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  1. In many traits, not only individual trait levels are under genetic control, but also the variation around that level. In other words, genotypes do not only differ in mean, but also in (residual) variation arou...

    Authors: E. Sell-Kubiak, N. Duijvesteijn, M. S. Lopes, L. L. G. Janss, E. F. Knol, P. Bijma and H. A. Mulder
    Citation: BMC Genomics 2015 16:1049
    Content type: Research article Published on:

  2. Pearl millet is a staple food for people in arid and semi-arid regions of Africa and South Asia due to its high drought tolerance and nutritional qualities. A better understanding of the genomic diversity and ...

    Authors: Zhenbin Hu, Bassirou Mbacké, Ramasamy Perumal, Mame Codou Guèye, Ousmane Sy, Sophie Bouchet, P. V. Vara Prasad and Geoffrey P. Morris
    Citation: BMC Genomics 2015 16:1048
    Content type: Research article Published on:

  3. Genotyping-by-sequencing (GBS) is becoming an attractive alternative to array-based methods for genotyping individuals for a large number of single nucleotide polymorphisms (SNPs). Costs can be lowered by redu...

    Authors: Ken G. Dodds, John C. McEwan, Rudiger Brauning, Rayna M. Anderson, Tracey C. van Stijn, Theodor Kristjánsson and Shannon M. Clarke
    Citation: BMC Genomics 2015 16:1047
    Content type: Methodology article Published on:

  4. Mycobacterium abscessus (MAB) is an emerging pathogen causing pulmonary infections in those with inflammatory lung disorders, such as Cystic Fibrosis (CF), and is associated with the h...

    Authors: Anna Aulicino, Adam M. Dinan, Aleksandra A. Miranda-CasoLuengo, John A. Browne, Kévin Rue-Albrecht, David E. MacHugh and Brendan J. Loftus
    Citation: BMC Genomics 2015 16:1046
    Content type: Research article Published on:

  5. Most currently-used normalization methods for miRNA array data are based on methods developed for mRNA arrays despite fundamental differences between the data characteristics. The application of conventional q...

    Authors: Anvar Suyundikov, John R. Stevens, Christopher Corcoran, Jennifer Herrick, Roger K. Wolff and Martha L. Slattery
    Citation: BMC Genomics 2015 16:1045
    Content type: Methodology Article Published on:

  6. Gene copy-number variation (CNVs), which provides the raw material for the evolution of novel genes, is widespread in natural populations. We investigated whether CNVs constitute a common mechanism of genetic ...

    Authors: James C. Farslow, Kendra J. Lipinski, Lucille B. Packard, Mark L. Edgley, Jon Taylor, Stephane Flibotte, Donald G. Moerman, Vaishali Katju and Ulfar Bergthorsson
    Citation: BMC Genomics 2015 16:1044
    Content type: Research article Published on:

  7. Over the last few years, continuous development of high-throughput sequencing platforms and sequence analysis tools has facilitated reliable identification and characterization of genetic variants in many catt...

    Authors: Ashutosh Das, Frank Panitz, Vivi Raundahl Gregersen, Christian Bendixen and Lars-Erik Holm
    Citation: BMC Genomics 2015 16:1043
    Content type: Research article Published on:

  8. Although much is known about the mechanism of action of Bacillus thuringiensis Cry toxins, the target tissue cellular responses to toxin activity is less understood. Previous transcriptomic studies indicated that...

    Authors: Pablo Emiliano Canton, Angeles Cancino-Rodezno, Sarjeet S. Gill, Mario Soberón and Alejandra Bravo
    Citation: BMC Genomics 2015 16:1042
    Content type: Research article Published on:

  10. Sorghum is a versatile cereal crop, with excellent heat and drought tolerance. However, it is susceptible to early-season cold stress (12–15 Â°C) which limits stand-establishment and seedling growth. To gain fu...

    Authors: Ratan Chopra, Gloria Burow, Chad Hayes, Yves Emendack, Zhanguo Xin and John Burke
    Citation: BMC Genomics 2015 16:1040
    Content type: Research article Published on:

  11. The large and complex hexaploid genome has greatly hindered genomics studies of common wheat (Triticum aestivum, AABBDD). Here, we investigated transcripts in common wheat developing caryopses using the emerging ...

    Authors: Lingli Dong, Hongfang Liu, Juncheng Zhang, Shuangjuan Yang, Guanyi Kong, Jeffrey S. C. Chu, Nansheng Chen and Daowen Wang
    Citation: BMC Genomics 2015 16:1039
    Content type: Research article Published on:

  12. Studies of non-model species are important for understanding the molecular processes underpinning phenotypic variation under natural ecological conditions. The common buzzard (Buteo buteo; Aves: Accipitriformes) ...

    Authors: Martina Pauli, Nayden Chakarov, Oliver Rupp, Jörn Kalinowski, Alexander Goesmann, Michael D. Sorenson, Oliver Krüger and Joseph Ivan Hoffman
    Citation: BMC Genomics 2015 16:1038
    Content type: Research article Published on:

  13. Members of the plant MAP Kinases superfamily have been mostly studied in Arabidopsis thaliana and little is known in most other species. In Solanum chacoense, a wild species close to the common potato, it had bee...

    Authors: Caroline Daigle and Daniel P. Matton
    Citation: BMC Genomics 2015 16:1037
    Content type: Research article Published on:

  14. 3′untranslated regions (3′UTRs) are poorly understood portions of eukaryotic mRNAs essential for post-transcriptional gene regulation. Sequence elements in 3′UTRs can be target sites for regulatory molecules s...

    Authors: Kasuen Kotagama, Cody S. Babb, Justin M. Wolter, Ronan P. Murphy and Marco Mangone
    Citation: BMC Genomics 2015 16:1036
    Content type: Research article Published on:

  15. High-density map is a valuable tool for genetic and genomic analysis. Although wax gourd is a widely distributed vegetable of Cucurbitaceae and has important medicinal and health value, no genetic map has been co...

    Authors: Biao Jiang, Wenrui Liu, Dasen Xie, Qingwu Peng, Xiaoming He, Yu’e Lin and Zhaojun Liang
    Citation: BMC Genomics 2015 16:1035
    Content type: Research article Published on:

  16. Determining whether two DNA samples originate from the same individual is difficult when the amount of retrievable DNA is limited. This is often the case for ancient, historic, and forensic samples. The most w...

    Authors: Samuel H. Vohr, Carlos Fernando Buen Abad Najar, Beth Shapiro and Richard E. Green
    Citation: BMC Genomics 2015 16:1034
    Content type: Methodology article Published on:

  17. The Egyptian Rousette bat (Rousettus aegyptiacus), a common fruit bat species found throughout Africa and the Middle East, was recently identified as a natural reservoir host of Marburg virus. With Ebola virus, M...

    Authors: Albert K. Lee, Kirsten A. Kulcsar, Oliver Elliott, Hossein Khiabanian, Elyse R. Nagle, Megan E.B. Jones, Brian R. Amman, Mariano Sanchez-Lockhart, Jonathan S. Towner, Gustavo Palacios and Raul Rabadan
    Citation: BMC Genomics 2015 16:1033
    Content type: Research Article Published on:

  18. While the taxonomy and genomics of environmental strains from the P. fluorescens species-complex has been reported, little is known about P. fluorescens strains from clinical samples. In this report, we provide t...

    Authors: Brittan S. Scales, John R. Erb-Downward, Ian M. Huffnagle, John J. LiPuma and Gary B. Huffnagle
    Citation: BMC Genomics 2015 16:1032
    Content type: Research article Published on:

  19. For plant species with unsequenced genomes, cDNA contigs created by de novo assembly of RNA-Seq reads are used as reference sequences for comparative analysis of RNA-Seq datasets and the detection of differential...

    Authors: Hanako Ono, Kazuo Ishii, Toshinori Kozaki, Isao Ogiwara, Motoki Kanekatsu and Tetsuya Yamada
    Citation: BMC Genomics 2015 16:1031
    Content type: Methodology article Published on:

  20. Transcriptional responses to small molecules can provide insights into drug mode of action (MOA). The capacity of the human malaria parasite, Plasmodium falciparum, to respond specifically to transcriptional pert...

    Authors: Geoffrey H. Siwo, Roger S. Smith, Asako Tan, Katrina A. Button-Simons, Lisa A. Checkley and Michael T. Ferdig
    Citation: BMC Genomics 2015 16:1030
    Content type: Research article Published on:

  21. Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or bet...

    Authors: Kuei-Han Lin, Ben-Yang Liao, Hao-Wei Chang, Shiao-Wei Huang, Ting-Yan Chang, Cheng-Yu Yang, Yu-Bin Wang, Yu-Teh Kirk Lin, Yu-Wei Wu, Sen-Lin Tang and Hon-Tsen Yu
    Citation: BMC Genomics 2015 16:1029
    Content type: Research article Published on:

  22. Since chemosensory genes play key roles in insect behaviour, they can potentially be used as new targets for pest control. The cabbage beetle, Colaphellus bowringi, is a serious insect pest of cruciferous vegetab...

    Authors: Xiao-Ming Li, Xiu-Yun Zhu, Zhi-Qiang Wang, Yi Wang, Peng He, Geng Chen, Liang Sun, Dao-Gui Deng and Ya-Nan Zhang
    Citation: BMC Genomics 2015 16:1028
    Content type: Research article Published on:

  23. Pooled samples are frequently used in experiments measuring gene expression. In this method, RNA from different individuals sharing the same experimental conditions and explanatory variables is blended and the...

    Authors: Henrik Rudolf, Gerd Nuernberg, Dirk Koczan, Jens Vanselow, Tanja Gempe, Martin Beye, Gérard Leboulle, Kaspar Bienefeld and Norbert Reinsch
    Citation: BMC Genomics 2015 16:1027
    Content type: Methodology Article Published on:

  24. MicroRNAs (miRNAs) play a vital role in growth, development, and stress response at the post-transcriptional level. Broccoli (Brassica oleracea L. var italic) is an important vegetable crop, and the yield and qua...

    Authors: Chi-Chien Chen, Shih-Feng Fu, Monma Norikazu, Yau-Wen Yang, Yu-Ju Liu, Kazuho Ikeo, Takashi Gojobori and Hao-Jen Huang
    Citation: BMC Genomics 2015 16:1026
    Content type: Research article Published on:

  25. Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfi...

    Authors: Ivett Baksa, Tibor Nagy, Endre Barta, Zoltán Havelda, Éva Várallyay, Dániel Silhavy, József Burgyán and György Szittya
    Citation: BMC Genomics 2015 16:1025
    Content type: Research article Published on:

  26. Fish reared under intensive conditions are repeatedly exposed to stress, which negatively impacts growth. Although most fish follow a conserved pattern of stress response, with increased concentrations of cort...

    Authors: Jorge E. Aedo, Jonathan Maldonado, Víctor Aballai, Juan M. Estrada, Macarena Bastias-Molina, Claudio Meneses, Cristian Gallardo-Escarate, Herman Silva, Alfredo Molina and Juan A. Valdés
    Citation: BMC Genomics 2015 16:1024
    Content type: Research article Published on:

  27. Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previo...

    Authors: Udo Wegmann, Donald A. MacKenzie, Jinshui Zheng, Alexander Goesmann, Stefan Roos, David Swarbreck, Jens Walter, Lisa C. Crossman and Nathalie Juge
    Citation: BMC Genomics 2015 16:1023
    Content type: Research article Published on:

  28. One major goal of large-scale cancer omics study is to identify molecular subtypes for more accurate cancer diagnoses and treatments. To deal with high-dimensional cancer multi-omics data, a promising strategy...

    Authors: Dingming Wu, Dongfang Wang, Michael Q. Zhang and Jin Gu
    Citation: BMC Genomics 2015 16:1022
    Content type: Methodology article Published on:

  29. Fusion transcripts are found in many tissues and have the potential to create novel functional products. Here, we investigate the genomic sequences around fusion junctions to better understand the transcriptio...

    Authors: John Lai, Jiyuan An, Inge Seim, Carina Walpole, Andrea Hoffman, Leire Moya, Srilakshmi Srinivasan, Joanna L. Perry-Keene, Chenwei Wang, Melanie L. Lehman, Colleen C. Nelson, Judith A. Clements and Jyotsna Batra
    Citation: BMC Genomics 2015 16:1021
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2016 17:424

  30. Genomic selection based on genotyping-by-sequencing (GBS) data could accelerate alfalfa yield gains, if it displayed moderate ability to predict parent breeding values. Its interest would be enhanced by predic...

    Authors: Paolo Annicchiarico, Nelson Nazzicari, Xuehui Li, Yanling Wei, Luciano Pecetti and E. Charles Brummer
    Citation: BMC Genomics 2015 16:1020
    Content type: Research article Published on:

  31. á…Ÿ

    Authors: Julie Earl, Daniel Rico, Enrique Carrillo-de-Santa-Pau, Benjamín Rodríguez-Santiago, Marinela Méndez-Pertuz, Herbert Auer, Gonzalo Gómez, H. Barton Grossman, David G. Pisano, Wolfgang A. Schulz, Luis A. Pérez-Jurado, Alfredo Carrato, Dan Theodorescu, Stephen Chanock, Alfonso Valencia and Francisco X. Real
    Citation: BMC Genomics 2015 16:1019
    Content type: Erratum Published on:

    The original article was published in BMC Genomics 2015 16:403

  33. The Tasmanian devil (Sarcophilus harrisii) is being threatened with extinction in the wild by a disease known as devil facial tumour disease (DFTD). In order to prevent the spread of this disease a thorough under...

    Authors: Katrina M. Morris, Yuanyuan Cheng, Wesley Warren, Anthony T. Papenfuss and Katherine Belov
    Citation: BMC Genomics 2015 16:1017
    Content type: Research article Published on:

  34. Larval nutrition and growth are key issues for wild and cultured cod. While it was shown previously that larval cod fed wild zooplankton grow faster than those fed only rotifers, the mechanisms involved in thi...

    Authors: Matthew L. Rise, Jennifer R. Hall, Gordon W. Nash, Xi Xue, Marije Booman, Tomer Katan and A. Kurt Gamperl
    Citation: BMC Genomics 2015 16:1016
    Content type: Research article Published on:

  35. Polyketide synthase (PKS) catalyzes the biosynthesis of polyketides, which are structurally and functionally diverse natural products in microorganisms and plants. Here, we have analyzed available full genome ...

    Authors: Ekaterina Shelest, Natalie Heimerl, Maximilian Fichtner and Severin Sasso
    Citation: BMC Genomics 2015 16:1015
    Content type: Research article Published on:

  36. Functions of most genes predicted in the soybean genome have not been clarified. A mutant library with a high mutation density would be helpful for functional studies and for identification of novel alleles us...

    Authors: Mai Tsuda, Akito Kaga, Toyoaki Anai, Takehiko Shimizu, Takashi Sayama, Kyoko Takagi, Kayo Machita, Satoshi Watanabe, Minoru Nishimura, Naohiro Yamada, Satomi Mori, Harumi Sasaki, Hiroyuki Kanamori, Yuichi Katayose and Masao Ishimoto
    Citation: BMC Genomics 2015 16:1014
    Content type: Research article Published on:

  37. The microstructure of trabecular bone is a composite trait governed by a complex interaction of multiple genetic determinants. Identifying these genetic factors should significantly improve our ability to pred...

    Authors: Roei Levy, Richard F. Mott, Fuad A. Iraqi and Yankel Gabet
    Citation: BMC Genomics 2015 16:1013
    Content type: Research article Published on:

  39. A central question for disease studies and crop improvements is how genetics variants drive phenotypes. Genome Wide Association Study (GWAS) provides a powerful tool for characterizing the genotype-phenotype r...

    Authors: Juexin Wang, Trupti Joshi, Babu Valliyodan, Haiying Shi, Yanchun Liang, Henry T. Nguyen, Jing Zhang and Dong Xu
    Citation: BMC Genomics 2015 16:1011
    Content type: Methodology article Published on:

  40. As a valuable medicinal plant, the yield of Panax ginseng is seriously affected by autotoxicity, which is a common phenomenon due to continuous cropping. However, the mechanism of autotoxicity in P. ginseng is st...

    Authors: Bin Wu, Qiliang Long, Yuan Gao, Zi Wang, Tianwei Shao, Yanan Liu, Yong Li and Wanlong Ding
    Citation: BMC Genomics 2015 16:1010
    Content type: Research article Published on:

  41. The largest of the tuna species, Atlantic bluefin tuna (Thunnus thynnus), inhabits the North Atlantic Ocean and the Mediterranean Sea and is considered to be an endangered species, largely a consequence of overfi...

    Authors: Željka Trumbić, Michaël Bekaert, John B. Taggart, James E. Bron, Karim Gharbi and Ivona Mladineo
    Citation: BMC Genomics 2015 16:1007
    Content type: Research article Published on:

  42. The Pacific white shrimp (Litopenaeus vannamei) is the world’s most prevalent cultured crustacean species. However, the supply of high-quality broodstocks is limited and baseline information related to its reprod...

    Authors: Jinxia Peng, Pinyuan Wei, Bin Zhang, Yongzhen Zhao, Digang Zeng, Xiuli Chen, Ming Li and Xiaohan Chen
    Citation: BMC Genomics 2015 16:1006
    Content type: Research article Published on:

  43. Plasmodium falciparum, the deadliest malaria-causing parasite, has an extremely AT-rich (80.7 %) genome. Because of high AT-content, sequence-based annotation of genes and functional e...

    Authors: Xueqing Maggie Lu, Evelien M. Bunnik, Neeti Pokhriyal, Sara Nasseri, Stefano Lonardi and Karine G. Le Roch
    Citation: BMC Genomics 2015 16:1005
    Content type: Methodology article Published on:

  44. The fungus Purpureocillium lilacinum is widely known as a biological control agent against plant parasitic nematodes. This research article consists of genomic annotation of the first draft of whole genome sequen...

    Authors: Pushplata Prasad, Deepti Varshney and Alok Adholeya
    Citation: BMC Genomics 2015 16:1004
    Content type: Research article Published on:

  45. Infinium HumanMethylation 450 BeadChip Arrays by Illumina (Illumina HM450K) are among the most popular CpG microarray platforms widely used in biological and medical research. Several recent studies highlighte...

    Authors: Patrycja Daca-Roszak, Aleksandra Pfeifer, Jadwiga Żebracka-Gala, Dagmara Rusinek, Aleksandra Szybińska, Barbara Jarząb, Michał Witt and Ewa Ziętkiewicz
    Citation: BMC Genomics 2015 16:1003
    Content type: Research article Published on:

  46. The clinical course of chronic lymphocytic leukemia (CLL) is highly variable; some patients follow an indolent course, but others progress to a more advanced stage. The mutational status of rearranged immunogl...

    Authors: Sally Yepes, Maria Mercedes Torres and Liliana López-Kleine
    Citation: BMC Genomics 2015 16:1002
    Content type: Research article Published on:

  47. Natural rubber, an important industrial raw material, is specifically synthesized in laticifers located inside the rubber tree (Hevea brasiliensis Muell. Arg.) trunk. Due to the absence of plasmodesmata, the lati...

    Authors: Zhi Zou, Jun Gong, Feng An, Guishui Xie, Jikun Wang, Yeyong Mo and Lifu Yang
    Citation: BMC Genomics 2015 16:1001
    Content type: Research article Published on:

  48. The analysis of differential gene expression is a fundamental tool to relate gene regulation with specific biological processes. Differential binding of transcription factors (TFs) can drive differential gene ...

    Authors: Jason Piper, Salam A. Assi, Pierre Cauchy, Christophe Ladroue, Peter N. Cockerill, Constanze Bonifer and Sascha Ott
    Citation: BMC Genomics 2015 16:1000
    Content type: Methodology article Published on:

  49. MicroRNAs (miRNAs) are small regulatory RNA that mediate RNA interference by binding to various mRNA target regions. There have been several computational methods for the identification of target mRNAs for miR...

    Authors: Asish Ghoshal, Raghavendran Shankar, Saurabh Bagchi, Ananth Grama and Somali Chaterji
    Citation: BMC Genomics 2015 16:999
    Content type: Research Article Published on:

    The Erratum to this article has been published in BMC Genomics 2016 17:216

  50. Whole-exome sequencing (WES) is rapidly evolving into a tool of choice for rapid, and inexpensive identification of molecular genetic lesions within targeted regions of the human genome. While biases in WES co...

    Authors: Praveen F. Cherukuri, Valerie Maduro, Karin V. Fuentes-Fajardo, Kevin Lam, David R. Adams, Cynthia J. Tifft, James C. Mullikin, William A. Gahl and Cornelius F. Boerkoel
    Citation: BMC Genomics 2015 16:998
    Content type: Research article Published on:

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BMC Genomics

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