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  1. Research article

    Atp8 is in the ground pattern of flatworm mitochondrial genomes

    To date, mitochondrial genomes of more than one hundred flatworms (Platyhelminthes) have been sequenced. They show a high degree of similarity and a strong taxonomic bias towards parasitic lineages. The mitoch...

    Bernhard Egger, Lutz Bachmann and Bastian Fromm

    BMC Genomics 2017 18:414

    Published on: 26 May 2017

  2. Research article

    Association mapping of loci controlling genetic and environmental interaction of soybean flowering time under various photo-thermal conditions

    Soybean (Glycine max (L.) Merr.) is a short day plant. Its flowering and maturity time are controlled by genetic and environmental factors, as well the interaction between the two factors. Previous studies have s...

    Tingting Mao, Jinyu Li, Zixiang Wen, Tingting Wu, Cunxiang Wu, Shi Sun, Bingjun Jiang, Wensheng Hou, Wenbin Li, Qijian Song, Dechun Wang and Tianfu Han

    BMC Genomics 2017 18:415

    Published on: 26 May 2017

  3. Research article

    Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers

    The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson’s drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits in...

    N. Sathyanarayana, Ranjith Kumar Pittala, Pankaj Kumar Tripathi, Ratan Chopra, Heikham Russiachand Singh, Vikas Belamkar, Pardeep Kumar Bhardwaj, Jeff J. Doyle and Ashley N. Egan

    BMC Genomics 2017 18:409

    Published on: 25 May 2017

  4. Research article

    Whole genome sequencing reveals within-host genetic changes in paired meningococcal carriage isolates from Ethiopia

    Meningococcal colonization is a prerequisite for transmission and disease, but the bacterium only very infrequently causes disease while asymptomatic carriage is common. Carriage is highly dynamic, showing a g...

    Guro K. Bårnes, Ola Brønstad Brynildsrud, Bente Børud, Bereket Workalemahu, Paul A. Kristiansen, Demissew Beyene, Abraham Aseffa and Dominique A. Caugant

    BMC Genomics 2017 18:407

    Published on: 25 May 2017

  5. Research article

    Long-lasting effect of obesity on skeletal muscle transcriptome

    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...

    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

    BMC Genomics 2017 18:411

    Published on: 25 May 2017

  6. Research article

    Genetic complexity of miscanthus cell wall composition and biomass quality for biofuels

    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...

    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

    BMC Genomics 2017 18:406

    Published on: 25 May 2017

  7. Research

    Statistical analysis of fractionation resistance by functional category and expression

    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...

    Eric C. H. Chen, Annie Morin, Jean-Hugues Chauchat and David Sankoff

    BMC Genomics 2017 18(Suppl 4):366

    Published on: 24 May 2017

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

  8. Research

    Efficient detection of viral transmissions with Next-Generation Sequencing data

    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 ...

    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

    BMC Genomics 2017 18(Suppl 4):372

    Published on: 24 May 2017

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

  9. Research Article

    Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability

    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 ...

    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

    BMC Genomics 2017 18:403

    Published on: 24 May 2017

  10. Research

    A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms

    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...

    Sing-Hoi Sze, Meaghan L. Pimsler, Jeffery K. Tomberlin, Corbin D. Jones and Aaron M. Tarone

    BMC Genomics 2017 18(Suppl 4):387

    Published on: 24 May 2017

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

  11. Research article

    A comprehensive proteogenomic study of the human Brucella vaccine strain 104 M

    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...

    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

    BMC Genomics 2017 18:402

    Published on: 23 May 2017

  12. Research article

    Identification of putative olfactory G-protein coupled receptors in Crown-of-Thorns starfish, Acanthaster planci

    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...

    Rebecca E. Roberts, Cherie A. Motti, Kenneth W. Baughman, Noriyuki Satoh, Michael R. Hall and Scott F. Cummins

    BMC Genomics 2017 18:400

    Published on: 23 May 2017

  13. Research article

    Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols

    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...

    Susan M. Corley, Karen L. MacKenzie, Annemiek Beverdam, Louise F. Roddam and Marc R. Wilkins

    BMC Genomics 2017 18:399

    Published on: 23 May 2017

  14. Research article

    De novo transcriptome analysis and glucosinolate profiling in watercress (Nasturtium officinale R. Br.)

    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...

    Jin Jeon, Sun Ju Bong, Jong Seok Park, Young-Kyu Park, Mariadhas Valan Arasu, Naif Abdullah Al-Dhabi and Sang Un Park

    BMC Genomics 2017 18:401

    Published on: 23 May 2017

  15. Research article

    A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing

    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

    Nam V. Hoang, Agnelo Furtado, Patrick J. Mason, Annelie Marquardt, Lakshmi Kasirajan, Prathima P. Thirugnanasambandam, Frederik C. Botha and Robert J. Henry

    BMC Genomics 2017 18:395

    Published on: 22 May 2017

  16. Research article

    Extremely low-coverage whole genome sequencing in South Asians captures population genomics information

    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...

    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

    BMC Genomics 2017 18:396

    Published on: 22 May 2017

  17. Research article

    Hierarchical genomic analysis of carried and invasive serogroup A Neisseria meningitidis during the 2011 epidemic in Chad

    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...

    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

    BMC Genomics 2017 18:398

    Published on: 22 May 2017

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