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  1. Lipids are a class of molecules that play an important role in cellular structure and metabolism in all cell types. In the last few decades, it has been reported that long-chain fatty acids (FAs) are involved ...

    Authors: Aline S. M. Cesar, Luciana C. A. Regitano, Mirele D. Poleti, Sónia C. S. Andrade, Polyana C. Tizioto, Priscila S. N. Oliveira, Andrezza M. Felício, Michele L. do Nascimento, Amália S. Chaves, Dante P. D. Lanna, Rymer R. Tullio, Renata T. Nassu, James E. Koltes, Eric Fritz-Waters, Gerson B. Mourão, Adhemar Zerlotini-Neto…
    Citation: BMC Genomics 2016 17:961
    Content type: Research article Published on:

  2. Hybridization is a prominent process in the evolution of crop plants that can give rise to gene expression variation, phenotypic novelty and heterosis. Maize is the most successful crop in utilizing heterosis....

    Authors: Xiaojiao Hu, Hongwu Wang, Xizhou Diao, Zhifang Liu, Kun Li, Yujin Wu, Qianjin Liang, Hui Wang and Changling Huang
    Citation: BMC Genomics 2016 17:959
    Content type: Research article Published on:

  4. The fight against grapevine diseases due to biotrophic pathogens usually requires the massive use of chemical fungicides with harmful environmental effects. An alternative strategy could be the use of compound...

    Authors: Marie-Cécile Dufour, Noël Magnin, Bernard Dumas, Sophie Vergnes and Marie-France Corio-Costet
    Citation: BMC Genomics 2016 17:957
    Content type: Research article Published on:

  5. Human central memory CD4 T cells are characterized by their capacity of proliferation and differentiation into effector memory CD4 T cells. Homeostasis of central memory CD4 T cells is considered a key factor ...

    Authors: Gustavo Olvera-García, Tania Aguilar-García, Fany Gutiérrez-Jasso, Iván Imaz-Rosshandler, Claudia Rangel-Escareño, Lorena Orozco, Irma Aguilar-Delfín, Joel A. Vázquez-Pérez, Joaquín Zúñiga, Santiago Pérez-Patrigeon and Enrique Espinosa
    Citation: BMC Genomics 2016 17:956
    Content type: Research article Published on:

  7. Plant allelochemicals act as toxins, inhibitors of digestion, and deterrents that affect the fecundity of insects. These compounds have attracted significant research attention in recent decades, and much is k...

    Authors: Lei Zhang, Yao Lu, Min Xiang, Qingli Shang and Xiwu Gao
    Citation: BMC Genomics 2016 17:954
    Content type: Research article Published on:

  8. The Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass species including the cereal crops barley and rye. A sexual stage has not been described, but se...

    Authors: Daniel Penselin, Martin Münsterkötter, Susanne Kirsten, Marius Felder, Stefan Taudien, Matthias Platzer, Kevin Ashelford, Konrad H. Paskiewicz, Richard J. Harrison, David J. Hughes, Thomas Wolf, Ekaterina Shelest, Jenny Graap, Jan Hoffmann, Claudia Wenzel, Nadine Wöltje…
    Citation: BMC Genomics 2016 17:953
    Content type: Research article Published on:

  9. G-quadruplexes are increasingly recognized as regulatory elements in human, animal, bacterial and plant genomes. The presence and function of G-quadruplexes are not well studied among herpesviruses; in particu...

    Authors: Banhi Biswas, Manish Kandpal, Utkarsh Kumar Jauhari and Perumal Vivekanandan
    Citation: BMC Genomics 2016 17:949
    Content type: Research article Published on:

  10. Synthetic biology approaches are promising new strategies for control of pest insects that transmit disease and cause agricultural damage. These strategies require characterised modular components that can dir...

    Authors: Elizabeth R. Sutton, Yachuan Yu, Sebastian M. Shimeld, Helen White-Cooper and and Luke Alphey
    Citation: BMC Genomics 2016 17:948
    Content type: Research article Published on:

  11. Whole genome sequencing (WGS) has rapidly become an important research tool in tuberculosis epidemiology and is likely to replace many existing methods in public health microbiology in the near future. WGS-bas...

    Authors: Tyler S. Brown, Apurva Narechania, John R. Walker, Paul J. Planet, Pablo J. Bifani, Sergios-Orestis Kolokotronis, Barry N. Kreiswirth and Barun Mathema
    Citation: BMC Genomics 2016 17:947
    Content type: Research article Published on:

  12. Maize (Zea mays) husk referring to the leafy outer enclosing the ear, plays an important role in grain production by directly contributing photosynthate and protecting ear from pathogen infection. Although the...

    Authors: Zhenhai Cui, Jinhong Luo, Chuangye Qi, Yanye Ruan, Jing Li, Ao Zhang, Xiaohong Yang and Yan He
    Citation: BMC Genomics 2016 17:946
    Content type: Research article Published on:

  13. Sweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more...

    Authors: Zengzhi Si, Bing Du, Jinxi Huo, Shaozhen He, Qingchang Liu and Hong Zhai
    Citation: BMC Genomics 2016 17:945
    Content type: Research article Published on:

  14. Mesenchymal Stromal/Stem Cells (MSCs), isolated under the criteria established by the ISCT, still have a poorly characterized phenotype that is difficult to distinguish from similar cell populations. Although ...

    Authors: Beatriz Roson-Burgo, Fermin Sanchez-Guijo, Consuelo Del Cañizo and Javier De Las Rivas
    Citation: BMC Genomics 2016 17:944
    Content type: Research Article Published on:

  15. Knowledge on population structure and genetic diversity in vegetable crops is essential for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for...

    Authors: F. Taranto, N. D’Agostino, B. Greco, T. Cardi and P. Tripodi
    Citation: BMC Genomics 2016 17:943
    Content type: Research article Published on:

  16. The gutless marine worm Olavius algarvensis has a completely reduced digestive and excretory system, and lives in an obligate nutritional symbiosis with bacterial symbionts. While considerable knowledge has been ...

    Authors: Juliane Wippler, Manuel Kleiner, Christian Lott, Alexander Gruhl, Paul E. Abraham, Richard J. Giannone, Jacque C. Young, Robert L. Hettich and Nicole Dubilier
    Citation: BMC Genomics 2016 17:942
    Content type: Research article Published on:

  17. Host genetics is one of several factors known to shape human gut microbiome composition, however, the physiological processes underlying the heritability are largely unknown. Inter-individual differences in ho...

    Authors: Emily R. Davenport, Julia K. Goodrich, Jordana T. Bell, Tim D. Spector, Ruth E. Ley and Andrew G. Clark
    Citation: BMC Genomics 2016 17:941
    Content type: Research article Published on:

  18. Graves’ disease is an autoimmune thyroid disease of complex inheritance. Multiple genetic susceptibility loci are thought to be involved in Graves’ disease and it is therefore likely that these can be identifi...

    Authors: Jwu Jin Khong, Kathryn P. Burdon, Yi Lu, Kate Laurie, Lefta Leonardos, Paul N. Baird, Srujana Sahebjada, John P. Walsh, Adam Gajdatsy, Peter R. Ebeling, Peter Shane Hamblin, Rosemary Wong, Simon P. Forehan, Spiros Fourlanos, Anthony P. Roberts, Matthew Doogue…
    Citation: BMC Genomics 2016 17:939
    Content type: Methodology article Published on:

  19. ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friend...

    Authors: Giovanna Ambrosini, René Dreos, Sunil Kumar and Philipp Bucher
    Citation: BMC Genomics 2016 17:938
    Content type: Software Published on:

  20. The large Gondwanan plant family Proteaceae is an early-diverging eudicot lineage renowned for its morphological, taxonomic and ecological diversity. Macadamia is the most economically important Proteaceae cro...

    Authors: Catherine J. Nock, Abdul Baten, Bronwyn J. Barkla, Agnelo Furtado, Robert J. Henry and Graham J. King
    Citation: BMC Genomics 2016 17:937
    Content type: Research article Published on:

  21. Diabetic nephropathy (DN) is a major complication of type1 and type 2 diabetes. Understanding how diabetes regulate transcriptome dynamics in DN is important for understanding the biology of the disease and fo...

    Authors: Ana Rubin, Anna C. Salzberg, Yuka Imamura, Anzor Grivitishvilli and Joyce Tombran-Tink
    Citation: BMC Genomics 2016 17:936
    Content type: Research article Published on:

  22. Hickory (Carya cathayensis), a woody plant with high nutritional and economic value, is widely planted in China. Due to its long juvenile phase, grafting is a useful technique for large-scale cultivation of hicko...

    Authors: Lingling Qiu, Bo Jiang, Jia Fang, Yike Shen, Zhongxiang Fang, Saravana Kumar RM, Keke Yi, Chenjia Shen, Daoliang Yan and Bingsong Zheng
    Citation: BMC Genomics 2016 17:935
    Content type: Research article Published on:

  24. Genetic recombination is a driving force in genome evolution. Among viruses it has a dual role. For genomes with higher fitness, it maintains genome integrity in the face of high mutation rates. Conversely, fo...

    Authors: Ann C. Gregory, Sergei A. Solonenko, J. Cesar Ignacio-Espinoza, Kurt LaButti, Alex Copeland, Sebastian Sudek, Ashley Maitland, Lauren Chittick, Filipa dos Santos, Joshua S. Weitz, Alexandra Z. Worden, Tanja Woyke and Matthew B. Sullivan
    Citation: BMC Genomics 2016 17:930
    Content type: Research article Published on:

  25. Symplocos paniculata, asiatic sweetleaf or sapphire berry, is a widespread shrub or small tree from Symplocaceae with high oil content and excellent fatty acid composition in fruit. It...

    Authors: Qiang Liu, Youping Sun, Jinzheng Chen, Peiwang Li, Changzhu Li, Genhua Niu and Lijuan Jiang
    Citation: BMC Genomics 2016 17:929
    Content type: Research article Published on:

  26. In mammals, CEACAM1 and closely related members represent paired receptors with similar extracellular ligand-binding regions and cytoplasmic domains with opposing functions. Human CEACAM1 and CEACAM3 which hav...

    Authors: Wolfgang Zimmermann and Robert Kammerer
    Citation: BMC Genomics 2016 17:928
    Content type: Research article Published on:

  28. Varroa mites are widely considered the biggest honey bee health problem worldwide. Until recently, Varroa jacobsoni has been found to live and reproduce only in Asian honey bee (Apis c...

    Authors: Gladys K. Andino, Michael Gribskov, Denis L. Anderson, Jay D. Evans and Greg J. Hunt
    Citation: BMC Genomics 2016 17:926
    Content type: Research article Published on:

  29. Recent (2013 and 2009) zoonotic transmission of avian or porcine influenza to humans highlights an increase in host range by evading species barriers. Gene reassortment or antigenic shift between viruses from ...

    Authors: Fatemeh Kargarfard, Ashkan Sami, Manijeh Mohammadi-Dehcheshmeh and Esmaeil Ebrahimie
    Citation: BMC Genomics 2016 17:925
    Content type: Research article Published on:

  30. While a few studies on the variations in mRNA expression and half-lives measured under different growth conditions have been used to predict patterns of regulation in bacterial organisms, the extent to which t...

    Authors: Joseph R. Peterson, ShengShee Thor, Lars Kohler, Petra R.A. Kohler, William W. Metcalf and Zaida Luthey-Schulten
    Citation: BMC Genomics 2016 17:924
    Content type: Research Article Published on:

  31. Mouse models have served a valuable role in deciphering various facets of Salivary Gland (SG) biology, from normal developmental programs to diseased states. To facilitate such studies, gene expression profili...

    Authors: Christian Gluck, Sangwon Min, Akinsola Oyelakin, Kirsten Smalley, Satrajit Sinha and Rose-Anne Romano
    Citation: BMC Genomics 2016 17:923
    Content type: Research article Published on:

  32. MicroRNAs (miRNAs) are critical regulators responding to acute environmental stresses in both plants and animals. By modulating gene expression, miRNAs either restore or reconstitute a new expression program t...

    Authors: I-Chen Hung, Yu-Chuan Hsiao, H. Sunny Sun, Tsung-Ming Chen and Shyh-Jye Lee
    Citation: BMC Genomics 2016 17:922
    Content type: Research article Published on:

  34. Yeast-to-hypha transition is a major morphological change in fungi. Molecular regulators and pathways that are involved in this process have been extensively studied in model species, including Saccharomyces cere...

    Authors: M. Nigg and L. Bernier
    Citation: BMC Genomics 2016 17:920
    Content type: Research article Published on:

  35. Hop (Humulus lupulus L.) plants are grown primarily for the brewing industry and have been used as a traditional medicinal herb for a long time. Severe hop stunt disease caused by the recently discovered Citrus b...

    Authors: Ajay Kumar Mishra, Ganesh Selvaraj Duraisamy, Jaroslav Matoušek, Sebastjan Radisek, Branka Javornik and Jernej Jakse
    Citation: BMC Genomics 2016 17:919
    Content type: Research article Published on:

  36. Sulfate-reducing bacteria (SRB) are key players of the carbon- and sulfur-cycles in the sediments of the world’s oceans. Habitat relevant SRBs are often members of the Desulfosarcina-Desulfococcus clade belonging...

    Authors: Marvin Dörries, Lars Wöhlbrand, Michael Kube, Richard Reinhardt and Ralf Rabus
    Citation: BMC Genomics 2016 17:918
    Content type: Research article Published on:

  37. The bacterial CRISPR system is fast becoming the most popular genetic and epigenetic engineering tool due to its universal applicability and adaptability. The desire to deploy CRISPR-based methods in a large v...

    Authors: Anna Köferle, Karolina Worf, Christopher Breunig, Valentin Baumann, Javier Herrero, Maximilian Wiesbeck, Lukas H. Hutter, Magdalena Götz, Christiane Fuchs, Stephan Beck and Stefan H. Stricker
    Citation: BMC Genomics 2016 17:917
    Content type: Methodology article Published on:

  38. Alpha satellite is the major repeated DNA element of primate centromeres. Evolution of these tandemly repeated sequences has led to the existence of numerous families of monomers exhibiting specific organizati...

    Authors: Lauriane Cacheux, Loïc Ponger, Michèle Gerbault-Seureau, Florence Anne Richard and Christophe Escudé
    Citation: BMC Genomics 2016 17:916
    Content type: Research article Published on:

  39. The maize kernel row number (KRN) is a key component that contributes to grain yield and has high broad-sense heritability (H 2 ). Quantitative tr...

    Authors: Changlin Liu, Qiang Zhou, Le Dong, Hui Wang, Fang Liu, Jianfeng Weng, Xinhai Li and Chuanxiao Xie
    Citation: BMC Genomics 2016 17:915
    Content type: Research article Published on:

  40. In a process known as phase variation, the marine bacterium and cholera pathogen Vibrio cholerae alternately expresses smooth or rugose colonial phenotypes, the latter being associated with advanced biofilm archi...

    Authors: Bliss Lambert, Maheshi Dassanayake, Dong-Ha Oh, Shana B. Garrett, Sang-Yeol Lee and Gregg S. Pettis
    Citation: BMC Genomics 2016 17:914
    Content type: Research article Published on:

  42. Next-generation sequencing (NGS) allows unbiased, in-depth interrogation of cancer genomes. Many somatic variant callers have been developed yet accurate ascertainment of somatic variants remains a considerabl...

    Authors: Jean-François Spinella, Pamela Mehanna, Ramon Vidal, Virginie Saillour, Pauline Cassart, Chantal Richer, Manon Ouimet, Jasmine Healy and Daniel Sinnett
    Citation: BMC Genomics 2016 17:912
    Content type: Software Published on:

  43. Gossypium hirsutum L., or upland cotton, is an important renewable resource for textile fiber. To enhance understanding of the genetic basis of cotton earliness, we constructed an intr...

    Authors: Xiaoyun Jia, Chaoyou Pang, Hengling Wei, Hantao Wang, Qifeng Ma, Jilong Yang, Shuaishuai Cheng, Junji Su, Shuli Fan, Meizhen Song, Nusireti Wusiman and Shuxun Yu
    Citation: BMC Genomics 2016 17:909
    Content type: Research article Published on:

  45. Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference ...

    Authors: Olivier Tremblay-Savard, Vladimir Reinharz and Jérôme Waldispühl
    Citation: BMC Genomics 2016 17(Suppl 10):862
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 10

  46. Transcriptome reconstruction, defined as the identification of all protein isoforms that may be expressed by a gene, is a notably difficult computational task. With real data, the best methods based on RNA-seq...

    Authors: Samuel Blanquart, Jean-Stéphane Varré, Paul Guertin, Amandine Perrin, Anne Bergeron and Krister M. Swenson
    Citation: BMC Genomics 2016 17(Suppl 10):786
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 10

  47. The most widely used state-of-the-art methods for reconstructing species phylogenies from genomic sequence data assume that sampled loci are identically and independently distributed. In principle, free recomb...

    Authors: Zhiwei Wang and Kevin J. Liu
    Citation: BMC Genomics 2016 17(Suppl 10):785
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 10

  49. Of the approximately two hundred sequenced plant genomes, how many and which ones were sequenced motivated by strictly or largely scientific considerations, and how many by chiefly economic, in a wide sense, i...

    Authors: Geneviève C. Vallée, Daniella Santos Muñoz and David Sankoff
    Citation: BMC Genomics 2016 17(Suppl 10):782
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 10

  50. Multiple sequence alignment is an important task in bioinformatics, and alignments of large datasets containing hundreds or thousands of sequences are increasingly of interest. While many alignment methods exi...

    Authors: Michael Nute and Tandy Warnow
    Citation: BMC Genomics 2016 17(Suppl 10):764
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 10

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BMC Genomics

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