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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  11. 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:

  12. 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:

  13. 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:

  14. Organisms utilize a multitude of mechanisms for responding to changing environmental conditions, maintaining their functional homeostasis and to overcome stress situations. One of the most important mechanisms...

    Authors: Vinicius A. C. Abreu, Sintia Almeida, Sandeep Tiwari, Syed Shah Hassan, Diego Mariano, Artur Silva, Jan Baumbach, Vasco Azevedo and Richard Röttger
    Citation: BMC Genomics 2015 16:452
    Content type: Database Published on:

  16. Terpenoids are abundant in the foliage of Eucalyptus, providing the characteristic smell as well as being valuable economically and influencing ecological interactions. Quantitative and qualitative inter- and int...

    Authors: Carsten Külheim, Amanda Padovan, Charles Hefer, Sandra T Krause, Tobias G Köllner, Alexander A Myburg, Jörg Degenhardt and William J Foley
    Citation: BMC Genomics 2015 16:450
    Content type: Research article Published on:

  17. 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:

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. Clostridium difficile and C. sordellii are two anaerobic, spore forming, gram positive pathogens with a broad host range and the ability to cause lethal infections. Despite strong similarities ...

    Authors: Joy Scaria, Haruo Suzuki, Christopher P. Ptak, Jenn-Wei Chen, Yongzhang Zhu, Xiao-Kui Guo and Yung-Fu Chang
    Citation: BMC Genomics 2015 16:448
    Content type: Research article Published on:

  38. Aliivibrio wodanis and Moritella viscosa have often been isolated concurrently from fish with winter-ulcer disease. Little is known about the interaction between the two bacterial species and h...

    Authors: Erik Hjerde, Christian Karlsen, Henning Sørum, Julian Parkhill, Nils Peder Willassen and Nicholas R. Thomson
    Citation: BMC Genomics 2015 16:447
    Content type: Research article Published on:

  39. Banana and plantain (Musa spp.) comprise an important part of diets for millions of people around the globe. Low temperature is one of the key environmental stresses which greatly affects the global banana produc...

    Authors: Qiao-Song Yang, Jie Gao, Wei-Di He, Tong-Xin Dou, Li-Jie Ding, Jun-Hua Wu, Chun-Yu Li, Xin-Xiang Peng, Sheng Zhang and Gan-Jun Yi
    Citation: BMC Genomics 2015 16:446
    Content type: Research article Published on:

  40. The amphinomid polychaete Hermodice carunculata is a cosmopolitan and ecologically important omnivore in coral reef ecosystems, preying on a diverse suite of reef organisms and potentially acting as a vector for ...

    Authors: Shaadi Mehr, Aida Verdes, Rob DeSalle, John Sparks, Vincent Pieribone and David F Gruber
    Citation: BMC Genomics 2015 16:445
    Content type: Research article Published on:

  42. Due to the absence of transcription initiation regulation of protein coding genes transcribed by RNA polymerase II, posttranscriptional regulation is responsible for the majority of gene expression changes in ...

    Authors: Pablo Smircich, Guillermo Eastman, Saloe Bispo, María Ana Duhagon, Eloise P Guerra-Slompo, Beatriz Garat, Samuel Goldenberg, David J Munroe, Bruno Dallagiovanna, Fabiola Holetz and Jose R Sotelo-Silveira
    Citation: BMC Genomics 2015 16:443
    Content type: Research article Published on:

  43. Amplified gene families on sex chromosomes can harbour genes with important biological functions, especially relating to fertility. The Y-linked heat shock transcription factor (HSFY) family has become amplified ...

    Authors: Benjamin M Skinner, Kim Lachani, Carole A Sargent, Fengtang Yang, Peter Ellis, Toby Hunt, Beiyuan Fu, Sandra Louzada, Carol Churcher, Chris Tyler-Smith and Nabeel A Affara
    Citation: BMC Genomics 2015 16:442
    Content type: Research article Published on:

  44. Hematophagy arose independently multiple times during metazoan evolution, with several lineages of vampire animals particularly diversified in invertebrates. However, the biochemistry of hematophagy has been s...

    Authors: Maria Vittoria Modica, Fabrizio Lombardo, Paolo Franchini and Marco Oliverio
    Citation: BMC Genomics 2015 16:441
    Content type: Research article Published on:

  45. In climacteric fruit-bearing species, the onset of fruit ripening is marked by a transient rise in respiration rate and autocatalytic ethylene production, followed by rapid deterioration in fruit quality. In n...

    Authors: Montserrat Saladié, Joaquin Cañizares, Michael A. Phillips, Manuel Rodriguez-Concepcion, Christian Larrigaudière, Yves Gibon, Mark Stitt, John Edward Lunn and Jordi Garcia-Mas
    Citation: BMC Genomics 2015 16:440
    Content type: Research article Published on:

  46. Multipartite mitochondrial genomes are very rare in animals but have been found previously in two insect orders with highly rearranged genomes, the Phthiraptera (parasitic lice), and the Psocoptera (booklice/b...

    Authors: Aaron M. Dickey, Vivek Kumar, J. Kent Morgan, Antonella Jara-Cavieres, Robert G. Shatters Jr., Cindy L. McKenzie and Lance S. Osborne
    Citation: BMC Genomics 2015 16:439
    Content type: Research article Published on:

  47. The Generation Scotland Scottish Family Health Study (GS:SFHS) includes 23,960 participants from across Scotland with records for many health-related traits and environmental covariates. Genotypes at ~700 K SN...

    Authors: Carmen Amador, Jennifer Huffman, Holly Trochet, Archie Campbell, David Porteous, James F Wilson, Nick Hastie, Veronique Vitart, Caroline Hayward, Pau Navarro and Chris S Haley
    Citation: BMC Genomics 2015 16:437
    Content type: Research article Published on:

  48. Lampreys are extant representatives of the jawless vertebrate lineage that diverged from jawed vertebrates around 500 million years ago. Lamprey genomes contain information crucial for understanding the evolut...

    Authors: Jianfeng Ren, Yu-Wen Chung-Davidson, Chu-Yin Yeh, Camille Scott, Titus Brown and Weiming Li
    Citation: BMC Genomics 2015 16:436
    Content type: Research article Published on:

  49. Recent technological advances in atmospheric plasmas have made the creation of non-thermal atmospheric pressure plasma (NTP) possible for utilization in the medical field. Although accumulated evidence suggest...

    Authors: Jue Hou, Jie Ma, K. N. Yu, Wei Li, Cheng Cheng, Lingzhi Bao and Wei Han
    Citation: BMC Genomics 2015 16:435
    Content type: Research article Published on:

  50. Authors: Amir M Hossini, Matthias Megges, Alessandro Prigione, Bjoern Lichtner, Mohammad R Toliat, Wasco Wruck, Friederike Schröter, Peter Nuernberg, Hartmut Kroll, Eugenia Makrantonaki, Christos C Zouboulis and James Adjaye
    Citation: BMC Genomics 2015 16:433
    Content type: Erratum Published on:

    The original article was published in BMC Genomics 2015 16:84

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