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  1. 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:

  2. 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:

  5. 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:

  6. 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:

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  16. In higher eukaryotes, the genome is partitioned into large "Topologically Associating Domains" (TADs) in which the chromatin displays favoured long-range contacts. While a crumpled/fractal globule organization...

    Authors: Vuthy Ea, Tom Sexton, Thierry Gostan, Laurie Herviou, Marie-Odile Baudement, Yunzhe Zhang, Soizik Berlivet, Marie-Noëlle Le Lay-Taha, Guy Cathala, Annick Lesne, Jean-Marc Victor, Yuhong Fan, Giacomo Cavalli and Thierry Forné
    Citation: BMC Genomics 2015 16:607
    Content type: Research article Published on:

  17. The maturation of the brain involves the coordinated expression of thousands of genes, proteins and regulatory elements over time. In sensory pathways, gene expression profiles are modified by age and sensory ...

    Authors: Troy A. Hackett, Yan Guo, Amanda Clause, Nicholas J. Hackett, Krassimira Garbett, Pan Zhang, Daniel B. Polley and Karoly Mirnics
    Citation: BMC Genomics 2015 16:606
    Content type: Research article Published on:

  18. Acanthus is a unique genus consisting of both true mangrove and terrestrial species; thus, it represents an ideal system for studying the origin and adaptive evolution of mangrove plan...

    Authors: Yuchen Yang, Shuhuan Yang, Jianfang Li, Yunfei Deng, Zhang Zhang, Shaohua Xu, Wuxia Guo, Cairong Zhong, Renchao Zhou and Suhua Shi
    Citation: BMC Genomics 2015 16:605
    Content type: Research article Published on:

  21. Deidentified newborn screening bloodspot samples (NBS) represent a valuable potential resource for genomic research if impediments to whole exome sequencing of NBS deoxyribonucleic acid (DNA), including the sm...

    Authors: Brandi L. Cantarel, Yunping Lei, Daniel Weaver, Huiping Zhu, Andrew Farrell, Graeme Benstead-Hume, Justin Reese and Richard H. Finnell
    Citation: BMC Genomics 2015 16:602
    Content type: Research article Published on:

  22. Insertions and deletions (indels) are the most abundant form of structural variation in all genomes. Indels have been increasingly recognized as an important source of molecular markers due to high-density occ...

    Authors: Jian Liu, Jingtao Qu, Cong Yang, Dengguo Tang, Jingwei Li, Hai Lan and Tingzhao Rong
    Citation: BMC Genomics 2015 16:601
    Content type: Research article Published on:

  23. Species showing complex life cycles provide excellent opportunities to study the genetic associations between life cycle stages, as selective pressures may differ before and after metamorphosis. The European e...

    Authors: J. M. Pujolar, M. W. Jacobsen, D. Bekkevold, J. Lobón-Cervià, B. Jónsson, L. Bernatchez and M. M. Hansen
    Citation: BMC Genomics 2015 16:600
    Content type: Research article Published on:

  24. Avocado (Persea americana) is an economically important tropical fruit considered to be a good source of fatty acids. Despite its importance, the molecular and cellular characterization of biochemical and develop...

    Authors: Enrique Ibarra-Laclette, Alfonso Méndez-Bravo, Claudia Anahí Pérez-Torres, Victor A. Albert, Keithanne Mockaitis, Aruna Kilaru, Rodolfo López-Gómez, Jacob Israel Cervantes-Luevano and Luis Herrera-Estrella
    Citation: BMC Genomics 2015 16:599
    Content type: Research article Published on:

  25. Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most fatal pests of soybean (Glycine max (L.) Merr.) worldwide and causes huge loss of soybean yield each year. Multiple sources of resistan...

    Authors: Yingpeng Han, Xue Zhao, Guanglu Cao, Yan Wang, Yinghui Li, Dongyuan Liu, Weili Teng, Zhiwu Zhang, Dongmei Li, Lijuan Qiu, Hongkun Zheng and Wenbin Li
    Citation: BMC Genomics 2015 16:598
    Content type: Research article Published on:

  26. Identifying the transcription start sites (TSS) of genes is essential for characterizing promoter regions. Several protocols have been developed to capture the 5′ end of transcripts via Cap Analysis of Gene Ex...

    Authors: Jason S. Cumbie, Maria G. Ivanchenko and Molly Megraw
    Citation: BMC Genomics 2015 16:597
    Content type: Methodology article Published on:

  27. Whole genome sequencing provides the most comprehensive collection of an organism’s genetic information. The availability of complete genome sequences is expected to dramatically deliver a high impact on biolo...

    Authors: Chenglin Chai, Yongqin Wang, Trupti Joshi, Babu Valliyodan, Silvas Prince, Lydia Michel, Dong Xu and Henry T. Nguyen
    Citation: BMC Genomics 2015 16:596
    Content type: Research article Published on:

  28. A complete genome sequence is an essential tool for the genetic improvement of wheat. Because the wheat genome is large, highly repetitive and complex due to its allohexaploid nature, the International Wheat G...

    Authors: Fuminori Kobayashi, Jianzhong Wu, Hiroyuki Kanamori, Tsuyoshi Tanaka, Satoshi Katagiri, Wataru Karasawa, Satoko Kaneko, Shota Watanabe, Toyotaka Sakaguchi, Yumiko Hanawa, Hiroko Fujisawa, Kanako Kurita, Chikako Abe, Julio C. M. Iehisa, Ryoko Ohno, Jan Šafář…
    Citation: BMC Genomics 2015 16:595
    Content type: Research article Published on:

  29. Base-resolution methylome data generated by whole-genome bisulfite sequencing (WGBS) is often used to segment the genome into domains with distinct methylation levels. However, most segmentation methods includ...

    Authors: Takao Yokoyama, Fumihito Miura, Hiromitsu Araki, Kohji Okamura and Takashi Ito
    Citation: BMC Genomics 2015 16:594
    Content type: Methodology article Published on:

  30. Bi-parental mapping populations have been commonly utilized to identify and characterize quantitative trait loci (QTL) controlling resistance to soybean cyst nematode (SCN, Heterodera glycines Ichinohe). Although...

    Authors: T. D. Vuong, H. Sonah, C. G. Meinhardt, R. Deshmukh, S. Kadam, R. L. Nelson, J. G. Shannon and H. T. Nguyen
    Citation: BMC Genomics 2015 16:593
    Content type: Research article Published on:

  31. Ameloblast differentiation is the most critical stepwise process in amelogenesis, and it is controlled by precise molecular events. To better understand the mechanism controlling pre-ameloblasts (PABs) differe...

    Authors: Chengcheng Liu, Yulong Niu, Xuedong Zhou, Xin Xu, Yi Yang, Yan Zhang and Liwei Zheng
    Citation: BMC Genomics 2015 16:592
    Content type: Research article Published on:

  32. Unlike mammals, zebrafish have the ability to regenerate damaged parts of their central nervous system (CNS) and regain functionality of the affected area. A better understanding of the molecular mechanisms in...

    Authors: Paula I. Fuller-Carter, Kim W. Carter, Denise Anderson, Alan R. Harvey, Keith M. Giles and Jennifer Rodger
    Citation: BMC Genomics 2015 16:591
    Content type: Research article Published on:

  33. Herbicide resistance in agrestal weeds is a global problem threatening food security. Non-target-site resistance (NTSR) endowed by mechanisms neutralising the herbicide or compensating for its action is consid...

    Authors: Jeanne Aude Christiane Gardin, Jérôme Gouzy, Sébastien Carrère and Christophe Délye
    Citation: BMC Genomics 2015 16:590
    Content type: Research article Published on:

  34. PCR amplicon sequencing has been widely used as a targeted approach for both DNA and RNA sequence analysis. High multiplex PCR has further enabled the enrichment of hundreds of amplicons in one simple reaction...

    Authors: Quan Peng, Ravi Vijaya Satya, Marcus Lewis, Pranay Randad and Yexun Wang
    Citation: BMC Genomics 2015 16:589
    Content type: Methodology article Published on:

  35. Trichoderma reesei is used for industry-scale production of plant cell wall-degrading enzymes, in particular cellulases, but also xylanases. The expression of the encoding genes was so...

    Authors: Thiago M. Mello-de-Sousa, Alice Rassinger, Marion E. Pucher, Lilian dos Santos Castro, Gabriela F. Persinoti, Rafael Silva-Rocha, Marcio J. Poças-Fonseca, Robert L. Mach, Roberto Nascimento Silva and Astrid R. Mach-Aigner
    Citation: BMC Genomics 2015 16:588
    Content type: Research article Published on:

  36. A systems toxicology investigation comparing and integrating transcriptomic and proteomic results was conducted to develop holistic effects characterizations for the wildlife bird model, Northern bobwhite (Colinu...

    Authors: Kurt A. Gust, Bindu Nanduri, Arun Rawat, Mitchell S. Wilbanks, Choo Yaw Ang, David R. Johnson, Ken Pendarvis, Xianfeng Chen, Michael J. Quinn Jr., Mark S. Johnson, Shane C. Burgess and Edward J. Perkins
    Citation: BMC Genomics 2015 16:587
    Content type: Research article Published on:

  37. The radioactive isotope Strontium-90 (90Sr) may be released as a component of fallout from nuclear accidents, or in the event of a radiological incident such as detonation of an improvised nuclear device, and if ...

    Authors: Shanaz A. Ghandhi, Waylon Weber, Dunstana Melo, Melanie Doyle-Eisele, Mashkura Chowdhury, Raymond Guilmette and Sally A. Amundson
    Citation: BMC Genomics 2015 16:586
    Content type: Research article Published on:

  38. The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region...

    Authors: Vikas Kumar, Verena E. Kutschera, Maria A. Nilsson and Axel Janke
    Citation: BMC Genomics 2015 16:585
    Content type: Research article Published on:

  39. The transcription factor p63 belongs to the p53/p63/p73 family and plays key functional roles during normal epithelial development and differentiation and in pathological states such as squamous cell carcinoma...

    Authors: Isha Sethi, Rose-Anne Romano, Christian Gluck, Kirsten Smalley, Borivoj Vojtesek, Michael J. Buck and Satrajit Sinha
    Citation: BMC Genomics 2015 16:584
    Content type: Research article Published on:

  41. Spounavirinae viruses have received an increasing interest as tools for the control of harmful bacteria due to their relatively broad host range and strictly virulent phenotype.

    Authors: Paul Tetteh Asare, Tae-Yong Jeong, Sangryeol Ryu, Jochen Klumpp, Martin J. Loessner, Bryan D. Merrill and Kwang-Pyo Kim
    Citation: BMC Genomics 2015 16:582
    Content type: Research article Published on:

  42. To promote the clinical application of next-generation sequencing, it is important to obtain accurate and consistent variants of target genomic regions at low cost. Ion Proton, the latest updated semiconductor...

    Authors: Guoqiang Zhang, Jianfeng Wang, Jin Yang, Wenjie Li, Yutian Deng, Jing Li, Jun Huang, Songnian Hu and Bing Zhang
    Citation: BMC Genomics 2015 16:581
    Content type: Research article Published on:

  43. Lobosphaera incisa, formerly known as Myrmecia incisa and then Parietochloris incisa, is an oleaginous unicellular green alga belonging to the class Trebouxiophyceae (Chlorophyta). It ...

    Authors: Nicolas J. Tourasse, Nastassia Shtaida, Inna Khozin-Goldberg, Sammy Boussiba and Olivier Vallon
    Citation: BMC Genomics 2015 16:580
    Content type: Research article Published on:

  44. The cereal rust fungi are destructive pathogens that affect grain production worldwide. Although the genomic and transcript sequences for three Puccinia species that attack wheat have been released, the functions...

    Authors: Chuntao Yin, Samantha I. Downey, Naeh L. Klages-Mundt, Sowmya Ramachandran, Xianming Chen, Les J. Szabo, Michael Pumphrey and Scot H. Hulbert
    Citation: BMC Genomics 2015 16:579
    Content type: Research article Published on:

  45. We present a genome-wide messenger RNA (mRNA) sequencing technique that converts small amounts of RNA from many samples into molecular phenotypes. It encompasses all steps from sample preparation to sequence a...

    Authors: John E. Collins, Neha Wali, Ian M. Sealy, James A. Morris, Richard J. White, Steven R. Leonard, David K. Jackson, Matthew C. Jones, Nathalie C. Smerdon, Jorge Zamora, Christopher M. Dooley, Samantha N. Carruthers, Jeffrey C. Barrett, Derek L. Stemple and Elisabeth M. Busch-Nentwich
    Citation: BMC Genomics 2015 16:578
    Content type: Methodology article Published on:

  46. Verticillium wilt (VW) and Fusarium wilt (FW), caused by the soil-borne fungi Verticillium dahliae and Fusarium oxysporum f. sp. vasinfectum, respectively, are two most destructive diseases in cotton production w...

    Authors: Jinfa Zhang, Jiwen Yu, Wenfeng Pei, Xingli Li, Joseph Said, Mingzhou Song and Soum Sanogo
    Citation: BMC Genomics 2015 16:577
    Content type: Research article Published on:

  48. Soil salinity is one of the most significant abiotic stresses affecting plant shoots and roots growth. The adjustment of root architecture to spatio-temporal heterogeneity in salinity is particularly critical ...

    Authors: Longxing Hu, Huiying Li, Liang Chen, Yanhong Lou, Erick Amombo and Jinmin Fu
    Citation: BMC Genomics 2015 16:575
    Content type: Research article Published on:

  49. Chickens are susceptible to infection with a limited number of Influenza A viruses and are a potential source of a human influenza pandemic. In particular, H5 and H7 haemagglutinin subtypes can evolve from low...

    Authors: Jacqueline Smith, Nikki Smith, Le Yu, Ian R. Paton, Maria Weronika Gutowska, Heather L. Forrest, Angela F. Danner, J. Patrick Seiler, Paul Digard, Robert G. Webster and David W. Burt
    Citation: BMC Genomics 2015 16:574
    Content type: Research article Published on:

  50. Dickeya zeae is a bacterial species that infects monocotyledons and dicotyledons. Two antibiotic-like phytotoxins named zeamine and zeamine II were reported to play an important role i...

    Authors: Jianuan Zhou, Yingying Cheng, Mingfa Lv, Lisheng Liao, Yufan Chen, Yanfang Gu, Shiyin Liu, Zide Jiang, Yuanyan Xiong and Lianhui Zhang
    Citation: BMC Genomics 2015 16:571
    Content type: Research article Published on:

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BMC Genomics

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