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  1. Molecular marker-assisted breeding provides an efficient tool to develop improved crop varieties. A major challenge for the broad application of markers in marker-assisted selection is that the marker phenotyp...

    Authors: Huaan Yang, Jianbo Jian, Xuan Li, Daniel Renshaw, Jonathan Clements, Mark W. Sweetingham, Cong Tan and Chengdao Li
    Citation: BMC Genomics 2015 16:660
    Content type: Research article Published on:

  2. Kalmegh (Andrographis paniculata) has been widely exploited in traditional medicine for the treatment of infectious diseases and health disorders. Ent-labdane-related diterpene (ent-LRD) specialized (i.e., second...

    Authors: Anchal Garg, Lalit Agrawal, Rajesh Chandra Misra, Shubha Sharma and Sumit Ghosh
    Citation: BMC Genomics 2015 16:659
    Content type: Research article Published on:

  3. Lophophora williamsii (commonly named peyote) is a small, spineless cactus with psychoactive alkaloids, particularly mescaline. Peyote utilizes crassulacean acid metabolism (CAM), an a...

    Authors: Enrique Ibarra-Laclette, Flor Zamudio-Hernández, Claudia Anahí Pérez-Torres, Victor A. Albert, Enrique Ramírez-Chávez, Jorge Molina-Torres, Araceli Fernández-Cortes, Carlos Calderón-Vázquez, José Luis Olivares-Romero, Alfredo Herrera-Estrella and Luis Herrera-Estrella
    Citation: BMC Genomics 2015 16:657
    Content type: Research article Published on:

  4. Head and neck squamous cell carcinoma (HNSCC) is a very heterogeneous disease resulting in huge differences in the treatment response. New individualized therapy strategies including molecular targeting might ...

    Authors: Isolde Summerer, Julia Hess, Adriana Pitea, Kristian Unger, Ludwig Hieber, Martin Selmansberger, Kirsten Lauber and Horst Zitzelsberger
    Citation: BMC Genomics 2015 16:654
    Content type: Research article Published on:

  5. To study the potential of genomic selection for heterosis resulting from multiplicative interactions between additive and antagonistic components, we focused on oil palm, where bunch production is the product ...

    Authors: David Cros, Marie Denis, Jean-Marc Bouvet and Leopoldo Sánchez
    Citation: BMC Genomics 2015 16:651
    Content type: Research article Published on:

  6. Whole genome sequencing (WGS) of Cryptosporidium spp. has previously relied on propagation of the parasite in animals to generate enough oocysts from which to extract DNA of sufficient quantity and purity for ana...

    Authors: Stephen J. Hadfield, Justin A. Pachebat, Martin T. Swain, Guy Robinson, Simon JS Cameron, Jenna Alexander, Matthew J. Hegarty, Kristin Elwin and Rachel M. Chalmers
    Citation: BMC Genomics 2015 16:650
    Content type: Research article Published on:

  8. Whole genome sequence construction is becoming increasingly feasible because of advances in next generation sequencing (NGS), including increasing throughput and read length. By simply overlapping paired-end r...

    Authors: Ting-Wen Chen, Ruei-Chi Gan, Yi-Feng Chang, Wei-Chao Liao, Timothy H. Wu, Chi-Ching Lee, Po-Jung Huang, Cheng-Yang Lee, Yi-Ywan M. Chen, Cheng-Hsun Chiu and Petrus Tang
    Citation: BMC Genomics 2015 16:648
    Content type: Research article Published on:

  9. While many studies have shown that extracellular proteins evolve rapidly, how selection acts on them remains poorly understood. We used snake venoms to understand the interaction between ecology, expression le...

    Authors: Steven D. Aird, Shikha Aggarwal, Alejandro Villar-Briones, Mandy Man-Ying Tin, Kouki Terada and Alexander S. Mikheyev
    Citation: BMC Genomics 2015 16:647
    Content type: Research article Published on:

  10. Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those within the grass tri...

    Authors: Yi Wang, Thomas Drader, Vijay K. Tiwari, Lingli Dong, Ajay Kumar, Naxin Huo, Farhad Ghavami, M. Javed Iqbal, Gerard R. Lazo, Jeff Leonard, Bikram S. Gill, Shahryar F. Kianian, Ming-Cheng Luo and Yong Q. Gu
    Citation: BMC Genomics 2015 16:646
    Content type: Research article Published on:

  11. Identification of marker genes associated with a specific tissue/cell type is a fundamental challenge in genetic and cell research. Marker genes are of great importance for determining cell identity, and for u...

    Authors: Khadija El Amrani, Harald Stachelscheid, Fritz Lekschas, Andreas Kurtz and Miguel A. Andrade-Navarro
    Citation: BMC Genomics 2015 16:645
    Content type: Methodology Article Published on:

  12. The cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Currently, there are two ...

    Authors: Shiguo Zhou, Steve Goldstein, Michael Place, Michael Bechner, Diego Patino, Konstantinos Potamousis, Prabu Ravindran, Louise Pape, Gonzalo Rincon, Juan Hernandez-Ortiz, Juan F. Medrano and David C. Schwartz
    Citation: BMC Genomics 2015 16:644
    Content type: Research article Published on:

  13. Infection outcome in some coevolving host-pathogens is characterised by host-pathogen genetic interactions, where particular host genotypes are susceptible only to a subset of pathogen genotypes. To identify c...

    Authors: Seanna J. McTaggart, Timothée Cézard, Jennie S. Garbutt, Phil J. Wilson and Tom J. Little
    Citation: BMC Genomics 2015 16:643
    Content type: Research article Published on:

  14. Almost all genome sequencing projects neglect the fact that diploid organisms contain two genome copies and consequently what is published is a composite of the two. This means that the relationship between al...

    Authors: Harry A. Noyes, Derek Daly, Ian Goodhead, Suzanne Kay, Steven J. Kemp, John Kenny, Ilik Saccheri, Robert D. Schnabel, Jeremy F. Taylor and Neil Hall
    Citation: BMC Genomics 2015 16:642
    Content type: Methodology article Published on:

  15. Haemophilus influenzae is an opportunistic bacterial pathogen that exclusively colonises humans and is associated with both acute and chronic disease. Despite its clinical significance...

    Authors: Erin P. Price, Derek S. Sarovich, Elizabeth Nosworthy, Jemima Beissbarth, Robyn L. Marsh, Janessa Pickering, Lea-Ann S. Kirkham, Anthony D. Keil, Anne B. Chang and Heidi C. Smith-Vaughan
    Citation: BMC Genomics 2015 16:641
    Content type: Research article Published on:

  16. Invasive aspergillosis is started after germination of Aspergillus fumigatus conidia that are inhaled by susceptible individuals. Fungal hyphae can grow in the lung through the epithelial tissue and disseminate h...

    Authors: Henriette Irmer, Sonia Tarazona, Christoph Sasse, Patrick Olbermann, Jürgen Loeffler, Sven Krappmann, Ana Conesa and Gerhard H. Braus
    Citation: BMC Genomics 2015 16:640
    Content type: Research article Published on:

  17. Butterflies and moths are emerging as model organisms in genetics and evolutionary studies. The family Hesperiidae (skippers) was traditionally viewed as a sister to other butterflies based on its moth-like mo...

    Authors: Qian Cong, Dominika Borek, Zbyszek Otwinowski and Nick V. Grishin
    Citation: BMC Genomics 2015 16:639
    Content type: Research article Published on:

  18. The Cold Shock proteins are RNA binding proteins involved in various cellular processes, including adaptation to low temperature, nutritional stress, cell growth and stationary phase. They may have an impact o...

    Authors: Juliana S. Santos, Carolina A. P. T. da Silva, Heloise Balhesteros, Rogério F. Lourenço and Marilis V. Marques
    Citation: BMC Genomics 2015 16:638
    Content type: Research article Published on:

  19. Legionella pneumophila (Lp) is a water-borne opportunistic pathogen. In water, Lp can survive for an extended period of time until it encounters a permissive host. Therefore, identifyi...

    Authors: Laam Li, Nilmini Mendis, Hana Trigui and Sébastien P. Faucher
    Citation: BMC Genomics 2015 16:637
    Content type: Research article Published on:

  21. Providing double-stranded RNA (dsRNA) to insects has been proven to silence target genes, and this approach has emerged as a potential method to control agricultural pests by engineering plants to express inse...

    Authors: Roberto de A. Camargo, Roberto H. Herai, Luana N. Santos, Flavia M M Bento, Joni E. Lima, Henrique Marques-Souza and Antonio Figueira
    Citation: BMC Genomics 2015 16:635
    Content type: Research article Published on:

  22. Sockeye Salmon are an iconic species widely distributed throughout the North Pacific. A devastating pathogen of Sockeye Salmon is infectious hematopoietic necrosis virus (IHNV, genus Novirhabdovirus, family Rhabd...

    Authors: Anita Müller, Ben J. G. Sutherland, Ben F. Koop, Stewart C. Johnson and Kyle A. Garver
    Citation: BMC Genomics 2015 16:634
    Content type: Research article Published on:

  23. Allergic airway diseases (AADs) such as asthma are characterized in part by granulocytic airway inflammation. The gene regulatory networks that govern granulocyte recruitment are poorly understood, but evidenc...

    Authors: Holly Rutledge, Jeanette Baran-Gale, Fernando Pardo-Manuel de Villena, Elissa J. Chesler, Gary A. Churchill, Praveen Sethupathy and Samir N. P. Kelada
    Citation: BMC Genomics 2015 16:633
    Content type: Research article Published on:

  25. In humans it is unknown if the composition of the gut microbiota alters the risk of Plasmodium falciparum infection or the risk of developing febrile malaria once P. falciparum infection is established. Here we c...

    Authors: Shibu Yooseph, Ewen F. Kirkness, Tuan M. Tran, Derek M. Harkins, Marcus B. Jones, Manolito G. Torralba, Elise O’Connell, Thomas B. Nutman, Safiatou Doumbo, Ogobara K. Doumbo, Boubacar Traore, Peter D. Crompton and Karen E. Nelson
    Citation: BMC Genomics 2015 16:631
    Content type: Research article Published on:

  26. Improved understanding of bacterial-fungal interactions in the rhizosphere should assist in the successful application of bacteria as biological control agents against fungal pathogens of plants, providing alt...

    Authors: Konstantia Gkarmiri, Roger D. Finlay, Sadhna Alström, Elizabeth Thomas, Marc A. Cubeta and Nils Högberg
    Citation: BMC Genomics 2015 16:630
    Content type: Research article Published on:

  27. The application of phages is a promising tool to reduce the number of Campylobacter along the food chain. Besides the efficacy against a broad range of strains, phages have to be safe in terms of their genomes.

    Authors: Claudia Jäckel, Jens A. Hammerl, Jochen Reetz, Andrew M. Kropinski and Stefan Hertwig
    Citation: BMC Genomics 2015 16:629
    Content type: Research article Published on:

  28. The hemibiotroph Colletotrichum lentis, causative agent of anthracnose on Lens culinaris (lentil) was recently described as a new species. During its interaction with the host plant, C. lentis likely secretes num...

    Authors: Vijai Bhadauria, Ron MacLachlan, Curtis Pozniak and Sabine Banniza
    Citation: BMC Genomics 2015 16:628
    Content type: Research article Published on:

  29. Root rot caused by Aphanomyces euteiches is one of the most destructive pea diseases while a distantly related species P. pisi has been recently described as the agent of pea and faba bean root rot. These two oom...

    Authors: Sara Hosseini, Malin Elfstrand, Fredrik Heyman, Dan Funck Jensen and Magnus Karlsson
    Citation: BMC Genomics 2015 16:627
    Content type: Research article Published on:

  30. 2,3,7,8–tetrachlorodibenzo-p-dixion (TCDD) is the most potent of the dioxin congeners, capable of causing a wide range of toxic effects across numerous animal models. Previous studies have demonstrated that males...

    Authors: Jamie Lee, Stephenie D. Prokopec, John D. Watson, Ren X. Sun, Raimo Pohjanvirta and Paul C. Boutros
    Citation: BMC Genomics 2015 16:625
    Content type: Research article Published on:

  31. In the male germline, neonatal prospermatogonia give rise to spermatogonia, which include stem cell population (undifferentiated spermatogonia) that supports continuous spermatogenesis in adults. Although the ...

    Authors: Naoki Kubo, Hidehiro Toh, Kenjiro Shirane, Takayuki Shirakawa, Hisato Kobayashi, Tetsuya Sato, Hidetoshi Sone, Yasuyuki Sato, Shin-ichi Tomizawa, Yoshinori Tsurusaki, Hiroki Shibata, Hirotomo Saitsu, Yutaka Suzuki, Naomichi Matsumoto, Mikita Suyama, Tomohiro Kono…
    Citation: BMC Genomics 2015 16:624
    Content type: Research article Published on:

  33. Cymbidium ensifolium is one of the most important ornamental flowers in China, with an elegant shape, beautiful appearance, and a fragrant aroma. Its unique flower shape has long attra...

    Authors: Xiaobai Li, Feng Jin, Liang Jin, Aaron Jackson, Xiang Ma, Xiaoli Shu, Dianxing Wu and Guoqiang Jin
    Citation: BMC Genomics 2015 16:622
    Content type: Research article Published on:

  35. Adaptive manipulation of animal behavior by parasites functions to increase parasite transmission through changes in host behavior. These changes can range from slight alterations in existing behaviors of the ...

    Authors: Charissa de Bekker, Robin A. Ohm, Raquel G. Loreto, Aswathy Sebastian, Istvan Albert, Martha Merrow, Andreas Brachmann and David P. Hughes
    Citation: BMC Genomics 2015 16:620
    Content type: Research article Published on:

  36. Transcriptome sequencing offers a great resource for the study of non-model plants such as Catharanthus roseus, which produces valuable monoterpenoid indole alkaloids (MIAs) via a complex biosynthetic pathway who...

    Authors: Thomas Dugé de Bernonville, Emilien Foureau, Claire Parage, Arnaud Lanoue, Marc Clastre, Monica Arias Londono, Audrey Oudin, Benjamin Houillé, Nicolas Papon, Sébastien Besseau, Gaëlle Glévarec, Lucia Atehortùa, Nathalie Giglioli-Guivarc’h, Benoit St-Pierre, Vincenzo De Luca, Sarah E. O’Connor…
    Citation: BMC Genomics 2015 16:619
    Content type: Research article Published on:

  37. An emerging field in biomedical research is focusing on the roles of aquaporin water channels in parasites that cause debilitating or lethal diseases to their vertebrate hosts. The primary vectorial agents are...

    Authors: Jon Anders Stavang, Francois Chauvigné, Heidi Kongshaug, Joan Cerdà, Frank Nilsen and Roderick Nigel Finn
    Citation: BMC Genomics 2015 16:618
    Content type: Research article Published on:

  38. Most biological processes are influenced by protein post-translational modifications (PTMs). Identifying novel PTM sites in different organisms, including humans and model organisms, has expedited our understa...

    Authors: Rima Chaudhuri, Arash Sadrieh, Nolan J. Hoffman, Benjamin L. Parker, Sean J. Humphrey, Jacqueline Stöckli, Adam P. Hill, David E. James and Jean Yee Hwa Yang
    Citation: BMC Genomics 2015 16:617
    Content type: Software Published on:

  41. Walnut (Juglans regia, 2n = 32, approximately 606 Mb per 1C genome) is an economically important tree crop. Resistance to anthracnose, caused by Colletotrichum gloeosporioides, is a major objective of walnut gene...

    Authors: Yufeng Zhu, Yanfei Yin, Keqiang Yang, Jihong Li, Yalin Sang, Long Huang and Shu Fan
    Citation: BMC Genomics 2015 16:614
    Content type: Research article Published on:

  42. Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput app...

    Authors: Stefanie Hartmann, Natascha Hasenkamp, Jens Mayer, Johan Michaux, Serge Morand, Camila J. Mazzoni, Alfred L. Roca and Alex D. Greenwood
    Citation: BMC Genomics 2015 16:613
    Content type: Research Article Published on:

  43. microRNA (miRNA) expression plays an influential role in cancer classification and malignancy, and miRNAs are feasible as alternative diagnostic markers for pancreatic cancer, a highly aggressive neoplasm with...

    Authors: Min-Seok Kwon, Yongkang Kim, Seungyeoun Lee, Junghyun Namkung, Taegyun Yun, Sung Gon Yi, Sangjo Han, Meejoo Kang, Sun Whe Kim, Jin-Young Jang and Taesung Park
    Citation: BMC Genomics 2015 16(Suppl 9):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 9

    The Erratum to this article has been published in BMC Genomics 2017 18:88

  44. Cancer is a disease characterized largely by the accumulation of out-of-control somatic mutations during the lifetime of a patient. Distinguishing driver mutations from passenger mutations has posed a challeng...

    Authors: Christopher Ma, Yixin Chen, Dawn Wilkins, Xiang Chen and Jinghui Zhang
    Citation: BMC Genomics 2015 16(Suppl 9):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 9

  45. The identification of genes and uncovering the role they play in diseases is an important and complex challenge. Genome-wide linkage and association studies have made advancements in identifying genetic varian...

    Authors: Fiona Browne, Haiying Wang and Huiru Zheng
    Citation: BMC Genomics 2015 16(Suppl 9):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 9

  46. Missing data is an inevitable phenomenon in gene expression microarray experiments due to instrument failure or human error. It has a negative impact on performance of downstream analysis. Technically, most ex...

    Authors: Huihui Li, Changbo Zhao, Fengfeng Shao, Guo-Zheng Li and Xiao Wang
    Citation: BMC Genomics 2015 16(Suppl 9):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 9

  47. Acidity is a major contributor to fruit quality. Several organic acids are present in apple fruit, but malic acid is predominant and determines fruit acidity. The trait is largely controlled by the Malic acid (Ma

    Authors: Yang Bai, Laura Dougherty, Lailiang Cheng, Gan-Yuan Zhong and Kenong Xu
    Citation: BMC Genomics 2015 16:612
    Content type: Research article Published on:

  48. Field pea (Pisum sativum L.) is a cool-season grain legume that is cultivated world-wide for both human consumption and stock-feed purposes. Enhancement of genetic and genomic resources for field pea will permit ...

    Authors: Shimna Sudheesh, Timothy I. Sawbridge, Noel OI Cogan, Peter Kennedy, John W. Forster and Sukhjiwan Kaur
    Citation: BMC Genomics 2015 16:611
    Content type: Research article Published on:

  49. Mycoplasma pneumoniae is a common pathogen that causes upper and lower respiratory tract infections in people of all ages, responsible for up to 40 % of community-acquired pneumonias. ...

    Authors: Li Xiao, Travis Ptacek, John D. Osborne, Donna M. Crabb, Warren L. Simmons, Elliot J. Lefkowitz, Ken B. Waites, T. Prescott Atkinson and Kevin Dybvig
    Citation: BMC Genomics 2015 16:610
    Content type: Research article Published on:

  50. Root-colonizing fluorescent pseudomonads are known for their excellent abilities to protect plants against soil-borne fungal pathogens. Some of these bacteria produce an insecticidal toxin (Fit) suggesting tha...

    Authors: Beat Ruffner, Maria Péchy-Tarr, Monica Höfte, Guido Bloemberg, Jürg Grunder, Christoph Keel and Monika Maurhofer
    Citation: BMC Genomics 2015 16:609
    Content type: Research article Published on:

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BMC Genomics

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