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  1. Isatis indigotica Fort. is one of the most commonly used traditional Chinese medicines. Its antiviral compound is a kind of lignan, which is formed with the action of dirigent proteins (DIR). DIR proteins are mem...

    Authors: Qing Li, Junfeng Chen, Ying Xiao, Peng Di, Lei Zhang and Wansheng Chen
    Citation: BMC Genomics 2014 15:388
    Content type: Research article Published on:

  2. Although the reference human genome sequence was declared finished in 2003, some regions of the genome remain incomplete due to their complex architecture. One such region, 1q21.1-q21.2, is of increasing inter...

    Authors: Majesta O’Bleness, Veronica B Searles, C Michael Dickens, David Astling, Derek Albracht, Angel C Y Mak, Yvonne Y Y Lai, Chin Lin, Catherine Chu, Tina Graves, Pui-Yan Kwok, Richard K Wilson and James M Sikela
    Citation: BMC Genomics 2014 15:387
    Content type: Research article Published on:

  3. The rapid growth of un-annotated missense variants poses challenges requiring novel strategies for their interpretation. From the thermodynamic point of view, amino acid changes can lead to a change in the int...

    Authors: Manuel Giollo, Alberto JM Martin, Ian Walsh, Carlo Ferrari and Silvio CE Tosatto
    Citation: BMC Genomics 2014 15(Suppl 4):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 4

  4. Reliable prediction of stability changes in protein variants is an important aspect of computational protein design. A number of machine learning methods that allow a classification of stability changes knowin...

    Authors: Lukas Folkman, Bela Stantic and Abdul Sattar
    Citation: BMC Genomics 2014 15(Suppl 4):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 4

  5. Genome wide association studies (GWAS) have revealed a large number of links between genome variation and complex disease. Among other benefits, it is expected that these insights will lead to new therapeutic ...

    Authors: Chen Cao and John Moult
    Citation: BMC Genomics 2014 15(Suppl 4):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 4

  6. Missense pharmacogenomic (PGx) variants refer to amino acid substitutions that potentially affect the pharmacokinetic (PK) or pharmacodynamic (PD) response to drug therapies. The PGx variants, as compared to d...

    Authors: Biao Li, Chet Seligman, Janita Thusberg, Jackson L Miller, Jim Auer, Michelle Whirl-Carrillo, Emidio Capriotti, Teri E Klein and Sean D Mooney
    Citation: BMC Genomics 2014 15(Suppl 4):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 4

  7. Inflammation has significant roles in all phases of tumor development, including initiation, progression and metastasis. Interleukin-10 (IL-10) is a well-known immuno-modulatory cytokine with an anti-inflammat...

    Authors: Ece Saliha Acuner-Ozbabacan, Billur Hatice Engin, Emine Guven-Maiorov, Guray Kuzu, Serena Muratcioglu, Alper Baspinar, Zhong Chen, Carter Van Waes, Attila Gursoy, Ozlem Keskin and Ruth Nussinov
    Citation: BMC Genomics 2014 15(Suppl 4):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 4

  8. RNA metabolism, including RNA synthesis and RNA degradation, is one of the most conserved biological systems and has been intensively studied; however, the degradation network of ribonucleases (RNases) and RNA...

    Authors: Hiromasa Ohyama, Tomofumi Sakai, Yoshihiro Agari, Kenji Fukui, Noriko Nakagawa, Akeo Shinkai, Ryoji Masui and Seiki Kuramitsu
    Citation: BMC Genomics 2014 15:386
    Content type: Research article Published on:

  9. Bacterial small RNAs (sRNAs) regulate gene expression by base-pairing with downstream target mRNAs to attenuate translation of mRNA into protein at the post-transcriptional level. In response to specific envir...

    Authors: Chris J Stubben, Sofiya N Micheva-Viteva, Yulin Shou, Sarah K Buddenborg, John M Dunbar and Elizabeth Hong-Geller
    Citation: BMC Genomics 2014 15:385
    Content type: Research article Published on:

  10. Novosphingobium sp. strain PP1Y is a marine α-proteobacterium adapted to grow at the water/fuel oil interface. It exploits the aromatic fraction of fuel oils as a carbon and energy source. PP1Y is able to grow on...

    Authors: Valeria D’Argenio, Eugenio Notomista, Mauro Petrillo, Piergiuseppe Cantiello, Valeria Cafaro, Viviana Izzo, Barbara Naso, Luca Cozzuto, Lorenzo Durante, Luca Troncone, Giovanni Paolella, Francesco Salvatore and Alberto Di Donato
    Citation: BMC Genomics 2014 15:384
    Content type: Research article Published on:

  11. Mosses are the largest of the three extant clades of gametophyte-dominant land plants and remain poorly studied using comparative genomic methods. Major monophyletic moss lineages are characterised by differen...

    Authors: Neil E Bell, Jeffrey L Boore, Brent D Mishler and Jaakko Hyvönen
    Citation: BMC Genomics 2014 15:383
    Content type: Research article Published on:

  12. The endothelial PAS domain protein 1 (EPAS1) activates genes that are involved in erythropoiesis and angiogenesis, thus favoring a better delivery of oxygen to the tissues and is a plausible candidate to influ...

    Authors: Sarah Voisin, Pawel Cieszczyk, Vladimir P Pushkarev, Dmitry A Dyatlov, Boris F Vashlyayev, Vladimir A Shumaylov, Agnieszka Maciejewska-Karlowska, Marek Sawczuk, Lidia Skuza, Zbigniew Jastrzebski, David J Bishop and Nir Eynon
    Citation: BMC Genomics 2014 15:382
    Content type: Research article Published on:

  13. Adipogenesis is a complex process, in which immature pre-adipocytes change morphology, micro-anatomy and physiology to become mature adipocytes. These store and accumulate fat and release diverse hormones. Mas...

    Authors: Silvia von der Heyde, Carolin Fromm-Dornieden, Gabriela Salinas-Riester, Tim Beissbarth and Bernhard G Baumgartner
    Citation: BMC Genomics 2014 15:381
    Content type: Research article Published on:

  14. Epidemiological studies in the recent years have investigated the relationship between dietary habits and disease risk demonstrating that diet has a direct effect on public health. Especially plant-based diets...

    Authors: David Westergaard, Jun Li, Kasper Jensen, Irene Kouskoumvekaki and Gianni Panagiotou
    Citation: BMC Genomics 2014 15:380
    Content type: Research article Published on:

  15. Allergic contact dermatitis (ACD) develops upon exposure to certain chemical compounds termed skin sensitizers. To reduce the occurrence of skin sensitizers, chemicals are regularly screened for their capacity...

    Authors: Andy Forreryd, Henrik Johansson, Ann-Sofie Albrekt and Malin Lindstedt
    Citation: BMC Genomics 2014 15:379
    Content type: Research article Published on:

  16. The rapid growth of the world’s population demands an increase in food production that no longer can be reached by increasing amounts of nitrogenous fertilizers. Plant growth promoting bacteria (PGPB) might be...

    Authors: Doumit Camilios-Neto, Paloma Bonato, Roseli Wassem, Michelle Z Tadra-Sfeir, Liziane CC Brusamarello-Santos, Glaucio Valdameri, Lucélia Donatti, Helisson Faoro, Vinicius A Weiss, Leda S Chubatsu, Fábio O Pedrosa and Emanuel M Souza
    Citation: BMC Genomics 2014 15:378
    Content type: Research article Published on:

  17. Mate preference behavior is an essential first step in sexual selection and is a critical determinant in evolutionary biology. Previously an environmental compound (the fungicide vinclozolin) was found to prom...

    Authors: Michael K Skinner, Marina I Savenkova, Bin Zhang, Andrea C Gore and David Crews
    Citation: BMC Genomics 2014 15:377
    Content type: Research article Published on:

  18. We have a limited understanding of genomic interactions that occur among partners for many symbioses. One of the most important symbioses in tropical reef habitats involves Symbiodinium. Most work examining Symbi...

    Authors: Ana Riesgo, Kristin Peterson, Crystal Richardson, Tyler Heist, Brian Strehlow, Mark McCauley, Carlos Cotman, Malcolm Hill and April Hill
    Citation: BMC Genomics 2014 15:376
    Content type: Research article Published on:

  19. Protein phosphorylation is one of the most important post-translational modifications involved in the regulation of plant growth and development as well as diverse stress response. As a member of the Poaceae, Bra...

    Authors: Dong-Wen Lv, Xin Li, Ming Zhang, Ai-Qin Gu, Shou-Min Zhen, Chang Wang, Xiao-Hui Li and Yue-Ming Yan
    Citation: BMC Genomics 2014 15:375
    Content type: Research article Published on:

  20. Nucleomorphs are residual nuclei derived from eukaryotic endosymbionts in chlorarachniophyte and cryptophyte algae. The endosymbionts that gave rise to nucleomorphs and plastids in these two algal groups were ...

    Authors: Goro Tanifuji, Naoko T Onodera, Matthew W Brown, Bruce A Curtis, Andrew J Roger, Gane Ka-Shu Wong, Michael Melkonian and John M Archibald
    Citation: BMC Genomics 2014 15:374
    Content type: Research article Published on:

  21. Preeclampsia is a significant cause of maternal and fetal mortality and morbidity worldwide. We previously reported associations between trichothiodystrophy (TTD) nucleotide excision repair (NER) and transcrip...

    Authors: Roxana Moslehi, Xavier Ambroggio, Vijayaraj Nagarajan, Anil Kumar and Amiran Dzutsev
    Citation: BMC Genomics 2014 15:373
    Content type: Research article Published on:

  22. Lotus is a diploid plant with agricultural, medicinal, and ecological significance. Genetic linkage maps are fundamental resources for genome and genetic study, and also provide molecular markers for breeding ...

    Authors: Qiong Zhang, Leiting Li, Robert VanBuren, Yanling Liu, Mei Yang, Liming Xu, John E Bowers, Caihong Zhong, Yuepeng Han, Shaohua Li and Ray Ming
    Citation: BMC Genomics 2014 15:372
    Content type: Research article Published on:

  23. Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mec...

    Authors: José B Pereira-Leal, Isabel A Abreu, Cláudia S Alabaça, Maria Helena Almeida, Paulo Almeida, Tânia Almeida, Maria Isabel Amorim, Susana Araújo, Herlânder Azevedo, Aleix Badia, Dora Batista, Andreas Bohn, Tiago Capote, Isabel Carrasquinho, Inês Chaves, Ana Cristina Coelho…
    Citation: BMC Genomics 2014 15:371
    Content type: Research article Published on:

  24. The gut of phloem feeding insects is critical for nutrition uptake and xenobiotics degradation. However, partly due to its tiny size, genomic information for the gut of phloem feeding insects is limited.

    Authors: Xiao-Dong Ye, Yun-Lin Su, Qiong-Yi Zhao, Wen-Qiang Xia, Shu-Sheng Liu and Xiao-Wei Wang
    Citation: BMC Genomics 2014 15:370
    Content type: Research article Published on:

  25. Nuclear receptors are a superfamily of transcription factors important in key biological, developmental and reproductive processes. Several of these receptors are ligand- activated and through their ability to...

    Authors: Susanne Vogeler, Tamara S Galloway, Brett P Lyons and Tim P Bean
    Citation: BMC Genomics 2014 15:369
    Content type: Research article Published on:

  26. As the architecture of complex traits incorporates a widening spectrum of genetic variation, analyses integrating common and rare variation are needed. Body mass index (BMI) represents a model trait, since com...

    Authors: Roseann E Peterson, Hermine H Maes, Peng Lin, John R Kramer, Victor M Hesselbrock, Lance O Bauer, John I Nurnberger Jr, Howard J Edenberg, Danielle M Dick and Bradley T Webb
    Citation: BMC Genomics 2014 15:368
    Content type: Research article Published on:

  27. Transgenesis by random integration of a transgene into the genome of a zygote has become a reliable and powerful method for the creation of new mouse strains that express exogenous genes, including human disea...

    Authors: Anuj Srivastava, Vivek M Philip, Ian Greenstein, Lucy B Rowe, Mary Barter, Cathleen Lutz and Laura G Reinholdt
    Citation: BMC Genomics 2014 15:367
    Content type: Methodology article Published on:

  28. Alternative splicing diversifies the pool of messenger RNA molecules encoded by individual genes. This diversity is particularly high when multiple splicing decisions cause a combinatorial arrangement of sever...

    Authors: Dominique A Glauser
    Citation: BMC Genomics 2014 15:364
    Content type: Research article Published on:

  29. Amycolatopsis orientalis is the type species of the genus and its industrial strain HCCB10007, derived from ATCC 43491, has been used for large-scale production of the vital antibiotic vancomycin. However, to dat...

    Authors: Li Xu, He Huang, Wei Wei, Yi Zhong, Biao Tang, Hua Yuan, Li Zhu, Weiyi Huang, Mei Ge, Shen Yang, Huajun Zheng, Weihong Jiang, Daijie Chen, Guo-Ping Zhao and Wei Zhao
    Citation: BMC Genomics 2014 15:363
    Content type: Research article Published on:

  30. Carolacton is a newly identified secondary metabolite causing altered cell morphology and death of Streptococcus mutans biofilm cells. To unravel key regulators mediating these effects, the transcriptional regula...

    Authors: Padhmanand Sudhakar, Michael Reck, Wei Wang, Feng Q He, Irene W Dobler and An-Ping Zeng
    Citation: BMC Genomics 2014 15:362
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2014 15:739

  31. Essential genes are critical for the development of all organisms and are associated with many human diseases. These genes have been a difficult category to study prior to the availability of balanced lethal s...

    Authors: Jeffrey Shih-Chieh Chu, Shu-Yi Chua, Kathy Wong, Ann Marie Davison, Robert Johnsen, David L Baillie and Ann M Rose
    Citation: BMC Genomics 2014 15:361
    Content type: Research article Published on:

  32. Studies have shown the strong association between histone modification levels and gene expression levels. The detailed relationships between the two can vary substantially due to differential regulation, and h...

    Authors: Yeonok Lee, Debashis Ghosh and Yu Zhang
    Citation: BMC Genomics 2014 15:360
    Content type: Methodology article Published on:

  36. In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted a...

    Authors: Milica Ciric, Christina D Moon, Sinead C Leahy, Christopher J Creevey, Eric Altermann, Graeme T Attwood, Jasna Rakonjac and Dragana Gagic
    Citation: BMC Genomics 2014 15:356
    Content type: Methodology article Published on:

  37. Shigella dysenteriae type 1 (Sd1) causes recurrent epidemics of dysentery associated with high mortality in many regions of the world. Sd1 infects humans at very low infectious doses (10 CFU), and treatment is co...

    Authors: Laurence Rohmer, Michael A Jacobs, Mitchell J Brittnacher, Christine Fong, Hillary S Hayden, Didier Hocquet, Eli J Weiss, Matthew Radey, Yves Germani, Kaisar Ali Talukder, Anthony J Hager, John M Kemner, Elizabeth H Sims-Day, Susana Matamouros, Kyle R Hager and Samuel I Miller
    Citation: BMC Genomics 2014 15:355
    Content type: Research article Published on:

  38. Next generation sequencing is helping to overcome limitations in organisms less accessible to classical or reverse genetic methods by facilitating whole genome mutational analysis studies. One traditionally in...

    Authors: Andrew Farrell, Bradley I Coleman, Brian Benenati, Kevin M Brown, Ira J Blader, Gabor T Marth and Marc-Jan Gubbels
    Citation: BMC Genomics 2014 15:354
    Content type: Research article Published on:

  39. Multiple infection sources for enterohemorrhagic Escherichia coli O157:H7 (EHEC) are known, including animal products, fruit and vegetables. The ecology of this pathogen outside its human host is largely unknown ...

    Authors: Richard Landstorfer, Svenja Simon, Steffen Schober, Daniel Keim, Siegfried Scherer and Klaus Neuhaus
    Citation: BMC Genomics 2014 15:353
    Content type: Research article Published on:

  40. Although more than one thousand complete mitochondrial DNA (mtDNA) sequences have been determined in teleostean fishes, only a few gene rearrangements have been observed, and genome-scale rearrangements are ev...

    Authors: Wei Shi, Xian-Guang Miao and Xiao-Yu Kong
    Citation: BMC Genomics 2014 15:352
    Content type: Research article Published on:

  41. Cultivated peanut, or groundnut (Arachis hypogaea L.), is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40). In recent years, many efforts have been made to construct linkage maps in cu...

    Authors: Xiaojing Zhou, Youlin Xia, Xiaoping Ren, Yulin Chen, Li Huang, Shunmou Huang, Boshou Liao, Yong Lei, Liyin Yan and Huifang Jiang
    Citation: BMC Genomics 2014 15:351
    Content type: Research article Published on:

  42. Considerable work has been carried out to understand the biology of tachyzoites and bradyzoites of Toxoplasma gondii in large part due to in vitro culture methods for these stages. However, culturing methods for ...

    Authors: Michael S Behnke, Tiange P Zhang, Jitender P Dubey and L David Sibley
    Citation: BMC Genomics 2014 15:350
    Content type: Research article Published on:

  43. Bacterial interactions with the environment- and/or host largely depend on the bacterial glycome. The specificities of a bacterial glycome are largely determined by glycosyltransferases (GTs), the enzymes invo...

    Authors: Aminael Sánchez-Rodríguez, Hanne LP Tytgat, Joris Winderickx, Jos Vanderleyden, Sarah Lebeer and Kathleen Marchal
    Citation: BMC Genomics 2014 15:349
    Content type: Research article Published on:

  44. Deep-sequencing has enabled the identification of large numbers of miRNAs and siRNAs, making the high-throughput target identification a main limiting factor in defining their function. In plants, several tool...

    Authors: Prashant K Srivastava, Taraka Ramji Moturu, Priyanka Pandey, Ian T Baldwin and Shree P Pandey
    Citation: BMC Genomics 2014 15:348
    Content type: Research article Published on:

  45. In eukaryotic organisms, packaging of DNA into nucleosomes controls gene expression by regulating access of the promoter to transcription factors. The human malaria parasite Plasmodium falciparum encodes relative...

    Authors: Evelien M Bunnik, Anton Polishko, Jacques Prudhomme, Nadia Ponts, Sarjeet S Gill, Stefano Lonardi and Karine G Le Roch
    Citation: BMC Genomics 2014 15:347
    Content type: Research article Published on:

  46. High-yielding cultivars of rice (Oryza sativa L.) have been developed in Japan from crosses between overseas indica and domestic japonica cultivars. Recently, next-generation sequencing technology and high-throug...

    Authors: Jun-ichi Yonemaru, Ritsuko Mizobuchi, Hiroshi Kato, Toshio Yamamoto, Eiji Yamamoto, Kazuki Matsubara, Hideyuki Hirabayashi, Yoshinobu Takeuchi, Hiroshi Tsunematsu, Takuro Ishii, Hisatoshi Ohta, Hideo Maeda, Kaworu Ebana and Masahiro Yano
    Citation: BMC Genomics 2014 15:346
    Content type: Research article Published on:

  47. Opioids are the cornerstone of treatment for moderate to severe pain, but chronic use leads to maladaptations that include: tolerance, dependence and opioid-induced hyperalgesia (OIH). These responses limit th...

    Authors: De-Yong Liang, Ming Zheng, Yuan Sun, Peyman Sahbaie, Sarah A Low, Gary Peltz, Grégory Scherrer, Cecilia Flores and J David Clark
    Citation: BMC Genomics 2014 15:345
    Content type: Research article Published on:

  48. Heat shock proteins (Hsps) perform a fundamental role in protecting plants against abiotic stresses. Although researchers have made great efforts on the functional analysis of individual family members, Hsps h...

    Authors: Yongfei Wang, Shoukai Lin, Qi Song, Kuan Li, Huan Tao, Jian Huang, Xinhai Chen, Shufu Que and Huaqin He
    Citation: BMC Genomics 2014 15:344
    Content type: Research article Published on:

  50. MicroRNAs (miRNAs) are small noncoding RNAs that play an important role in the regulation of various biological processes through their interaction with cellular mRNAs. A significant amount of miRNAs has been ...

    Authors: Francesco Russo, Sebastiano Di Bella, Vincenzo Bonnici, Alessandro Laganà, Giuseppe Rainaldi, Marco Pellegrini, Alfredo Pulvirenti, Rosalba Giugno and Alfredo Ferro
    Citation: BMC Genomics 2014 15(Suppl 3):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 3

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BMC Genomics

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