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  1. DNA methylation is associated with aberrant gene expression in cancer, and has been shown to correlate with therapeutic response and disease prognosis in some types of cancer. We sought to investigate the biol...

    Authors: Steven H Lin, Jing Wang, Pierre Saintigny, Chia-Chin Wu, Uma Giri, Jing Zhang, Toshi Menju, Lixia Diao, Lauren Byers, John N Weinstein, Kevin R Coombes, Luc Girard, Ritsuko Komaki, Ignacio I Wistuba, Hiroshi Date, John D Minna…
    Citation: BMC Genomics 2014 15:1079
    Content type: Research article Published on:

  2. Sumoylation, which is a reversible and dynamic post-translational modification, is one of the vital processes in a cell. Before a protein matures to perform its function, sumoylation may alter its localization...

    Authors: Ahmet Sinan Yavuz and Osman Ugur Sezerman
    Citation: BMC Genomics 2014 15(Suppl 9):S18
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  3. With the rapid accumulation of proteomic and genomic datasets in terms of genome-scale features and interaction networks through high-throughput experimental techniques, the process of manual predicting functi...

    Authors: Qingyao Wu, Yunming Ye, Shen-Shyang Ho and Shuigeng Zhou
    Citation: BMC Genomics 2014 15(Suppl 9):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  4. Altered expression profiles of microRNAs (miRNAs) are linked to many diseases including lung cancer. miRNA expression profiling is reproducible and miRNAs are very stable. These characteristics of miRNAs make ...

    Authors: Renhua Song, Qian Liu, Gyorgy Hutvagner, Hung Nguyen, Kotagiri Ramamohanarao, Limsoon Wong and Jinyan Li
    Citation: BMC Genomics 2014 15(Suppl 9):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  5. G-quadruplexes are four-stranded structures formed in guanine-rich nucleotide sequences. Several functional roles of DNA G-quadruplexes have so far been investigated, where their putative functional roles duri...

    Authors: Masato Yano and Yuki Kato
    Citation: BMC Genomics 2014 15(Suppl 9):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  6. RNA interference (RNAi) is involved in genome defense as well as diverse cellular, developmental, and physiological processes. Key components of RNAi are Argonaute, Dicer, and RNA-dependent RNA polymerase (RdR...

    Authors: Jaeyoung Choi, Ki-Tae Kim, Jongbum Jeon, Jiayao Wu, Hyeunjeong Song, Fred O Asiegbu and Yong-Hwan Lee
    Citation: BMC Genomics 2014 15(Suppl 9):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  7. Current ChIP-seq studies are interested in comparing multiple epigenetic profiles across several cell types and tissues simultaneously for studying constitutive and differential regulation. Simultaneous analys...

    Authors: Kuan-Bei Chen, Ross Hardison and Yu Zhang
    Citation: BMC Genomics 2014 15(Suppl 9):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  8. Recently, large bio-projects dealing with the release of different genomes have transpired. Most of these projects use next-generation sequencing platforms. As a consequence, many de novo assembly tools have evol...

    Authors: Mostafa M Abbas, Qutaibah M Malluhi and Ponnuraman Balakrishnan
    Citation: BMC Genomics 2014 15(Suppl 9):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  9. Computational prediction of major histocompatibility complex class II (MHC-II) binding peptides can assist researchers in understanding the mechanism of immune systems and developing peptide based vaccines. Al...

    Authors: Yichang Xu, Cheng Luo, Mingjie Qian, Xiaodi Huang and Shanfeng Zhu
    Citation: BMC Genomics 2014 15(Suppl 9):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  10. Long noncoding RNAs (lncRNAs) constitute a major, but poorly characterized part of human transcriptome. Recent evidence indicates that many lncRNAs are involved in cancer and can be used as predictive and prog...

    Authors: Aliaksandr A Yarmishyn, Arsen O Batagov, Jovina Z Tan, Gopinath M Sundaram, Prabha Sampath, Vladimir A Kuznetsov and Igor V Kurochkin
    Citation: BMC Genomics 2014 15(Suppl 9):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  11. Histone modification and remodeling play crucial roles in regulating gene transcription. These post-translational modifications of histones function in a combinatorial fashion and can be recognized by specific...

    Authors: Po-Cheng Hung, Tzu-Hsien Yang, Hung-Jiun Liaw and Wei-Sheng Wu
    Citation: BMC Genomics 2014 15(Suppl 9):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  12. The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the g...

    Authors: JeHoon Jun, Yun Sung Cho, Haejin Hu, Hak-Min Kim, Sungwoong Jho, Priyvrat Gadhvi, Kyung Mi Park, Jeongheui Lim, Woon Kee Paek, Kyudong Han, Andrea Manica, Jeremy S Edwards and Jong Bhak
    Citation: BMC Genomics 2014 15(Suppl 9):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  13. A number of microtubule disassembly blocking agents and inhibitors of tubulin polymerization have been elements of great interest in anti-cancer therapy, some of them even entering into the clinical trials. On...

    Authors: Chetna Tyagi, Ankita Gupta, Sukriti Goyal, Jaspreet Kaur Dhanjal and Abhinav Grover
    Citation: BMC Genomics 2014 15(Suppl 9):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  14. Non-small cell lung cancer (NSCLC) remains lethal despite the development of numerous drug therapy technologies. About 85% to 90% of lung cancers are NSCLC and the 5-year survival rate is at best still below 5...

    Authors: Hideaki Umeyama, Mitsuo Iwadate and Y-h Taguchi
    Citation: BMC Genomics 2014 15(Suppl 9):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  15. Proteomics research is enabled with the high-throughput technologies, but our ability to identify expressed proteome is limited in small samples. The coverage and consistency of proteome expression are critica...

    Authors: Jing Sun, Guang Lan Zhang, Siyang Li, Alexander R Ivanov, David Fenyo, Frederique Lisacek, Shashi K Murthy, Barry L Karger and Vladimir Brusic
    Citation: BMC Genomics 2014 15(Suppl 9):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  16. Bacterial wilt caused by Ralstonia solanacearum is a serious soil-borne disease of peanut (Arachis hypogaea L). The molecular basis of peanut response to R. solanacearum remains unknown. To understand the resista...

    Authors: Yuning Chen, Xiaoping Ren, Xiaojing Zhou, Li Huang, Liying Yan, Yong Lei, Boshou Liao, Jinyong Huang, Shunmou Huang, Wenhui Wei and Huifang Jiang
    Citation: BMC Genomics 2014 15:1078
    Content type: Research article Published on:

  17. Grapevine (Vitis vinifera L.) is one of the most important fruit crops in the world and serves as a valuable model for fruit development in woody species. A major breakthrough in grapevine genomics was achieved i...

    Authors: Jérôme Grimplet, Anne-Françoise Adam-Blondon, Pierre-François Bert, Oliver Bitz, Dario Cantu, Christopher Davies, Serge Delrot, Mario Pezzotti, Stéphane Rombauts and Grant R Cramer
    Citation: BMC Genomics 2014 15:1077
    Content type: Methodology article Published on:

  18. Maintenance of metal homeostasis is crucial in bacterial pathogenicity as metal starvation is the most important mechanism in the nutritional immunity strategy of host cells. Thus, pathogenic bacteria have evo...

    Authors: Elke Eckelt, Michael Jarek, Cornelia Frömke, Jochen Meens and Ralph Goethe
    Citation: BMC Genomics 2014 15:1076
    Content type: Research article Published on:

  19. Strains of Escherichia coli cause a wide variety of intestinal and extra-intestinal diseases in both humans and animals, and are also often found in healthy individuals or the environment. Broadly, a strong phylo...

    Authors: Robert J Goldstone, Roman Popat, Hans-Joachim Schuberth, Olivier Sandra, I Martin Sheldon and David GE Smith
    Citation: BMC Genomics 2014 15:1075
    Content type: Research article Published on:

  20. Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have often been suggested to possess the most ancie...

    Authors: John F Mulley, Adam D Hargreaves, Matthew J Hegarty, R Scott Heller and Martin T Swain
    Citation: BMC Genomics 2014 15:1074
    Content type: Research article Published on:

  22. Vertebrate organogenesis is a highly complex process involving sequential cascades of transcription factor activation or repression. Interestingly a single developmental control gene can occasionally be essent...

    Authors: Sumantra Chatterjee, V Sivakamasundari, Sook Peng Yap, Petra Kraus, Vibhor Kumar, Xing Xing, Siew Lan Lim, Joel Sng, Shyam Prabhakar and Thomas Lufkin
    Citation: BMC Genomics 2014 15:1072
    Content type: Research article Published on:

  23. Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their h...

    Authors: Raúl Castanera, Gúmer Pérez, Leticia López, Rubén Sancho, Francisco Santoyo, Manuel Alfaro, Toni Gabaldón, Antonio G Pisabarro, José A Oguiza and Lucía Ramírez
    Citation: BMC Genomics 2014 15:1071
    Content type: Research article Published on:

  24. Lactobacillus crispatus is a ubiquitous micro-organism encountered in a wide range of host-associated habitats. It can be recovered from the gastrointestinal tract of animals and it is a common constituent of the...

    Authors: Teija Ojala, Matti Kankainen, Joana Castro, Nuno Cerca, Sanna Edelman, Benita Westerlund-Wikström, Lars Paulin, Liisa Holm and Petri Auvinen
    Citation: BMC Genomics 2014 15:1070
    Content type: Research article Published on:

  25. Some species of fungi can cause serious human diseases, particularly to immuno-compromised individuals. Opportunistic fungal infections are a leading cause of mortality, and present an emerging challenge that ...

    Authors: Manish Datt and Amit Sharma
    Citation: BMC Genomics 2014 15:1069
    Content type: Research article Published on:

  26. A previous study reported a comprehensive quantitative trait locus (QTL) and genome wide association study (GWAS) of southern leaf blight (SLB) resistance in the maize Nested Association Mapping (NAM) panel. S...

    Authors: Yang Bian, Qin Yang, Peter J Balint-Kurti, Randall J Wisser and James B Holland
    Citation: BMC Genomics 2014 15:1068
    Content type: Research article Published on:

  27. Comparison of toxicogenomic data facilitates the identification of deregulated gene patterns and maximizes health risk prediction in human.

    Authors: Immacolata Porreca, Fulvio D’Angelo, Daniela Gentilcore, Emanuele Carchia, Angela Amoresano, Andrea Affuso, Michele Ceccarelli, Pasquale De Luca, Libera Esposito, Francesco M Guadagno, Massimo Mallardo, Antonio Nardone, Sergio Maccarone, Francesca Pane, Marzia Scarfò, Paolo Sordino…
    Citation: BMC Genomics 2014 15:1067
    Content type: Research article Published on:

  28. The reliable identification of proteins containing 50 or fewer amino acids is difficult due to the limited information content in short sequences. The 37 amino acid CydX protein in Escherichia coli is a member of...

    Authors: Rondine J Allen, Evan P Brenner, Caitlin E VanOrsdel, Jessica J Hobson, David J Hearn and Matthew R Hemm
    Citation: BMC Genomics 2014 15:946
    Content type: Research article Published on:

  29. Bacteria in the genus Ruminococcus are ubiquitous members of the mammalian gastrointestinal tract. In particular, they are important in ruminants where they digest a wide range of plant cell wall polysaccharides....

    Authors: Melissa R Christopherson, John A Dawson, David M Stevenson, Andrew C Cunningham, Shanti Bramhacharya, Paul J Weimer, Christina Kendziorski and Garret Suen
    Citation: BMC Genomics 2014 15:1066
    Content type: Research article Published on:

  30. Corynebacterium pseudotuberculosis biovar ovis is a facultative intracellular pathogen, and the etiological agent of caseous lymphadenitis in small ruminants. During the infection process, the bacterium is subjec...

    Authors: Wanderson M Silva, Rodrigo D Carvalho, Siomar C Soares, Isabela FS Bastos, Edson L Folador, Gustavo HMF Souza, Yves Le Loir, Anderson Miyoshi, Artur Silva and Vasco Azevedo
    Citation: BMC Genomics 2014 15:1065
    Content type: Research article Published on:

  31. In the filamentous cyanobacterium Nostoc punctiforme ATCC 29133, removal of combined nitrogen induces the differentiation of heterocysts, a cell-type specialized in N2 fixation. The differentiation involves genom...

    Authors: Gustaf Sandh, Margareta Ramström and Karin Stensjö
    Citation: BMC Genomics 2014 15:1064
    Content type: Research article Published on:

  33. A low birth weight has been extensively related to poor adult health outcomes. Birth weight can be seen as a proxy for environmental conditions during prenatal development. Identical twin pairs discordant for ...

    Authors: Qihua Tan, Morten Frost, Bastiaan T Heijmans, Jacob von Bornemann Hjelmborg, Elmar W Tobi, Kaare Christensen and Lene Christiansen
    Citation: BMC Genomics 2014 15:1062
    Content type: Research article Published on:

  34. Largely because of their direct, negative impacts on human health, the venoms of front-fanged snakes of the families Viperidae and Elapidae have been extensively characterized proteomically, transcriptomically...

    Authors: James J McGivern, Kenneth P Wray, Mark J Margres, Michelle E Couch, Stephen P Mackessy and Darin R Rokyta
    Citation: BMC Genomics 2014 15:1061
    Content type: Research article Published on:

  35. The wine industry needs better-adapted yeasts to grow at low temperature because it is interested in fermenting at low temperature to improve wine aroma. Elucidating the response to cold in Saccharomyces cerevisi...

    Authors: Estéfani García-Ríos, María López-Malo and José Manuel Guillamón
    Citation: BMC Genomics 2014 15:1059
    Content type: Research article Published on:

  36. The in vivo gene response associated with hyperthermia is poorly understood. Here, we perform a global, multiorgan characterization of the gene response to heat stress using an in vivo conscious rat model.

    Authors: Jonathan D Stallings, Danielle L Ippolito, Vineet Rakesh, Christine E Baer, William E Dennis, Bryan G Helwig, David A Jackson, Lisa R Leon, John A Lewis and Jaques Reifman
    Citation: BMC Genomics 2014 15:1058
    Content type: Research article Published on:

  37. The oral GPCR nutrient/taste receptor gene repertoire consists of the Tas1r family (sweet and umami tastes), the Tas2r family (bitter taste) as well as several other potential candidate sensors of amino acids, pe...

    Authors: Elizabete C da Silva, Nadia de Jager, William Burgos-Paz, Antonio Reverter, Miguel Perez-Enciso and Eugeni Roura
    Citation: BMC Genomics 2014 15:1057
    Content type: Research article Published on:

  38. Understanding gene expression and metabolic re-programming that occur in response to limiting nitrogen (N) conditions in crop plants is crucial for the ongoing progress towards the development of varieties wit...

    Authors: Viktoriya Coneva, Caitlin Simopoulos, José A Casaretto, Ashraf El-kereamy, David R Guevara, Jonathan Cohn, Tong Zhu, Lining Guo, Danny C Alexander, Yong-Mei Bi, Paul D McNicholas and Steven J Rothstein
    Citation: BMC Genomics 2014 15:1056
    Content type: Research article Published on:

  39. Neonicotinoid insecticides are widely known for their broad-spectrum control of arthropod pests. Recently, their effects on plant physiological mechanisms have been characterized as producing a stress shield, ...

    Authors: Mitchell D Stamm, Laramy S Enders, Teresa J Donze-Reiner, Frederick P Baxendale, Blair D Siegfried and Tiffany M Heng-Moss
    Citation: BMC Genomics 2014 15:1055
    Content type: Research article Published on:

  40. Lactococcus lactis is the most used species in the dairy industry. Its ability to adapt to technological stresses, such as oxidative stress encountered during stirring in the first stages of the cheese-making pro...

    Authors: Marina Cretenet, Gwenaëlle Le Gall, Udo Wegmann, Sergine Even, Claire Shearman, Régis Stentz and Sophie Jeanson
    Citation: BMC Genomics 2014 15:1054
    Content type: Research article Published on:

  41. Research on the aryl hydrocarbon receptor (AHR) has largely focused on variations in toxic outcomes resulting from its activation by halogenated aromatic hydrocarbons. But the AHR also plays key roles in regul...

    Authors: Ren X Sun, Lauren C Chong, Trent T Simmons, Kathleen E Houlahan, Stephenie D Prokopec, John D Watson, Ivy D Moffat, Sanna Lensu, Jere Lindén, Christine P'ng, Allan B Okey, Raimo Pohjanvirta and Paul C Boutros
    Citation: BMC Genomics 2014 15:1053
    Content type: Research article Published on:

  42. Changes to the environment as a result of human activities can result in a range of impacts on reef building corals that include coral bleaching (reduced concentrations of algal symbionts), decreased coral gro...

    Authors: Nedeljka Rosic, Paulina Kaniewska, Chon-Kit Kenneth Chan, Edmund Yew Siang Ling, David Edwards, Sophie Dove and Ove Hoegh-Guldberg
    Citation: BMC Genomics 2014 15:1052
    Content type: Research article Published on:

  43. Global change will affect patterns of nutrient upwelling in marine environments, potentially becoming even stricter regulators of phytoplankton primary productivity. To better understand phytoplankton nutrient...

    Authors: Sebastian D Rokitta, Peter Von Dassow, Björn Rost and Uwe John
    Citation: BMC Genomics 2014 15:1051
    Content type: Research article Published on:

  44. Chrysanthemum is an important ornamental plant all over the world. It is easily attacked by aphid, Macrosiphoniella sanbourni. The molecular mechanisms of plant defense responses to aphid are only partially under...

    Authors: Xiaolong Xia, Yafeng Shao, Jiafu Jiang, Liping Ren, Fadi Chen, Weimin Fang, Zhiyong Guan and Sumei Chen
    Citation: BMC Genomics 2014 15:1050
    Content type: Research article Published on:

  46. Genomic selection (GS) may improve selection response over conventional pedigree-based selection if markers capture more detailed information than pedigrees in recently domesticated tree species and/or make it...

    Authors: Jean Beaulieu, Trevor K Doerksen, John MacKay, André Rainville and Jean Bousquet
    Citation: BMC Genomics 2014 15:1048
    Content type: Research article Published on:

  47. In eukaryotes, transcriptional regulation is usually mediated by interactions of multiple transcription factors (TFs) with their respective specific cis-regulatory elements (CREs) in the so-called cis-regulatory ...

    Authors: Meng Niu, Ehsan S Tabari and Zhengchang Su
    Citation: BMC Genomics 2014 15:1047
    Content type: Methodology article Published on:

  48. Availability of molecular markers has proven to be an efficient tool in facilitating progress in plant breeding, which is particularly important in the case of less researched crops such as cotton. Considering...

    Authors: Ximei Li, Wenhui Gao, Huanle Guo, Xianlong Zhang, David D Fang and Zhongxu Lin
    Citation: BMC Genomics 2014 15:1046
    Content type: Research article Published on:

  49. RNA-seq studies have an important role for both large-scale analysis of gene expression and for transcriptome reconstruction. However, the lack of software specifically developed for the analysis of the transc...

    Authors: Alessandro Sardu, Laura Treu and Stefano Campanaro
    Citation: BMC Genomics 2014 15:1045
    Content type: Research article Published on:

  50. Driver mutations are positively selected during the evolution of cancers. The relative frequency of a particular mutation within a gene is typically used as a criterion for identifying a driver mutation. Howev...

    Authors: Jason Roszik and Scott E Woodman
    Citation: BMC Genomics 2014 15:1044
    Content type: Methodology article Published on:

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BMC Genomics

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