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  1. Previously we reported extensive gene expression reprogramming during epithelial to mesenchymal transition (EMT) of primary prostate cells. Here we investigated the hypothesis that specific histone and DNA met...

    Authors: Xi-Song Ke, Yi Qu, Yang Cheng, Wen-Cheng Li, Varda Rotter, Anne Margrete Øyan and Karl-Henning Kalland
    Citation: BMC Genomics 2010 11:669
    Content type: Research article Published on:

  2. Identifying the bacteria and viruses present in a complex sample is useful in disease diagnostics, product safety, environmental characterization, and research. Array-based methods have proven utility to detec...

    Authors: Shea N Gardner, Crystal J Jaing, Kevin S McLoughlin and Tom R Slezak
    Citation: BMC Genomics 2010 11:668
    Content type: Research article Published on:

  3. Adherent and invasive Escherichia coli (AIEC) are commonly found in ileal lesions of Crohn's Disease (CD) patients, where they adhere to intestinal epithelial cells and invade into and survive in epithelial cells...

    Authors: John HE Nash, Andre Villegas, Andrew M Kropinski, Renan Aguilar-Valenzuela, Paulina Konczy, Mariola Mascarenhas, Kim Ziebell, Alfredo G Torres, Mohamed A Karmali and Brian K Coombes
    Citation: BMC Genomics 2010 11:667
    Content type: Research article Published on:

  4. Gene expression regulation is still poorly documented in bacteria with highly reduced genomes. Understanding the evolution and mechanisms underlying the regulation of gene transcription in Buchnera aphidicola, th...

    Authors: Lilia Brinza, Federica Calevro, Gabrielle Duport, Karen Gaget, Christian Gautier and Hubert Charles
    Citation: BMC Genomics 2010 11:666
    Content type: Research article Published on:

  6. Recently, we identified c ysteine- r ich with E GF- l ike d omains 2 (CRELD2) as a novel endoplasmic reticulum (ER) stress-inducible gene and characterized its transcriptional regulation by ATF6 under ER stress c...

    Authors: Kentaro Oh-hashi, Hisashi Koga, Shun Ikeda, Kiyo Shimada, Yoko Hirata and Kazutoshi Kiuchi
    Citation: BMC Genomics 2010 11:664
    Content type: Research article Published on:

  7. Comprehensive annotation and quantification of transcriptomes are outstanding problems in functional genomics. While high throughput mRNA sequencing (RNA-Seq) has emerged as a powerful tool for addressing thes...

    Authors: Jeffrey Martin, Vincent M Bruno, Zhide Fang, Xiandong Meng, Matthew Blow, Tao Zhang, Gavin Sherlock, Michael Snyder and Zhong Wang
    Citation: BMC Genomics 2010 11:663
    Content type: Methodology article Published on:

  8. Gene expression profiling is an important approach for detecting diagnostic and prognostic biomarkers, and predicting drug safety. The development of a wide range of technologies and platforms for measuring mR...

    Authors: Alison S Devonshire, Ramnath Elaswarapu and Carole A Foy
    Citation: BMC Genomics 2010 11:662
    Content type: Research article Published on:

  9. Post-transcriptional regulation by small RNAs (sRNAs) in bacteria is now recognized as a wide-spread regulatory mechanism modulating a variety of physiological responses including virulence. In Streptococcus pneu...

    Authors: Patrick Marx, Michael Nuhn, Martá Kovács, Regine Hakenbeck and Reinhold Brückner
    Citation: BMC Genomics 2010 11:661
    Content type: Research article Published on:

  10. The yeast Saccharomyces cerevisiae is able to adapt and in situ detoxify lignocellulose derived inhibitors such as furfural and HMF. The length of lag phase for cell growth in response to the inhibitor challenge ...

    Authors: Menggen Ma and Z Lewis Liu
    Citation: BMC Genomics 2010 11:660
    Content type: Research article Published on:

  11. The molecular mechanisms underlying the sex differences in human muscle morphology and function remain to be elucidated. The sex differences in the skeletal muscle transcriptome in both the resting state and f...

    Authors: Dongmei Liu, Maureen A Sartor, Gustavo A Nader, Laurie Gutmann, Mary K Treutelaar, Emidio E Pistilli, Heidi B IglayReger, Charles F Burant, Eric P Hoffman and Paul M Gordon
    Citation: BMC Genomics 2010 11:659
    Content type: Research article Published on:

  12. The posterior genes of the HoxD cluster play a crucial role in the patterning of the tetrapod limb. This region is under the control of a global, long-range enhancer that is present in all vertebrates. Variation ...

    Authors: An Mannaert, Chris T Amemiya and Franky Bossuyt
    Citation: BMC Genomics 2010 11:658
    Content type: Research article Published on:

  14. Genetic populations provide the basis for a wide range of genetic and genomic studies and have been widely used in genetic mapping, gene discovery and genomics-assisted breeding. Chromosome segment substitutio...

    Authors: Jianjun Xu, Qiang Zhao, Peina Du, Chenwu Xu, Baohe Wang, Qi Feng, Qiaoquan Liu, Shuzhu Tang, Minghong Gu, Bin Han and Guohua Liang
    Citation: BMC Genomics 2010 11:656
    Content type: Research article Published on:

  15. Repeat-induced point mutation (RIP) is a fungal genome defence mechanism guarding against transposon invasion. RIP mutates the sequence of repeated DNA and over time renders the affected regions unrecognisable...

    Authors: James K Hane and Richard P Oliver
    Citation: BMC Genomics 2010 11:655
    Content type: Research article Published on:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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

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BMC Genomics

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