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  1. The bacterial genus Listeria contains pathogenic and non-pathogenic species, including the pathogens L. monocytogenes and L. ivanovii, both of which carry homologous virulence gene clusters such as the prfA clust...

    Authors: Henk C den Bakker, Craig A Cummings, Vania Ferreira, Paolo Vatta, Renato H Orsi, Lovorka Degoricija, Melissa Barker, Olga Petrauskene, Manohar R Furtado and Martin Wiedmann
    Citation: BMC Genomics 2010 11:688
    Content type: Research article Published on:

  2. The increasing numbers of 3D compounds and protein complexes stored in databases contribute greatly to current advances in biotechnology, being employed in several pharmaceutical and industrial applications. H...

    Authors: Daniel L Clinciu, Yen-Fu Chen, Cheng-Neng Ko, Chi-Chun Lo and Jinn-Moon Yang
    Citation: BMC Genomics 2010 11(Suppl 4):S26
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  3. Mutation impact extraction is a hitherto unaccomplished task in state of the art mutation extraction systems. Protein mutations and their impacts on protein properties are hidden in scientific literature, maki...

    Authors: Jonas B Laurila, Nona Naderi, René Witte, Alexandre Riazanov, Alexandre Kouznetsov and Christopher JO Baker
    Citation: BMC Genomics 2010 11(Suppl 4):S24
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  4. While the accuracy and precision of deep sequencing data is significantly better than those obtained by the earlier generation of hybridization-based high throughput technologies, the digital nature of deep se...

    Authors: Manhong Dai, Robert C Thompson, Christopher Maher, Rafael Contreras-Galindo, Mark H Kaplan, David M Markovitz, Gil Omenn and Fan Meng
    Citation: BMC Genomics 2010 11(Suppl 4):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 4

  5. 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:

  6. De novo assembly of transcript sequences produced by short-read DNA sequencing technologies offers a rapid approach to obtain expressed gene catalogs for non-model organisms. A draft genome sequence will be produ...

    Authors: Eshchar Mizrachi, Charles A Hefer, Martin Ranik, Fourie Joubert and Alexander A Myburg
    Citation: BMC Genomics 2010 11:681
    Content type: Research article Published on:

  7. 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

  8. Significant interest exists in establishing radiologic imaging as a valid biomarker for assessing the response of cancer to a variety of treatments. To address this problem, we have chosen to study patients wi...

    Authors: Walker H Land, Dan Margolis, Ronald Gottlieb, Elizabeth A Krupinski and Jack Y Yang
    Citation: BMC Genomics 2010 11(Suppl 3):S15
    Content type: Research Published on:

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

  9. 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

  10. The increasing resistance of Plasmodium, the malaria parasites, to multiple commonly used drugs has underscored the urgent need to develop effective antimalarial drugs and vaccines. The new direction of genomics-...

    Authors: Hong Cai, Jianying Gu and Yufeng Wang
    Citation: BMC Genomics 2010 11(Suppl 3):S13
    Content type: Research Published on:

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

  11. 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

  12. Response of cells to changing endogenous or exogenous conditions is governed by intricate molecular interactions, or regulatory networks. To lead to appropriate responses, regulatory network should be 1) conte...

    Authors: Jia Meng, Mingzhu Lu, Yidong Chen, Shou-Jiang Gao and Yufei Huang
    Citation: BMC Genomics 2010 11(Suppl 3):S11
    Content type: Research Published on:

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

  13. 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

  14. Small animal MRI at 7 Tesla (T) provides a useful tool for adiposity research. For adiposity researchers, separation of fat from surrounding tissues and its subsequent quantitative or semi- quantitative analys...

    Authors: Yang Tang, Susan Lee, Marvin D Nelson Jr, Simerly Richard and Rex A Moats
    Citation: BMC Genomics 2010 11(Suppl 3):S9
    Content type: Research Published on:

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

  15. The identification and quantification of proteins using label-free Liquid Chromatography/Mass Spectrometry (LC/MS) play crucial roles in biological and biomedical research. Increasing evidence has shown that b...

    Authors: Jianqiu Zhang and William Haskins
    Citation: BMC Genomics 2010 11(Suppl 3):S8
    Content type: Research Published on:

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

  16. 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

  17. Understanding the biomedical implications of data from high throughput experiments requires solutions for effective cross-scale and cross-domain data exploration. However, existing solutions do not provide suf...

    Authors: Weijian Xuan, Manhong Dai, Josh Buckner, Barbara Mirel, Jean Song, Brian Athey, Stanley J Watson and Fan Meng
    Citation: BMC Genomics 2010 11(Suppl 3):S6
    Content type: Research Published on:

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

  18. 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

  19. Military and industrial activities have lead to reported release of 2,4-dinitrotoluene (2,4DNT) into soil, groundwater or surface water. It has been reported that 2,4DNT can induce toxic effects on humans and ...

    Authors: Sudhir Chowbina, Youping Deng, Junmei Ai, Xiaogang Wu, Xin Guan, Mitchell S Wilbanks, Barbara Lynn Escalon, Sharon A Meyer, Edward J Perkins and Jake Y Chen
    Citation: BMC Genomics 2010 11(Suppl 3):S4
    Content type: Research Published on:

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

  20. The challenge today is to develop a modeling and simulation paradigm that integrates structural, molecular and genetic data for a quantitative understanding of physiology and behavior of biological processes a...

    Authors: Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal K Das and Chaoyang Zhang
    Citation: BMC Genomics 2010 11(Suppl 3):S3
    Content type: Research Published on:

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

  21. Short interfering RNAs (siRNAs) can be used to knockdown gene expression in functional genomics. For a target gene of interest, many siRNA molecules may be designed, whereas their efficiency of expression inhi...

    Authors: Liangjiang Wang, Caiyan Huang and Jack Y Yang
    Citation: BMC Genomics 2010 11(Suppl 3):S2
    Content type: Research Published on:

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

  22. Effector secretion is a common strategy of pathogen in mediating host-pathogen interaction. Eight EPIYA-motif containing effectors have recently been discovered in six pathogens. Once these effectors enter hos...

    Authors: Shunfu Xu, Chao Zhang, Yi Miao, Jianjiong Gao and Dong Xu
    Citation: BMC Genomics 2010 11(Suppl 3):S1
    Content type: Research Published on:

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

  23. 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:

  24. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  48. 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:

  49. 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:

  50. 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:

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