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  1. Major secondary metabolites, including flavonoids, caffeine, and theanine, are important components of tea products and are closely related to the taste, flavor, and health benefits of tea. Secondary metabolit...

    Authors: Chun-Fang Li, Yan Zhu, Yao Yu, Qiong-Yi Zhao, Sheng-Jun Wang, Xin-Chao Wang, Ming-Zhe Yao, Da Luo, Xuan Li, Liang Chen and Ya-Jun Yang
    Citation: BMC Genomics 2015 16:560
    Content type: Research article Published on:

  2. One of the most important global pathogens infecting all age groups is Streptococcus pneumoniae (the ‘pneumococcus’). Pneumococci reside in the paediatric nasopharynx, where they compete for space and resources, ...

    Authors: Carlijn Bogaardt, Andries J van Tonder and Angela B Brueggemann
    Citation: BMC Genomics 2015 16:554
    Content type: Research article Published on:

  3. Two major mycoparasitic lineages, the family Hypocreaceae and the genus Tolypocladium, exist within the fungal order, Hypocreales. Peptaibiotics are a group of secondary metabolites almost exclusively described f...

    Authors: C. Alisha Quandt, Kathryn E. Bushley and Joseph W. Spatafora
    Citation: BMC Genomics 2015 16:553
    Content type: Research article Published on:

  6. Vernalization is an obligatory requirement of extended exposure to low temperatures to induce flowering in certain plants. It is the most important factor affecting flowering time and quality in Easter lily (Lili...

    Authors: Carlos Villacorta-Martin, Francisco F. Núñez de Cáceres González, Jorn de Haan, Kitty Huijben, Paul Passarinho, Maya Lugassi-Ben Hamo and Michele Zaccai
    Citation: BMC Genomics 2015 16:550
    Content type: Research article Published on:

  7. The role of viruses as members of the human microbiome has gained broader attention with the discovery that human body surfaces are inhabited by sizeable viral communities. The majority of the viruses identifi...

    Authors: Tasha M. Santiago-Rodriguez, Mayuri Naidu, Shira R. Abeles, Tobias K. Boehm, Melissa Ly and David T. Pride
    Citation: BMC Genomics 2015 16:549
    Content type: Research article Published on:

  8. Massively parallel cDNA sequencing (RNA-seq) experiments are gradually superseding microarrays in quantitative gene expression profiling. However, many biologists are uncertain about the choice of differential...

    Authors: Anto P. Rajkumar, Per Qvist, Ross Lazarus, Francesco Lescai, Jia Ju, Mette Nyegaard, Ole Mors, Anders D. Børglum, Qibin Li and Jane H. Christensen
    Citation: BMC Genomics 2015 16:548
    Content type: Research article Published on:

  9. Although the responses to many pathogen associated molecular patterns (PAMPs) in cell cultures and extracted organs are well characterized, there is little known of transcriptome responses to PAMPs in whole or...

    Authors: Shuxin Yang, Rubén Marín-Juez, Annemarie H. Meijer and Herman P. Spaink
    Citation: BMC Genomics 2015 16:547
    Content type: Research article Published on:

  10. Silene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this spe...

    Authors: N Blavet, H Blavet, A Muyle, J Käfer, R Cegan, C Deschamps, N Zemp, S Mousset, S Aubourg, R Bergero, D Charlesworth, R Hobza, A Widmer and GAB Marais
    Citation: BMC Genomics 2015 16:546
    Content type: Research article Published on:

  11. Nr2e1 (nuclear receptor subfamily 2, group e, member 1) encodes a transcription factor important in neocortex development. Previous work has shown that nuclear receptors can have hundr...

    Authors: Jean-François Schmouth, David Arenillas, Ximena Corso-Díaz, Yuan-Yun Xie, Slavita Bohacec, Kathleen G. Banks, Russell J. Bonaguro, Siaw H. Wong, Steven J. M. Jones, Marco A. Marra, Elizabeth M. Simpson and Wyeth W. Wasserman
    Citation: BMC Genomics 2015 16:545
    Content type: Research article Published on:

  12. Accurate genome assembly and gene model annotation are critical for comparative species and gene functional analyses. Here we present the completed genome sequence and annotation of the reference strain PH-1 of F...

    Authors: Robert King, Martin Urban, Michael C. U. Hammond-Kosack, Keywan Hassani-Pak and Kim E. Hammond-Kosack
    Citation: BMC Genomics 2015 16:544
    Content type: Research article Published on:

  13. Serine/threonine kinase 33 (STK33) has been shown to be conserved across all major vertebrate classes including reptiles, mammals, amphibians and fish, suggesting its importance within vertebrates. It has been...

    Authors: Tobias Lautwein, Steffen Lerch, Daniel Schäfer and Erwin R. Schmidt
    Citation: BMC Genomics 2015 16:543
    Content type: Research article Published on:

  14. Recent developments in sequencing technology have facilitated widespread investigations of genomic variants, including continuous stretches of homozygous genomic regions. For cattle, a large proportion of thes...

    Authors: Qianqian Zhang, Bernt Guldbrandtsen, Mirte Bosse, Mogens S Lund and Goutam Sahana
    Citation: BMC Genomics 2015 16:542
    Content type: Research article Published on:

  15. There is a limited capacity to repair damage in the mammalian heart after birth, which is primarily due to the inability of cardiomyocytes to proliferate after birth. This is in contrast to zebrafish and salam...

    Authors: Janna L Morrison, Song Zhang, Ross L Tellam, Doug A Brooks, I Caroline McMillen, Enzo R Porrello and Kimberley J Botting
    Citation: BMC Genomics 2015 16:541
    Content type: Research article Published on:

  16. Defence mechanisms of organisms are shaped by their lifestyle, environment and pathogen pressure. Carpenter ants are social insects which live in huge colonies comprising genetically closely related individual...

    Authors: Shishir K. Gupta, Maria Kupper, Carolin Ratzka, Heike Feldhaar, Andreas Vilcinskas, Roy Gross, Thomas Dandekar and Frank Förster
    Citation: BMC Genomics 2015 16:540
    Content type: Research article Published on:

  17. Plant growth-promoting rhizobacteria (PGPR) can protect plants against pathogenic microbes through a diversity of mechanisms including competition for nutrients, production of antibiotics, and stimulation of t...

    Authors: Roeland L. Berendsen, Marcel C. van Verk, Ioannis A. Stringlis, Christos Zamioudis, Jan Tommassen, Corné M. J. Pieterse and Peter A. H. M. Bakker
    Citation: BMC Genomics 2015 16:539
    Content type: Research article Published on:

  18. Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not...

    Authors: Dario Copetti, Jianwei Zhang, Moaine El Baidouri, Dongying Gao, Jun Wang, Elena Barghini, Rosa M. Cossu, Angelina Angelova, Carlos E. Maldonado L., Stefan Roffler, Hajime Ohyanagi, Thomas Wicker, Chuanzhu Fan, Andrea Zuccolo, Mingsheng Chen, Antonio Costa de Oliveira…
    Citation: BMC Genomics 2015 16:538
    Content type: Methodology article Published on:

  19. Wine produced at low temperature is often considered to improve sensory qualities. However, there are certain drawbacks to low temperature fermentations: e.g. low growth rate, long lag phase, and sluggish or s...

    Authors: María López-Malo, Estéfani García-Rios, Bruno Melgar, Monica R Sanchez, Maitreya J Dunham and José Manuel Guillamón
    Citation: BMC Genomics 2015 16:537
    Content type: Research article Published on:

  20. Differences in gene expression have a significant role in the diversity of phenotypes in humans. Here we integrated human public data from ENCODE, 1000 Genomes and Geuvadis to explore the populational landscap...

    Authors: André M. Ribeiro-dos-Santos, Vandeclécio L. da Silva, Jorge E.S. de Souza and Sandro J. de Souza
    Citation: BMC Genomics 2015 16:536
    Content type: Research article Published on:

  21. Major histocompatibility complex (MHC) class I genes are found in the genomes of all jawed vertebrates. The evolution of this gene family is closely tied to the evolution of the vertebrate genome. Family membe...

    Authors: Anthony T Papenfuss, Zhi-Ping Feng, Katina Krasnec, Janine E Deakin, Michelle L Baker and Robert D Miller
    Citation: BMC Genomics 2015 16:535
    Content type: Research article Published on:

  22. Sweet sorghum is an annual C4 crop considered to be one of the most promising bio-energy crops due to its high sugar content in stem, yet it is poorly understood how this plant increases its sugar content in r...

    Authors: Na Sui, Zhen Yang, Mingli Liu and Baoshan Wang
    Citation: BMC Genomics 2015 16:534
    Content type: Research article Published on:

  23. Protein phosphorylation regulated by plant hormone is involved in the coordination of fundamental plant development. Brassinosteroids (BRs), a group of phytohormones, regulated phosphorylation dynamics remains...

    Authors: Li-Ling Lin, Chia-Lang Hsu, Chia-Wei Hu, Shiao-Yun Ko, Hsu-Liang Hsieh, Hsuan-Cheng Huang and Hsueh-Fen Juan
    Citation: BMC Genomics 2015 16:533
    Content type: Research article Published on:

  24. Insects use pheromones, chemical signals that underlie all animal behaviors, for communication and for attracting mates. Synthetic pheromones are widely used in pest control strategies because they are environ...

    Authors: Binu Antony, Alan Soffan, Jernej Jakše, Sulieman Alfaifi, Koko D. Sutanto, Saleh A. Aldosari, Abdulrahman S. Aldawood and Arnab Pain
    Citation: BMC Genomics 2015 16:532
    Content type: Research article Published on:

  25. Entomopathogenic associations between nematodes in the genera Steinernema and Heterorhabdus with their cognate bacteria from the bacterial genera Xenorhabdus and Photorhabdus, respectively, are extensively studie...

    Authors: Feseha Abebe-Akele, Louis S. Tisa, Vaughn S. Cooper, Philip J. Hatcher, Eyualem Abebe and W. Kelley Thomas
    Citation: BMC Genomics 2015 16:531
    Content type: Research article Published on:

  26. Genome-wide association studies show that most human traits and diseases are caused by a combination of environmental and genetic causes, with each one of these having a relatively small effect. In contrast, m...

    Authors: Miguel Angel Varela
    Citation: BMC Genomics 2015 16:530
    Content type: Research article Published on:

  27. The airway epithelial cell plays a central role in coordinating the pulmonary response to injury and inflammation. Here, transforming growth factor-β (TGFβ) activates gene expression programs to induce stem ce...

    Authors: Bing Tian, Xueling Li, Mridul Kalita, Steven G. Widen, Jun Yang, Suresh K. Bhavnani, Bryant Dang, Andrzej Kudlicki, Mala Sinha, Fanping Kong, Thomas G. Wood, Bruce A. Luxon and Allan R. Brasier
    Citation: BMC Genomics 2015 16:529
    Content type: Research article Published on:

  28. Most microbial eukaryotes are uncultivated and thus poorly suited to standard genomic techniques. This is the case for Polykrikos lebouriae, a dinoflagellate with ultrastructurally aberrant plastids. It has been ...

    Authors: Gregory S. Gavelis, Richard A. White III, Curtis A. Suttle, Patrick J. Keeling and Brian S. Leander
    Citation: BMC Genomics 2015 16:528
    Content type: Research article Published on:

  29. Genome wide sequence analyses of malaria parasites from widely separated areas of the world have identified contrasting population structures and signatures of selection. To compare relatively closely situated...

    Authors: Craig W. Duffy, Samuel A. Assefa, James Abugri, Nicholas Amoako, Seth Owusu-Agyei, Thomas Anyorigiya, Bronwyn MacInnis, Dominic P. Kwiatkowski, David J. Conway and Gordon A. Awandare
    Citation: BMC Genomics 2015 16:527
    Content type: Research article Published on:

  31. Neurotransmitter signaling systems play crucial roles in multiple physiological and behavioral processes in insects. Genome wide analyses of de novo transcriptome sequencing and gene specific expression profiling...

    Authors: Gang Xu, Shun-Fan Wu, Ya-Su Wu, Gui-Xiang Gu, Qi Fang and Gong-Yin Ye
    Citation: BMC Genomics 2015 16:525
    Content type: Research article Published on:

  32. The Xanthomonas citri pv. citri (X. citri) is a phytopathogenic bacterium that infects different species of citrus plants where it causes canker disease. The adaptation to different habitats is related to the abi...

    Authors: Cristiane Tambascia Pereira, Alexandre Moutran, Melissa Fessel and Andrea Balan
    Citation: BMC Genomics 2015 16:524
    Content type: Research article Published on:

  33. Transcriptional enhancers are generally known to regulate gene transcription from afar. Their activation involves a series of changes in chromatin marks and recruitment of protein factors. These enhancers may ...

    Authors: Juan González-Vallinas, Amadís Pagès, Babita Singh and Eduardo Eyras
    Citation: BMC Genomics 2015 16:523
    Content type: Research article Published on:

  34. Next-generation sequencing technologies are rapidly generating whole-genome datasets for an increasing number of organisms. However, phylogenetic reconstruction of genomic data remains difficult because de novo a...

    Authors: Huan Fan, Anthony R. Ives, Yann Surget-Groba and Charles H. Cannon
    Citation: BMC Genomics 2015 16:522
    Content type: Methodology article Published on:

  35. The blue crab, Callinectes sapidus, is economically and ecologically important in western Atlantic and Gulf of Mexico coastal estuaries. In 2010 blue crabs in the northern Gulf of Mexico were exposed to crude oil...

    Authors: Bree K. Yednock, Timothy J. Sullivan and Joseph E. Neigel
    Citation: BMC Genomics 2015 16:521
    Content type: Research article Published on:

  36. SWEET (MtN3_saliva) domain proteins, a recently identified group of efflux transporters, play an indispensable role in sugar efflux, phloem loading, plant-pathogen interaction and reproductive tissue development....

    Authors: Gunvant Patil, Babu Valliyodan, Rupesh Deshmukh, Silvas Prince, Bjorn Nicander, Mingzhe Zhao, Humira Sonah, Li Song, Li Lin, Juhi Chaudhary, Yang Liu, Trupti Joshi, Dong Xu and Henry T. Nguyen
    Citation: BMC Genomics 2015 16:520
    Content type: Research article Published on:

  37. Drosophila melanogaster activates a variety of immune responses against microbial infections. However, information on the Drosophila immune response to entomopathogenic nematode infect...

    Authors: Julio C. Castillo, Todd Creasy, Priti Kumari, Amol Shetty, Upasana Shokal, Luke J. Tallon and Ioannis Eleftherianos
    Citation: BMC Genomics 2015 16:519
    Content type: Research article Published on:

  38. With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ec...

    Authors: Zachary L. Fuller, Elina L. Niño, Harland M. Patch, Oscar C. Bedoya-Reina, Tracey Baumgarten, Elliud Muli, Fiona Mumoki, Aakrosh Ratan, John McGraw, Maryann Frazier, Daniel Masiga, Stephen Schuster, Christina M. Grozinger and Webb Miller
    Citation: BMC Genomics 2015 16:518
    Content type: Research article Published on:

  39. Resident macrophages in the CNS microglia become activated and produce proinflammatory molecules upon encountering bacteria or viruses. TLRs are a phylogenetically conserved diverse family of sensors that driv...

    Authors: Amitabh Das, Jin Choul Chai, Sun Hwa Kim, Young Seek Lee, Kyoung Sun Park, Kyoung Hwa Jung and Young Gyu Chai
    Citation: BMC Genomics 2015 16:517
    Content type: Research article Published on:

  40. The presence of variability in the response of pigs to Porcine Reproductive and Respiratory Syndrome virus (PRRSv) infection, and recent demonstration of significant genetic control of such responses, leads us...

    Authors: Martine Schroyen, Juan P. Steibel, James E. Koltes, Igseo Choi, Nancy E. Raney, Christopher Eisley, Eric Fritz-Waters, James M. Reecy, Jack C. M. Dekkers, Robert R. R. Rowland, Joan K. Lunney, Catherine W. Ernst and Christopher K. Tuggle
    Citation: BMC Genomics 2015 16:516
    Content type: Research article Published on:

  42. Identification of the causative genes of retinitis pigmentosa (RP) is important for the clinical care of patients with RP. However, a comprehensive genetic study has not been performed in Korean RP patients. M...

    Authors: Chang-Ki Yoon, Nayoung K. D. Kim, Je-Gun Joung, Joo Young Shin, Jung Hyun Park, Hye-Hyun Eum, Hae-ock Lee, Woong-Yang Park and Hyeong Gon Yu
    Citation: BMC Genomics 2015 16:515
    Content type: Research article Published on:

  43. Laboratory evolution is an important tool for developing robust yeast strains for bioethanol production since the biological basis behind combined tolerance requires complex alterations whose proper regulation...

    Authors: Valeria Wallace-Salinas, Daniel P. Brink, Dag Ahrén and Marie F. Gorwa-Grauslund
    Citation: BMC Genomics 2015 16:514
    Content type: Research article Published on:

  45. Acyl-coA binding proteins (ACBPs) bind long chain acyl-CoA esters with very high affinity. Their possible involvement in fatty acid transportation from the plastid to the endoplasmic reticulum, prior to the fo...

    Authors: Nadia Haingotiana Raboanatahiry, Yongtai Yin, Li Chen and Maoteng Li
    Citation: BMC Genomics 2015 16:512
    Content type: Research article Published on:

  46. Messenger RNA polyadenylation is an essential step for the maturation of most eukaryotic mRNAs. Accurate determination of poly(A) sites helps define the 3’-ends of genes, which is important for genome annotati...

    Authors: Xiaohui Wu, Yong Zeng, Jinting Guan, Guoli Ji, Rongting Huang and Qingshun Q. Li
    Citation: BMC Genomics 2015 16:511
    Content type: Research article Published on:

  47. Host-range restricted poxviruses make promising vaccine vectors due to their safety profile and immunogenicity. An understanding of the host innate immune responses produced by different poxvirus vectors would...

    Authors: Kristy Offerman, Armin Deffur, Olivia Carulei, Robert Wilkinson, Nicola Douglass and Anna-Lise Williamson
    Citation: BMC Genomics 2015 16:510
    Content type: Research article Published on:

  48. Metabolic syndrome is a multi-component disorder associated to a high risk of cardiovascular disease. Its etiology is the result of a complex interaction between genetic and environmental factors, including di...

    Authors: Oriol Alberto Rangel-Zúñiga, Antonio Camargo, Carmen Marin, Patricia Peña-Orihuela, Pablo Pérez-Martínez, Javier Delgado-Lista, Lorena González-Guardia, Elena M. Yubero-Serrano, Francisco J. Tinahones, María M. Malagón, Francisco Pérez-Jiménez, Helen M. Roche and José López-Miranda
    Citation: BMC Genomics 2015 16:509
    Content type: Research article Published on:

  49. Like other structural variants, transposable element insertions can be highly polymorphic across individuals. Their functional impact, however, remains poorly understood. Current genome-wide approaches for gen...

    Authors: Alexandre Kuhn, Yao Min Ong, Stephen R. Quake and William F. Burkholder
    Citation: BMC Genomics 2015 16:508
    Content type: Methodology article Published on:

  50. The presence of methyl groups on cytosine nucleotides across an organism’s genome (methylation) is a major regulator of genome stability, crossing over, and gene regulation. The capacity for DNA methylation to...

    Authors: Jack M. Colicchio, Fumihito Miura, John K. Kelly, Takashi Ito and Lena C. Hileman
    Citation: BMC Genomics 2015 16:507
    Content type: Research article Published on:

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BMC Genomics

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