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  1. Potato virus Y (PVY) is one of the most important plant viruses affecting potato production. The interactions between potato and PVY are complex and the outcome of the interactions depends on the potato genoty...

    Authors: Aymeric Goyer, Launa Hamlin, James M. Crosslin, Alex Buchanan and Jeff H. Chang
    Citation: BMC Genomics 2015 16:472
    Content type: Research article Published on:

  2. Chronic bacterial infections occur as a result of the infecting pathogen’s ability to live within a biofilm, hence escaping the detrimental effects of antibiotics and the immune defense system. Burkholderia pseud...

    Authors: Chui-Yoke Chin, Yuka Hara, Ahmad-Kamal Ghazali, Soon-Joo Yap, Cin Kong, Yee-Chin Wong, Naufal Rozali, Seng-Fook Koh, Chee-Choong Hoh, Savithri D. Puthucheary and Sheila Nathan
    Citation: BMC Genomics 2015 16:471
    Content type: Research article Published on:

  4. Trunk diseases threaten the longevity and productivity of grapevines in all viticulture production systems. They are caused by distantly-related fungi that form chronic wood infections. Variation in wood-decay...

    Authors: Abraham Morales-Cruz, Katherine C. H. Amrine, Barbara Blanco-Ulate, Daniel P. Lawrence, Renaud Travadon, Philippe E. Rolshausen, Kendra Baumgartner and Dario Cantu
    Citation: BMC Genomics 2015 16:469
    Content type: Research article Published on:

  5. Caecilians, with a discrete lifestyle, are the least explored group of amphibians. Though with distinct traits, many aspects of their biology are poorly investigated. Obtaining the caecilian genomic sequences ...

    Authors: Riga Wu, Qingfeng Liu, Shaoquan Meng, Peng Zhang and Dan Liang
    Citation: BMC Genomics 2015 16:468
    Content type: Research article Published on:

  6. Single-stranded non-protein coding small RNAs, 18–25 nucleotides in length, are ubiquitous throughout plants genomes and are involved in post-transcriptional gene regulation. Several types of DNA markers have ...

    Authors: Nang Myint Phyu Sin Htwe, Zhong-Qin Luo, Long-Guo Jin, Brian Nadon, Ke-Jing Wang and Li-Juan Qiu
    Citation: BMC Genomics 2015 16:467
    Content type: Research article Published on:

  7. Floral transition is a critical event in the life cycle of a flowering plant as it determines its reproductive success. Despite extensive studies of specific genes that regulate this process, the global change...

    Authors: Anna V. Klepikova, Maria D. Logacheva, Sergey E. Dmitriev and Aleksey A. Penin
    Citation: BMC Genomics 2015 16:466
    Content type: Research article Published on:

  8. Idiopathic epilepsy is a common neurological disease in human and domestic dogs but relatively few risk genes have been identified to date. The seizure characteristics, including focal and generalised seizures...

    Authors: Lotta L. E. Koskinen, Eija H. Seppälä, Janelle M. Belanger, Meharji Arumilli, Osmo Hakosalo, Päivi Jokinen, Elisa M. Nevalainen, Ranno Viitmaa, Tarja S. Jokinen, Anita M. Oberbauer and Hannes Lohi
    Citation: BMC Genomics 2015 16:465
    Content type: Research article Published on:

  9. The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, th...

    Authors: Konstantin Kozlov, Dmitri Chebotarev, Mehedi Hassan, Martin Triska, Petr Triska, Pavel Flegontov and Tatiana V Tatarinova
    Citation: BMC Genomics 2015 16(Suppl 8):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  10. Over the past 50,000 years, shifts in human-environmental or human-human interactions shaped genetic differences within and among human populations, including variants under positive selection. Shaped by envir...

    Authors: Samuel K Handelman, Michal Seweryn, Ryan M Smith, Katherine Hartmann, Danxin Wang, Maciej Pietrzak, Andrew D Johnson, Andrzej Kloczkowski and Wolfgang Sadee
    Citation: BMC Genomics 2015 16(Suppl 8):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  11. The recent improvement of the high-throughput sequencing technologies is having a strong impact on the detection of genetic variations associated with cancer. Several institutions worldwide have been sequencin...

    Authors: Rui Tian, Malay K Basu and Emidio Capriotti
    Citation: BMC Genomics 2015 16(Suppl 8):S7
    Content type: Review Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  12. Enrichment analysis is a widely applied procedure for shedding light on the molecular mechanisms and functions at the basis of phenotypes, for enlarging the dataset of possibly related genes/proteins and for h...

    Authors: Pietro Di Lena, Pier Luigi Martelli, Piero Fariselli and Rita Casadio
    Citation: BMC Genomics 2015 16(Suppl 8):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  13. Many cancer cells show distorted epigenetic landscapes. The Cancer Genome Atlas (TCGA) project profiles thousands of tumors, allowing the discovery of somatic alterations in the epigenetic machinery and the id...

    Authors: Florian Gnad, Sophia Doll, Gerard Manning, David Arnott and Zemin Zhang
    Citation: BMC Genomics 2015 16(Suppl 8):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  14. There are now over 2000 loci in the human genome where genome wide association studies (GWAS) have found one or more SNPs to be associated with altered risk of a complex trait disease. At each of these loci, t...

    Authors: Lipika R Pal, Chen-Hsin Yu, Stephen M Mount and John Moult
    Citation: BMC Genomics 2015 16(Suppl 8):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  15. The invention of high throughput sequencing technologies has led to the discoveries of hundreds of thousands of genetic variants associated with thousands of human diseases. Many of these genetic variants are ...

    Authors: Meng Ma, Ying Ru, Ling-Shiang Chuang, Nai-Yun Hsu, Li-Song Shi, Jörg Hakenberg, Wei-Yi Cheng, Andrew Uzilov, Wei Ding, Benjamin S Glicksberg and Rong Chen
    Citation: BMC Genomics 2015 16(Suppl 8):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  16. A vast amount of DNA variation is being identified by increasingly large-scale exome and genome sequencing projects. To be useful, variants require accurate functional annotation and a wide range of tools are ...

    Authors: Adam Frankish, Barbara Uszczynska, Graham RS Ritchie, Jose M Gonzalez, Dmitri Pervouchine, Robert Petryszak, Jonathan M Mudge, Nuno Fonseca, Alvis Brazma, Roderic Guigo and Jennifer Harrow
    Citation: BMC Genomics 2015 16(Suppl 8):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  17. Elucidating the effects of naturally occurring genetic variation is one of the major challenges for personalized health and personalized medicine. Here, we introduce SNAP2, a novel neural network based classif...

    Authors: Maximilian Hecht, Yana Bromberg and Burkhard Rost
    Citation: BMC Genomics 2015 16(Suppl 8):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  19. Many recent studies using ChIP-seq approaches cross-referenced to trascriptome data and also to potentially unbiased in vitro DNA binding selection experiments are detailing with increasing precision the p53-dire...

    Authors: Toma Tebaldi, Sara Zaccara, Federica Alessandrini, Alessandra Bisio, Yari Ciribilli and Alberto Inga
    Citation: BMC Genomics 2015 16:464
    Content type: Research article Published on:

  20. Pyropia yezoensis is a model organism often used to investigate the mechanisms underlying stress tolerance in intertidal zones. The digital gene expression (DGE) approach was used to characteri...

    Authors: Peipei Sun, Yunxiang Mao, Guiyang Li, Min Cao, Fanna Kong, Li Wang and Guiqi Bi
    Citation: BMC Genomics 2015 16:463
    Content type: Research article Published on:

  21. Piwi-interacting RNAs (piRNAs) are a class of small RNAs; distinct types of piRNAs are expressed in the mammalian testis at different stages of development. The function of piRNAs expressed in the adult testis...

    Authors: Jennifer Yamtich, Seok-Jin Heo, Joseph Dhahbi, David IK Martin and Dario Boffelli
    Citation: BMC Genomics 2015 16:462
    Content type: Research article Published on:

  22. The genus Microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. Microbotryum lychnidis-dioicae infects Silene latifolia and replaces host pollen with fungal spo...

    Authors: Michael H Perlin, Joelle Amselem, Eric Fontanillas, Su San Toh, Zehua Chen, Jonathan Goldberg, Sebastien Duplessis, Bernard Henrissat, Sarah Young, Qiandong Zeng, Gabriela Aguileta, Elsa Petit, Helene Badouin, Jared Andrews, Dominique Razeeq, Toni Gabaldón…
    Citation: BMC Genomics 2015 16:461
    Content type: Research article Published on:

  23. Insect mitochondrial genomes (mitogenomes) are the most extensively used genetic marker for evolutionary and population genetics studies of insects. The Pentatomoidea superfamily is economically important and ...

    Authors: Ming-Long Yuan, Qi-Lin Zhang, Zhong-Long Guo, Juan Wang and Yu-Ying Shen
    Citation: BMC Genomics 2015 16:460
    Content type: Research article Published on:

  24. Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural materials on earth. It consists of complex carbohydrates and a...

    Authors: Youzhi Miao, Dongyang Liu, Guangqi Li, Pan Li, Yangchun Xu, Qirong Shen and Ruifu Zhang
    Citation: BMC Genomics 2015 16:459
    Content type: Research article Published on:

  25. The European shore crab, Carcinus maenas, is used widely in biomonitoring, ecotoxicology and for studies into host-pathogen interactions. It is also an important invasive species in numerous global locations. How...

    Authors: Bas Verbruggen, Lisa K. Bickley, Eduarda M. Santos, Charles R. Tyler, Grant D. Stentiford, Kelly S. Bateman and Ronny van Aerle
    Citation: BMC Genomics 2015 16:458
    Content type: Research article Published on:

  26. microRNAs (miRNAs) in fish have not been as extensively studied as those in mammals. The fish species Takifugu rubripes is an intensively studied model organism whose genome has been sequenced. The T. rubripes ge...

    Authors: Chaninya Wongwarangkana, Kazuhiro E. Fujimori, Masaki Akiba, Shigeharu Kinoshita, Morimi Teruya, Maiko Nezuo, Tsukahara Masatoshi, Shugo Watabe and Shuichi Asakawa
    Citation: BMC Genomics 2015 16:457
    Content type: Research article Published on:

  28. The advent of the NGS technologies has permitted profiling of whole-genome transcriptomes (i.e., RNA-Seq) at unprecedented speed and very low cost. RNA-Seq provides a far more precise measurement of transcript...

    Authors: Chen Chu, Zhaoben Fang, Xing Hua, Yaning Yang, Enguo Chen, Allen W. Cowley Jr., Mingyu Liang, Pengyuan Liu and Yan Lu
    Citation: BMC Genomics 2015 16:455
    Content type: Methodology article Published on:

  29. The human malaria parasite Plasmodium falciparum has a complex and multi-stage life cycle that requires extensive and precise gene regulation to allow invasion and hijacking of host cells, transmission, and immun...

    Authors: Kate M Broadbent, Jill C Broadbent, Ulf Ribacke, Dyann Wirth, John L Rinn and Pardis C Sabeti
    Citation: BMC Genomics 2015 16:454
    Content type: Research article Published on:

  30. The substantially large bread wheat genome, organized into highly similar three sub-genomes, renders genomic research challenging. The construction of BAC-based physical maps of individual chromosomes reduces ...

    Authors: Bala Ani Akpinar, Federica Magni, Meral Yuce, Stuart J. Lucas, Hana Šimková, Jan Šafář, Sonia Vautrin, Hélène Bergès, Federica Cattonaro, Jaroslav Doležel and Hikmet Budak
    Citation: BMC Genomics 2015 16:453
    Content type: Research article Published on:

  31. In bright beer, haze formation is a serious quality problem, degrading beer quality and reducing its shelf life. The quality of barley (Hordeum vulgare L) malt, as the main raw material for beer brewing, largely ...

    Authors: Lingzhen Ye, Yuqing Huang, Fei Dai, Huajiang Ning, Chengdao Li, Meixue Zhou and Guoping Zhang
    Citation: BMC Genomics 2015 16:449
    Content type: Research article Published on:

  32. Gene regulation is dynamic across cellular conditions and disease subtypes. From the aspect of regulation under modulation, regulation strength between a pair of genes can be modulated by (dependent on) expres...

    Authors: Yu-Chiao Chiu, Chin-Ting Wu, Tzu-Hung Hsiao, Yi-Pin Lai, Chuhsing Kate Hsiao, Yidong Chen and Eric Y Chuang
    Citation: BMC Genomics 2015 16(Suppl 7):S19
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  33. Pathway analysis has been widely used to gain insight into essential mechanisms of the response to myocardial infarction (MI). Currently, there exist multiple pathway databases that organize molecular datasets...

    Authors: Nguyen T Nguyen, Merry L Lindsey and Yu-Fang Jin
    Citation: BMC Genomics 2015 16(Suppl 7):S18
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  34. One major challenge in personalized medicine research is to identify the environmental factors that can alter drug response, and to investigate their molecular mechanisms. These environmental factors include c...

    Authors: Santosh Philips, Jing Zhou, Zhigao Li, Todd C Skaar and Lang Li
    Citation: BMC Genomics 2015 16(Suppl 7):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  35. Enzymes are known as the molecular machines that drive the metabolism of an organism; hence identification of the full enzyme complement of an organism is essential to build the metabolic blueprint of that spe...

    Authors: Akram Mohammed and Chittibabu Guda
    Citation: BMC Genomics 2015 16(Suppl 7):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  36. Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao (A. mongolicus, family Leguminosae) is one of the most important traditional Chinese herbs. Among many secondary metabolites it produces, the effective bi...

    Authors: Jing Chen, Xue-Ting Wu, Yi-Qin Xu, Yang Zhong, Yi-Xue Li, Jia-Kuan Chen, Xuan Li and Peng Nan
    Citation: BMC Genomics 2015 16(Suppl 7):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  37. RNA sequencing (RNA-seq) is a powerful tool for genome-wide expression profiling of biological samples with the advantage of high-throughput and high resolution. There are many existing algorithms nowadays for...

    Authors: Hung-I Harry Chen, Yuanhang Liu, Yi Zou, Zhao Lai, Devanand Sarkar, Yufei Huang and Yidong Chen
    Citation: BMC Genomics 2015 16(Suppl 7):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  38. Motifs are regulatory elements that will activate or inhibit the expression of related genes when proteins (such as transcription factors, TFs) bind to them. Therefore, motif finding is important to understand...

    Authors: Yizhe Zhang, Yupeng He, Guangyong Zheng and Chaochun Wei
    Citation: BMC Genomics 2015 16(Suppl 7):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  39. High-throughput in vivo protein-DNA interaction experiments are currently widely used in gene regulation studies. Hitherto, comprehensive data analysis remains a challenge and for that reason most computational m...

    Authors: Junbai Wang, Agnieszka Malecka, Gunhild Trøen and Jan Delabie
    Citation: BMC Genomics 2015 16(Suppl 7):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  40. Regulatory regions (e.g. promoters and enhancers) play an essential role in human development and disease. Many computational approaches have been developed to predict the regulatory regions using various geno...

    Authors: Woochang Hwang, Verity F Oliver, Shannath L Merbs, Heng Zhu and Jiang Qian
    Citation: BMC Genomics 2015 16(Suppl 7):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  41. Identification of protein interaction network is a very important step for understanding the molecular mechanisms in cancer. Several methods have been developed to integrate protein-protein interaction (PPI) d...

    Authors: Xu Shi, Xiao Wang, Ayesha Shajahan, Leena Hilakivi-Clarke, Robert Clarke and Jianhua Xuan
    Citation: BMC Genomics 2015 16(Suppl 7):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  42. Malaria is the most deadly parasitic infectious disease. Existing drug treatments have limited efficacy in malaria elimination, and the complex pathogenesis of the disease is not fully understood. Detecting no...

    Authors: Yang Chen and Rong Xu
    Citation: BMC Genomics 2015 16(Suppl 7):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  43. Defective tumor suppressor genes (TSGs) and hyperactive oncogenes (OCGs) heavily contribute to cell proliferation and apoptosis during cancer development through genetic variations such as somatic mutations an...

    Authors: Kevin Zhu, Qi Liu, Yubo Zhou, Cui Tao, Zhongming Zhao, Jingchun Sun and Hua Xu
    Citation: BMC Genomics 2015 16(Suppl 7):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  44. Cancers are complex diseases with heterogeneous genetic causes and clinical outcomes. It is critical to classify patients into subtypes and associate the subtypes with clinical outcomes for better prognosis an...

    Authors: Xue Zhong, Hushan Yang, Shuyang Zhao, Yu Shyr and Bingshan Li
    Citation: BMC Genomics 2015 16(Suppl 7):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  45. Personalized genomics instability, e.g., somatic mutations, is believed to contribute to the heterogeneous drug responses in patient cohorts. However, it is difficult to discover personalized driver mutations ...

    Authors: Lin Wang, Fuhai Li, Jianting Sheng and Stephen TC Wong
    Citation: BMC Genomics 2015 16(Suppl 7):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  46. It is well known that carcinogenesis is in part dictated by dysregulated transcription events and signal pathways. Large-scale transcriptional profiling studies in each cancer type have reported aberrant gene ...

    Authors: Jing Wang, Qi Liu and Yu Shyr
    Citation: BMC Genomics 2015 16(Suppl 7):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  47. Dietary intakes of red meat and fat are established risk factors for both colorectal cancer (CRC) and cardiovascular disease (CVDs). Recent studies have shown a mechanistic link between TMAO, an intestinal mic...

    Authors: Rong Xu, QuanQiu Wang and Li Li
    Citation: BMC Genomics 2015 16(Suppl 7):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  48. Prostate cancer (PCa) is a leading cause of cancer-related death of men worldwide. There is an urgent need to develop novel biomarkers for PCa prognosis and diagnosis in the post prostate specific antigen era....

    Authors: Weirong Cui, Yulan Qian, Xiaoke Zhou, Yuxin Lin, Junfeng Jiang, Jiajia Chen, Zhongming Zhao and Bairong Shen
    Citation: BMC Genomics 2015 16(Suppl 7):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  49. The lack of consensus among reported gene signature subsets (GSSs) in multi-gene biomarker discovery studies is often a concern for researchers and clinicians. Subsequently, it discourages larger scale prospec...

    Authors: Ghim Siong Ow and Vladimir A Kuznetsov
    Citation: BMC Genomics 2015 16(Suppl 7):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  50. Here we present a summary of the 2014 International Conference on Intelligent Biology and Medicine (ICIBM 2014) and the editorial report of the supplement to BMC Genomics and BMC Systems Biology that includes ...

    Authors: Jianhua Ruan, Victor Jin, Yufei Huang, Hua Xu, Jeremy S Edwards, Yidong Chen and Zhongming Zhao
    Citation: BMC Genomics 2015 16(Suppl 7):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

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