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  2. Recent progress in high-throughput technologies has greatly contributed to the development of DNA methylation profiling. Although there are several reports that describe methylome detection of whole genome bis...

    Authors: Liu Yang, Kunlin Zhang, Wei Dai, Ximiao He, Qian Zhao, Jing Wang and Zhong Sheng Sun
    Citation: BMC Genomics 2011 12:10
    Content type: Research article Published on:

  3. Macrophomina phaseolina is an emerging and devastating fungal pathogen that causes significant losses in crop production under high temperatures and drought stress. An increasing number of disease incidence repor...

    Authors: Wellington Muchero, Jeffrey D Ehlers, Timothy J Close and Philip A Roberts
    Citation: BMC Genomics 2011 12:8
    Content type: Research article Published on:

  4. Most agronomic plant traits result from complex molecular networks involving multiple genes and from environmental factors. One such trait is the enzymatic discoloration of fruit and tuber tissues initiated by...

    Authors: Claude Urbany, Benjamin Stich, Lysann Schmidt, Ludwig Simon, Hergen Berding, Holger Junghans, Karl-Heinz Niehoff, Alexander Braun, Eckhard Tacke, Hans-Rheinhardt Hofferbert, Jens Lübeck, Josef Strahwald and Christiane Gebhardt
    Citation: BMC Genomics 2011 12:7
    Content type: Research article Published on:

  5. Peptide spectrum matching (PSM) is the standard method in shotgun proteomics data analysis. It relies on the availability of an accurate and complete sample proteome that is used to make interpretation of the ...

    Authors: Koos Rooijers, Carolin Kolmeder, Catherine Juste, Joël Doré, Mark de Been, Sjef Boeren, Pilar Galan, Christian Beauvallet, Willem M de Vos and Peter J Schaap
    Citation: BMC Genomics 2011 12:6
    Content type: Research article Published on:

  6. Understanding the genetic elements that contribute to key aspects of coffee biology will have an impact on future agronomical improvements for this economically important tree. During the past years, EST colle...

    Authors: Isabelle Privat, Amélie Bardil, Aureliano Bombarely Gomez, Dany Severac, Christelle Dantec, Ivanna Fuentes, Lukas Mueller, Thierry Joët, David Pot, Séverine Foucrier, Stéphane Dussert, Thierry Leroy, Laurent Journot, Alexandre de Kochko, Claudine Campa, Marie-Christine Combes…
    Citation: BMC Genomics 2011 12:5
    Content type: Methodology article Published on:

  7. Linkage maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical map construction follows a well-established workflow: an initial discovery phase where gene...

    Authors: Yada Chutimanitsakun, Rick W Nipper, Alfonso Cuesta-Marcos, Luis Cistué, Ann Corey, Tanya Filichkina, Eric A Johnson and Patrick M Hayes
    Citation: BMC Genomics 2011 12:4
    Content type: Research article Published on:

  8. DNA methylation is an epigenetic mechanism associated with regulation of gene expression and it is modulated during chemical carcinogenesis. The zebrafish is increasingly employed as a human disease model; how...

    Authors: Leda Mirbahai, Timothy D Williams, Huiqing Zhan, Zhiyuan Gong and J Kevin Chipman
    Citation: BMC Genomics 2011 12:3
    Content type: Research article Published on:

  9. The radiation bystander effect is an important component of the overall biological response of tissues and organisms to ionizing radiation, but the signaling mechanisms between irradiated and non-irradiated by...

    Authors: Shanaz A Ghandhi, Anshu Sinha, Marianthi Markatou and Sally A Amundson
    Citation: BMC Genomics 2011 12:2
    Content type: Research article Published on:

  10. Kraits (genus Bungarus) and cobras (genus Naja) are two representative toxic genera of elapids in the old world. Although they are closely related genera and both of their venoms are very toxic, the compositions ...

    Authors: Yu Jiang, Yan Li, Wenhui Lee, Xun Xu, Yue Zhang, Ruoping Zhao, Yun Zhang and Wen Wang
    Citation: BMC Genomics 2011 12:1
    Content type: Research article Published on:

  11. Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. With the availability of a sequenced planarian geno...

    Authors: Josep F Abril, Francesc Cebrià, Gustavo Rodríguez-Esteban, Thomas Horn, Susanna Fraguas, Beatriz Calvo, Kerstin Bartscherer and Emili Saló
    Citation: BMC Genomics 2010 11:731
    Content type: Research article Published on:

  12. Grain endosperm chalkiness of rice is a varietal characteristic that negatively affects not only the appearance and milling properties but also the cooking texture and palatability of cooked rice. However, gra...

    Authors: Xiaolu Liu, Tao Guo, Xiangyuan Wan, Haiyang Wang, Mingzhu Zhu, Aili Li, Ning Su, Yingyue Shen, Bigang Mao, Huqu Zhai, Long Mao and Jianmin Wan
    Citation: BMC Genomics 2010 11:730
    Content type: Research article Published on:

  13. Salmonella paratyphi C is one of the few human-adapted pathogens along with S. typhi, S. paratyphi A and S. paratyphi B that cause typhoid, but it is not clear whether these bacteria cause the disease by the same...

    Authors: Qing-Hua Zou, Qing-Hai Li, Hong-Yun Zhu, Ye Feng, Yong-Guo Li, Randal N Johnston, Gui-Rong Liu and Shu-Lin Liu
    Citation: BMC Genomics 2010 11:729
    Content type: Research article Published on:

  14. Corynebacterium pseudotuberculosis is generally regarded as an important animal pathogen that rarely infects humans. Clinical strains are occasionally recovered from human cases of lymphadenitis, such as C. pseud...

    Authors: Eva Trost, Lisa Ott, Jessica Schneider, Jasmin Schröder, Sebastian Jaenicke, Alexander Goesmann, Peter Husemann, Jens Stoye, Fernanda Alves Dorella, Flavia Souza Rocha, Siomar de Castro Soares, Vívian D'Afonseca, Anderson Miyoshi, Jeronimo Ruiz, Artur Silva, Vasco Azevedo…
    Citation: BMC Genomics 2010 11:728
    Content type: Research article Published on:

  15. Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experimen...

    Authors: Shiaoman Chao, Jorge Dubcovsky, Jan Dvorak, Ming-Cheng Luo, Stephen P Baenziger, Rustam Matnyazov, Dale R Clark, Luther E Talbert, James A Anderson, Susanne Dreisigacker, Karl Glover, Jianli Chen, Kim Campbell, Phil L Bruckner, Jackie C Rudd, Scott Haley…
    Citation: BMC Genomics 2010 11:727
    Content type: Research article Published on:

  16. The tuberous root of sweetpotato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism und...

    Authors: Zhangying Wang, Boping Fang, Jingyi Chen, Xiongjian Zhang, Zhongxia Luo, Lifei Huang, Xinliang Chen and Yujun Li
    Citation: BMC Genomics 2010 11:726
    Content type: Research article Published on:

  17. Type A1 Clostridium botulinum strains are a group of Gram-positive, spore-forming anaerobic bacteria that produce a genetically, biochemically, and biophysically indistinguishable 150 kD protein that causes botul...

    Authors: Ping-Ke Fang, Brian H Raphael, Susan E Maslanka, Shuowei Cai and Bal Ram Singh
    Citation: BMC Genomics 2010 11:725
    Content type: Research article Published on:

  18. As we enter an era when testing millions of SNPs in a single gene association study will become the standard, consideration of multiple comparisons is an essential part of determining statistical significance....

    Authors: Randall C Johnson, George W Nelson, Jennifer L Troyer, James A Lautenberger, Bailey D Kessing, Cheryl A Winkler and Stephen J O'Brien
    Citation: BMC Genomics 2010 11:724
    Content type: Research article Published on:

  19. The need for rapid and efficient microbial cell factory design and construction are possible through the enabling technology, metabolic engineering, which is now being facilitated by systems biology approaches...

    Authors: José Manuel Otero, Wanwipa Vongsangnak, Mohammad A Asadollahi, Roberto Olivares-Hernandes, Jérôme Maury, Laurent Farinelli, Loïc Barlocher, Magne Østerås, Michel Schalk, Anthony Clark and Jens Nielsen
    Citation: BMC Genomics 2010 11:723
    Content type: Research article Published on:

  20. Physical protein-protein interaction (PPI) is a critical phenomenon for the function of most proteins in living organisms and a significant fraction of PPIs are the result of domain-domain interactions. Exon s...

    Authors: Douglas V Cancherini, Gustavo S França and Sandro J de Souza
    Citation: BMC Genomics 2010 11(Suppl 5):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  21. A large number of probabilistic models used in sequence analysis assign non-zero probability values to most input sequences. To decide when a given probability is sufficient the most common way is bayesian bin...

    Authors: Ariane Machado-Lima, André Yoshiaki Kashiwabara and Alan Mitchell Durham
    Citation: BMC Genomics 2010 11(Suppl 5):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  22. The genome-wide identification of both morbid genes, i.e., those genes whose mutations cause hereditary human diseases, and druggable genes, i.e., genes coding for proteins whose modulation by small molecules ...

    Authors: Pedro R Costa, Marcio L Acencio and Ney Lemke
    Citation: BMC Genomics 2010 11(Suppl 5):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  23. The need to manage large amounts of data is a clear demand for laboratories nowadays. The use of Laboratory Information Management Systems (LIMS) to achieve this is growing each day. A LIMS is a complex comput...

    Authors: Alexandre Melo, Alessandra Faria-Campos, Daiane Mariele DeLaat, Rodrigo Keller, Vinícius Abreu and Sérgio Campos
    Citation: BMC Genomics 2010 11(Suppl 5):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  24. G. diazotrophicus and A. vinelandii are aerobic nitrogen-fixing bacteria. Although oxygen is essential for the survival of these organisms, it irreversibly inhibits nitrogenase, the complex responsible for nitrog...

    Authors: Letícia MS Lery, Mainá Bitar, Mauricio GS Costa, Shaila CS Rössle and Paulo M Bisch
    Citation: BMC Genomics 2010 11(Suppl 5):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  25. Molecular docking simulation is the Rational Drug Design (RDD) step that investigates the affinity between protein receptors and ligands. Typically, molecular docking algorithms consider receptors as rigid bod...

    Authors: Karina S Machado, Ana T Winck, Duncan DA Ruiz and Osmar Norberto de Souza
    Citation: BMC Genomics 2010 11(Suppl 5):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  26. Cathepsin B (catB) is a promising target for anti-cancer drug design due to its implication in several steps of tumorigenesis. catB activity and inhibition are pH-dependent, making it difficult to identify eff...

    Authors: Mauricio GS Costa, Paulo R Batista, Cláudio S Shida, Charles H Robert, Paulo M Bisch and Pedro G Pascutti
    Citation: BMC Genomics 2010 11(Suppl 5):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  27. Alternative splicing (AS) is a central mechanism in the generation of genomic complexity and is a major contributor to transcriptome and proteome diversity. Alterations of the splicing process can lead to dere...

    Authors: Elisa N Ferreira, Maria CR Rangel, Pedro F Galante, Jorge E de Souza, Gustavo C Molina, Sandro J de Souza and Dirce M Carraro
    Citation: BMC Genomics 2010 11(Suppl 5):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  28. Retrieving pertinent information from biological scientific literature requires cutting-edge text mining methods which may be able to recognize the meaning of the very ambiguous names of biological entities. A...

    Authors: Roney S Coimbra, Dana E Vanderwall and Guilherme C Oliveira
    Citation: BMC Genomics 2010 11(Suppl 5):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  29. The thymus is a central lymphoid organ, in which bone marrow-derived T cell precursors undergo a complex process of maturation. Developing thymocytes interact with thymic microenvironment in a defined spatial ...

    Authors: Leandra Linhares-Lacerda, Marcelo Ribeiro-Alves, Ana Cristina Martins de Almeida Nogueira, Daniella Areas Mendes-da-Cruz, Danielle Aparecida Magalhães, Mireille Dardenne, Geraldo Aleixo Passos and Wilson Savino
    Citation: BMC Genomics 2010 11(Suppl 5):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  30. The link between reproductive life history and incidence of ovarian tumors is well known. Periods of reduced ovulations may confer protection against ovarian cancer. Using phenotypic data available for mouse, ...

    Authors: Ulises Urzúa, Garrison A Owens, Gen-Mu Zhang, James M Cherry, John J Sharp and David J Munroe
    Citation: BMC Genomics 2010 11(Suppl 5):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 5

  31. Acute enteritis caused by Salmonella is a public health concern. Salmonella infection is also known to increase the risk of inflammatory bowel diseases and cancer. Therefore, it is important to understand how Sal...

    Authors: Xingyin Liu, Rong Lu, Yinglin Xia and Jun Sun
    Citation: BMC Genomics 2010 11:722
    Content type: Research article Published on:

  32. Members of the makorin (mkrn) gene family encode RING/C3H zinc finger proteins with U3 ubiquitin ligase activity. Although these proteins have been described in a variety of eukaryotes such as plants, fungi, inve...

    Authors: Astrid Böhne, Amandine Darras, Helena D'Cotta, Jean-Francois Baroiller, Delphine Galiana-Arnoux and Jean-Nicolas Volff
    Citation: BMC Genomics 2010 11:721
    Content type: Research article Published on:

  34. The AP2/ERF protein family contains transcription factors that play a crucial role in plant growth and development and in response to biotic and abiotic stress conditions in plants. Grapevine (Vitis vinifera) is ...

    Authors: Francesco Licausi, Federico M Giorgi, Sara Zenoni, Fabio Osti, Mario Pezzotti and Pierdomenico Perata
    Citation: BMC Genomics 2010 11:719
    Content type: Research article Published on:

  35. Although the importance and widespread occurrence of iron limitation in the contemporary ocean is well documented, we still know relatively little about genetic adaptation of phytoplankton to these environment...

    Authors: Markus Lommer, Alexandra-Sophie Roy, Markus Schilhabel, Stefan Schreiber, Philip Rosenstiel and Julie LaRoche
    Citation: BMC Genomics 2010 11:718
    Content type: Research article Published on:

  36. While the number of newly sequenced genomes and genes is constantly increasing, elucidation of their function still is a laborious and time-consuming task. This has led to the development of a wide range of me...

    Authors: Samira Jaeger, Christine T Sers and Ulf Leser
    Citation: BMC Genomics 2010 11:717
    Content type: Research article Published on:

  37. MicroRNAs are small non-coding RNA transcripts that regulate post-transcriptional gene expression. The millions of short sequence reads generated by next generation sequencing technologies make this technique ...

    Authors: Henk PJ Buermans, Yavuz Ariyurek, Gertjan van Ommen, Johan T den Dunnen and Peter AC 't Hoen
    Citation: BMC Genomics 2010 11:716
    Content type: Methodology article Published on:

  38. MicroRNAs (miRNAs) are key regulators of biological processes. To define miRNA function in the eye, it is essential to determine a high-resolution profile of their spatial and temporal distribution.

    Authors: Marianthi Karali, Ivana Peluso, Vincenzo A Gennarino, Marchesa Bilio, Roberta Verde, Giampiero Lago, Pascal Dollé and Sandro Banfi
    Citation: BMC Genomics 2010 11:715
    Content type: Research article Published on:

  39. Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. We recently constructed the first physical map of a...

    Authors: Camille Rustenholz, Pete E Hedley, Jenny Morris, Frédéric Choulet, Catherine Feuillet, Robbie Waugh and Etienne Paux
    Citation: BMC Genomics 2010 11:714
    Content type: Research article Published on:

  40. Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution t...

    Authors: Taryn P Stewart, Hyoung Yon Kim, Arnold M Saxton and Jung Han Kim
    Citation: BMC Genomics 2010 11:713
    Content type: Research article Published on:

  43. The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two oth...

    Authors: Alexandra Sirota-Madi, Tsviya Olender, Yael Helman, Colin Ingham, Ina Brainis, Dalit Roth, Efrat Hagi, Leonid Brodsky, Dena Leshkowitz, Vladimir Galatenko, Vladimir Nikolaev, Raja C Mugasimangalam, Sharron Bransburg-Zabary, David L Gutnick, Doron Lancet and Eshel Ben-Jacob
    Citation: BMC Genomics 2010 11:710
    Content type: Research article Published on:

  44. Arsenic is present in numerous ecosystems and microorganisms have developed various mechanisms to live in such hostile environments. Herminiimonas arsenicoxydans, a bacterium isolated from arsenic contaminated sl...

    Authors: Jessica Cleiss-Arnold, Sandrine Koechler, Caroline Proux, Marie-Laure Fardeau, Marie-Agnès Dillies, Jean-Yves Coppee, Florence Arsène-Ploetze and Philippe N Bertin
    Citation: BMC Genomics 2010 11:709
    Content type: Research article Published on:

  45. In recent years numerous studies have undertaken to measure the impact of patents, material transfer agreements, data-withholding and commercialization pressures on biomedical researchers. Of particular concer...

    Authors: Matthew R Voell, Lily Farris, Edwin Levy and Emily Marden
    Citation: BMC Genomics 2010 11:708
    Content type: Correspondence Published on:

  46. Considerations in applying association mapping (AM) to plant breeding are population structure and size: not accounting for structure and/or using small populations can lead to elevated false-positive rates. T...

    Authors: Alfonso Cuesta-Marcos, Péter Szűcs, Timothy J Close, Tanya Filichkin, Gary J Muehlbauer, Kevin P Smith and Patrick M Hayes
    Citation: BMC Genomics 2010 11:707
    Content type: Research article Published on:

  47. Single nucleotide polymorphisms (SNPs) represent the most widespread type of DNA variation in vertebrates and may be used as genetic markers for a range of applications. This has led to an increased interest i...

    Authors: Rune Andreassen, Sigbjørn Lunner and Bjørn Høyheim
    Citation: BMC Genomics 2010 11:706
    Content type: Research article Published on:

  48. Oryza longistaminata, an AA genome type (2 n = 24), originates from Africa and is closely related to Asian cultivated rice (O. sativa L.). It contains various valuable traits with respect to tolerance to biotic a...

    Authors: Haiyuan Yang, Liwei Hu, Thomas Hurek and Barbara Reinhold-Hurek
    Citation: BMC Genomics 2010 11:705
    Content type: Research article Published on:

  50. Changes in promoter DNA methylation pattern of genes involved in key biological pathways have been reported in glioblastoma. Genome-wide assessments of DNA methylation levels are now required to decipher the e...

    Authors: Amandine Etcheverry, Marc Aubry, Marie de Tayrac, Elodie Vauleon, Rachel Boniface, Frederique Guenot, Stephan Saikali, Abderrahmane Hamlat, Laurent Riffaud, Philippe Menei, Veronique Quillien and Jean Mosser
    Citation: BMC Genomics 2010 11:701
    Content type: Research article Published on:

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