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  1. 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:

  2. 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:

  3. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  13. 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:

  15. 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:

  16. 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:

  18. 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:

  19. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  34. Potato virus Y (PVY) is one of the most important plant viruses affecting potato production. The interactions between potato and PVY are complex and the outcome of the interactions depends on the potato genoty...

    Authors: Aymeric Goyer, Launa Hamlin, James M. Crosslin, Alex Buchanan and Jeff H. Chang
    Citation: BMC Genomics 2015 16:472
    Content type: Research article Published on:

  35. Chronic bacterial infections occur as a result of the infecting pathogen’s ability to live within a biofilm, hence escaping the detrimental effects of antibiotics and the immune defense system. Burkholderia pseud...

    Authors: Chui-Yoke Chin, Yuka Hara, Ahmad-Kamal Ghazali, Soon-Joo Yap, Cin Kong, Yee-Chin Wong, Naufal Rozali, Seng-Fook Koh, Chee-Choong Hoh, Savithri D. Puthucheary and Sheila Nathan
    Citation: BMC Genomics 2015 16:471
    Content type: Research article Published on:

  37. Trunk diseases threaten the longevity and productivity of grapevines in all viticulture production systems. They are caused by distantly-related fungi that form chronic wood infections. Variation in wood-decay...

    Authors: Abraham Morales-Cruz, Katherine C. H. Amrine, Barbara Blanco-Ulate, Daniel P. Lawrence, Renaud Travadon, Philippe E. Rolshausen, Kendra Baumgartner and Dario Cantu
    Citation: BMC Genomics 2015 16:469
    Content type: Research article Published on:

  38. Caecilians, with a discrete lifestyle, are the least explored group of amphibians. Though with distinct traits, many aspects of their biology are poorly investigated. Obtaining the caecilian genomic sequences ...

    Authors: Riga Wu, Qingfeng Liu, Shaoquan Meng, Peng Zhang and Dan Liang
    Citation: BMC Genomics 2015 16:468
    Content type: Research article Published on:

  39. Single-stranded non-protein coding small RNAs, 18–25 nucleotides in length, are ubiquitous throughout plants genomes and are involved in post-transcriptional gene regulation. Several types of DNA markers have ...

    Authors: Nang Myint Phyu Sin Htwe, Zhong-Qin Luo, Long-Guo Jin, Brian Nadon, Ke-Jing Wang and Li-Juan Qiu
    Citation: BMC Genomics 2015 16:467
    Content type: Research article Published on:

  40. Idiopathic epilepsy is a common neurological disease in human and domestic dogs but relatively few risk genes have been identified to date. The seizure characteristics, including focal and generalised seizures...

    Authors: Lotta L. E. Koskinen, Eija H. Seppälä, Janelle M. Belanger, Meharji Arumilli, Osmo Hakosalo, Päivi Jokinen, Elisa M. Nevalainen, Ranno Viitmaa, Tarja S. Jokinen, Anita M. Oberbauer and Hannes Lohi
    Citation: BMC Genomics 2015 16:465
    Content type: Research article Published on:

  41. The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, th...

    Authors: Konstantin Kozlov, Dmitri Chebotarev, Mehedi Hassan, Martin Triska, Petr Triska, Pavel Flegontov and Tatiana V Tatarinova
    Citation: BMC Genomics 2015 16(Suppl 8):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  42. Over the past 50,000 years, shifts in human-environmental or human-human interactions shaped genetic differences within and among human populations, including variants under positive selection. Shaped by envir...

    Authors: Samuel K Handelman, Michal Seweryn, Ryan M Smith, Katherine Hartmann, Danxin Wang, Maciej Pietrzak, Andrew D Johnson, Andrzej Kloczkowski and Wolfgang Sadee
    Citation: BMC Genomics 2015 16(Suppl 8):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  43. The recent improvement of the high-throughput sequencing technologies is having a strong impact on the detection of genetic variations associated with cancer. Several institutions worldwide have been sequencin...

    Authors: Rui Tian, Malay K Basu and Emidio Capriotti
    Citation: BMC Genomics 2015 16(Suppl 8):S7
    Content type: Review Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  44. Enrichment analysis is a widely applied procedure for shedding light on the molecular mechanisms and functions at the basis of phenotypes, for enlarging the dataset of possibly related genes/proteins and for h...

    Authors: Pietro Di Lena, Pier Luigi Martelli, Piero Fariselli and Rita Casadio
    Citation: BMC Genomics 2015 16(Suppl 8):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  45. Many cancer cells show distorted epigenetic landscapes. The Cancer Genome Atlas (TCGA) project profiles thousands of tumors, allowing the discovery of somatic alterations in the epigenetic machinery and the id...

    Authors: Florian Gnad, Sophia Doll, Gerard Manning, David Arnott and Zemin Zhang
    Citation: BMC Genomics 2015 16(Suppl 8):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  46. There are now over 2000 loci in the human genome where genome wide association studies (GWAS) have found one or more SNPs to be associated with altered risk of a complex trait disease. At each of these loci, t...

    Authors: Lipika R Pal, Chen-Hsin Yu, Stephen M Mount and John Moult
    Citation: BMC Genomics 2015 16(Suppl 8):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  47. The invention of high throughput sequencing technologies has led to the discoveries of hundreds of thousands of genetic variants associated with thousands of human diseases. Many of these genetic variants are ...

    Authors: Meng Ma, Ying Ru, Ling-Shiang Chuang, Nai-Yun Hsu, Li-Song Shi, Jörg Hakenberg, Wei-Yi Cheng, Andrew Uzilov, Wei Ding, Benjamin S Glicksberg and Rong Chen
    Citation: BMC Genomics 2015 16(Suppl 8):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  48. A vast amount of DNA variation is being identified by increasingly large-scale exome and genome sequencing projects. To be useful, variants require accurate functional annotation and a wide range of tools are ...

    Authors: Adam Frankish, Barbara Uszczynska, Graham RS Ritchie, Jose M Gonzalez, Dmitri Pervouchine, Robert Petryszak, Jonathan M Mudge, Nuno Fonseca, Alvis Brazma, Roderic Guigo and Jennifer Harrow
    Citation: BMC Genomics 2015 16(Suppl 8):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  49. Elucidating the effects of naturally occurring genetic variation is one of the major challenges for personalized health and personalized medicine. Here, we introduce SNAP2, a novel neural network based classif...

    Authors: Maximilian Hecht, Yana Bromberg and Burkhard Rost
    Citation: BMC Genomics 2015 16(Suppl 8):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

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