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  1. Rice blast caused by the fungus Magnaporthe oryzae is an important disease in virtually every rice growing region of the world, which leads to significant annual decreases of grain quality and yield. To prevent d...

    Authors: Chenxi Chen, Bi Lian, Jinnan Hu, Huanchen Zhai, Xingxing Wang, RC Venu, Erming Liu, Zhilong Wang, Meilian Chen, Baohua Wang, Guo-Liang Wang, Zonghua Wang and Thomas K Mitchell
    Citation: BMC Genomics 2013 14:887
    Content type: Research article Published on:

  2. Microsatellites are ubiquitous in genomes of various organisms. With the realization that they play roles in developmental and physiological processes, rather than exist as ‘junk’ DNA, microsatellites are rece...

    Authors: Zhimin Gao, Jie Wu, Zheng’an Liu, Liangsheng Wang, Hongxu Ren and Qingyan Shu
    Citation: BMC Genomics 2013 14:886
    Content type: Research article Published on:

  3. Through the diversity of cytokinin regulated processes, this phytohormone has a profound impact on plant growth and development. Cytokinin signaling is involved in the control of apical and lateral meristem ac...

    Authors: Juha Immanen, Kaisa Nieminen, Héctor Duchens Silva, Fernanda Rodríguez Rojas, Lee A Meisel, Herman Silva, Victor A Albert, Torgeir R Hvidsten and Ykä Helariutta
    Citation: BMC Genomics 2013 14:885
    Content type: Research article Published on:

  4. Five-needle pines are important forest species that have been devastated by white pine blister rust (WPBR, caused by Cronartium ribicola) across North America. Currently little transcriptomic and genomic data are...

    Authors: Jun-Jun Liu, Rona N Sturrock and Ross Benton
    Citation: BMC Genomics 2013 14:884
    Content type: Research article Published on:

  5. Rice false smut caused by Villosiclava virens is a devastating fungal disease that spreads in major rice-growing regions throughout the world. However, the genomic information for this fungal pathogen is limited ...

    Authors: Xiaoming Wang, Qingli Liu, Hao Wang, Chao-Xi Luo, Gejiao Wang and Meizhong Luo
    Citation: BMC Genomics 2013 14:883
    Content type: Research article Published on:

  7. A population reference database of complete human mitochondrial genome (mtGenome) sequences is needed to enable the use of mitochondrial DNA (mtDNA) coding region data in forensic casework applications. Howeve...

    Authors: Elizabeth A Lyons, Melissa K Scheible, Kimberly Sturk-Andreaggi, Jodi A Irwin and Rebecca S Just
    Citation: BMC Genomics 2013 14:881
    Content type: Methodology article Published on:

  9. Despite the advances in our understanding of aging-associated behavioral decline, relatively little is known about how aging affects neural circuits that regulate specific behaviors, particularly the expressio...

    Authors: Beena M Kadakkuzha, Komolitdin Akhmedov, Tom R Capo, Anthony C Carvalloza, Mohammad Fallahi and Sathyanarayanan V Puthanveettil
    Citation: BMC Genomics 2013 14:880
    Content type: Research article Published on:

  10. Mycobacterium abscessus is a rapidly growing mycobacterium that is often associated with human infections. The taxonomy of this species has undergone several revisions and is still being debated. In this study, w...

    Authors: Joon Liang Tan, Tsung Fei Khang, Yun Fong Ngeow and Siew Woh Choo
    Citation: BMC Genomics 2013 14:879
    Content type: Methodology article Published on:

  11. Data normalization is a key step in gene expression analysis by qPCR. Endogenous control genes are used to estimate variations and experimental errors occurring during sample preparation and expression measure...

    Authors: Mauricio González-Agüero, Miguel García-Rojas, Alex Di Genova, José Correa, Alejandro Maass, Ariel Orellana and Patricio Hinrichsen
    Citation: BMC Genomics 2013 14:878
    Content type: Methodology article Published on:

  12. Maize is an increasingly important food crop in southeast Asia. The elucidation of its genetic architecture, accomplished by exploring quantitative trait loci and useful alleles in various lines across numerou...

    Authors: Nepolean Thirunavukkarasu, Firoz Hossain, Kaliyugam Shiriga, Swati Mittal, Kanika Arora, Abhishek Rathore, Sweta Mohan, Trushar Shah, Rinku Sharma, Pottekatt Mohanlal Namratha, Amitha SV Mithra, Trilochan Mohapatra and Hari Shankar Gupta
    Citation: BMC Genomics 2013 14:877
    Content type: Research article Published on:

  13. Natural selection has molded evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern catt...

    Authors: Laercio R Porto-Neto, Tad S Sonstegard, George E Liu, Derek M Bickhart, Marcos VB Da Silva, Marco A Machado, Yuri T Utsunomiya, Jose F Garcia, Cedric Gondro and Curtis P Van Tassell
    Citation: BMC Genomics 2013 14:876
    Content type: Research article Published on:

  14. Psorophora mosquitoes are exclusively found in the Americas and have been associated with transmission of encephalitis and West Nile fever viruses, among other arboviruses. Mosquito salivary glands represent the ...

    Authors: Andrezza C Chagas, Eric Calvo, Claudia M Rios-Velásquez, Felipe AC Pessoa, Jansen F Medeiros and José MC Ribeiro
    Citation: BMC Genomics 2013 14:875
    Content type: Research article Published on:

  15. The Hunt bumble bee (Bombus huntii Greene, Hymenoptera: Apidae) is a holometabolous, social insect important as a pollinator in natural and agricultural ecosystems in western North America. Bumble bees spend a si...

    Authors: Junhuan Xu, James P Strange, Dennis L Welker and Rosalind R James
    Citation: BMC Genomics 2013 14:874
    Content type: Research article Published on:

  16. Bacteroides thetaiotaomicron, a predominant member of the human gut microbiota, is characterized by its ability to utilize a wide variety of polysaccharides using the extensive saccharolytic machinery that is con...

    Authors: Dmitry A Ravcheev, Adam Godzik, Andrei L Osterman and Dmitry A Rodionov
    Citation: BMC Genomics 2013 14:873
    Content type: Research article Published on:

  17. Studies of normal human mammary gland development and function have mostly relied on cell culture, limited surgical specimens, and rodent models. Although RNA extracted from human milk has been used to assay t...

    Authors: Danielle G Lemay, Russell C Hovey, Stella R Hartono, Katie Hinde, Jennifer T Smilowitz, Frank Ventimiglia, Kimberli A Schmidt, Joyce WS Lee, Alma Islas-Trejo, Pedro Ivo Silva, Ian Korf, Juan F Medrano, Peter A Barry and J Bruce German
    Citation: BMC Genomics 2013 14:872
    Content type: Research article Published on:

  18. Influenza A H5N1 has killed millions of birds and raises serious public health concern because of its potential to spread to humans and cause a global pandemic. While the early focus was in Asia, recent eviden...

    Authors: Matthew Scotch, Changjiang Mei, Yilma J Makonnen, Julio Pinto, AbdelHakim Ali, Sally Vegso, Michael Kane, Indra Neil Sarkar and Peter Rabinowitz
    Citation: BMC Genomics 2013 14:871
    Content type: Research article Published on:

  19. Lichens are symbiotic organisms with a fungal and an algal or a cyanobacterial partner. Lichens inhabit some of the harshest climates on earth and most lichen species are desiccation-tolerant. Lichen desiccati...

    Authors: Sini Junttila, Asta Laiho, Attila Gyenesei and Stephen Rudd
    Citation: BMC Genomics 2013 14:870
    Content type: Research article Published on:

  20. Although transposable element (TE) derived DNA accounts for more than half of mammalian genomes and initiates a significant proportion of RNA transcripts, high throughput methods are rarely leveraged specifica...

    Authors: Veena P Gnanakkan, Andrew E Jaffe, Lixin Dai, Jie Fu, Sarah J Wheelan, Hyam I Levitsky, Jef D Boeke and Kathleen H Burns
    Citation: BMC Genomics 2013 14:869
    Content type: Methodology article Published on:

  21. Alloplasmic lines provide a unique tool to study nuclear-cytoplasmic interactions. Three alloplasmic lines, with nuclear genomes from Triticum aestivum and harboring cytoplasm from Aegilops uniaristata, Aegilops ...

    Authors: Cristina Crosatti, Lydia Quansah, Caterina Maré, Lorenzo Giusti, Enrica Roncaglia, Sergio G Atienza, Luigi Cattivelli and Aaron Fait
    Citation: BMC Genomics 2013 14:868
    Content type: Research article Published on:

  23. In fleshy fruit, abscission of fully ripe fruit is a process intimately linked to the ripening process. In many fruit-tree species, such as olive (Olea europaea L. cv. Picual), there is a coupling of the full rip...

    Authors: Ruben Parra, Miguel A Paredes, Isabel M Sanchez-Calle and Maria C Gomez-Jimenez
    Citation: BMC Genomics 2013 14:866
    Content type: Research article Published on:

  24. Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) that associate with clinical phenotypes, but these SNPs usually explain just a small part of the herita...

    Authors: Harish Dharuri, Peter Henneman, Ayse Demirkan, Jan Bert van Klinken, Dennis Owen Mook-Kanamori, Rui Wang-Sattler, Christian Gieger, Jerzy Adamski, Kristina Hettne, Marco Roos, Karsten Suhre, Cornelia M Van Duijn, Ko Willems van Dijk and Peter AC 't Hoen
    Citation: BMC Genomics 2013 14:865
    Content type: Research article Published on:

  25. The Miscanthus genus of perennial C4 grasses contains promising biofuel crops for temperate climates. However, few genomic resources exist for Miscanthus, which limits understanding of its interesting biology and...

    Authors: Adam Barling, Kankshita Swaminathan, Therese Mitros, Brandon T James, Juliette Morris, Ornella Ngamboma, Megan C Hall, Jessica Kirkpatrick, Magdy Alabady, Ashley K Spence, Matthew E Hudson, Daniel S Rokhsar and Stephen P Moose
    Citation: BMC Genomics 2013 14:864
    Content type: Research article Published on:

  26. Somatic mosaicism of copy number variants (CNVs) in human body organs and de novo CNV event in monozygotic twins suggest that de novo CNVs can occur during mitotic recombination. These de novo CNV events are i...

    Authors: Seung-Hyun Jung, Seon-Hee Yim, Hyun Ju Oh, Jung Eun Park, Min Jung Kim, Geon A Kim, Tae-Min Kim, Jin-Soo Kim, Byeong Chun Lee and Yeun-Jun Chung
    Citation: BMC Genomics 2013 14:863
    Content type: Research article Published on:

  27. Development of a cancerous cell takes place when it ceases to respond to growth-inhibiting signals and multiplies uncontrollably and can detach and move to other parts of the body; the process called as metast...

    Authors: Chetna Tyagi, Sonam Grover, Jaspreet Kaur Dhanjal, Sukriti Goyal, Manisha Goyal and Abhinav Grover
    Citation: BMC Genomics 2013 14(Suppl 8):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 8

  28. Over the last decade, genome-wide association studies (GWAS) have discovered many risk associated single nucleotide polymorphisms (SNPs) of prostate cancer (PCa). However, the majority of the associated PCa SN...

    Authors: Junfeng Jiang, Weirong Cui, Wanwipa Vongsangnak, Guang Hu and Bairong Shen
    Citation: BMC Genomics 2013 14(Suppl 8):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 8

  29. Genome-wide association studies (GWAS) have identified hundreds of genetic variants associated with complex human diseases, clinical conditions and traits. Genetic mapping of expression quantitative trait loci...

    Authors: Arindom Chakraborty, Guanglong Jiang, Malaz Boustani, Yunlong Liu, Todd Skaar and Lang Li
    Citation: BMC Genomics 2013 14(Suppl 8):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 8

  30. Selecting genes and pathways indicative of disease is a central problem in computational biology. This problem is especially challenging when parsing multi-dimensional genomic data. A number of tools, such as L1-...

    Authors: Wen Zhang, Ying-wooi Wan, Genevera I Allen, Kaifang Pang, Matthew L Anderson and Zhandong Liu
    Citation: BMC Genomics 2013 14(Suppl 8):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 8

  31. The gene Polymorphic derived intron-containing, known as Pldi, is a long non-coding RNA (lncRNA) first discovered in mouse. Although parts of its sequence were reported to be conserved in rat and human, it can on...

    Authors: Yulin Dai, Shengdi Li, Xiao Dong, Han Sun, Chao Li, Zhi Liu, Beili Ying, Guohui Ding and Yixue Li
    Citation: BMC Genomics 2013 14(Suppl 8):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 8

  32. Tandem mass spectrometry (MS/MS) technology has been applied to identify proteins, as an ultimate approach to confirm the original genome annotation. To be able to identify gene fusion proteins, a special data...

    Authors: Han Sun, Xiaobin Xing, Jing Li, Fengli Zhou, Yunqin Chen, Ying He, Wei Li, Guangwu Wei, Xiao Chang, Jia Jia, Yixue Li and Lu Xie
    Citation: BMC Genomics 2013 14(Suppl 8):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 8

  33. Advances in next-generation sequencing (NGS) technology has provided us with an opportunity to analyze and evaluate the rich microbial communities present in all natural environments. The shorter reads obtaine...

    Authors: Satish M Srinivasan and Chittibabu Guda
    Citation: BMC Genomics 2013 14(Suppl 8):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 8

  34. Many computational programs have been developed to identify enriched regions for a single biological ChIP-seq sample. Given that many biological questions are often asked to compare the difference between two ...

    Authors: Bin Liu, Jimmy Yi, Aishwarya SV, Xun Lan, Yilin Ma, Tim HM Huang, Gustavo Leone and Victor X Jin
    Citation: BMC Genomics 2013 14(Suppl 8):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 8

  36. The 2013 International Conference on Intelligent Biology and Medicine (ICIBM 2013) was held on August 11-13, 2013 in Nashville, Tennessee, USA. The conference included six scientific sessions, two tutorial ses...

    Authors: Bing Zhang, Yufei Huang, Jason E McDermott, Rebecca H Posey, Hua Xu and Zhongming Zhao
    Citation: BMC Genomics 2013 14(Suppl 8):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 8

  37. A number of spider species within the family Theridiidae exhibit a dramatic abdominal (opisthosomal) color polymorphism. The polymorphism is inherited in a broadly Mendelian fashion and in some species consist...

    Authors: Peter JP Croucher, Michael S Brewer, Christopher J Winchell, Geoff S Oxford and Rosemary G Gillespie
    Citation: BMC Genomics 2013 14:862
    Content type: Research article Published on:

  38. Group B Sox domain transcription factors play conserved roles in the specification and development of the nervous system in higher metazoans. However, we know comparatively little about how these transcription...

    Authors: Jelena Aleksic, Enrico Ferrero, Bettina Fischer, Shih Pei Shen and Steven Russell
    Citation: BMC Genomics 2013 14:861
    Content type: Research article Published on:

  39. In genomic prediction, an important measure of accuracy is the correlation between the predicted and the true breeding values. Direct computation of this quantity for real datasets is not possible, because the...

    Authors: Sidi Boubacar Ould Estaghvirou, Joseph O Ogutu, Torben Schulz-Streeck, Carsten Knaak, Milena Ouzunova, Andres Gordillo and Hans-Peter Piepho
    Citation: BMC Genomics 2013 14:860
    Content type: Research article Published on:

  40. Ralstonia solanacearum is a soil-borne beta-proteobacterium that causes bacterial wilt disease in many food crops and is a major problem for agriculture in intertropical regions. R. solanacearum is a heterogeneou...

    Authors: Nemo Peeters, Sébastien Carrère, Maria Anisimova, Laure Plener, Anne-Claire Cazalé and Stephane Genin
    Citation: BMC Genomics 2013 14:859
    Content type: Research article Published on:

  41. Septoria tritici blotch is an important leaf disease of European winter wheat. In our survey, we analyzed Septoria tritici blotch resistance in field trials with a large population of 1,055 elite hybrids and t...

    Authors: Thomas Miedaner, Yusheng Zhao, Manje Gowda, C Friedrich H Longin, Viktor Korzun, Erhard Ebmeyer, Ebrahim Kazman and Jochen C Reif
    Citation: BMC Genomics 2013 14:858
    Content type: Research article Published on:

  42. Isatis indigotica is a widely used herb for the clinical treatment of colds, fever, and influenza in Traditional Chinese Medicine (TCM). Various structural classes of compounds have been identified as effective i...

    Authors: Junfeng Chen, Xin Dong, Qing Li, Xun Zhou, Shouhong Gao, Ruibing Chen, Lianna Sun, Lei Zhang and Wansheng Chen
    Citation: BMC Genomics 2013 14:857
    Content type: Research article Published on:

  43. Target enrichment and resequencing is a widely used approach for identification of cancer genes and genetic variants associated with diseases. Although cost effective compared to whole genome sequencing, analy...

    Authors: Eva C Berglund, Carl Mårten Lindqvist, Shahina Hayat, Elin Övernäs, Niklas Henriksson, Jessica Nordlund, Per Wahlberg, Erik Forestier, Gudmar Lönnerholm and Ann-Christine Syvänen
    Citation: BMC Genomics 2013 14:856
    Content type: Methodology article Published on:

  44. Recent studies have demonstrated an unexpected complexity of transcription in eukaryotes. The majority of the genome is transcribed and only a little fraction of these transcripts is annotated as protein codin...

    Authors: Claudia Calabrese, Marina Mangiulli, Caterina Manzari, Anna Maria Paluscio, Mariano Francesco Caratozzolo, Flaviana Marzano, Ivana Kurelac, Anna Maria D’Erchia, Domenica D’Elia, Flavio Licciulli, Sabino Liuni, Ernesto Picardi, Marcella Attimonelli, Giuseppe Gasparre, Anna Maria Porcelli, Graziano Pesole…
    Citation: BMC Genomics 2013 14:855
    Content type: Methodology article Published on:

  45. Recently, questions have been raised regarding the ability of animal models to recapitulate human disease at the molecular level. It has also been demonstrated that cellular kinases, individually or as a colle...

    Authors: Brett Trost, Jason Kindrachuk, Erin Scruten, Philip Griebel, Anthony Kusalik and Scott Napper
    Citation: BMC Genomics 2013 14:854
    Content type: Research article Published on:

  46. Lysosomes play important roles in multiple aspects of physiology, but the problem of how the transcription of lysosomal genes is coordinated remains incompletely understood. The goal of this study was to illum...

    Authors: Louise M Brignull, Zsolt Czimmerer, Hafida Saidi, Bence Daniel, Izabel Villela, Nathan W Bartlett, Sebastian L Johnston, Lisiane B Meira, Laszlo Nagy and Axel Nohturfft
    Citation: BMC Genomics 2013 14:853
    Content type: Research article Published on:

  47. Cotton Verticillium wilt is a serious soil-borne vascular disease that causes great economic loss each year. However, due to the lack of resistant varieties of upland cotton, the molecular mechanisms of resist...

    Authors: Quan Sun, Huaizhong Jiang, Xiaoyan Zhu, Weina Wang, Xiaohong He, Yuzhen Shi, Youlu Yuan, Xiongming Du and Yingfan Cai
    Citation: BMC Genomics 2013 14:852
    Content type: Research article Published on:

  48. Cavendish, the most widely grown banana cultivar, is relatively resistant to Race 1 of Fusarium oxysporum f. sp. cubense (Foc1) which caused widespread Panama disease during the first half of the 20th century but...

    Authors: Chunqiang Li, Jiaofang Shao, Yejun Wang, Wenbin Li, Dianjing Guo, Bin Yan, Yiji Xia and Ming Peng
    Citation: BMC Genomics 2013 14:851
    Content type: Research article Published on:

  49. Wood-feeding insects often work in collaboration with microbial symbionts to degrade lignin biopolymers and release glucose and other fermentable sugars from recalcitrant plant cell wall carbohydrates, includi...

    Authors: Erin D Scully, Kelli Hoover, John E Carlson, Ming Tien and Scott M Geib
    Citation: BMC Genomics 2013 14:850
    Content type: Research article Published on:

  50. Small non-coding RNAs (sRNA) are emerging as major components of the cell’s regulatory network, several possessing their own regulons. A few sRNAs have been reported as being involved in general or toxic-metab...

    Authors: Keerthi P Venkataramanan, Shawn W Jones, Kevin P McCormick, Sridhara G Kunjeti, Matthew T Ralston, Blake C Meyers and Eleftherios T Papoutsakis
    Citation: BMC Genomics 2013 14:849
    Content type: Research article Published on:

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BMC Genomics

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