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  1. The avalanche of integromics and panomics approaches shifted the deciphering of aging mechanisms from single molecular entities to communities of them. In this orientation, we explore the cardiac aging mechani...

    Authors: Konstantina Dimitrakopoulou, Aristidis G Vrahatis and Anastasios Bezerianos
    Citation: BMC Genomics 2015 16:147
    Content type: Research article Published on:

  2. Since 2011, the level of pyrethroid resistance in the major malaria mosquito, Anopheles coluzzi, has increased to such an extent in Burkina Faso that none of the long lasting insecticide treated nets (LLINs) curr...

    Authors: Kobié H Toé, Sagnon N’Falé, Roch K Dabiré, Hilary Ranson and Christopher M Jones
    Citation: BMC Genomics 2015 16:146
    Content type: Research article Published on:

  3. Strand specific RNAseq data is now more common in RNAseq projects. Visualizing RNAseq data has become an important matter in Analysis of sequencing data. The most widely used visualization tool is the UCSC gen...

    Authors: Jiyuan An, John Lai, David L A Wood, Atul Sajjanhar, Chenwei Wang, Gregor Tevz, Melanie L Lehman and Colleen C Nelson
    Citation: BMC Genomics 2015 16:145
    Content type: Software Published on:

  4. Mammalian CpG islands (CGIs) normally escape DNA methylation in all adult tissues and developmental stages. However, in our previous study we unexpectedly identified many methylated CGIs in human peripheral bl...

    Authors: Hiroki Miyahara, Osamu Hirose, Kenji Satou and Yoichi Yamada
    Citation: BMC Genomics 2015 16:144
    Content type: Research article Published on:

  5. Identifying insertion/deletion polymorphisms (INDELs) with high confidence has been intrinsically challenging in short-read sequencing data. Here we report our approach for improving INDEL calling accuracy by ...

    Authors: Danny Challis, Lilian Antunes, Erik Garrison, Eric Banks, Uday S Evani, Donna Muzny, Ryan Poplin, Richard A Gibbs, Gabor Marth and Fuli Yu
    Citation: BMC Genomics 2015 16:143
    Content type: Research article Published on:

  6. Next-generation sequencing techniques such as ChIP-seq allow researchers to investigate the genomic position of nuclear components and events. These experiments provide researchers with thousands of regions of...

    Authors: RyangGuk Kim, Owen K Smith, Wing Chung Wong, Alex M Ryan, Michael C Ryan and Mirit I Aladjem
    Citation: BMC Genomics 2015 16:142
    Content type: Software Published on:

  7. Transposable Elements (TEs) are key components that shape the organization and evolution of genomes. Fungi have developed defense mechanisms against TE invasion such as RIP (Repeat-Induced Point mutation), MIP...

    Authors: Joëlle Amselem, Marc-Henri Lebrun and Hadi Quesneville
    Citation: BMC Genomics 2015 16:141
    Content type: Research article Published on:

  10. Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with diseases of the colon including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). Howe...

    Authors: Imge Hulur, Eric R Gamazon, Andrew D Skol, Rosa M Xicola, Xavier Llor, Kenan Onel, Nathan A Ellis and Sonia S Kupfer
    Citation: BMC Genomics 2015 16:138
    Content type: Research article Published on:

  12. The analysis of differential splicing (DS) is crucial for understanding physiological processes in cells and organs. In particular, aberrant transcripts are known to be involved in various diseases including c...

    Authors: Karin Zimmermann, Marcel Jentsch, Axel Rasche, Michael Hummel and Ulf Leser
    Citation: BMC Genomics 2015 16:136
    Content type: Research Article Published on:

  13. The marine medaka Oryzias melastigma has been demonstrated as a novel model for marine ecotoxicological studies. However, the lack of genome and transcriptome reference has largely restricted the use of O. melast...

    Authors: Keng Po Lai, Jing-Woei Li, Simon Yuan Wang, Jill Man-Ying Chiu, Anna Tse, Karen Lau, Si Lok, Doris Wai-Ting Au, William Ka-Fai Tse, Chris Kong-Chu Wong, Ting-Fung Chan, Richard Yuen-Chong Kong and Rudolf Shiu-Sun Wu
    Citation: BMC Genomics 2015 16:135
    Content type: Research article Published on:

  15. Next-generation sequencing technology provides a means to study genetic exchange at a higher resolution than was possible using earlier technologies. However, this improvement presents challenges as the alignm...

    Authors: Jahangheer S Shaik, Asis Khan, Stephen M Beverley and L David Sibley
    Citation: BMC Genomics 2015 16:133
    Content type: Software Published on:

  16. Root system architecture is important for water acquisition and nutrient acquisition for all crops. In soybean breeding programs, wild soybean alleles have been used successfully to enhance yield and seed comp...

    Authors: Silvas J Prince, Li Song, Dan Qiu, Joao V Maldonado dos Santos, Chenglin Chai, Trupti Joshi, Gunvant Patil, Babu Valliyodan, Tri D Vuong, Mackensie Murphy, Konstantinos Krampis, Dominic M Tucker, Ruslan Biyashev, Anne E Dorrance, MA Saghai Maroof, Dong Xu…
    Citation: BMC Genomics 2015 16:132
    Content type: Research article Published on:

  17. Guatemala is a multiethnic and multilingual country located in Central America. The main population groups separate ‘Ladinos’ (mixed Native American-African-Spanish), and Native indigenous people of Maya desce...

    Authors: Jens Söchtig, Vanesa Álvarez-Iglesias, Ana Mosquera-Miguel, Miguel Gelabert-Besada, Alberto Gómez-Carballa and Antonio Salas
    Citation: BMC Genomics 2015 16:131
    Content type: Research article Published on:

  18. Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show...

    Authors: Sunjin Moon, Tae-Hun Kim, Kyung-Tai Lee, Woori Kwak, Taeheon Lee, Si-Woo Lee, Myung-Jick Kim, Kyuho Cho, Namshin Kim, Won-Hyong Chung, Samsun Sung, Taesung Park, Seoae Cho, Martien AM Groenen, Rasmus Nielsen, Yuseob Kim…
    Citation: BMC Genomics 2015 16:130
    Content type: Research article Published on:

  19. In recent years, dozens of Arabidopsis and rice CCCH-type zinc finger genes have been functionally studied, many of which confer important traits, such as abiotic and biotic stress tolerance, delayed leaf sene...

    Authors: Shaoxun Yuan, Bin Xu, Jing Zhang, Zheni Xie, Qiang Cheng, Zhimin Yang, Qingsheng Cai and Bingru Huang
    Citation: BMC Genomics 2015 16:129
    Content type: Research article Published on:

  20. Gibberellins are well known for their growth control function in flower, fruit and seed development, and as such, exogenous gibberellic acid (GA) application plays an important role in viticulture. Unfortunate...

    Authors: Chenxia Cheng, Chen Jiao, Stacy D Singer, Min Gao, Xiaozhao Xu, Yiming Zhou, Zhi Li, Zhangjun Fei, Yuejin Wang and Xiping Wang
    Citation: BMC Genomics 2015 16:128
    Content type: Research article Published on:

  21. Pseudoplusia includens single nucleopolyhedrovirus (PsinSNPV-IE) is a baculovirus recently identified in our laboratory, with high pathogenicity to the soybean looper, Chrysodeixis includens (L...

    Authors: Saluana R Craveiro, Peter W Inglis, Roberto C Togawa, Priscila Grynberg, Fernando L Melo, Zilda Maria A Ribeiro, Bergmann M Ribeiro, Sônia N Báo and Maria Elita B Castro
    Citation: BMC Genomics 2015 16:127
    Content type: Research article Published on:

  22. Recent advances in studies of the Schistosoma japonicum genome have opened new avenues for the elucidation of parasite biology and the identification of novel targets for vaccines, drug development and early diag...

    Authors: Nan Hou, Xianyu Piao, Pengfei Cai, Chuang Wu, Shuai Liu, Yan Xiao and Qijun Chen
    Citation: BMC Genomics 2015 16:126
    Content type: Research article Published on:

  23. Wheat (Triticum aestivum) is one of the most important cereal crops, providing food for humans and feed for other animals. However, its productivity is challenged by various biotic and abiotic stresses such as fu...

    Authors: Zhen-Yong Chen, Xiao-Jiang Guo, Zhong-Xu Chen, Wei-Ying Chen, Deng-Cai Liu, You-Liang Zheng, Ya-Xi Liu, Yu-Ming Wei and Ji-Rui Wang
    Citation: BMC Genomics 2015 16:125
    Content type: Research article Published on:

  24. Hepatocellular carcinoma (HCC) is on the rise and the sixth most common cancer worldwide. To combat HCC effectively research is directed towards its early detection and the development of targeted therapies. G...

    Authors: Jürgen Borlak, Prashant Singh and Giuseppe Gazzana
    Citation: BMC Genomics 2015 16:124
    Content type: Research article Published on:

  25. Climate change will lead in the future to an occurrence of heat waves with a higher frequency and duration than observed today, which has the potential to cause severe damage to seedlings of temperate maize ge...

    Authors: Felix P Frey, Claude Urbany, Bruno Hüttel, Richard Reinhardt and Benjamin Stich
    Citation: BMC Genomics 2015 16:123
    Content type: Research article Published on:

  26. Many species of the genus Prevotella are pathogens that cause oral diseases. Prevotella intermedia is known to cause various oral disorders e.g. periodontal disease, periapical periodontitis and noma as well as c...

    Authors: Yunfeng Ruan, Lu Shen, Yan Zou, Zhengnan Qi, Jun Yin, Jie Jiang, Liang Guo, Lin He, Zijiang Chen, Zisheng Tang and Shengying Qin
    Citation: BMC Genomics 2015 16:122
    Content type: Research article Published on:

  27. Several recently developed experimental methods, each an extension of the chromatin conformation capture (3C) assay, have enabled the genome-wide profiling of chromatin contacts between pairs of genomic loci i...

    Authors: Ferhat Ay, Thanh H Vu, Michael J Zeitz, Nelle Varoquaux, Jan E Carette, Jean-Philippe Vert, Andrew R Hoffman and William S Noble
    Citation: BMC Genomics 2015 16:121
    Content type: Research Article Published on:

  28. Plants attenuate their responses to a variety of bacterial and fungal pathogens, leading to higher incidences of pathogen infection at night. However, little is known about the molecular mechanism responsible ...

    Authors: You-Xin Yang, Meng-Meng Wang, Yan-Ling Yin, Eugen Onac, Guo-Fu Zhou, Sheng Peng, Xiao-Jian Xia, Kai Shi, Jing-Quan Yu and Yan-Hong Zhou
    Citation: BMC Genomics 2015 16:120
    Content type: Research article Published on:

  29. microRNAs (miRNAs) are important regulators of translation and have been implicated in the pathogenesis of a number of cardiovascular diseases, including stroke, and suggested as possible prognostic biomarkers...

    Authors: Anne Holt Müller, Gro Klitgaard Povlsen, Claus Heiner Bang-Berthelsen, Lars Schack Kruse, Janne Nielsen, Karin Warfvinge and Lars Edvinsson
    Citation: BMC Genomics 2015 16:119
    Content type: Research article Published on:

  30. Extensive focus is placed on the comparative analyses of consensus genotypes in the study of West Nile virus (WNV) emergence. Few studies account for genetic change in the underlying WNV quasispecies populatio...

    Authors: Cornell Kortenhoeven, Fourie Joubert, Armanda DS Bastos and Celia Abolnik
    Citation: BMC Genomics 2015 16:118
    Content type: Methodology article Published on:

  31. In plants, RNA silencing plays a fundamental role as defence mechanism against viruses. During last years deep-sequencing technology has allowed to analyze the sRNA profile of a large variety of virus-infected...

    Authors: Mari Carmen Herranz, Jose Antonio Navarro, Evelien Sommen and Vicente Pallas
    Citation: BMC Genomics 2015 16:117
    Content type: Research article Published on:

  32. NdgR is an IclR-type transcription factor that regulates leucine biosynthesis and other metabolic pathways in Streptomyces coelicolor. Recent study revealed that NdgR is one of the regulatory targets of SigR, an ...

    Authors: Ji-Nu Kim, Yujin Jeong, Ji Sun Yoo, Jung-Hye Roe, Byung-Kwan Cho and Byung-Gee Kim
    Citation: BMC Genomics 2015 16:116
    Content type: Research article Published on:

  33. The paradigm of resistance evolution to chemotherapeutic agents is that a key coding mutation in a specific gene drives resistance to a particular drug. In the case of resistance to the anti-malarial drug chlo...

    Authors: Geoffrey H Siwo, Asako Tan, Katrina A Button-Simons, Upeka Samarakoon, Lisa A Checkley, Richard S Pinapati and Michael T Ferdig
    Citation: BMC Genomics 2015 16:115
    Content type: Research article Published on:

  34. Social plasticity is a pervasive feature of animal behavior. Animals adjust the expression of their social behavior to the daily changes in social life and to transitions between life-history stages, and this ...

    Authors: José M Simões, Eduardo N Barata, Rayna M Harris, Lauren A O’Connell, Hans A Hofmann and Rui F Oliveira
    Citation: BMC Genomics 2015 16:114
    Content type: Research article Published on:

  35. Recent studies have shown that some pseudogenes are transcribed and contribute to cancer when dysregulated. In particular, pseudogene transcripts can function as competing endogenous RNAs (ceRNAs). The high si...

    Authors: Joshua D Welch, Jeanette Baran-Gale, Charles M Perou, Praveen Sethupathy and Jan F Prins
    Citation: BMC Genomics 2015 16:113
    Content type: Research article Published on:

  36. Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic to...

    Authors: Isabelle Lesur, Grégoire Le Provost, Pascal Bento, Corinne Da Silva, Jean-Charles Leplé, Florent Murat, Saneyoshi Ueno, Jerôme Bartholomé, Céline Lalanne, François Ehrenmann, Céline Noirot, Christian Burban, Valérie Léger, Joelle Amselem, Caroline Belser, Hadi Quesneville…
    Citation: BMC Genomics 2015 16:112
    Content type: Research article Published on:

  37. Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating rice disease worldwide. Xa39 is a resistance (R) gene with a broad-spectrum hypersensitive response (BSHR) to Xoo. Nevertheless, t...

    Authors: Fan Zhang, Li-Yu Huang, Fan Zhang, Jauhar Ali, Casiana Vera Cruz, Da-Long Zhuo, Zheng-Lin Du, Zhi-kang Li and Yong-Li Zhou
    Citation: BMC Genomics 2015 16:111
    Content type: Research article Published on:

  38. Members of Comamonas testosteroni are environmental microorganisms that are usually found in polluted environment samples. They utilize steroids and aromatic compounds but rarely sugars, and show resistance to mu...

    Authors: Lin Liu, Wentao Zhu, Zhan Cao, Biao Xu, Gejiao Wang and Meizhong Luo
    Citation: BMC Genomics 2015 16:110
    Content type: Research article Published on:

  39. Epistasis (synergistic interaction) among SNPs governing gene expression is likely to arise within transcriptional networks. However, the power to detect it is limited by the large number of combinations to be...

    Authors: Darren J Fitzpatrick, Colm J Ryan, Naisha Shah, Derek Greene, Cliona Molony and Denis C Shields
    Citation: BMC Genomics 2015 16:109
    Content type: Research article Published on:

  40. One of the reasons hard red winter wheat cultivar ‘Duster’ (PI 644016) is widely grown in the southern Great Plains is that it confers a consistently high level of resistance to biotype GP of Hessian fly (Hf)....

    Authors: Genqiao Li, Ying Wang, Ming-Shun Chen, Erena Edae, Jesse Poland, Edward Akhunov, Shiaoman Chao, Guihua Bai, Brett F Carver and Liuling Yan
    Citation: BMC Genomics 2015 16:108
    Content type: Research article Published on:

  41. Meiotic recombination has traditionally been explained based on the structural requirement to stabilize homologous chromosome pairs to ensure their proper meiotic segregation. Competing hypotheses seek to expl...

    Authors: Caitlin R Ross, Dominick S DeFelice, Greg J Hunt, Kate E Ihle, Gro V Amdam and Olav Rueppell
    Citation: BMC Genomics 2015 16:107
    Content type: Research article Published on:

  42. Ophiocordyceps sinensis, a worm and fungus combined mixture which Hirsutella sinensis is parasitic on the caterpillar body, has been used as a traditional medicine or healthy food in China for ...

    Authors: Zhi-Qiang Liu, Shan Lin, Peter James Baker, Ling-Fang Wu, Xiao-Rui Wang, Hui Wu, Feng Xu, Hong-Yan Wang, Mgavi Elombe Brathwaite and Yu-Guo Zheng
    Citation: BMC Genomics 2015 16:106
    Content type: Research article Published on:

  43. Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global...

    Authors: Judith Burstin, Pauline Salloignon, Marianne Chabert-Martinello, Jean-Bernard Magnin-Robert, Mathieu Siol, Françoise Jacquin, Aurélie Chauveau, Caroline Pont, Grégoire Aubert, Catherine Delaitre, Caroline Truntzer and Gérard Duc
    Citation: BMC Genomics 2015 16:105
    Content type: Research Article Published on:

  46. Epigenetic modifications play important roles in the regulation of plant development. DNA methylation is an important epigenetic modification that dynamically regulates gene expression during developmental pro...

    Authors: Jihong Hu, Xiaojun Chen, Hongyuan Zhang and Yi Ding
    Citation: BMC Genomics 2015 16:102
    Content type: Research article Published on:

  47. The anthers and pollen grains are critical for male fertility and hybrid rice breeding. The development of rice mature anther and pollen consists of multiple continuous stages. However, molecular mechanisms re...

    Authors: Sheng Ling, Caisheng Chen, Yang Wang, Xiaocong Sun, Zhanhua Lu, Yidan Ouyang and Jialing Yao
    Citation: BMC Genomics 2015 16:101
    Content type: Research article Published on:

  48. Small RNAs include different classes essential for endogenous gene regulation and cellular defence against genomic parasites. However, a comprehensive analysis of the small RNA pathways in the germline of the ...

    Authors: Leandro Castellano, Ermanno Rizzi, Jonathan Krell, Manlio Di Cristina, Roberto Galizi, Ayako Mori, Janis Tam, Gianluca De Bellis, Justin Stebbing, Andrea Crisanti and Tony Nolan
    Citation: BMC Genomics 2015 16:100
    Content type: Research article Published on:

  50. Interferons (IFN) are cytokines secreted by vertebrate cells involved in activation of signaling pathways that direct the synthesis of antiviral genes. To gain a global understanding of antiviral genes induced...

    Authors: Cheng Xu, Øystein Evensen and Hetron Mweemba Munang’andu
    Citation: BMC Genomics 2015 16:96
    Content type: Research article Published on:

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BMC Genomics

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