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  1. Whilst being closely related to the model actinomycete Streptomyces coelicolor A3(2), S. lividans 66 differs from it in several significant and phenotypically observable ways, including antibiotic production. Pre...

    Authors: Richard A Lewis, Emma Laing, Nicholas Allenby, Giselda Bucca, Volker Brenner, Marcus Harrison, Andrzej M Kierzek and Colin P Smith
    Citation: BMC Genomics 2010 11:682
    Content type: Research article Published on:

  2. Glioblastoma is the most common primary brain tumor in adults. Though a lot of research has been focused on this disease, the causes and pathogenesis of glioblastoma have not been indentified clearly.

    Authors: Hua Dong, Hoicheong Siu, Li Luo, Xiangzhong Fang, Li Jin and Momiao Xiong
    Citation: BMC Genomics 2010 11(Suppl 3):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  3. Identifying the regions associated with protein function is a singularly important task in the post-genomic era. Biological studies often identify functional enzyme residues by amino acid sequences, particular...

    Authors: Che-Lun Hung, Chihan Lee, Chun-Yuan Lin, Chih-Hung Chang, Yeh-Ching Chung and Chuan Yi Tang
    Citation: BMC Genomics 2010 11(Suppl 3):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  4. MicroRNAs (miRNAs) are single-stranded non-coding RNAs shown to plays important regulatory roles in a wide range of biological processes and diseases. The functions and regulatory mechanisms of most of miRNAs ...

    Authors: Hui Liu, Dong Yue, Lin Zhang, Yidong Chen, Shou-Jiang Gao and Yufei Huang
    Citation: BMC Genomics 2010 11(Suppl 3):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  5. The increasing availability of large-scale protein-protein interaction data has made it possible to understand the basic components and organization of cell machinery from the network level. The arising challe...

    Authors: Jianxin Wang, Min Li, Youping Deng and Yi Pan
    Citation: BMC Genomics 2010 11(Suppl 3):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  6. Comprehensive exploration of protein-protein interactions is a challenging route to understand biological processes. For efficiently enlarging protein interactions annotated with residue-based binding models, ...

    Authors: Yu-Shu Lo, Yung-Chiang Chen and Jinn-Moon Yang
    Citation: BMC Genomics 2010 11(Suppl 3):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  7. Cancer is a complex disease. So far, many genes have been reported to involve in the development of cancer. Rather than the traditional approach to studying individual genes or loci, a systematic investigation...

    Authors: Jingchun Sun and Zhongming Zhao
    Citation: BMC Genomics 2010 11(Suppl 3):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  8. Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, tho...

    Authors: James B McKinlay, Maris Laivenieks, Bryan D Schindler, Anastasia A McKinlay, Shivakumara Siddaramappa, Jean F Challacombe, Stephen R Lowry, Alicia Clum, Alla L Lapidus, Kirk B Burkhart, Victoria Harkins and Claire Vieille
    Citation: BMC Genomics 2010 11:680
    Content type: Research article Published on:

  9. Lantibiotics are lanthionine-containing, post-translationally modified antimicrobial peptides. These peptides have significant, but largely untapped, potential as preservatives and chemotherapeutic agents. Typ...

    Authors: Alan J Marsh, Orla O'Sullivan, R Paul Ross, Paul D Cotter and Colin Hill
    Citation: BMC Genomics 2010 11:679
    Content type: Research article Published on:

  11. The computational prediction of transcription start sites is an important unsolved problem. Some recent progress has been made, but many promoters, particularly those not associated with CpG islands, are still...

    Authors: David G Dineen, Markus Schröder, Desmond G Higgins and Pádraig Cunningham
    Citation: BMC Genomics 2010 11:677
    Content type: Research article Published on:

  12. Treatment of non-small cell lung cancer with novel targeted therapies is a major unmet clinical need. Alternative splicing is a mechanism which generates diverse protein products and is of functional relevance...

    Authors: Wolfram Langer, Florian Sohler, Gabriele Leder, Georg Beckmann, Henrik Seidel, Jörn Gröne, Michael Hummel and Anette Sommer
    Citation: BMC Genomics 2010 11:676
    Content type: Research article Published on:

  13. Age- and sex-related susceptibility to adverse drug reactions and disease is a key concern in understanding drug safety and disease progression. We hypothesize that the underlying suite of hepatic genes expres...

    Authors: Joshua C Kwekel, Varsha G Desai, Carrie L Moland, William S Branham and James C Fuscoe
    Citation: BMC Genomics 2010 11:675
    Content type: Research article Published on:

  14. Riverine ecosystems, highly sensitive to climate change and human activities, are characterized by rapid environmental change to fluctuating water levels and siltation, causing stress on their biological compo...

    Authors: Olga Pechanova, Chuan-Yu Hsu, Joshua P Adams, Tibor Pechan, Lindsay Vandervelde, Jenny Drnevich, Sara Jawdy, Ardeshir Adeli, Jeffrey C Suttle, Amanda M Lawrence, Timothy J Tschaplinski, Armand Séguin and Cetin Yuceer
    Citation: BMC Genomics 2010 11:674
    Content type: Research article Published on:

  15. Copy number variation (CNV) has been recently identified in human and other mammalian genomes, and there is a growing awareness of CNV's potential as a major source for heritable variation in complex traits. G...

    Authors: Eyal Seroussi, Giora Glick, Andrey Shirak, Emanuel Yakobson, Joel I Weller, Ephraim Ezra and Yoel Zeron
    Citation: BMC Genomics 2010 11:673
    Content type: Research article Published on:

  16. Significant interest exists in establishing synergistic research in bioinformatics, systems biology and intelligent computing. Supported by the United States National Science Foundation (NSF), International So...

    Authors: Jack Y Yang, Andrzej Niemierko, Ruzena Bajcsy, Dong Xu, Brian D Athey, Aidong Zhang, Okan K Ersoy, Guo-zheng Li, Mark Borodovsky, Joe C Zhang, Hamid R Arabnia, Youping Deng, A Keith Dunker, Yunlong Liu and Arif Ghafoor
    Citation: BMC Genomics 2010 11(Suppl 3):I1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  17. At present, very little is known about how Burkholderia pseudomallei (B. pseudomallei) interacts with its host to elicit melioidosis symptoms. We established a murine acute-phase melioidosis model and used DNA mi...

    Authors: Chui-Yoke Chin, Denise M Monack and Sheila Nathan
    Citation: BMC Genomics 2010 11:672
    Content type: Research article Published on:

  18. Proteins may evolve through the recruitment and modification of discrete domains, and in many cases, protein action can be dissected at the domain level. PDZ domains are found in many important structural and ...

    Authors: Nicolas Lenfant, Jolanta Polanowska, Sophie Bamps, Shizue Omi, Jean-Paul Borg and Jérôme Reboul
    Citation: BMC Genomics 2010 11:671
    Content type: Research article Published on:

  19. The Beijing genotype of M. tuberculosis is a virulent strain that is disseminating worldwide and has a strong association with drug resistance. In the Western Cape of South Africa, epidemiological studies have id...

    Authors: Thomas R Ioerger, Yicheng Feng, Xiaohua Chen, Karen M Dobos, Thomas C Victor, Elizabeth M Streicher, Robin M Warren, Nicolaas C Gey van Pittius, Paul D Van Helden and James C Sacchettini
    Citation: BMC Genomics 2010 11:670
    Content type: Research article Published on:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

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