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  1. Understanding genetic control of tassel and ear architecture in maize (Zea mays L. ssp. mays) is important due to their relationship with grain yield. High resolution QTL mapping is critical for understanding the...

    Authors: Zongliang Chen, Baobao Wang, Xiaomei Dong, Han Liu, Longhui Ren, Jian Chen, Andrew Hauck, Weibin Song and Jinsheng Lai
    Citation: BMC Genomics 2014 15:433
    Content type: Research article Published on:

  2. Comparative transcriptomics and functional studies of different Saccharomyces species have opened up the possibility of studying and understanding new yeast abilities. This is the case of yeast adaptation to stre...

    Authors: Jordi Tronchoni, Victor Medina, Jose Manuel Guillamón, Amparo Querol and Roberto Pérez-Torrado
    Citation: BMC Genomics 2014 15:432
    Content type: Research article Published on:

  3. Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such...

    Authors: Feng Ding, Peng Cui, Zhenyu Wang, Shoudong Zhang, Shahjahan Ali and Liming Xiong
    Citation: BMC Genomics 2014 15:431
    Content type: Research article Published on:

  4. The Firmicutes often possess three conspicuous genome features: marked Purine Asymmetry (PAS) across two strands of replication, Strand-biased Gene Distribution (SGD) and presence of two isoforms of DNA polyme...

    Authors: Sanjoy Kumar Saha, Aranyak Goswami and Chitra Dutta
    Citation: BMC Genomics 2014 15:430
    Content type: Research article Published on:

  5. Bacteroides fragilis is a Gram-negative anaerobe that is normally a human gut commensal; it comprises a small percentage of the gut Bacteroides but is the most frequently isolated Bacteroides from human infection...

    Authors: Yaligara Veeranagouda, Fasahath Husain, Elizabeth L Tenorio and Hannah M Wexler
    Citation: BMC Genomics 2014 15:429
    Content type: Research article Published on:

  6. Cysticercosis remains a major neglected tropical disease of humanity in many regions, especially in sub-Saharan Africa, Central America and elsewhere. Owing to the emerging drug resistance and the inability of...

    Authors: Hong-Bin Yan, Zhong-Zi Lou, Li Li, Paul J Brindley, Yadong Zheng, Xuenong Luo, Junling Hou, Aijiang Guo, Wan-Zhong Jia and Xuepeng Cai
    Citation: BMC Genomics 2014 15:428
    Content type: Research article Published on:

  7. Within the last decade, Salmonella enterica subsp. enterica serovar Cerro (S. Cerro) has become one of the most common serovars isolated from cattle and dairy farm environments in the northeastern US. The fact th...

    Authors: Lorraine D Rodriguez-Rivera, Andrea I Moreno Switt, Lovorka Degoricija, Rixun Fang, Craig A Cummings, Manohar R Furtado, Martin Wiedmann and Henk C den Bakker
    Citation: BMC Genomics 2014 15:427
    Content type: Research article Published on:

  8. Crosstalk between the signalling pathways responding to light–dark cycles and those triggering the adaptation of metabolism to the environment is known to occur in various organisms. This interrelationship of ...

    Authors: Doris Tisch, Andre Schuster and Monika Schmoll
    Citation: BMC Genomics 2014 15:425
    Content type: Research article Published on:

  9. Boar taint is an offensive urine or faecal-like odour, affecting the smell and taste of cooked pork from some mature non-castrated male pigs. Androstenone and skatole in fat are the molecules responsible. In m...

    Authors: Suzanne J Rowe, Burak Karacaören, Dirk-Jan de Koning, Boris Lukic, Nicola Hastings-Clark, Ingela Velander, Chris S Haley and Alan L Archibald
    Citation: BMC Genomics 2014 15:424
    Content type: Research article Published on:

  10. miRNAs play a key role in normal physiology and various diseases. miRNA profiling through next generation sequencing (miRNA-seq) has become the main platform for biological research and biomarker discovery. Ho...

    Authors: Zhifu Sun, Jared Evans, Aditya Bhagwate, Sumit Middha, Matthew Bockol, Huihuang Yan and Jean-Pierre Kocher
    Citation: BMC Genomics 2014 15:423
    Content type: Software Published on:

  11. Cabbage (Brassica oleracea) is one of the most important leaf vegetables grown worldwide. The entire cabbage genome sequence and more than fifty thousand proteins have been obtained to date. However a high degree...

    Authors: Senthil Kumar Thamilarasan, Jong-In Park, Hee-Jeong Jung and Ill-Sup Nou
    Citation: BMC Genomics 2014 15:422
    Content type: Research article Published on:

  12. Plants respond to diverse environmental cues including microbial perturbations by coordinated regulation of thousands of genes. These intricate transcriptional regulatory interactions depend on the recognition...

    Authors: Joel P Tully, Aubrey E Hill, Hadia MR Ahmed, Ryan Whitley, Anthony Skjellum and M Shahid Mukhtar
    Citation: BMC Genomics 2014 15:421
    Content type: Research article Published on:

  13. The soybean-Bradyrhizobium symbiosis can be highly efficient in fixing nitrogen, but few genomic sequences of elite inoculant strains are available. Here we contribute with information on the genomes of two comme...

    Authors: Arthur Fernandes Siqueira, Ernesto Ormeño-Orrillo, Rangel Celso Souza, Elisete Pains Rodrigues, Luiz Gonzaga Paula Almeida, Fernando Gomes Barcellos, Jesiane Stefânia Silva Batista, Andre Shigueyoshi Nakatani, Esperanza Martínez-Romero, Ana Tereza Ribeiro Vasconcelos and Mariangela Hungria
    Citation: BMC Genomics 2014 15:420
    Content type: Research article Published on:

  14. RNA sequencing (RNA-Seq) is often used for transcriptome profiling as well as the identification of novel transcripts and alternative splicing events. Typically, RNA-Seq libraries are prepared from total RNA u...

    Authors: Wei Zhao, Xiaping He, Katherine A Hoadley, Joel S Parker, David Neil Hayes and Charles M Perou
    Citation: BMC Genomics 2014 15:419
    Content type: Research article Published on:

  16. Microtus fortis is a non-permissive host of Schistosoma japonicum. It has natural resistance against schistosomes, although the precise resistance mechanisms remain unclear. The paucity of genetic information for...

    Authors: Yuan Hu, Yuxin Xu, Weiyuan Lu, Zhongying Yuan, Hong Quan, Yujuan Shen and Jianping Cao
    Citation: BMC Genomics 2014 15:417
    Content type: Research article Published on:

  17. Patient-derived tumour xenografts are an attractive model for preclinical testing of anti-cancer drugs. Insights into tumour biology and biomarkers predictive of responses to chemotherapeutic drugs can also be...

    Authors: Nicholas C Wong, Vivek A Bhadri, Jovana Maksimovic, Mandy Parkinson-Bates, Jane Ng, Jeff M Craig, Richard Saffery and Richard B Lock
    Citation: BMC Genomics 2014 15:416
    Content type: Research article Published on:

  18. Mycobacterium avium subsp. paratuberculosis (MAP) is an obligate intracellular pathogen that infects many ruminant species. The acquisition of foreign genes via horizontal gene transfer has been postulated to con...

    Authors: Joyce Wang, Justin R Pritchard, Louis Kreitmann, Alexandre Montpetit and Marcel A Behr
    Citation: BMC Genomics 2014 15:415
    Content type: Research article Published on:

  19. Erwinia amylovora is a phytopathogenic bacterium and causal agent of fire blight disease in apples and pears. Although many virulence factors have been characterized, the coordination of expression of these virul...

    Authors: Quan Zeng and George W Sundin
    Citation: BMC Genomics 2014 15:414
    Content type: Research article Published on:

  20. The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evalu...

    Authors: Cristina Óvilo, Rita Benítez, Almudena Fernández, Yolanda Núñez, Miriam Ayuso, Ana Isabel Fernández, Carmen Rodríguez, Beatriz Isabel, Ana Isabel Rey, Clemente López-Bote and Luis Silió
    Citation: BMC Genomics 2014 15:413
    Content type: Research article Published on:

  21. Eggplant (Solanum melongena L.) and turkey berry (S. torvum Sw.), a wild ally of eggplant with promising multi-disease resistance traits, are of great economic, medicinal and genetic importance, but genomic resou...

    Authors: Xu Yang, Yu-Fu Cheng, Cao Deng, Yan Ma, Zhi-Wen Wang, Xue-Hao Chen and Lin-Bao Xue
    Citation: BMC Genomics 2014 15:412
    Content type: Research article Published on:

  22. Many eukaryotes have been shown to use alternative schemes to the universal genetic code. While most Saccharomycetes, including Saccharomyces cerevisiae, use the standard genetic code translating the CUG codon as...

    Authors: Stefanie Mühlhausen and Martin Kollmar
    Citation: BMC Genomics 2014 15:411
    Content type: Software Published on:

  23. The growth and development of the posterior silk gland and the biosynthesis of the silk core protein at the fifth larval instar stage of Bombyx mori are of paramount importance for silk production.

    Authors: Jisheng Li, Yimei Cai, Lupeng Ye, Shaohua Wang, Jiaqian Che, Zhengying You, Jun Yu and Boxiong Zhong
    Citation: BMC Genomics 2014 15:410
    Content type: Research article Published on:

  24. V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies. In leukemia, they are used to quantify the minimal residual disease during patient fo...

    Authors: Mathieu Giraud, Mikaël Salson, Marc Duez, Céline Villenet, Sabine Quief, Aurélie Caillault, Nathalie Grardel, Christophe Roumier, Claude Preudhomme and Martin Figeac
    Citation: BMC Genomics 2014 15:409
    Content type: Methodology article Published on:

  25. Some association studies, as the implemented in VEGAS, ALIGATOR, i-GSEA4GWAS, GSA-SNP and other software tools, use genes as the unit of analysis. These genes include the coding sequence plus flanking sequence...

    Authors: Cristina Rodriguez-Fontenla, Manuel Calaza and Antonio Gonzalez
    Citation: BMC Genomics 2014 15:408
    Content type: Methodology article Published on:

  26. Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus are lactic acid producing bacteria that are largely used in dairy industries, notably in cheese-making and yogurt production. An earlier in-depth study of...

    Authors: Hela El Kafsi, Johan Binesse, Valentin Loux, Julien Buratti, Samira Boudebbouze, Rozenn Dervyn, Sean Kennedy, Nathalie Galleron, Benoît Quinquis, Jean-Michel Batto, Bouziane Moumen, Emmanuelle Maguin and Maarten van de Guchte
    Citation: BMC Genomics 2014 15:407
    Content type: Research article Published on:

  27. A colony of the hydrozoan Hydractinia symbiolongicarpus comprises genetically identical yet morphologically distinct and functionally specialized polyp types. The main labor divisions are between feeding, reprodu...

    Authors: Steven M Sanders, Mariya Shcheglovitova and Paulyn Cartwright
    Citation: BMC Genomics 2014 15:406
    Content type: Research article Published on:

  28. Rhazya stricta is native to arid regions in South Asia and the Middle East and is used extensively in folk medicine to treat a wide range of diseases. In addition to generating genomic resources for this medicina...

    Authors: Seongjun Park, Tracey A Ruhlman, Jamal SM Sabir, Mohammed HZ Mutwakil, Mohammed N Baeshen, Meshaal J Sabir, Nabih A Baeshen and Robert K Jansen
    Citation: BMC Genomics 2014 15:405
    Content type: Research article Published on:

  29. Pantoea ananatis is found in a wide range of natural environments, including water, soil, as part of the epi- and endophytic flora of various plant hosts, and in the insect gut. Some strains have proven effective...

    Authors: Pieter De Maayer, Wai Yin Chan, Enrico Rubagotti, Stephanus N Venter, Ian K Toth, Paul R J Birch and Teresa A Coutinho
    Citation: BMC Genomics 2014 15:404
    Content type: Research article Published on:

  30. American eel (Anguilla rostrata) is one of the few species for which panmixia has been demonstrated at the scale of the entire species. As such, the development of long term local adaptation is impossible. Howeve...

    Authors: Caroline L Côté, Martin Castonguay, McWilliam Svetlana Kalujnaia, Gordon Cramb and Louis Bernatchez
    Citation: BMC Genomics 2014 15:403
    Content type: Research article Published on:

  31. Glandular trichomes are production and storage organs of specialized metabolites such as terpenes, which play a role in the plant’s defense system. The present study aimed to shed light on the regulation of te...

    Authors: Eleni A Spyropoulou, Michel A Haring and Robert C Schuurink
    Citation: BMC Genomics 2014 15:402
    Content type: Research article Published on:

  32. A major hurdle to transcriptome profiling by deep-sequencing technologies is that abundant transcripts, such as rRNAs, can overwhelm the libraries, severely reducing transcriptome-wide coverage. Methods for de...

    Authors: Stuart K Archer, Nikolay E Shirokikh and Thomas Preiss
    Citation: BMC Genomics 2014 15:401
    Content type: Methodology article Published on:

    The Related Article to this article has been published in Nature Protocols 2017 12:nprot.2016.189

  33. Sexually dimorphic phenotypes are generally associated with differential gene expression between the sexes. The study of molecular evolution and genomic location of these differentially expressed, or sex-biase...

    Authors: Eshita Sharma, Axel Künstner, Bonnie A Fraser, Gideon Zipprich, Verena A Kottler, Stefan R Henz, Detlef Weigel and Christine Dreyer
    Citation: BMC Genomics 2014 15:400
    Content type: Research article Published on:

  34. Many Poaceae species show a gametophytic self-incompatibility (GSI) system, which is controlled by at least two independent and multiallelic loci, S and Z. Until currently, the gene products for S and Z were unkn...

    Authors: Qingyuan Zhou, Junting Jia, Xing Huang, Xueqing Yan, Liqin Cheng, Shuangyan Chen, Xiaoxia Li, Xianjun Peng and Gongshe Liu
    Citation: BMC Genomics 2014 15:399
    Content type: Research article Published on:

  35. Genetic association studies are conducted to discover genetic loci that contribute to an inherited trait, identify the variants behind these associations and ascertain their functional role in determining the ...

    Authors: Edwin S Iversen, Gary Lipton, Merlise A Clyde and Alvaro NA Monteiro
    Citation: BMC Genomics 2014 15:398
    Content type: Methodology article Published on:

  36. Upland cotton (Gossypium hirsutum L.) accounts for about 95% of world cotton production. Improving Upland cotton cultivars has been the focus of world-wide cotton breeding programs. Negative correlation between y...

    Authors: David D Fang, Johnie N Jenkins, Dewayne D Deng, Jack C McCarty, Ping Li and Jixiang Wu
    Citation: BMC Genomics 2014 15:397
    Content type: Research article Published on:

  37. Brassica juncea (AABB) is an allotetraploid species containing genomes of B. rapa (AA) and B. nigra (BB). It is a major oilseed crop in South Asia, and grown on approximately 6–7 million hectares of land in India...

    Authors: Kumar Paritosh, Vibha Gupta, Satish K Yadava, Priyansha Singh, Akshay K Pradhan and Deepak Pental
    Citation: BMC Genomics 2014 15:396
    Content type: Research article Published on:

  38. microRNAs (miRNAs) play crucial roles in major biological processes and their deregulations are often associated with human malignancies. As such, they represent appealing candidates as targets of innovative t...

    Authors: Marjorie Monleau, Sophie Bonnel, Thierry Gostan, Dominique Blanchard, Valérie Courgnaud and Charles-Henri Lecellier
    Citation: BMC Genomics 2014 15:395
    Content type: Methodology article Published on:

  39. Closely spaced long inverted repeats, also known as DNA palindromes, can undergo intrastrand annealing to form DNA hairpins. The ability to form these hairpins results in genome instability, difficulties in ma...

    Authors: Hui Yang, Natalia Volfovsky, Alison Rattray, Xiongfong Chen, Hisashi Tanaka and Jeffrey Strathern
    Citation: BMC Genomics 2014 15:394
    Content type: Methodology article Published on:

  40. Development of cancer therapeutics partially depends upon selection of appropriate animal models. Therefore, improvements to model selection are beneficial.

    Authors: Melinda G Hollingshead, Luke H Stockwin, Sergio Y Alcoser, Dianne L Newton, Benjamin C Orsburn, Carrie A Bonomi, Suzanne D Borgel, Raymond Divelbiss, Kelly M Dougherty, Elizabeth J Hager, Susan L Holbeck, Gurmeet Kaur, David J Kimmel, Mark W Kunkel, Angelena Millione, Michael E Mullendore…
    Citation: BMC Genomics 2014 15:393
    Content type: Research article Published on:

  41. The genus Clavibacter harbors economically important plant pathogens infecting agricultural crops such as potato and tomato. Although the vast majority of Clavibacter strains are pathogenic, there is an increasin...

    Authors: Joanna Załuga, Pieter Stragier, Steve Baeyen, Annelies Haegeman, Johan Van Vaerenbergh, Martine Maes and Paul De Vos
    Citation: BMC Genomics 2014 15:392
    Content type: Research article Published on:

  42. The DA rat strain is particularly susceptible to the induction of a number of chronic inflammatory diseases, such as models for rheumatoid arthritis and multiple sclerosis. Here we sequenced the genomes of two...

    Authors: Liselotte Bäckdahl, Diana Ekman, Maja Jagodic, Tomas Olsson and Rikard Holmdahl
    Citation: BMC Genomics 2014 15:391
    Content type: Research article Published on:

  43. The analysis of cellular networks and pathways involved in oncogenesis has increased our knowledge about the pathogenic mechanisms that underlie tumour biology and has unmasked new molecular targets that may l...

    Authors: Carlos Aya-Bonilla, Emily Camilleri, Larisa M Haupt, Rod Lea, Maher K Gandhi and Lyn R Griffiths
    Citation: BMC Genomics 2014 15:390
    Content type: Research article Published on:

  44. Salmonella enterica subsp. enterica serovar Virchow has been recognized as a significant health burden in Asia, Australia and Europe. In addition to its global distribution, S. Virchow is clinically significant d...

    Authors: Nathan L Bachmann, Nicola K Petty, Nouri L Ben Zakour, Jan M Szubert, John Savill and Scott A Beatson
    Citation: BMC Genomics 2014 15:389
    Content type: Research article Published on:

  45. Sex allocation of offspring in mammals is usually considered as a matter of chance, being dependent on whether an X- or a Y-chromosome-bearing spermatozoon reaches the oocyte first. Here we investigated the al...

    Authors: Carmen Almiñana, Ignacio Caballero, Paul Roy Heath, Saeedeh Maleki-Dizaji, Inmaculada Parrilla, Cristina Cuello, Maria Antonia Gil, Jose Luis Vazquez, Juan Maria Vazquez, Jordi Roca, Emilio Arsenio Martinez, William Vincent Holt and Alireza Fazeli
    Citation: BMC Genomics 2014 15:293
    Content type: Research article Published on:

  47. RNA-related applications of the next-generation sequencing (NGS) technologies require context-specific interpretations: e.g., sequence mismatches may indicate sites of RNA editing, or uneven read coverage ofte...

    Authors: Ammar Naqvi, Tiange Cui and Andrey Grigoriev
    Citation: BMC Genomics 2014 15(Suppl 4):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 4

  48. Next Generation Sequencing (NGS) of whole exomes or genomes is increasingly being used in human genetic research and diagnostics. Sharing NGS data with third parties can help physicians and researchers to iden...

    Authors: Björn Stade, Dominik Seelow, Ingo Thomsen, Michael Krawczak and Andre Franke
    Citation: BMC Genomics 2014 15(Suppl 4):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 4

  49. Recent studies have shown that human populations have experienced a complex demographic history, including a recent epoch of rapid population growth that led to an excess in the proportion of rare genetic vari...

    Authors: Feng Gao and Alon Keinan
    Citation: BMC Genomics 2014 15(Suppl 4):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 4

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BMC Genomics

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