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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  9. 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:

  10. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. Atherosclerosis is a heterogeneously distributed disease of arteries in which the endothelium plays an important central role. Spatial transcriptome profiling of endothelium in pre-lesional arteries has demons...

    Authors: Yi-Zhou Jiang, Elisabetta Manduchi, Christian J. Stoeckert Jr and Peter F. Davies
    Citation: BMC Genomics 2015 16:506
    Content type: Research article Published on:

  19. Since drought can seriously affect plant growth and development and little is known about how the oscillations of gene expression during the drought stress-acclimation response in soybean is affected, we appli...

    Authors: Fabiana Aparecida Rodrigues, Renata Fuganti-Pagliarini, Juliana Marcolino-Gomes, Thiago Jonas Nakayama, Hugo Bruno Correa Molinari, Francisco Pereira Lobo, Frank G Harmon and Alexandre Lima Nepomuceno
    Citation: BMC Genomics 2015 16:505
    Content type: Research article Published on:

  20. Solanum elaeagnifolium, an invasive weed of the Solanaceae family, is poorly studied although it poses a significant threat to crops. Here the analysis of the transcriptome of S. elaea...

    Authors: Aphrodite Tsaballa, Alexandros Nikolaidis, Foteini Trikka, Codruta Ignea, Sotirios C. Kampranis, Antonios M. Makris and Anagnostis Argiriou
    Citation: BMC Genomics 2015 16:504
    Content type: Research article Published on:

  22. Alfalfa (Medicago sativa L.) is the primary forage legume crop species in the United States and plays essential economic and ecological roles in agricultural systems across the country. Modern alfalfa is the resu...

    Authors: Jamie A. O’Rourke, Fengli Fu, Bruna Bucciarelli, S. Sam Yang, Deborah A. Samac, JoAnn F. S. Lamb, Maria J. Monteros, Michelle A. Graham, John W. Gronwald, Nick Krom, Jun Li, Xinbin Dai, Patrick X. Zhao and Carroll P. Vance
    Citation: BMC Genomics 2015 16:502
    Content type: Research article Published on:

  23. MetastamiRs have momentous clinical relevance and have been correlated with disease progression in many tumors. In this study, we identified neuroblastoma metastamiRs exploiting unique mouse models of favorabl...

    Authors: Faizan H Khan, Vijayabaskar Pandian, Satishkumar Ramraj, Sheeja Aravindan, Terence S Herman and Natarajan Aravindan
    Citation: BMC Genomics 2015 16:501
    Content type: Research article Published on:

  24. Hygienic behavior is a complex, genetically-based quantitative trait that serves as a key defense mechanism against parasites and diseases in Apis mellifera. Yet, the genomic basis and functional pathways involve...

    Authors: Sébastien Boutin, Mohamed Alburaki, Pierre-Luc Mercier, Pierre Giovenazzo and Nicolas Derome
    Citation: BMC Genomics 2015 16:500
    Content type: Research article Published on:

  25. Trypanosoma cruzi, the etiologic agent of Chagas disease, is currently divided into six discrete typing units (DTUs), named TcI–TcVI. CL Brener, the reference strain of the T. cruzi ge...

    Authors: João Luís Reis-Cunha, Gabriela F. Rodrigues-Luiz, Hugo O. Valdivia, Rodrigo P. Baptista, Tiago A. O. Mendes, Guilherme Loss de Morais, Rafael Guedes, Andrea M. Macedo, Caryn Bern, Robert H. Gilman, Carlos Talavera Lopez, Björn Andersson, Ana Tereza Vasconcelos and Daniella C. Bartholomeu
    Citation: BMC Genomics 2015 16:499
    Content type: Research article Published on:

  26. The genome of Campylobacter jejuni contains two iron activated Fur-family transcriptional regulators, CjFur and CjPerR, which are primarily responsible for regulating iron homeostasis and oxidative stress respect...

    Authors: James Butcher, Rebecca A. Handley, Arnoud H. M. van Vliet and Alain Stintzi
    Citation: BMC Genomics 2015 16:498
    Content type: Research article Published on:

  27. Copy number variation is an important dimension of genetic diversity and has implications in development and disease. As an important model organism, the mouse is a prime candidate for copy number variant (CNV...

    Authors: M Elizabeth O Locke, Maja Milojevic, Susan T Eitutis, Nisha Patel, Andrea E Wishart, Mark Daley and Kathleen A Hill
    Citation: BMC Genomics 2015 16:497
    Content type: Research article Published on:

  28. Horizontal gene transfer (HGT) has been widely identified in complete prokaryotic genomes. However, the roles of HGT among members of a microbial community and in evolution remain largely unknown. With the eme...

    Authors: Jiangtao Guo, Qi Wang, Xiaoqi Wang, Fumeng Wang, Jinxian Yao and Huaiqiu Zhu
    Citation: BMC Genomics 2015 16:496
    Content type: Research article Published on:

  29. Piscirickettsiosis or Salmonid Rickettsial Septicaemia (SRS) is a bacterial disease that has a major economic impact on the Chilean salmon farming industry. Despite the fact that Piscirickettsia salmonis has b...

    Authors: Rodrigo Pulgar, Christian Hödar, Dante Travisany, Alejandro Zuñiga, Calixto Domínguez, Alejandro Maass, Mauricio González and Verónica Cambiazo
    Citation: BMC Genomics 2015 16:495
    Content type: Research article Published on:

  30. The complex microbiome of the gut has an enormous impact on human health. Analysis of the transcriptional activity of microorganisms through mRNA sequencing (metatranscriptomics) opens a completely new window ...

    Authors: Michael Reck, Jürgen Tomasch, Zhiluo Deng, Michael Jarek, Peter Husemann and Irene Wagner-Döbler
    Citation: BMC Genomics 2015 16:494
    Content type: Research article Published on:

  32. Carotenoids are isoprenoid compounds synthesized by all photosynthetic organisms. Despite much research on carotenoid biosynthesis in the model plant Arabidopsis thaliana, there is a lack of information on the ca...

    Authors: Peirong Li, Shujiang Zhang, Shifan Zhang, Fei Li, Hui Zhang, Feng Cheng, Jian Wu, Xiaowu Wang and Rifei Sun
    Citation: BMC Genomics 2015 16:492
    Content type: Research article Published on:

  33. Oriental river prawn, Macrobrachium nipponense, is a commercially important species found in brackish and fresh waters throughout China. Chronic hypoxia is a major physiological challenge for prawns in culture, a...

    Authors: Shengming Sun, Fujun Xuan, Hongtuo Fu, Jian Zhu, Xianping Ge and Zhimin Gu
    Citation: BMC Genomics 2015 16:491
    Content type: Research article Published on:

  35. Multifactor dimensionality reduction (MDR) is widely used to analyze interactions of genes to determine the complex relationship between diseases and polymorphisms in humans. However, the astronomical number o...

    Authors: Cheng-Hong Yang, Yu-Da Lin, Cheng-San Yang and Li-Yeh Chuang
    Citation: BMC Genomics 2015 16:489
    Content type: Methodology article Published on:

  36. The formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants. Although several studies have explored gene expression during flo...

    Authors: Patrick T. Ryan, Diarmuid S. Ó’Maoiléidigh, Hajk-Georg Drost, Kamila Kwaśniewska, Alexander Gabel, Ivo Grosse, Emmanuelle Graciet, Marcel Quint and Frank Wellmer
    Citation: BMC Genomics 2015 16:488
    Content type: Research article Published on:

  38. Barbarea vulgaris contains two genotypes: the glabrous type (G-type), which confers resistance to the diamondback moth (DBM) and other insect pests, and the pubescent type (P-type), which is su...

    Authors: Xiaohui Zhang, Tongjin Liu, Xiaochun Wei, Yang Qiu, Jiangping Song, Haiping Wang, Di Shen, Niels Agerbirk and Xixiang Li
    Citation: BMC Genomics 2015 16:486
    Content type: Research article Published on:

  39. Next Generation DNA Sequencing (NGS) and genome mining of actinomycetes and other microorganisms is currently one of the most promising strategies for the discovery of novel bioactive natural products, potenti...

    Authors: Juan Pablo Gomez-Escribano, Jean Franco Castro, Valeria Razmilic, Govind Chandra, Barbara Andrews, Juan A. Asenjo and Mervyn J. Bibb
    Citation: BMC Genomics 2015 16:485
    Content type: Research article Published on:

  40. The Solanaceae are an economically important family of plants that include tobacco (Nicotiana tabacum L.), tomato, and potato. Drought is a major cause of crop losses.

    Authors: Roel C Rabara, Prateek Tripathi, R Neil Reese, Deena L Rushton, Danny Alexander, Michael P Timko, Qingxi J Shen and Paul J Rushton
    Citation: BMC Genomics 2015 16:484
    Content type: Research article Published on:

  41. Triptolide is a therapeutic diterpenoid derived from the Chinese herb Tripterygium wilfordii Hook f. Triptolide has been shown to induce apoptosis by activation of pro-apoptotic proteins, inhibiting NFkB and c-KI...

    Authors: Lata Chauhan, Gregory D. Jenkins, Neha Bhise, Tanya Feldberg, Taraswi Mitra-Ghosh, Brooke L. Fridley and Jatinder K. Lamba
    Citation: BMC Genomics 2015 16:483
    Content type: Research article Published on:

  42. Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced use...

    Authors: Lars M.T. Eijssen, Varshna S. Goelela, Thomas Kelder, Michiel E. Adriaens, Chris T. Evelo and Marijana Radonjic
    Citation: BMC Genomics 2015 16:482
    Content type: Software Published on:

  44. MicroRNAs (miRs) are an abundant class of small non-coding RNAs (~22 nt) that reprogram gene expression by targeting mRNA degradation and translational disruption. An emerging concept implicates miR coupling w...

    Authors: Andrea Masotti, Gloria Donninelli, Letizia Da Sacco, Barbara Varano, Manuela Del Cornò and Sandra Gessani
    Citation: BMC Genomics 2015 16:480
    Content type: Research article Published on:

  45. Mycobacteria inhabit diverse niches and display high metabolic versatility. They can colonise both humans and animals and are also able to survive in the environment. In order to succeed, response to environme...

    Authors: Ricardo J. C. Balhana, Ashima Singla, Mahmudul Hasan Sikder, Mike Withers and Sharon L. Kendall
    Citation: BMC Genomics 2015 16:479
    Content type: Research article Published on:

  46. The b-Zip transcription factor AtfA plays a key role in regulating stress responses in the filamentous fungus Aspergillus nidulans. To identify the core regulons of AtfA, we examined genome-wide expression change...

    Authors: Tamás Emri, Vera Szarvas, Erzsébet Orosz, Károly Antal, HeeSoo Park, Kap-Hoon Han, Jae-Hyuk Yu and István Pócsi
    Citation: BMC Genomics 2015 16:478
    Content type: Research article Published on:

  47. The morphogenesis of single-celled cotton fiber includes extreme elongation and staged cell wall differentiation. Designing strategies for improving cotton fiber for textiles and other uses relies on uncoverin...

    Authors: John R. Tuttle, Gyoungju Nah, Mary V. Duke, Danny C. Alexander, Xueying Guan, Qingxin Song, Z. Jeffrey Chen, Brian E. Scheffler and Candace H. Haigler
    Citation: BMC Genomics 2015 16:477
    Content type: Research article Published on:

  48. Keratinocytes (KCs) are the most frequent cells in the epidermis, and they are often isolated and cultured in vitro to study the molecular biology of the skin. Cultured primary cells and various immortalized cell...

    Authors: Shintaro Katayama, Tiina Skoog, Eeva-Mari Jouhilahti, H. Annika Siitonen, Kristo Nuutila, Mari H Tervaniemi, Jyrki Vuola, Anna Johnsson, Peter Lönnerberg, Sten Linnarsson, Outi Elomaa, Esko Kankuri and Juha Kere
    Citation: BMC Genomics 2015 16:476
    Content type: Research article Published on:

  49. To understand cardiac and skeletal muscle function, it is important to define and explore their molecular constituents and also to identify similarities and differences in the gene expression in these two diff...

    Authors: Cecilia Lindskog, Jerker Linné, Linn Fagerberg, Björn M Hallström, Carl Johan Sundberg, Malene Lindholm, Mikael Huss, Caroline Kampf, Howard Choi, David A Liem, Peipei Ping, Leif Väremo, Adil Mardinoglu, Jens Nielsen, Erik Larsson, Fredrik Pontén…
    Citation: BMC Genomics 2015 16:475
    Content type: Research article Published on:

  50. The domestic dog is a rich resource for mapping the genetic components of phenotypic variation due to its unique population history involving strong artificial selection. Genome-wide association studies have r...

    Authors: Matthew T. Webster, Nona Kamgari, Michele Perloski, Marc P. Hoeppner, Erik Axelsson, Åke Hedhammar, Gerli Pielberg and Kerstin Lindblad-Toh
    Citation: BMC Genomics 2015 16:474
    Content type: Research article Published on:

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BMC Genomics

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