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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  14. 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

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. Serum concentrations of total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and triglycerides (TG) are highly heritable traits that are used clinic...

    Authors: Congying Chen, Bin Yang, Zhijun Zeng, Hui Yang, Chenlong Liu, Jun Ren and Lusheng Huang
    Citation: BMC Genomics 2013 14:848
    Content type: Research article Published on:

  30. The filamentous fungus Aspergillus nidulans has been a tractable model organism for cell biology and genetics for over 60 years. It is among a large number of Aspergilli whose genomes have been sequenced since 20...

    Authors: Christopher Sibthorp, Huihai Wu, Gwendolyn Cowley, Prudence W H Wong, Paulius Palaima, Igor Y Morozov, Gareth D Weedall and Mark X Caddick
    Citation: BMC Genomics 2013 14:847
    Content type: Research article Published on:

  31. Orb-web and cob-web weaving spiders spin dragline silk fibers that are among the strongest materials known. Draglines are primarily composed of MaSp1 and MaSp2, two spidroins (spider fibrous proteins) expresse...

    Authors: Amanda Kelly Lane, Cheryl Y Hayashi, Gregg B Whitworth and Nadia A Ayoub
    Citation: BMC Genomics 2013 14:846
    Content type: Research article Published on:

  32. Porcine fatty acid composition is a key factor for quality and nutritive value of pork. Several QTLs for fatty acid composition have been reported in diverse fat tissues. The results obtained so far seem to po...

    Authors: María Muñoz, M Carmen Rodríguez, Estefânia Alves, Josep María Folch, Noelia Ibañez-Escriche, Luis Silió and Ana Isabel Fernández
    Citation: BMC Genomics 2013 14:845
    Content type: Research article Published on:

  33. Glucocorticoids (GCs) are natural stress induced steroid hormones causing cell cycle arrest and cell death in lymphoid tissues. Therefore they are the central component in the treatment of lymphoid malignancie...

    Authors: Tatsiana Aneichyk, Daniel Bindreither, Christine Mantinger, Daniela Grazio, Katrin Goetsch, Reinhard Kofler and Johannes Rainer
    Citation: BMC Genomics 2013 14:844
    Content type: Research article Published on:

  34. In pigs, adipose tissue is one of the principal organs involved in the regulation of lipid metabolism. It is particularly involved in the overall fatty acid synthesis with consequences in other lipid-target or...

    Authors: Jordi Corominas, Yuliaxis Ramayo-Caldas, Anna Puig-Oliveras, Jordi Estellé, Anna Castelló, Estefania Alves, Ramona N Pena, Maria Ballester and Josep M Folch
    Citation: BMC Genomics 2013 14:843
    Content type: Research article Published on:

  36. Abscisic acid (ABA) can regulate the expressions of many stress-responsive genes in plants. However, in defense responses to pathogens, mounting evidence suggests that ABA plays variable roles. Little informat...

    Authors: Yan Wang, Xiang Tao, Xiao-Mei Tang, Liang Xiao, Jiao-long Sun, Xue-Feng Yan, Dan Li, Hong-Yuan Deng and Xin-Rong Ma
    Citation: BMC Genomics 2013 14:841
    Content type: Research article Published on:

  37. Brassica seeds are important as basic units of plant growth and sources of vegetable oil. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporal...

    Authors: Ram Kumar Basnet, Natalia Moreno-Pachon, Ke Lin, Johan Bucher, Richard G F Visser, Chris Maliepaard and Guusje Bonnema
    Citation: BMC Genomics 2013 14:840
    Content type: Research article Published on:

  38. Dynamics of polyadenylation vs. deadenylation determine the fate of several developmentally regulated genes. Decay of a subset of maternal mRNAs and new transcription define the maternal-to-zygotic transition,...

    Authors: Sarita S Paranjpe, Ulrike G Jacobi, Simon J van Heeringen and Gert Jan C Veenstra
    Citation: BMC Genomics 2013 14:762
    Content type: Research article Published on:

  39. Basic leucine zipper (bZIP) transcription factors are present exclusively in eukaryotes and constitute one of the largest and most diverse transcription factor families. The proteins are responsible for centra...

    Authors: Wenwu Ye, Yang Wang, Suomeng Dong, Brett M Tyler and Yuanchao Wang
    Citation: BMC Genomics 2013 14:839
    Content type: Research article Published on:

  40. Acetic acid is mostly known as a toxic by-product of alcoholic fermentation carried out by Saccharomyces cerevisiae, which it frequently impairs. The more recent finding that acetic acid triggers apoptotic progra...

    Authors: Marlene Sousa, Ana Marta Duarte, Tânia R Fernandes, Susana R Chaves, Andreia Pacheco, Cecília Leão, Manuela Côrte-Real and Maria João Sousa
    Citation: BMC Genomics 2013 14:838
    Content type: Research article Published on:

  41. Hansenula polymorpha DL1 is a methylotrophic yeast, widely used in fundamental studies of methanol metabolism, peroxisome biogenesis and function, and also as a microbial cell factory for production of recombinan...

    Authors: Nikolai V Ravin, Michael A Eldarov, Vitaly V Kadnikov, Alexey V Beletsky, Jessica Schneider, Eugenia S Mardanova, Elena M Smekalova, Maria I Zvereva, Olga A Dontsova, Andrey V Mardanov and Konstantin G Skryabin
    Citation: BMC Genomics 2013 14:837
    Content type: Research article Published on:

  42. Radish (Raphanus sativus L.), is an important root vegetable crop worldwide. Glucosinolates in the fleshy taproot significantly affect the flavor and nutritional quality of radish. However, little is known about ...

    Authors: Yan Wang, Yan Pan, Zhe Liu, Xianwen Zhu, Lulu Zhai, Liang Xu, Rugang Yu, Yiqin Gong and Liwang Liu
    Citation: BMC Genomics 2013 14:836
    Content type: Research article Published on:

  43. The tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world. It was domesticated in Latin America and Italy and Spain are considered secondary centers of diversification. This food crop ha...

    Authors: Giandomenico Corrado, Pietro Piffanelli, Martina Caramante, Mariangela Coppola and Rosa Rao
    Citation: BMC Genomics 2013 14:835
    Content type: Research article Published on:

  44. Chromatin immunoprecipitation combined with massive parallel sequencing (ChIP-seq) is widely used to study protein-chromatin interactions or chromatin modifications at genome-wide level. Sequence reads that ac...

    Authors: Marco-Antonio Mendoza-Parra, Malgorzata Nowicka, Wouter Van Gool and Hinrich Gronemeyer
    Citation: BMC Genomics 2013 14:834
    Content type: Software Published on:

  45. Cytochrome P450 2S1 (CYP2S1) is an orphan P450 with an unknown biological function. Data from our laboratory and others suggest that CYP2S1 may have an important physiological role in modulating the synthesis ...

    Authors: Thushara W Madanayake, Ingrid E Lindquist, Nicholas P Devitt, Joann Mudge and Aaron M Rowland
    Citation: BMC Genomics 2013 14:833
    Content type: Research article Published on:

  46. Alzheimer’s disease affects more than 35 million people worldwide but there is no known cure. Age is the strongest risk factor for Alzheimer’s disease but it is not clear how age-related changes impact the dis...

    Authors: Harriet M Jackson, Ileana Soto, Leah C Graham, Gregory W Carter and Gareth R Howell
    Citation: BMC Genomics 2013 14:831
    Content type: Research article Published on:

  47. Cellular differentiation is characterized by the acquisition of specialized structures and functions, cell cycle exit, and global attenuation of the DNA damage response. It is largely unknown how these diverse...

    Authors: Xiangwei Wang, Jeong-Hyeon Choi, Jane Ding, Liqun Yang, Lambert C Ngoka, Eun J Lee, Yunhong Zha, Ling Mao, Bilian Jin, Mingqiang Ren, John Cowell, Shuang Huang, Huidong Shi, Hongjuan Cui and Han-Fei Ding
    Citation: BMC Genomics 2013 14:830
    Content type: Research article Published on:

  48. Xanthomonas fragariae (Xf) is a bacterial strawberry pathogen and an A2 quarantine organism on strawberry planting stock in the EU. It is taxonomically and metabolically distinct within the genus Xanthomonas, and...

    Authors: Joachim Vandroemme, Bart Cottyn, Steve Baeyen, Paul De Vos and Martine Maes
    Citation: BMC Genomics 2013 14:829
    Content type: Research article Published on:

  49. Gene regulatory processes are largely resulting from binding of transcription factors to specific genomic targets. Leucine-responsive Regulatory Protein (Lrp) is a prevalent transcription factor family in prok...

    Authors: Trong Nguyen-Duc, Liesbeth van Oeffelen, Ningning Song, Gholamreza Hassanzadeh-Ghassabeh, Serge Muyldermans, Daniel Charlier and Eveline Peeters
    Citation: BMC Genomics 2013 14:828
    Content type: Research article Published on:

  50. Anthurium andraeanum is one of the most popular tropical flowers. In temperate and cold zones, a much greater risk of cold stress occurs in the supply of Anthurium plants. Unlike the freeze-tolerant model plants,...

    Authors: Dan-Qing Tian, Xiao-Yun Pan, Yong-Ming Yu, Wei-Yong Wang, Fei Zhang, Ya-Ying Ge, Xiao-Lan Shen, Fu-Quan Shen and Xiao-Jing Liu
    Citation: BMC Genomics 2013 14:827
    Content type: Research article Published on:

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BMC Genomics

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