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  1. Reduced physical activity and increased intake of calorically-dense diets are the main risk factors for obesity, glucose intolerance, and type 2 diabetes. Chronic overnutrition and hyperglycemia can alter gene...

    Authors: Ilhem Messaoudi, Mithila Handu, Maham Rais, Suhas Sureshchandra, Byung S. Park, Suzanne S. Fei, Hollis Wright, Ashley E. White, Ruhee Jain, Judy L. Cameron, Kerri M. Winters-Stone and Oleg Varlamov
    Citation: BMC Genomics 2017 18:411
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2017 18:471

  3. Miscanthus sinensis is a high yielding perennial grass species with great potential as a bioenergy feedstock. One of the challenges that currently impedes commercial cellulosic biofuel...

    Authors: Tim van der Weijde, Claire L. Alvim Kamei, Edouard I. Severing, Andres F. Torres, Leonardo D. Gomez, Oene Dolstra, Chris A. Maliepaard, Simon J. McQueen-Mason, Richard G. F. Visser and Luisa M. Trindade
    Citation: BMC Genomics 2017 18:406
    Content type: Research article Published on:

  4. Differences in DNA methylation are known to contribute to the development of immune-related disorders in humans but relatively little is known about how methylation regulates immune function in cattle. Utilizi...

    Authors: Filiz T. Korkmaz and David E. Kerr
    Citation: BMC Genomics 2017 18:405
    Content type: Research article Published on:

  5. Intellectual Disability (ID) is among the most common global disorders, yet etiology is unknown in ~30% of patients despite clinical assessment. Whole genome sequencing (WGS) is able to interrogate the entire ...

    Authors: Farah R. Zahir, Jill C. Mwenifumbo, Hye-Jung E. Chun, Emilia L. Lim, Clara D. M. Van Karnebeek, Madeline Couse, Karen L. Mungall, Leora Lee, Nancy Makela, Linlea Armstrong, Cornelius F. Boerkoel, Sylvie L. Langlois, Barbara M. McGillivray, Steven J. M. Jones, Jan M. Friedman and Marco A. Marra
    Citation: BMC Genomics 2017 18:403
    Content type: Research Article Published on:

  6. As crucial markers in identifying biological elements and processes in mammalian genomes, CpG islands (CGI) play important roles in DNA methylation, gene regulation, epigenetic inheritance, gene mutation, chro...

    Authors: Ning Yu, Xuan Guo, Alexander Zelikovsky and Yi Pan
    Citation: BMC Genomics 2017 18(Suppl 4):392
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 4

  7. With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing trans...

    Authors: Sing-Hoi Sze, Meaghan L. Pimsler, Jeffery K. Tomberlin, Corbin D. Jones and Aaron M. Tarone
    Citation: BMC Genomics 2017 18(Suppl 4):387
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 4

  8. Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections associated with unsafe injection practices, drug diversion, and other exposures ...

    Authors: Inna Rytsareva, David S. Campo, Yueli Zheng, Seth Sims, Sharma V. Thankachan, Cansu Tetik, Jain Chirag, Sriram P. Chockalingam, Amanda Sue, Srinivas Aluru and Yury Khudyakov
    Citation: BMC Genomics 2017 18(Suppl 4):372
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 4

  9. The current literature establishes the importance of gene functional category and expression in promoting or suppressing duplicate gene loss after whole genome doubling in plants, a process known as fractionat...

    Authors: Eric C. H. Chen, Annie Morin, Jean-Hugues Chauchat and David Sankoff
    Citation: BMC Genomics 2017 18(Suppl 4):366
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 4

  10. The recent advancement of whole genome alignment software has made it possible to align two genomes very efficiently and with only a small sacrifice in sensitivity. Yet it becomes very slow if the extra sensit...

    Authors: Huijun Mai, Tak-Wah Lam and Hing-Fung Ting
    Citation: BMC Genomics 2017 18(Suppl 4):362
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 4

  11. The ability to estimate the evolutionary distance between extant genomes plays a crucial role in many phylogenomic studies. Often such estimation is based on the parsimony assumption, implying that the distanc...

    Authors: Nikita Alexeev and Max A. Alekseyev
    Citation: BMC Genomics 2017 18(Suppl 4):356
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 4

  12. Brucella spp. are Gram-negative, facultative intracellular pathogens that cause brucellosis in both humans and animals. The B. abortus vaccine strain 104 M is the only vaccine availabl...

    Authors: Xiaodong Zai, Qiaoling Yang, Kun Liu, Ruihua Li, Mengying Qian, Taoran Zhao, Yaohui Li, Ying Yin, Dayong Dong, Ling Fu, Shanhu Li, Junjie Xu and Wei Chen
    Citation: BMC Genomics 2017 18:402
    Content type: Research article Published on:

  13. Watercress (Nasturtium officinale R. Br.) is an aquatic herb species that is a rich source of secondary metabolites such as glucosinolates. Among these glucosinolates, watercress contains high amounts of gluconas...

    Authors: Jin Jeon, Sun Ju Bong, Jong Seok Park, Young-Kyu Park, Mariadhas Valan Arasu, Naif Abdullah Al-Dhabi and Sang Un Park
    Citation: BMC Genomics 2017 18:401
    Content type: Research article Published on:

  14. In marine organisms, and in particular for benthic invertebrates including echinoderms, olfaction is a dominant sense with chemosensation being a critical signalling process. Until recently natural product che...

    Authors: Rebecca E. Roberts, Cherie A. Motti, Kenneth W. Baughman, Noriyuki Satoh, Michael R. Hall and Scott F. Cummins
    Citation: BMC Genomics 2017 18:400
    Content type: Research article Published on:

  15. RNA-Seq is now widely used as a research tool. Choices must be made whether to use paired-end (PE) or single-end (SE) sequencing, and whether to use strand-specific or non-specific (NS) library preparation kit...

    Authors: Susan M. Corley, Karen L. MacKenzie, Annemiek Beverdam, Louise F. Roddam and Marc R. Wilkins
    Citation: BMC Genomics 2017 18:399
    Content type: Research article Published on:

  16. Serogroup A Neisseria meningitidis (NmA) was the cause of the 2011 meningitis epidemics in Chad. This bacterium, often carried asymptomatically, is considered to be an “accidental pathogen”; however, the transiti...

    Authors: Kanny Diallo, Kadija Gamougam, Doumagoum M. Daugla, Odile B. Harrison, James E. Bray, Dominique A. Caugant, Jay Lucidarme, Caroline L. Trotter, Musa Hassan-King, James M. Stuart, Olivier Manigart, Brian M. Greenwood and Martin C. J. Maiden
    Citation: BMC Genomics 2017 18:398
    Content type: Research article Published on:

  17. Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics be...

    Authors: J. B. Butler, R. E. Vaillancourt, B. M. Potts, D. J. Lee, G. J. King, A. Baten, M. Shepherd and J. S. Freeman
    Citation: BMC Genomics 2017 18:397
    Content type: Research article Published on:

  18. The cost of Whole Genome Sequencing (WGS) has decreased tremendously in recent years due to advances in next-generation sequencing technologies. Nevertheless, the cost of carrying out large-scale cohort studie...

    Authors: Navin Rustagi, Anbo Zhou, W. Scott Watkins, Erika Gedvilaite, Shuoguo Wang, Naveen Ramesh, Donna Muzny, Richard A. Gibbs, Lynn B. Jorde, Fuli Yu and Jinchuan Xing
    Citation: BMC Genomics 2017 18:396
    Content type: Research article Published on:

  19. Despite the economic importance of sugarcane in sugar and bioenergy production, there is not yet a reference genome available. Most of the sugarcane transcriptomic studies have been based on Saccharum officinarum

    Authors: Nam V. Hoang, Agnelo Furtado, Patrick J. Mason, Annelie Marquardt, Lakshmi Kasirajan, Prathima P. Thirugnanasambandam, Frederik C. Botha and Robert J. Henry
    Citation: BMC Genomics 2017 18:395
    Content type: Research article Published on:

  20. Transversions (Tv’s) are more likely to alter the amino acid sequence of proteins than transitions (Ts’s), and local deviations in the Ts:Tv ratio are indicative of evolutionary selection on genes. Whether the...

    Authors: Cong Guo, Ian C. McDowell, Michael Nodzenski, Denise M. Scholtens, Andrew S. Allen, William L. Lowe and Timothy E. Reddy
    Citation: BMC Genomics 2017 18:394
    Content type: Research article Published on:

  22. Pikes represent an important genus (Esox) harbouring a pre-duplication karyotype (2n = 2x = 50) of economically important salmonid pseudopolyploids. Here, we have characterized the 5S ribosomal RNA genes (rDNA) i...

    Authors: Radka Symonová, Konrad Ocalewicz, Lech Kirtiklis, Giovanni Battista Delmastro, Šárka Pelikánová, Sonia Garcia and Aleš Kovařík
    Citation: BMC Genomics 2017 18:391
    Content type: Research article Published on:

  23. Complete and accurate annotation of sequenced genomes is of paramount importance to their utility and analysis. Differences in gene prediction pipelines mean that genome annotations for a species can differ co...

    Authors: Michael P. Dunne and Steven Kelly
    Citation: BMC Genomics 2017 18:390
    Content type: Software Published on:

    The Erratum to this article has been published in BMC Genomics 2017 18:488

  25. Bats are an extremely successful group of mammals and possess a variety of unique characteristics, including their ability to co-exist with a diverse range of pathogens. The major histocompatibility complex (M...

    Authors: Justin H. J. Ng, Mary Tachedjian, Lin-Fa Wang and Michelle L. Baker
    Citation: BMC Genomics 2017 18:388
    Content type: Research article Published on:

  26. Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Usin...

    Authors: Christopher M. Seabury, David L. Oldeschulte, Mahdi Saatchi, Jonathan E. Beever, Jared E. Decker, Yvette A. Halley, Eric K. Bhattarai, Maral Molaei, Harvey C. Freetly, Stephanie L. Hansen, Helen Yampara-Iquise, Kristen A. Johnson, Monty S. Kerley, JaeWoo Kim, Daniel D. Loy, Elisa Marques…
    Citation: BMC Genomics 2017 18:386
    Content type: Research article Published on:

  28. Transcriptional elongation is a generic function, but is also regulated to allow rapid transcription responses. Following relatively long initiation and promoter clearance, RNA polymerase II can pause and then...

    Authors: Haiwang Yang, Denis Basquin, Daniel Pauli and Brian Oliver
    Citation: BMC Genomics 2017 18:384
    Content type: Research article Published on:

  29. Development of primary open-angle glaucoma (POAG) is associated with the malfunctioning trabecular meshwork (TM). Cell therapy offers great potential for the treatment of POAG, but requires the generation of f...

    Authors: Padmapriya Sathiyanathan, Cheryl Y. Tay and Lawrence W. Stanton
    Citation: BMC Genomics 2017 18:383
    Content type: Research article Published on:

  30. The mosquito Aedes aegypti is the primary vector for medically important arthropod-borne viruses, including chikungunya virus (CHIKV). Following oral acquisition, an arbovirus has to persistently infect several o...

    Authors: Shengzhang Dong, Susanta K. Behura and Alexander W. E. Franz
    Citation: BMC Genomics 2017 18:382
    Content type: Research article Published on:

  32. Long noncoding RNAs (lncRNAs) are now considered important regulatory factors, with a variety of biological functions in many species including insects. Some lncRNAs have the ability to show rapid responses to...

    Authors: Bin Zhu, Manyu Xu, Haiyan Shi, Xiwu Gao and Pei Liang
    Citation: BMC Genomics 2017 18:380
    Content type: Research article Published on:

  33. Genome editing technologies developed around the CRISPR-Cas9 nuclease system have facilitated the investigation of a broad range of biological questions. These nucleases also hold tremendous promise for treati...

    Authors: Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Hervé Pagès, Alper Kucukural, Manuel Garber and Scot A. Wolfe
    Citation: BMC Genomics 2017 18:379
    Content type: Software Published on:

  34. Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools cap...

    Authors: Jake Lin, Lenka Kramna, Reija Autio, Heikki Hyöty, Matti Nykter and Ondrej Cinek
    Citation: BMC Genomics 2017 18:378
    Content type: Software Published on:

  36. Superoxide dismutases (SODs) are a key antioxidant enzyme family, which have been implicated in protecting plants against the toxic effects of reactive oxygen species. Despite current studies have shown that t...

    Authors: Wei Wang, Xiaopei Zhang, Fenni Deng, Rui Yuan and Fafu Shen
    Citation: BMC Genomics 2017 18:376
    Content type: Research article Published on:

  37. Recent studies have suggested that combinations of multiple epigenetic modifications are essential for controlling gene expression. Despite numerous computational approaches have been developed to decipher the...

    Authors: Qi Liu, Russell Bonneville, Tianbao Li and Victor X. Jin
    Citation: BMC Genomics 2017 18:375
    Content type: Methodology article Published on:

  38. The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its gen...

    Authors: Soichiro Nagano, Kenta Shirasawa, Hideki Hirakawa, Fumi Maeda, Masami Ishikawa and Sachiko N. Isobe
    Citation: BMC Genomics 2017 18:374
    Content type: Research article Published on:

  39. Huntington’s disease (HD) is a fatal neurodegenerative disorder caused by a CAG expansion in the Huntingtin (HTT) gene. Proteolytic cleavage of mutant huntingtin (Htt) protein with an expanded polyglutamine (poly...

    Authors: Martijn van Hagen, Diewertje G. E. Piebes, Wim C. de Leeuw, Ilona M. Vuist, Willeke M. C. van Roon-Mom, Perry D. Moerland and Pernette J. Verschure
    Citation: BMC Genomics 2017 18:373
    Content type: Research article Published on:

  40. Indigenous cattle in Africa have adapted to various local environments to acquire superior phenotypes that enhance their survival under harsh conditions. While many studies investigated the adaptation of overa...

    Authors: Soo-Jin Kim, Sojeong Ka, Jung-Woo Ha, Jaemin Kim, DongAhn Yoo, Kwondo Kim, Hak-Kyo Lee, Dajeong Lim, Seoae Cho, Olivier Hanotte, Okeyo Ally Mwai, Tadelle Dessie, Stephen Kemp, Sung Jong Oh and Heebal Kim
    Citation: BMC Genomics 2017 18:371
    Content type: Research article Published on:

  41. Whiteflies threaten agricultural crop production worldwide, are polyphagous in nature, and transmit hundreds of plant viruses. Little is known how whitefly gene expression is altered due to feeding on plants i...

    Authors: Navneet Kaur, Wenbo Chen, Yi Zheng, Daniel K. Hasegawa, Kai-Shu Ling, Zhangjun Fei and William M. Wintermantel
    Citation: BMC Genomics 2017 18:370
    Content type: Research article Published on:

  42. Fatty acid composition contributes importantly to meat quality and is essential to the nutritional value of the meat. Identification of genetic factors underlying levels of fatty acids can be used to breed for...

    Authors: Maren van Son, Eli Gjerlaug Enger, Harald Grove, Roger Ros-Freixedes, Matthew P. Kent, Sigbjørn Lien and Eli Grindflek
    Citation: BMC Genomics 2017 18:369
    Content type: Research article Published on:

  44. Cymbidium goeringii is a very famous traditional orchid plant in China, which is well known for its spectacular and diverse flower morphology. In particular, the multi-tepal mutants ha...

    Authors: Fengxi Yang, Genfa Zhu, Zhen Wang, Hailin Liu, Qingquan Xu, Dan huang and Chaoyi Zhao
    Citation: BMC Genomics 2017 18:367
    Content type: Research article Published on:

  45. The pPT23A family of plasmids appears to be indigenous to the plant pathogen Pseudomonas syringae and these plasmids are widely distributed and widely transferred among pathovars of P. syringae and related specie...

    Authors: José A. Gutiérrez-Barranquero, Francisco M. Cazorla, Antonio de Vicente and George W. Sundin
    Citation: BMC Genomics 2017 18:365
    Content type: Research article Published on:

  46. Evidence in diverse organisms suggests that codon optimality is a major determinant of mRNA translation and degradation. Codon optimality is thought to act by modulating the efficiency of ribosome elongation. In

    Authors: Yuriko Harigaya and Roy Parker
    Citation: BMC Genomics 2017 18:364
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2017 18:704

  47. Litchi (Litchi chinensis Sonn.) is an economically important evergreen fruit tree widely cultivated in subtropical areas. Low temperature is absolutely required for floral induction of litchi, but its molecular m...

    Authors: Hongna Zhang, Jiyuan Shen, Yongzan Wei and Houbin Chen
    Citation: BMC Genomics 2017 18:363
    Content type: Research article Published on:

  49. RNA editing by ADAR (adenosine deaminase acting on RNA) proteins is a form of transcriptional regulation that is widespread among humans and other primates. Based on high-throughput scans used to identify puta...

    Authors: Scott A. Funkhouser, Juan P. Steibel, Ronald O. Bates, Nancy E. Raney, Darius Schenk and Catherine W. Ernst
    Citation: BMC Genomics 2017 18:360
    Content type: Research article Published on:

  50. Cold tolerance is a key determinant of temperate insect distribution and performance. Chill-susceptible insects lose ion and water homeostasis during cold exposure, but prior cold acclimation improves both col...

    Authors: Lauren E. Des Marteaux, Alexander H McKinnon, Hiroko Udaka, Jantina Toxopeus and Brent J. Sinclair
    Citation: BMC Genomics 2017 18:357
    Content type: Research article Published on:

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BMC Genomics

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