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  1. Research article

    Genome-wide expression profiling in leaves and roots of date palm (Phoenix dactylifera L.) exposed to salinity

    Date palm, as one of the most important fruit crops in North African and West Asian countries including Oman, is facing serious growth problems due to salinity, arising from persistent use of saline water for ...

    Mahmoud W. Yaish, Himanshu V. Patankar, Dekoum V. M. Assaha, Yun Zheng, Rashid Al-Yahyai and Ramanjulu Sunkar

    BMC Genomics 2017 18:246

    Published on: 22 March 2017

  2. Research article

    A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs

    Animal’s efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of ...

    Florence Gondret, Annie Vincent, Magalie Houée-Bigot, Anne Siegel, Sandrine Lagarrigue, David Causeur, Hélène Gilbert and Isabelle Louveau

    BMC Genomics 2017 18:244

    Published on: 21 March 2017

  3. Research article

    Interferon signaling in ascites-associated macrophages is linked to a favorable clinical outcome in a subgroup of ovarian carcinoma patients

    Although tumor-associated macrophages (TAMs) are essential for cancer progression, connections between different clinical outcomes and transcriptional networks have not been reported. We have addressed this is...

    Till Adhikary, Annika Wortmann, Florian Finkernagel, Sonja Lieber, Andrea Nist, Thorsten Stiewe, Uwe Wagner, Sabine Müller-Brüsselbach, Silke Reinartz and Rolf Müller

    BMC Genomics 2017 18:243

    Published on: 21 March 2017

  4. Research article

    Exploring the nature of prediagnostic blood transcriptome markers of chronic lymphocytic leukemia by assessing their overlap with the transcriptome at the clinical stage

    We recently identified 700 genes whose expression levels were predictive of chronic lymphocytic leukemia (CLL) in a genome-wide gene expression analysis of prediagnostic blood from future cases and matched con...

    Jelle Vlaanderen, Max Leenders, Marc Chadeau-Hyam, Lützen Portengen, Soterios A. Kyrtopoulos, Ingvar A. Bergdahl, Ann-Sofie Johansson, Dennie D.G.A.J. Hebels, Theo M.C.M. de Kok, Paolo Vineis and Roel C.H. Vermeulen

    BMC Genomics 2017 18:239

    Published on: 20 March 2017

  5. Research article

    Quorum sensing of Streptococcus mutans is activated by Aggregatibacter actinomycetemcomitans and by the periodontal microbiome

    The oral cavity is inhabited by complex microbial communities forming biofilms that can cause caries and periodontitis. Cell-cell communication might play an important role in modulating the physiologies of in...

    Szymon P. Szafrański, Zhi-Luo Deng, Jürgen Tomasch, Michael Jarek, Sabin Bhuju, Manfred Rohde, Helena Sztajer and Irene Wagner-Döbler

    BMC Genomics 2017 18:238

    Published on: 20 March 2017

  6. Research article

    Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development

    Gut microbial colonization and development of immune competence are intertwined and are influenced by early-life nutritional, environmental, and management factors. Perturbation of the gut microbiome at young ...

    Dirkjan Schokker, Alfons J. M. Jansman, Gosse Veninga, Naomi de Bruin, Stephanie A. Vastenhouw, Freddy M. de Bree, Alex Bossers, Johanna M. J. Rebel and Mari A. Smits

    BMC Genomics 2017 18:241

    Published on: 20 March 2017

  7. Erratum

    Erratum to: Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

    Hisham Abdelrahman, Mohamed ElHady, Acacia Alcivar-Warren, Standish Allen, Rafet Al-Tobasei, Lisui Bao, Ben Beck, Harvey Blackburn, Brian Bosworth, John Buchanan, Jesse Chappell, William Daniels, Sheng Dong, Rex Dunham, Evan Durland, Ahmed Elaswad…

    BMC Genomics 2017 18:235

    Published on: 16 March 2017

    The original article was published in BMC Genomics 2017 18:191

  8. Research

    Active module identification in intracellular networks using a memetic algorithm with a new binary decoding scheme

    Active modules are connected regions in biological network which show significant changes in expression over particular conditions. The identification of such modules is important since it may reveal the regul...

    Dong Li, Zhisong Pan, Guyu Hu, Zexuan Zhu and Shan He

    BMC Genomics 2017 18(Suppl 2):209

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 18 Supplement 2

  9. Research

    Using the entrapment sequence method as a standard to evaluate key steps of proteomics data analysis process

    The mass spectrometry based technical pipeline has provided a high-throughput, high-sensitivity and high-resolution platform for post-genomic biology. Varied models and algorithms are implemented by different ...

    Xiao-dong Feng, Li-wei Li, Jian-hong Zhang, Yun-ping Zhu, Cheng Chang, Kun-xian Shu and Jie Ma

    BMC Genomics 2017 18(Suppl 2):143

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 18 Supplement 2

  10. Research

    P-Hint-Hunt: a deep parallelized whole genome DNA methylation detection tool

    The increasing studies have been conducted using whole genome DNA methylation detection as one of the most important part of epigenetics research to find the significant relationships among DNA methylation and...

    Shaoliang Peng, Shunyun Yang, Ming Gao, Xiangke Liao, Jie Liu, Canqun Yang, Chengkun Wu and Wenqiang Yu

    BMC Genomics 2017 18(Suppl 2):134

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 18 Supplement 2

  11. Research

    Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi

    Emerging evidence indicates that plant miRNAs can present within human circulating system through dietary intake and regulate human gene expression. Hence we deduced that comestible plants miRNAs can be identi...

    Yu-Chen Liu, Wen Liang Chen, Wei-Hsiang Kung and Hsien-Da Huang

    BMC Genomics 2017 18(Suppl 2):112

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 18 Supplement 2

  12. Research

    Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling

    Cancer is a complex disease driven by somatic genomic alterations (SGAs) that perturb signaling pathways and consequently cellular function. Identifying patterns of pathway perturbations would provide insights...

    Vicky Chen, John Paisley and Xinghua Lu

    BMC Genomics 2017 18(Suppl 2):105

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 18 Supplement 2

  13. Research article

    Genetics and fine mapping of a purple leaf gene, BoPr, in ornamental kale (Brassica oleracea L. var. acephala)

    Due to its variegated and colorful leaves, ornamental kale (Brassica oleracea L. var. acephala) has become a popular ornamental plant. In this study, we report the fine mapping and analysis of a candidate purple ...

    Xiao-ping Liu, Bao-zhen Gao, Feng-qing Han, Zhi-yuan Fang, Li-mei Yang, Mu Zhuang, Hong-hao Lv, Yu-mei Liu, Zhan-sheng Li, Cheng-cheng Cai, Hai-long Yu, Zhi-yuan Li and Yang-yong Zhang

    BMC Genomics 2017 18:230

    Published on: 14 March 2017

  14. Research

    Mathematical modelling for variations of inbreeding populations fitness with single and polygenic traits

    Inbreeding mating has been widely accepted as the key mechanism to enhance homozygosity which normally will decrease the fitness of the population. Although this result has been validated by a large amount of ...

    Shuhao Sun, Fima Klebaner and Tianhai Tian

    BMC Genomics 2017 18(Suppl 2):196

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 18 Supplement 2

  15. Research

    A clustering-based approach for efficient identification of microRNA combinatorial biomarkers

    MicroRNAs (miRNAs) have great potential serving as tumor biomarkers and therapeutic targets. As the rapid development of high-throughput experimental technology, gene expression experiments have become more an...

    Yang Yang, Ning Huang, Luning Hao and Wei Kong

    BMC Genomics 2017 18(Suppl 2):210

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 18 Supplement 2

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