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  1. There is interest in improving the flavor of commercial strawberry (Fragaria × ananassa) varieties. Fruit flavor is shaped by combinations of sugars, acids and volatile compounds. Many efforts seek to use genomic...

    Authors: Alan H Chambers, Jeremy Pillet, Anne Plotto, Jinhe Bai, Vance M Whitaker and Kevin M Folta
    Citation: BMC Genomics 2014 15:217
    Content type: Research article Published on:

  2. Understanding the basis for volatile organic compound (VOC) biosynthesis and regulation is of great importance for the genetic improvement of fruit flavor. Lactones constitute an essential group of fatty acid-...

    Authors: José F Sánchez-Sevilla, Eduardo Cruz-Rus, Victoriano Valpuesta, Miguel A Botella and Iraida Amaya
    Citation: BMC Genomics 2014 15:218
    Content type: Research article Published on:

  3. The zygomycete fungi like Rhizomucor miehei have been extensively exploited for the production of various enzymes. As a thermophilic fungus, R. miehei is capable of growing at temperatures that approach the upper...

    Authors: Peng Zhou, Guoqiang Zhang, Shangwu Chen, Zhengqiang Jiang, Yanbin Tang, Bernard Henrissat, Qiaojuan Yan, Shaoqing Yang, Chin-Fu Chen, Bing Zhang and Zhenglin Du
    Citation: BMC Genomics 2014 15:294
    Content type: Research article Published on:

  5. WUSCHEL (WUS)-related homeobox (WOX) protein family members play important roles in the maintenance and proliferation of the stem cell niche in the shoot apical meristem (SAM), root apical meristem (RAM), and ...

    Authors: Bobin Liu, Lin Wang, Jin Zhang, Jianbo Li, Huanquan Zheng, Jun Chen and Mengzhu Lu
    Citation: BMC Genomics 2014 15:296
    Content type: Research article Published on:

  6. Sprague and Tatum (1942) introduced the concepts of general combining ability (GCA) and specific combining ability (SCA) to evaluate the breeding parents and F1 hybrid performance, respectively. Since then, th...

    Authors: Gaoyuan Song, Zhibin Guo, Zhenwei Liu, Xuefeng Qu, Daiming Jiang, Wei Wang, Yingguo Zhu and Daichang Yang
    Citation: BMC Genomics 2014 15:297
    Content type: Research article Published on:

  8. Variation in seed oil composition and content among soybean varieties is largely attributed to differences in transcript sequences and/or transcript accumulation of oil production related genes in seeds. Disco...

    Authors: Wolfgang Goettel, Eric Xia, Robert Upchurch, Ming-Li Wang, Pengyin Chen and Yong-Qiang Charles An
    Citation: BMC Genomics 2014 15:299
    Content type: Research article Published on:

  11. The soil worm Enchytraeus crypticus (Oligochaeta) is an ecotoxicology model species that, until now, was without genome or transcriptome sequence information. The present research aims at studying the transcripto...

    Authors: Marta P Castro-Ferreira, Tjalf E de Boer, John K Colbourne, Riet Vooijs, Cornelis AM van Gestel, Nico M van Straalen, Amadeu MVM Soares, Mónica JB Amorim and Dick Roelofs
    Citation: BMC Genomics 2014 15:302
    Content type: Research article Published on:

  12. The endosteum of the bone marrow provides a specialized hypoxic niche that may serve to preserve the integrity, pluripotency, longevity and stemness of resident mesenchymal stem cells (MSCs). To explore the mo...

    Authors: Xinyang Hu, Rongrong Wu, Lina A Shehadeh, Qing Zhou, Cizhong Jiang, Xin Huang, Ling Zhang, Feng Gao, Xianbao Liu, Hong Yu, Keith A Webster and Jian’an Wang
    Citation: BMC Genomics 2014 15:303
    Content type: Research article Published on:

  13. The progress in mapping RNA-protein and RNA-RNA interactions at the transcriptome-wide level paves the way to decipher possible combinatorial patterns embedded in post-transcriptional regulation of gene expres...

    Authors: Gianluca Corrado, Toma Tebaldi, Giulio Bertamini, Fabrizio Costa, Alessandro Quattrone, Gabriella Viero and Andrea Passerini
    Citation: BMC Genomics 2014 15:304
    Content type: Methodology article Published on:

  14. With its plumage color dimorphism and unique history in North America, including a recent population expansion and an epizootic of Mycoplasma gallisepticum (MG), the house finch (Haemorhous mexicanus) is a model ...

    Authors: Qu Zhang, Geoffrey E Hill, Scott V Edwards and Niclas Backström
    Citation: BMC Genomics 2014 15:305
    Content type: Research article Published on:

  15. Phenotypic plasticity in defensive traits occurs in many species when facing heterogeneous predator regimes. The waterflea Daphnia is well-known for showing a variety of these so called inducible defences. Howeve...

    Authors: Kathrin A Otte, Thomas Fröhlich, Georg J Arnold and Christian Laforsch
    Citation: BMC Genomics 2014 15:306
    Content type: Research article Published on:

  16. A large number of single nucleotide polymorphisms (SNPs) have been identified in common carp (Cyprinus carpio) but, as yet, no high-throughput genotyping platform is available for this species. C. carpio is an im...

    Authors: Jian Xu, Zixia Zhao, Xiaofeng Zhang, Xianhu Zheng, Jiongtang Li, Yanliang Jiang, Youyi Kuang, Yan Zhang, Jianxin Feng, Chuangju Li, Juhua Yu, Qiang Li, Yuanyuan Zhu, Yuanyuan Liu, Peng Xu and Xiaowen Sun
    Citation: BMC Genomics 2014 15:307
    Content type: Research article Published on:

  17. Next generation sequencing based technologies are being extensively used to study transcriptomes. Among these, cap analysis of gene expression (CAGE) is specialized in detecting the most 5’ ends of RNA molecul...

    Authors: Hiroko Ohmiya, Morana Vitezic, Martin C Frith, Masayoshi Itoh, Piero Carninci, Alistair RR Forrest, Yoshihide Hayashizaki and Timo Lassmann
    Citation: BMC Genomics 2014 15:269
    Content type: Software Published on:

  18. Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome s...

    Authors: Ekaterina N Chernyaeva, Marina V Shulgina, Mikhail S Rotkevich, Pavel V Dobrynin, Serguei A Simonov, Egor A Shitikov, Dmitry S Ischenko, Irina Y Karpova, Elena S Kostryukova, Elena N Ilina, Vadim M Govorun, Vyacheslav Y Zhuravlev, Olga A Manicheva, Peter K Yablonsky, Yulia D Isaeva, Elena Y Nosova…
    Citation: BMC Genomics 2014 15:308
    Content type: Database Published on:

  19. Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is inval...

    Authors: Ngoot-Chin Ting, Johannes Jansen, Sean Mayes, Festo Massawe, Ravigadevi Sambanthamurthi, Leslie Cheng-Li Ooi, Cheuk Weng Chin, Xaviar Arulandoo, Tzer-Ying Seng, Sharifah Shahrul Rabiah Syed Alwee, Maizura Ithnin and Rajinder Singh
    Citation: BMC Genomics 2014 15:309
    Content type: Research article Published on:

  20. The human gastric pathogen Helicobacter pylori is a paradigm for chronic bacterial infections. Its persistence in the stomach mucosa is facilitated by several mechanisms of immune evasion and immune modulation, b...

    Authors: Wolfgang Fischer, Ute Breithaupt, Beate Kern, Stella I Smith, Carolin Spicher and Rainer Haas
    Citation: BMC Genomics 2014 15:310
    Content type: Research article Published on:

  21. Micro-organisms inhabiting teeth surfaces grow on biofilms where a specific and complex succession of bacteria has been described by co-aggregation tests and DNA-based studies. Although the composition of oral...

    Authors: Alfonso Benítez-Páez, Pedro Belda-Ferre, Aurea Simón-Soro and Alex Mira
    Citation: BMC Genomics 2014 15:311
    Content type: Research article Published on:

  22. Medicago truncatula, a close relative of alfalfa, is a preeminent model for studying nitrogen fixation, symbiosis, and legume genomics. The Medicago sequencing project began in 2003 with the goal to decipher sequ...

    Authors: Haibao Tang, Vivek Krishnakumar, Shelby Bidwell, Benjamin Rosen, Agnes Chan, Shiguo Zhou, Laurent Gentzbittel, Kevin L Childs, Mark Yandell, Heidrun Gundlach, Klaus FX Mayer, David C Schwartz and Christopher D Town
    Citation: BMC Genomics 2014 15:312
    Content type: Research article Published on:

  23. Pyrenochaeta lycopersici is a soil-dwelling ascomycete pathogen that causes corky root rot disease in tomato (Solanum lycopersicum) and other Solanaceous crops, reducing fruit yields by up to 75%. Fungal pathogen...

    Authors: Maria Aragona, Andrea Minio, Alberto Ferrarini, Maria Teresa Valente, Paolo Bagnaresi, Luigi Orrù, Paola Tononi, Gianpiero Zamperin, Alessandro Infantino, Giampiero Valè, Luigi Cattivelli and Massimo Delledonne
    Citation: BMC Genomics 2014 15:313
    Content type: Research article Published on:

  24. Mining novel biomarkers from gene expression profiles for accurate disease classification is challenging due to small sample size and high noise in gene expression measurements. Several studies have proposed i...

    Authors: Rendong Yang, Yun Bai, Zhaohui Qin and Tianwei Yu
    Citation: BMC Genomics 2014 15:314
    Content type: Methodology article Published on:

  25. Induced resistance (IR) can be part of a sustainable plant protection strategy against important plant diseases. β-aminobutyric acid (BABA) can induce resistance in a wide range of plants against several types...

    Authors: Therese Bengtsson, Deborah Weighill, Estelle Proux-Wéra, Fredrik Levander, Svante Resjö, Dharani Dhar Burra, Laith Ibrahim Moushib, Pete E Hedley, Erland Liljeroth, Dan Jacobson, Erik Alexandersson and Erik Andreasson
    Citation: BMC Genomics 2014 15:315
    Content type: Research article Published on:

  26. Mnemiopsis leidyi is a ctenophore native to the coastal waters of the western Atlantic Ocean. A number of studies on Mnemiopsis have led to a better understanding of many key biological processes, and these studi...

    Authors: R Travis Moreland, Anh-Dao Nguyen, Joseph F Ryan, Christine E Schnitzler, Bernard J Koch, Katherine Siewert, Tyra G Wolfsberg and Andreas D Baxevanis
    Citation: BMC Genomics 2014 15:316
    Content type: Database Published on:

  27. Using motif detection programs it is fairly straightforward to identify conserved cis-sequences in promoters of co-regulated genes. In contrast, the identification of the transcription factors (TFs) interacting w...

    Authors: Christian Dubos, Zsolt Kelemen, Alvaro Sebastian, Lorenz Bülow, Gunnar Huep, Wenjia Xu, Damaris Grain, Fabien Salsac, Cecile Brousse, Loïc Lepiniec, Bernd Weisshaar, Bruno Contreras-Moreira and Reinhard Hehl
    Citation: BMC Genomics 2014 15:317
    Content type: Research article Published on:

  28. Pseudomonas aeruginosa is an opportunistic pathogen with a high incidence of hospital infections that represents a threat to immune compromised patients. Genomic studies have shown that, in contrast to other path...

    Authors: María-Victoria Grosso-Becerra, Christian Santos-Medellín, Abigail González-Valdez, José-Luis Méndez, Gabriela Delgado, Rosario Morales-Espinosa, Luis Servín-González, Luis-David Alcaraz and Gloria Soberón-Chávez
    Citation: BMC Genomics 2014 15:318
    Content type: Research article Published on:

  29. Gene-based analysis has become popular in genomic research because of its appealing biological and statistical properties compared with those of a single-locus analysis. However, only a few, if any, studies ha...

    Authors: Hsin-Chou Yang, Chien-Wei Lin, Chia-Wei Chen and James J Chen
    Citation: BMC Genomics 2014 15:319
    Content type: Research article Published on:

  30. Efficient light acclimation of photosynthetic cells is a basic and important property of plants. The process of acclimation depends on transformation of retrograde signals in gene expression, transcript accumu...

    Authors: Marie-Luise Oelze, Meenakumari Muthuramalingam, Marc Oliver Vogel and Karl-Josef Dietz
    Citation: BMC Genomics 2014 15:320
    Content type: Research article Published on:

  31. In metazoans, Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis ele...

    Authors: Jia-Jia Wang, Dong-Ya Cui, Tengfei Xiao, Xubin Sun, Peng Zhang, Runsheng Chen, Shunmin He and Da-Wei Huang
    Citation: BMC Genomics 2014 15:321
    Content type: Research article Published on:

  32. Cytoplasmic male sterility (CMS) is not only important for exploiting heterosis in crop plants, but also as a model for investigating nuclear-cytoplasmic interaction. CMS may be caused by mutations, rearrangem...

    Authors: Shuangping Heng, Chao Wei, Bing Jing, Zhengjie Wan, Jing Wen, Bin Yi, Chaozhi Ma, Jinxing Tu, Tingdong Fu and Jinxiong Shen
    Citation: BMC Genomics 2014 15:322
    Content type: Research article Published on:

  33. Actinobacteria of the genus Nocardia usually live in soil or water and play saprophytic roles, but they also opportunistically infect the respiratory system, skin, and other organs of humans and animals. Primaril...

    Authors: Hisayuki Komaki, Natsuko Ichikawa, Akira Hosoyama, Azusa Takahashi-Nakaguchi, Tetsuhiro Matsuzawa, Ken-ichiro Suzuki, Nobuyuki Fujita and Tohru Gonoi
    Citation: BMC Genomics 2014 15:323
    Content type: Research article Published on:

  34. Verticillium dahliae is a soil-borne fungus that causes vascular wilt diseases in a wide range of plant hosts. V. dahliae produces multicelled, melanized resting bodies, also known as microsclerotia (MS) that can...

    Authors: Dianguang Xiong, Yonglin Wang, Jie Ma, Steven J Klosterman, Shuxiao Xiao and Chengming Tian
    Citation: BMC Genomics 2014 15:324
    Content type: Research article Published on:

  36. Compared with other Populus species, Populus euphratica Oliv. exhibits better tolerance to abiotic stress, especially those involving extreme temperatures. However, little is known about gene regulation and signa...

    Authors: Jinhuan Chen, Qianqian Tian, Tao Pang, Libo Jiang, Rongling Wu, Xinli Xia and Weilun Yin
    Citation: BMC Genomics 2014 15:326
    Content type: Research article Published on:

  37. It is believed that the main factors of low prenatal growth in mammals are genetic and environmental. We used isogenic mice maintained in standard conditions to analyze how natural non-genetic microsomia (low ...

    Authors: Alberto Miranda, Angela P López-Cardona, Ricardo Laguna-Barraza, Alexandra Calle, Irene López-Vidriero, Belén Pintado and Alfonso Gutiérrez-Adán
    Citation: BMC Genomics 2014 15:327
    Content type: Research article Published on:

  38. Heat-induced browning (Hbs) of seed coats is caused by high temperatures which discolors the seed coats of many legumes, affecting the visual appearance and quality of seeds. The genetic determinants underlying H...

    Authors: Marti Pottorff, Philip A Roberts, Timothy J Close, Stefano Lonardi, Steve Wanamaker and Jeffrey D Ehlers
    Citation: BMC Genomics 2014 15:328
    Content type: Research article Published on:

  39. Intrachromosomal segmental duplications provide the substrate for non-allelic homologous recombination, facilitating extensive copy number variation in the human genome. Many multi-copy gene families are embed...

    Authors: Stuart Cantsilieris, Patrick S Western, Paul N Baird and Stefan J White
    Citation: BMC Genomics 2014 15:329
    Content type: Research article Published on:

  41. The precise nature of how cell type specific chromatin structures at enhancer sites affect gene expression is largely unknown. Here we identified cell type specific enhancers coupled with gene expression in tw...

    Authors: Suhn Kyong Rhie, Dennis J Hazelett, Simon G Coetzee, Chunli Yan, Houtan Noushmehr and Gerhard A Coetzee
    Citation: BMC Genomics 2014 15:331
    Content type: Research article Published on:

  42. The HUGO Pan-Asian SNP Consortium (PASNP) has generated a genetic resource of almost 55,000 autosomal single nucleotide polymorphisms (SNPs) across more than 1,800 individuals from 73 urban and indigenous popu...

    Authors: Xuanyao Liu, Woei-Yuh Saw, Mohammad Ali, Rick Twee-Hee Ong and Yik-Ying Teo
    Citation: BMC Genomics 2014 15:332
    Content type: Research article Published on:

  43. Tomato (Solanum lycopersicum), one of the world’s most important vegetable crops, is highly susceptible to necrotrophic fungal pathogens such as Botrytis cinerea and Alternaria solani. Improving resistance throug...

    Authors: Jonathon E Smith, Bemnet Mengesha, Hua Tang, Tesfaye Mengiste and Burton H Bluhm
    Citation: BMC Genomics 2014 15:334
    Content type: Research article Published on:

  45. The white mold fungus Sclerotinia sclerotiorum is a devastating necrotrophic plant pathogen with a remarkably broad host range. The interaction of necrotrophs with their hosts is more complex than initially thoug...

    Authors: Koanna Guyon, Claudine Balagué, Dominique Roby and Sylvain Raffaele
    Citation: BMC Genomics 2014 15:336
    Content type: Research article Published on:

  46. Populus euphratica Oliv and P. pruinosa Schrenk (Salicaceae) both grow in dry desert areas with high summer temperatures. However, P. euphratica is distributed in dry deserts with deep underground water whereas P...

    Authors: Jian Zhang, Jianju Feng, Jing Lu, Yongzhi Yang, Xu Zhang, Dongshi Wan and Jianquan Liu
    Citation: BMC Genomics 2014 15:337
    Content type: Research article Published on:

  47. Nephrotoxicity is the most prominent one among the various toxicities of ochratoxin A (OTA). MicroRNAs (miRNAs) are small non-coding RNAs that have an impact on a wide range of biological processes by regulati...

    Authors: Qiu Dai, Jue Zhao, Xiaozhe Qi, Wentao Xu, Xiaoyun He, Mingzhang Guo, Harsh Dweep, Wen-Hsing Cheng, Yunbo Luo, Kai Xia, Norbert Gretz and Kunlun Huang
    Citation: BMC Genomics 2014 15:333
    Content type: Research article Published on:

  48. Bidirectional gene pairs exist as a specific form of gene organization in microorganisms and mammals as well as in model plant species, such as Arabidopsis and rice. Little is known about bidirectional gene pairs...

    Authors: Xiaoqing Liu, Xiaojin Zhou, Ye Li, Jian Tian, Qiuxue Zhang, Suzhen Li, Lei Wang, Jun Zhao, Rumei Chen and Yunliu Fan
    Citation: BMC Genomics 2014 15:338
    Content type: Research article Published on:

  49. Molecular biology laboratories require extensive metadata to improve data collection and analysis. The heterogeneity of the collected metadata grows as research is evolving in to international multi-disciplina...

    Authors: Massimiliano Izzo, Francesco Mortola, Gabriele Arnulfo, Marco M Fato and Luigi Varesio
    Citation: BMC Genomics 2014 15(Suppl 3):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 3

  50. MicroRNAs (miRNAs) are small noncoding RNAs that play an important role in the regulation of various biological processes through their interaction with cellular mRNAs. A significant amount of miRNAs has been ...

    Authors: Francesco Russo, Sebastiano Di Bella, Vincenzo Bonnici, Alessandro Laganà, Giuseppe Rainaldi, Marco Pellegrini, Alfredo Pulvirenti, Rosalba Giugno and Alfredo Ferro
    Citation: BMC Genomics 2014 15(Suppl 3):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 3

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