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  1. Piper nigrum L., or “black pepper”, is an economically important spice crop in tropical regions. Black pepper production is markedly affected by foot rot disease caused by Phytophthora...

    Authors: Chaoyun Hao, Zhiqiang Xia, Rui Fan, Lehe Tan, Lisong Hu, Baoduo Wu and Huasong Wu
    Citation: BMC Genomics 2016 17:822
    Content type: Research article Published on:

  2. The Arabidopsis FLOWERING LOCUS T (FT) gene, a member of the phosphatidylethanolamine binding protein (PEBP) family, is a major controller of flowering in response to photoperiod, vernalization and light quality....

    Authors: Michał Książkiewicz, Sandra Rychel, Matthew N. Nelson, Katarzyna Wyrwa, Barbara Naganowska and Bogdan Wolko
    Citation: BMC Genomics 2016 17:820
    Content type: Research article Published on:

  3. Higher plants have to cope with increasing concentrations of pollutants of both natural and anthropogenic origin. Given their capacity to concentrate and metabolize various compounds including pollutants, plan...

    Authors: Anne-Sophie Dumas, Ludivine Taconnat, Evangelos Barbas, Guillem Rigaill, Olivier Catrice, Delphine Bernard, Abdelilah Benamar, David Macherel, Abdelhak El Amrani and Richard Berthomé
    Citation: BMC Genomics 2016 17:818
    Content type: Research article Published on:

  4. Human-induced pluripotent stem cells (hiPSCs) are a potentially invaluable resource for regenerative medicine, including the in vitro manufacture of blood products. HiPSC-derived red blood cells are an attract...

    Authors: Alison T. Merryweather-Clarke, Alex J. Tipping, Abigail A. Lamikanra, Rui Fa, Basel Abu-Jamous, Hoi Pat Tsang, Lee Carpenter, Kathryn J. H. Robson, Asoke K. Nandi and David J. Roberts
    Citation: BMC Genomics 2016 17:817
    Content type: Research article Published on:

  5. ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. As part of this procedure, immunoprecipitated DNA must undergo “library preparation” to enable subsequent high-throug...

    Authors: Arvind Y. M. Sundaram, Timothy Hughes, Shea Biondi, Nathalie Bolduc, Sarah K. Bowman, Andrew Camilli, Yap C. Chew, Catherine Couture, Andrew Farmer, John P. Jerome, David W. Lazinski, Andrew McUsic, Xu Peng, Kamran Shazand, Feng Xu, Robert Lyle…
    Citation: BMC Genomics 2016 17:816
    Content type: Research article Published on:

  6. Grapevine (Vitis vinifera L.) is an economically important crop with a wide geographical distribution, reflecting its ability to grow successfully in a range of climates. However, many vineyards are located in re...

    Authors: Silvia Dal Santo, Alberto Palliotti, Sara Zenoni, Giovanni Battista Tornielli, Marianna Fasoli, Paola Paci, Sergio Tombesi, Tommaso Frioni, Oriana Silvestroni, Andrea Bellincontro, Claudio d’Onofrio, Fabiola Matarese, Matteo Gatti, Stefano Poni and Mario Pezzotti
    Citation: BMC Genomics 2016 17:815
    Content type: Research article Published on:

  7. RNA-seq is a well-established method for studying the transcriptome. Popular methods for library preparation in RNA-seq such as Illumina TruSeq® RNA v2 kit use a poly-A pulldown strategy. Such methods can caus...

    Authors: Jaime I. Davila, Numrah M. Fadra, Xiaoke Wang, Amber M. McDonald, Asha A. Nair, Barbara, R. Crusan, Xianglin Wu, Joseph H. Blommel, Jin Jen, Kandelaria M. Rumilla, Robert B. Jenkins, Umut Aypar, Eric W. Klee, Benjamin R. Kipp and Kevin C. Halling
    Citation: BMC Genomics 2016 17:814
    Content type: Research article Published on:

  9. Analyses of sequence variants of two distinct and highly inbred chicken lines allowed characterization of genomic variation that may be associated with phenotypic differences between breeds. These lines were t...

    Authors: D. S. Fleming, J. E. Koltes, E. R. Fritz-Waters, M. F. Rothschild, C. J. Schmidt, C. M. Ashwell, M. E. Persia, J. M. Reecy and S. J. Lamont
    Citation: BMC Genomics 2016 17:812
    Content type: Research article Published on:

  10. Epithelial ovarian cancer (EOC) is the fifth leading cause of cancer death among women in the United States (5 % of cancer deaths). The standard treatment for patients with advanced EOC is initial debulking su...

    Authors: Rama Raghavan, Stephen Hyter, Harsh B. Pathak, Andrew K. Godwin, Gottfried Konecny, Chen Wang, Ellen L. Goode and Brooke L. Fridley
    Citation: BMC Genomics 2016 17:811
    Content type: Research article Published on:

  11. Muscle fibre hyperplasia stops in most fish when they reach approximately 50 % of their maximum body length. However, new small-diameter muscle fibres can be produced de novo in aged fish after muscle injury. Giv...

    Authors: Jerôme Montfort, Aurelie Le Cam, Jean-Charles Gabillard and Pierre-Yves Rescan
    Citation: BMC Genomics 2016 17:810
    Content type: Research article Published on:

  12. Nitric oxide (NO) functions as a critical signaling molecule in the low-temperature stress responses in plants, including polarized pollen tube growth in Camellia sinensis. Despite this, the potential mechanisms ...

    Authors: Junting Pan, Weidong Wang, Dongqin Li, Zaifa Shu, Xiaoli Ye, Pinpin Chang and Yuhua Wang
    Citation: BMC Genomics 2016 17:809
    Content type: Research article Published on:

  13. Inversions and other structural polymorphisms often reduce the rate of recombination between sex chromosomes, making it impossible to fine map sex-determination loci using traditional genetic mapping technique...

    Authors: William J. Gammerdinger, Matthew A. Conte, Jean-François Baroiller, Helena D’Cotta and Thomas D. Kocher
    Citation: BMC Genomics 2016 17:808
    Content type: Research article Published on:

  14. Alzheimer’s disease (AD) is a complex progressive neurodegenerative disorder commonly characterized by short term memory loss. Presently no effective therapeutic treatments exist that can completely cure this ...

    Authors: Salma Jamal, Sukriti Goyal, Asheesh Shanker and Abhinav Grover
    Citation: BMC Genomics 2016 17:807
    Content type: Research article Published on:

  15. African trypanosomes cause lethal diseases in humans and animals and escape host immune attack by switching the expression of Variant Surface Glycoprotein (VSG) genes. The expressed VSGs are located at the ends o...

    Authors: Sebastian Hutchinson, Lucy Glover and David Horn
    Citation: BMC Genomics 2016 17:806
    Content type: Research article Published on:

  18. Genome-wide association studies (GWAS) have become a mainstay of biological research concerned with discovering genetic variation linked to phenotypic traits and diseases. Both discrete and continuous traits c...

    Authors: Sajjad Karim, Hend Fakhri NourEldin, Heba Abusamra, Nada Salem, Elham Alhathli, Joel Dudley, Max Sanderford, Laura B. Scheinfeldt and Sudhir Kumar
    Citation: BMC Genomics 2016 17(Suppl 9):770
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 9

    The Erratum to this article has been published in BMC Genomics 2017 18:281

  19. Preterm birth (PTB), birth at <37 weeks of gestation, is a significant global public health problem. World-wide, about 15 million babies are born preterm each year resulting in more than a million deaths of ch...

    Authors: Ishfaq A. Sheikh, Ejaz Ahmad, Mohammad S. Jamal, Mohd Rehan, Mourad Assidi, Iftikhar A. Tayubi, Samera F. AlBasri, Osama S. Bajouh, Rola F. Turki, Adel M. Abuzenadah, Ghazi A. Damanhouri, Mohd A. Beg and Mohammed Al-Qahtani
    Citation: BMC Genomics 2016 17(Suppl 9):759
    Content type: Review Published on:

    This article is part of a Supplement: Volume 17 Supplement 9

  20. The identification of charge clusters (runs of charged residues) in proteins and their mapping within the protein structure sequence is an important step toward a comprehensive analysis of how these particular...

    Authors: Najla Kharrat, Sabrine Belmabrouk, Rania Abdelhedi, Riadh Benmarzoug, Mourad Assidi, Mohammed H. Al Qahtani and Ahmed Rebai
    Citation: BMC Genomics 2016 17(Suppl 9):758
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 9

  21. Epilepsy is genetically complex but common brain disorder of the world affecting millions of people with almost of all age groups. Novel Copy number variations (CNVs) are considered as important reason for the...

    Authors: Muhammad I. Naseer, Adeel G. Chaudhary, Mahmood Rasool, Gauthaman Kalamegam, Fai T. Ashgan, Mourad Assidi, Farid Ahmed, Shakeel A. Ansari, Syed Kashif Zaidi, Mohammed M. Jan and Mohammad H. Al-Qahtani
    Citation: BMC Genomics 2016 17(Suppl 9):757
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 9

  22. The role of small non-coding microRNAs (miRNAs) in several types of cancer has been evident. However, its expression studies have never been performed in gastric cancer (GC) patients from Saudi population. Fir...

    Authors: Fehmida Bibi, Muhammad I. Naseer, Sana Akhtar Alvi, Muhammad Yasir, Asif A. Jiman-Fatani, Ali Sawan, Adel M. Abuzenadah, Mohammed H. Al-Qahtani and Esam I. Azhar
    Citation: BMC Genomics 2016 17(Suppl 9):751
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 9

  23. Although the primary objective of forensic DNA analyses of unidentified human remains is positive identification, cases involving historical or archaeological skeletal remains often lack reference samples for ...

    Authors: Angie D. Ambers, Jennifer D. Churchill, Jonathan L. King, Monika Stoljarova, Harrell Gill-King, Mourad Assidi, Muhammad Abu-Elmagd, Abdelbaset Buhmeida and Bruce Budowle
    Citation: BMC Genomics 2016 17(Suppl 9):750
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 9

    The Erratum to this article has been published in BMC Genomics 2017 18:312

  24. Loss of function in genes required for telomere maintenance result in disorders known as telomeropathies, which are characterized by a pattern of symptoms including generalized and specific lymphocytopenias as...

    Authors: Brody Holohan, Wanil Kim, Tsung-Po Lai, Hirotoshi Hoshiyama, Ning Zhang, Anas M. Alazami, Woodring E. Wright, M. Stephen Meyn, Fowzan S. Alkuraya and Jerry W. Shay
    Citation: BMC Genomics 2016 17(Suppl 9):749
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 9

  25. Polycystic ovary syndrome (PCOS) is characterized by the growth of a number of small cysts on the ovaries which leads to sex hormonal imbalance. Women who are affected by this syndrome suffer from irregular me...

    Authors: Assila Ben Salem, Fatma Megdich, Olfa Kacem, Malek Souayeh, Faten Hachani Ben Ali, Sondes Hizem, Faouzi Janhai, Mounir Ajina, Muhammad Abu-Elmagd, Mourad Assidi, Mohammed H. Al Qahtani and Touhami Mahjoub
    Citation: BMC Genomics 2016 17(Suppl 9):748
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 9

  26. The Third International Genomic Medicine Conference (3rd IGMC) was organised by the Centre of Excellence in Genomic Medicine Research (CEGMR) at the King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia (KSA...

    Authors: Muhammad Abu-Elmagd, Mourad Assidi, Ashraf Dallol, Abdelbaset Buhmeida, Peter Natesan Pushparaj, Gauthaman Kalamegam, Emad Al-Hamzi, Jerry W. Shay, Stephen W. Scherer, Ashok Agarwal, Bruce Budowle, Mamdooh Gari, Adeel Chaudhary, Adel Abuzenadah and Mohammed Al-Qahtani
    Citation: BMC Genomics 2016 17(Suppl 9):747
    Content type: Meeting report Published on:

    This article is part of a Supplement: Volume 17 Supplement 9

  28. Sugarcane smut, which is caused by Sporisorium scitamineum, has been threatening global sugarcane production. Breeding smut resistant sugarcane varieties has been proven to be the most effective method of control...

    Authors: Yachun Su, Liping Xu, Zhuqing Wang, Qiong Peng, Yuting Yang, Yun Chen and Youxiong Que
    Citation: BMC Genomics 2016 17:800
    Content type: Research article Published on:

  29. DNA copy number profiles from microarray and sequencing experiments sometimes contain wave artefacts which may be introduced during sample preparation and cannot be removed completely by existing preprocessing...

    Authors: Ni Ai, Haoyang Cai, Caius Solovan and Michael Baudis
    Citation: BMC Genomics 2016 17:799
    Content type: ORIGINAL PAPER Published on:

  30. ‘Honeycrisp’ is an apple cultivar that is susceptible to soft scald, a chilling injury expressed as necrotic patches on the peel. Improved understanding of metabolism associated with the disorder would improve...

    Authors: Rachel S. Leisso, Nigel E. Gapper, James P. Mattheis, Nathanael L. Sullivan, Christopher B. Watkins, James J. Giovannoni, Robert J. Schaffer, Jason W. Johnston, Ines Hanrahan, Maarten L. A. T. M. Hertog, Bart M. Nicolaï and David R. Rudell
    Citation: BMC Genomics 2016 17:798
    Content type: Research article Published on:

  31. Autophagy is a cellular degradation process that is highly evolutionarily-conserved in yeast, plants, and animals. In plants, autophagy plays important roles in regulating intracellular degradation and recycli...

    Authors: Weiwei Li, Ming Chen, Erhui Wang, Liqin Hu, Malcolm J. Hawkesford, Li Zhong, Zhu Chen, Zhaoshi Xu, Liancheng Li, Yongbin Zhou, Changhong Guo and Youzhi Ma
    Citation: BMC Genomics 2016 17:797
    Content type: Research article Published on:

  32. The ability to establish root nodule symbioses is restricted to four different plant orders. Soil actinobacteria of the genus Frankia can establish a symbiotic relationship with a diverse group of plants within e...

    Authors: Thanh Van Nguyen, Daniel Wibberg, Kai Battenberg, Jochen Blom, Brian Vanden Heuvel, Alison M. Berry, Jörn Kalinowski and Katharina Pawlowski
    Citation: BMC Genomics 2016 17:796
    Content type: Research article Published on:

  33. Early ripening is an important desirable attribute for fruit crops. ‘Kyoho’ is a popular table grape cultivar in many Asian countries. ‘Fengzao’ is a bud mutant of ‘Kyoho’ and ripens nearly 30 days earlier tha...

    Authors: Da-Long Guo, Fei-Fei Xi, Yi-He Yu, Xiao-Yu Zhang, Guo-Hai Zhang and Gan-Yuan Zhong
    Citation: BMC Genomics 2016 17:795
    Content type: Research article Published on:

  34. Pre-harvest sprouting (PHS) in wheat can cause substantial reduction in grain yield and end-use quality. Grain color (GC) together with other components affect PHS resistance. Several quantitative trait loci (...

    Authors: Meng Lin, Dadong Zhang, Shubing Liu, Guorong Zhang, Jianming Yu, Allan K. Fritz and Guihua Bai
    Citation: BMC Genomics 2016 17:794
    Content type: Research article Published on:

  35. Diachasmimorpha longicaudata (Hymenoptera: Braconidae) is a solitary parasitoid of Tephritidae (Diptera) fruit flies of economic importance currently being mass-reared in bio-factories...

    Authors: M. Constanza Mannino, Máximo Rivarola, Alejandra C. Scannapieco, Sergio González, Marisa Farber, Jorge L. Cladera and Silvia B. Lanzavecchia
    Citation: BMC Genomics 2016 17:793
    Content type: Research article Published on:

  36. Ras-related proteins in brain (Rab)-family proteins are key members of the membrane trafficking pathway in cells. In addition, these proteins have been identified to have diverse functions such as cross-talkin...

    Authors: Sudeep Kumar, Hyun Joo Lee, Hee-Sae Park and Keesook Lee
    Citation: BMC Genomics 2016 17:792
    Content type: Research article Published on:

  37. As an intracellular human pathogen, Mycobacterium tuberculosis (Mtb) is facing multiple stressful stimuli inside the macrophage and the granuloma. Understanding Mtb responses to stress is essential to identify ne...

    Authors: Amine Namouchi, Marta Gómez-Muñoz, Stephan A. Frye, Line Victoria Moen, Torbjørn Rognes, Tone Tønjum and Seetha V. Balasingham
    Citation: BMC Genomics 2016 17:791
    Content type: Research article Published on:

  38. Acute kidney injury (AKI) caused by drug and toxicant ingestion is a serious clinical condition associated with high mortality rates. We currently lack detailed knowledge of the underlying molecular mechanisms...

    Authors: Mohamed Diwan M. AbdulHameed, Danielle L. Ippolito, Jonathan D. Stallings and Anders Wallqvist
    Citation: BMC Genomics 2016 17:790
    Content type: Research article Published on:

  39. Lycoris aurea is a medicine-valuable and ornamental herb widely distributed in China. Former studied have showed that methyl jasmonate (MJ) treatment could increase the content of glan...

    Authors: Sheng Xu, Yumei Jiang, Ning Wang, Bing Xia, Yilong Jiang, Xiaodan Li, Zhengzhi Zhang, Yikui Li and Ren Wang
    Citation: BMC Genomics 2016 17:789
    Content type: Research article Published on:

  40. Transmitted by the whitefly Bemisia tabaci, tomato yellow leaf curly virus (TYLCV) has posed serious threats to plant growth and development. Plant innate immune systems against various threats involve WRKY Group...

    Authors: Ying Huang, Meng-Yao Li, Peng Wu, Zhi-Sheng Xu, Feng Que, Feng Wang and Ai-Sheng Xiong
    Citation: BMC Genomics 2016 17:788
    Content type: Research article Published on:

  41. Alternative mRNA splicing is critical to proteomic diversity and tissue and species differentiation. Exclusion of cassette exons, also called exon skipping, is the most common type of alternative splicing in m...

    Authors: Michael Wainberg, Babak Alipanahi and Brendan Frey
    Citation: BMC Genomics 2016 17:787
    Content type: Research Article Published on:

  42. Pulmonary arterial hypertension (PAH) is a lethal disease with pronounced narrowing of pulmonary vessels due to abnormal cell proliferation. The platelet-derived growth factor BB (PDGF-BB) is well known as a p...

    Authors: Jidong Chen, Xiaolei Cui, Zhengjiang Qian, Yanjiao Li, Kang Kang, Junle Qu, Li Li and Deming Gou
    Citation: BMC Genomics 2016 17:781
    Content type: Research article Published on:

  44. As a major epigenetic component, DNA methylation plays important functions in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited d...

    Authors: Yang Zhou, Lingyang Xu, Derek M. Bickhart, El Hamidi abdel Hay, Steven G. Schroeder, Erin E. Connor, Leeson J. Alexander, Tad S. Sonstegard, Curtis P. Van Tassell, Hong Chen and George E. Liu
    Citation: BMC Genomics 2016 17:779
    Content type: Research article Published on:

  45. Authors: Giovanna Linguiti, Rachele Antonacci, Gianluca Tasco, Francesco Grande, Rita Casadio, Serafina Massari, Vito Castelli, Arianna Consiglio, Marie-Paule Lefranc and Salvatrice Ciccarese
    Citation: BMC Genomics 2016 17:778
    Content type: Erratum Published on:

    The original article was published in BMC Genomics 2016 17:634

  46. MicroRNAs (miRNAs) are short non-coding RNAs that are emerging as important post-transcriptional regulators of neuronal and synaptic development. The precise impact of miRNAs on presynaptic function and neurot...

    Authors: Vivian Y. Poon, Minxia Gu, Fang Ji, Antonius M. VanDongen and Marc Fivaz
    Citation: BMC Genomics 2016 17:777
    Content type: Research article Published on:

  47. MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression mainly through translational repression of target mRNA molecules. More than 2700 human miRNAs have been identified and some are known...

    Authors: Christian Wake, Adam Labadorf, Alexandra Dumitriu, Andrew G. Hoss, Joli Bregu, Kenneth H. Albrecht, Anita L. DeStefano and Richard H. Myers
    Citation: BMC Genomics 2016 17:776
    Content type: Research article Published on:

  48. Manganese (Mn) has several essential functions in plants, including a role as cofactor in the oxygen evolving complex (OEC) of photosystem II (PSII). Manganese deficiency is a major plant nutritional disorder ...

    Authors: Florian Leplat, Pai Rosager Pedas, Søren Kjærsgaard Rasmussen and Søren Husted
    Citation: BMC Genomics 2016 17:775
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2016 17:805

  49. Drought stress tolerance for crop improvement is an important goal worldwide. Drought is a complex trait, and it is vital to understand the complex physiological, biochemical, and molecular mechanisms of droug...

    Authors: Chandra Prakash, S. V. Amitha Mithra, Praveen K. Singh, T. Mohapatra and N. K. Singh
    Citation: BMC Genomics 2016 17:774
    Content type: Research article Published on:

  50. Whole-genome genotyping techniques like Genotyping-by-sequencing (GBS) are being used for genetic studies such as Genome-Wide Association (GWAS) and Genomewide Selection (GS), where different strategies for im...

    Authors: Sofía P. Brandariz, Agustín González Reymúndez, Bettina Lado, Marcos Malosetti, Antonio Augusto Franco Garcia, Martín Quincke, Jarislav von Zitzewitz, Marina Castro, Iván Matus, Alejandro del Pozo, Ariel J. Castro and Lucía Gutiérrez
    Citation: BMC Genomics 2016 17:773
    Content type: Research article Published on:

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BMC Genomics

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