lu, Klas Kullander, Robert W Williams and Elena Jazin
    Citation: BMC Genomics 2010 11:614
    Content type: Research article Published on:

  42. Long branch attraction (LBA) is a problem that afflicts both the parsimony and maximum likelihood phylogenetic analysis techniques. Research has shown that parsimony is particularly vulnerable to inferring the...

    Authors: Timothy O’Connor, Kenneth Sundberg, Hyrum Carroll, Mark Clement and Quinn Snell
    Citation: BMC Genomics 2010 11(Suppl 2):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  43. Starches are the main storage polysaccharides in plants and are distributed widely throughout plants including seeds, roots, tubers, leaves, stems and so on. Currently, microscopic observation is one of the mo...

    Authors: Shengwen Guo, Jinshan Tang, Youping Deng and Qun Xia
    Citation: BMC Genomics 2010 11(Suppl 2):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  44. A large amount of functional genomic data have provided enough knowledge in predicting gene function computationally, which uses known functional annotations and relationship between unknown genes and known on...

    Authors: Yiming Chen, Zhoujun Li, Xiaofeng Wang, Jiali Feng and Xiaohua Hu
    Citation: BMC Genomics 2010 11(Suppl 2):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  45. Ultrasound imaging technology has wide applications in cattle reproduction and has been used to monitor individual follicles and determine the patterns of follicular development. However, the speckles in ultra...

    Authors: Jinshan Tang, Shengwen Guo, Qingling Sun, Youping Deng and Dongfeng Zhou
    Citation: BMC Genomics 2010 11(Suppl 2):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  46. Existing clustering approaches for microarray data do not adequately differentiate between subsets of co-expressed genes. We devised a novel approach that integrates expression and sequence data in order to ge...

    Authors: Viktor Martyanov and Robert H Gross
    Citation: BMC Genomics 2010 11(Suppl 2):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  47. Acetylation is a crucial post-translational modification for histones, and plays a key role in gene expression regulation. Due to limited data and lack of a clear acetylation consensus sequence, a few research...

    Authors: Chen Zhao, Hui Liu, Jiang Li, Youping Deng and Tieliu Shi
    Citation: BMC Genomics 2010 11(Suppl 2):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  49. Identification of differentially expressed genes from microarray datasets is one of the most important analyses for microarray data mining. Popular algorithms such as statistical t-test rank genes based on a s...

    Authors: Jianjun Hu and Jia Xu
    Citation: BMC Genomics 2010 11(Suppl 2):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  50. Genomic islands (GIs) are clusters of alien genes in some bacterial genomes, but not be seen in the genomes of other strains within the same genus. The detection of GIs is extremely important to the medical an...

    Authors: Dongsheng Che, Cory Hockenbury, Robert Marmelstein and Khaled Rasheed
    Citation: BMC Genomics 2010 11(Suppl 2):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

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