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  1. Microalgae hold promise for yielding a biofuel feedstock that is sustainable, carbon-neutral, distributed, and only minimally disruptive for the production of food and feed by traditional agriculture. Amongst ...

    Authors: István Molnár, David Lopez, Jennifer H Wisecaver, Timothy P Devarenne, Taylor L Weiss, Matteo Pellegrini and Jeremiah D Hackett
    Citation: BMC Genomics 2012 13:576
    Content type: Research article Published on:

  2. Lichens are symbiotic organisms that have a remarkable ability to survive in some of the most extreme terrestrial climates on earth. Lichens can endure frequent desiccation and wetting cycles and are able to s...

    Authors: Sini Junttila and Stephen Rudd
    Citation: BMC Genomics 2012 13:575
    Content type: Research article Published on:

  3. The majority of published gene-expression studies have used RNA isolated from whole cells, overlooking the potential impact of including nuclear transcriptome in the analyses. In this study, mRNA fractions fro...

    Authors: Beata Werne Solnestam, Henrik Stranneheim, Jimmie Hällman, Max Käller, Emma Lundberg, Joakim Lundeberg and Pelin Akan
    Citation: BMC Genomics 2012 13:574
    Content type: Research article Published on:

  4. Wine aroma results from the combination of numerous volatile compounds, some produced by yeast and others produced in the grapes and further metabolized by yeast. However, little is known about the consequence...

    Authors: Damien Steyer, Chloe Ambroset, Christian Brion, Patricia Claudel, Pierre Delobel, Isabelle Sanchez, Claude Erny, Bruno Blondin, Francis Karst and Jean-Luc Legras
    Citation: BMC Genomics 2012 13:573
    Content type: Research article Published on:

  5. A proper balance between different T helper (Th) cell subsets is necessary for normal functioning of the adaptive immune system. Revealing key genes and pathways driving the differentiation to distinct Th cell...

    Authors: Tarmo Äijö, Sanna M Edelman, Tapio Lönnberg, Antti Larjo, Henna Kallionpää, Soile Tuomela, Emilia Engström, Riitta Lahesmaa and Harri Lähdesmäki
    Citation: BMC Genomics 2012 13:572
    Content type: Research article Published on:

  6. Molecular breeding of pepper (Capsicum spp.) can be accelerated by developing DNA markers associated with transcriptomes in breeding germplasm. Before the advent of next generation sequencing (NGS) technologies, ...

    Authors: Hamid Ashrafi, Theresa Hill, Kevin Stoffel, Alexander Kozik, JiQiang Yao, Sebastian Reyes Chin-Wo and Allen Van Deynze
    Citation: BMC Genomics 2012 13:571
    Content type: Research article Published on:

  7. The significant mortality associated with breast cancer (BCa) suggests a need to improve current research strategies to identify new genes that predispose women to breast cancer. Differential allele-specific e...

    Authors: Chuan Gao, Karthik Devarajan, Yan Zhou, Carolyn M Slater, Mary B Daly and Xiaowei Chen
    Citation: BMC Genomics 2012 13:570
    Content type: Research article Published on:

  8. We applied comparative phylogenomics (whole genome comparisons of microbes using DNA microarrays combined with Bayesian-based phylogenies) to investigate S. pneumoniae isolates from West Africa, with the aim of p...

    Authors: Eric S Donkor, Richard A Stabler, Jason Hinds, Richard A Adegbola, Martin Antonio and Brendan W Wren
    Citation: BMC Genomics 2012 13:569
    Content type: Research article Published on:

  9. Alfalfa, a perennial, outcrossing species, is a widely planted forage legume producing highly nutritious biomass. Currently, improvement of cultivated alfalfa mainly relies on recurrent phenotypic selection. M...

    Authors: Xuehui Li, Ananta Acharya, Andrew D Farmer, John A Crow, Arvind K Bharti, Robin S Kramer, Yanling Wei, Yuanhong Han, Jiqing Gou, Gregory D May, Maria J Monteros and E Charles Brummer
    Citation: BMC Genomics 2012 13:568
    Content type: Research article Published on:

  10. The deep-sea bacterium Photobacterium profundum is an established model for studying high pressure adaptation. In this paper we analyse the parental strain DB110 and the toxR mutant TW30 by massively parallel cDN...

    Authors: Stefano Campanaro, Fabio De Pascale, Andrea Telatin, Riccardo Schiavon, Douglas H Bartlett and Giorgio Valle
    Citation: BMC Genomics 2012 13:567
    Content type: Research article Published on:

  11. The organization of higher order chromatin is an emerging epigenetic mechanism for understanding development and disease. We and others have previously observed dynamic changes during differentiation and oncog...

    Authors: Bo Wen, Hao Wu, Yuin-Han Loh, Eirikur Briem, George Q Daley and Andrew P Feinberg
    Citation: BMC Genomics 2012 13:566
    Content type: Research article Published on:

  12. About 6 million Americans suffer from heart failure and 70% of heart failure cases are caused by myocardial infarction (MI). Following myocardial infarction, increased cytokines induce two major types of macro...

    Authors: Yunji Wang, Tianyi Yang, Yonggang Ma, Ganesh V Halade, Jianqiu Zhang, Merry L Lindsey and Yu-Fang Jin
    Citation: BMC Genomics 2012 13(Suppl 6):S21
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  13. DNA methylation occurs in the context of a CpG dinucleotide. It is an important epigenetic modification, which can be inherited through cell division. The two major types of methylation include hypomethylation...

    Authors: Lin Zhang, Jia Meng, Hui Liu and Yufei Huang
    Citation: BMC Genomics 2012 13(Suppl 6):S20
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  14. Until recently, sequencing has primarily been carried out in large genome centers which have invested heavily in developing the computational infrastructure that enables genomic sequence analysis. The recent a...

    Authors: Uday S Evani, Danny Challis, Jin Yu, Andrew R Jackson, Sameer Paithankar, Matthew N Bainbridge, Adinarayana Jakkamsetti, Peter Pham, Cristian Coarfa, Aleksandar Milosavljevic and Fuli Yu
    Citation: BMC Genomics 2012 13(Suppl 6):S19
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  15. One method to understand and evaluate an experiment that produces a large set of genes, such as a gene expression microarray analysis, is to identify overrepresentation or enrichment for biological pathways. B...

    Authors: Mark S Doderer, Zachry Anguiano, Uthra Suresh, Ravi Dashnamoorthy, Alexander JR Bishop and Yidong Chen
    Citation: BMC Genomics 2012 13(Suppl 6):S18
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  16. Network pharmacology has emerged as a new topic of study in recent years. It aims to study the myriad relationships among proteins, drugs, and disease phenotypes. The concept of molecular connectivity maps has...

    Authors: Hui Huang, Xiaogang Wu, Ragini Pandey, Jiao Li, Guoling Zhao, Sara Ibrahim and Jake Y Chen
    Citation: BMC Genomics 2012 13(Suppl 6):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  17. Whole genome sequencing enables a high resolution view of the human genome and provides unique insights into genome structure at an unprecedented scale. There have been a number of tools to infer copy number v...

    Authors: Angel Janevski, Vinay Varadan, Sitharthan Kamalakaran, Nilanjana Banerjee and Nevenka Dimitrova
    Citation: BMC Genomics 2012 13(Suppl 6):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  18. Genome-wide association studies (GWAS) have generated a wealth of valuable genotyping data for complex diseases/traits. A large proportion of these data are embedded with many weakly associated markers that ha...

    Authors: Peilin Jia and Zhongming Zhao
    Citation: BMC Genomics 2012 13(Suppl 6):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  19. Advances in whole genome profiling have revolutionized the cancer research field, but at the same time have raised new bioinformatics challenges. For next generation sequencing (NGS), these include data storag...

    Authors: Benjamin AT Rodriguez, David Frankhouser, Mark Murphy, Michael Trimarchi, Hok-Hei Tam, John Curfman, Rita Huang, Michael WY Chan, Hung-Cheng Lai, Deval Parikh, Bryan Ball, Sebastian Schwind, William Blum, Guido Marcucci, Pearlly Yan and Ralf Bundschuh
    Citation: BMC Genomics 2012 13(Suppl 6):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  20. Despite initial response in adjuvant chemotherapy, ovarian cancer patients treated with the combination of paclitaxel and carboplatin frequently suffer from recurrence after few cycles of treatment, and the un...

    Authors: Fang-Han Hsu, Erchin Serpedin, Tzu-Hung Hsiao, Alexander JR Bishop, Edward R Dougherty and Yidong Chen
    Citation: BMC Genomics 2012 13(Suppl 6):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  21. Multi-target therapeutics has been shown to be effective for treating complex diseases, and currently, it is a common practice to combine multiple drugs to treat such diseases to optimize the therapeutic outco...

    Authors: Mansuck Kim and Byung-Jun Yoon
    Citation: BMC Genomics 2012 13(Suppl 6):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  22. Molecularly targeted agents (MTAs) are increasingly used for cancer treatment, the goal being to improve the efficacy and selectivity of cancer treatment by developing agents that block the growth of cancer ce...

    Authors: Xiangfang Li, Lijun Qian, Jianping Hua, Michael L Bittner and Edward R Dougherty
    Citation: BMC Genomics 2012 13(Suppl 6):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  23. The Steady State (SS) probability distribution is an important quantity needed to characterize the steady state behavior of many stochastic biochemical networks. In this paper, we propose an efficient and accu...

    Authors: Shahriar Karim, Gregery T Buzzard and David M Umulis
    Citation: BMC Genomics 2012 13(Suppl 6):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  24. Numerous approaches exist for modeling of genetic regulatory networks (GRNs) but the low sampling rates often employed in biological studies prevents the inference of detailed models from experimental data. In...

    Authors: Saad Haider and Ranadip Pal
    Citation: BMC Genomics 2012 13(Suppl 6):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  25. Metastatic breast cancer is a leading cause of cancer-related deaths in women worldwide. DNA microarray has become an important tool to help identify biomarker genes for improving the prognosis of breast cance...

    Authors: Md Jamiul Jahid and Jianhua Ruan
    Citation: BMC Genomics 2012 13(Suppl 6):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  26. A current challenge in gene annotation is to define the gene function in the context of the network of relationships instead of using single genes. The inference of gene networks (GNs) has emerged as an approa...

    Authors: Fábio FR Vicente, Fabrício M Lopes, Ronaldo F Hashimoto and Roberto M Cesar Jr
    Citation: BMC Genomics 2012 13(Suppl 6):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  27. Estrogens control multiple functions of hormone-responsive breast cancer cells. They regulate diverse physiological processes in various tissues through genomic and non-genomic mechanisms that result in activa...

    Authors: Heng-Yi Wu, Pengyue Zheng, Guanglong Jiang, Yunlong Liu, Kenneth P Nephew, Tim HM Huang and Lang Li
    Citation: BMC Genomics 2012 13(Suppl 6):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  28. Cancer and other gene related diseases are usually caused by a failure in the signaling pathway between genes and cells. These failures can occur in different areas of the gene regulatory network, but can be a...

    Authors: Pey-Chang Kent Lin and Sunil P Khatri
    Citation: BMC Genomics 2012 13(Suppl 6):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  29. Oxidative stress is a consequence of normal and abnormal cellular metabolism and is linked to the development of human diseases. The effective functioning of the pathway responding to oxidative stress protects...

    Authors: Sriram Sridharan, Ritwik Layek, Aniruddha Datta and Jijayanagaram Venkatraj
    Citation: BMC Genomics 2012 13(Suppl 6):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  30. Regulation of gene expression has been shown to involve not only the binding of transcription factor at target gene promoters but also the characterization of histone around which DNA is wrapped around. Some h...

    Authors: Cenny Taslim, Shili Lin, Kun Huang and Tim Hui-Ming Huang
    Citation: BMC Genomics 2012 13(Suppl 6):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  31. Mass spectrometry is a complex technique used for large-scale protein profiling with clinical and pharmaceutical applications. While individual components in the system have been studied extensively, little wo...

    Authors: Youting Sun, Ulisses Braga-Neto and Edward R Dougherty
    Citation: BMC Genomics 2012 13(Suppl 6):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  33. The green algal genus Ulva Linnaeus (Ulvaceae, Ulvales, Chlorophyta) is well known for its wide distribution in marine, freshwater, and brackish environments throughout the world. The Ulva species are also highly...

    Authors: Xiaowen Zhang, Naihao Ye, Chengwei Liang, Shanli Mou, Xiao Fan, Jianfang Xu, Dong Xu and Zhimeng Zhuang
    Citation: BMC Genomics 2012 13:565
    Content type: Research article Published on:

  35. The core protein (HBc) of hepatitis B virus (HBV) has been implicated in the malignant transformation of chronically-infected hepatocytes and displays pleiotropic functions, including RNA- and DNA-binding acti...

    Authors: Yanhai Guo, Wei Kang, Xiaoying Lei, Yongnian Li, An Xiang, Yonglan Liu, Jinrong Zhao, Ju Zhang and Zhen Yan
    Citation: BMC Genomics 2012 13:563
    Content type: Research article Published on:

  36. Synthetic biology allows the development of new biochemical pathways for the production of chemicals from renewable sources. One major challenge is the identification of suitable microorganisms to hold these p...

    Authors: Lucas P Parizzi, Maria Carolina B Grassi, Luige A Llerena, Marcelo F Carazzolle, Verônica L Queiroz, Inês Lunardi, Ane F Zeidler, Paulo JPL Teixeira, Piotr Mieczkowski, Johana Rincones and Gonçalo AG Pereira
    Citation: BMC Genomics 2012 13:562
    Content type: Research article Published on:

  38. Despite the known importance of somatic cells for oocyte developmental competence acquisition, the overall mechanisms underlying the acquisition of full developmental competence are far from being understood, ...

    Authors: Cathy Charlier, Jérôme Montfort, Olivier Chabrol, Daphné Brisard, Thaovi Nguyen, Aurélie Le Cam, Laurent Richard-Parpaillon, François Moreews, Pierre Pontarotti, Svetlana Uzbekova, Franck Chesnel and Julien Bobe
    Citation: BMC Genomics 2012 13:560
    Content type: Research article Published on:

  39. Pan-genomic studies aim, for instance, at defining the core, dispensable and unique genes within a species. A pan-genomics study for vaccine design tries to assess the best candidates for a vaccine against a s...

    Authors: Anderson R Santos, Adriana Carneiro, Alfonso Gala-García, Anne Pinto, Debmalya Barh, Eudes Barbosa, Flávia Aburjaile, Fernanda Dorella, Flávia Rocha, Luis Guimarães, Meritxell Zurita-Turk, Rommel Ramos, Sintia Almeida, Siomar Soares, Ulisses Pereira, Vinícius C Abreu…
    Citation: BMC Genomics 2012 13(Suppl 5):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 5

  40. Analysis of DNA copy number alterations and gene expression changes in human samples have been used to find potential target genes in complex diseases. Recent studies have combined these two types of data usin...

    Authors: Celia Fontanillo, Sara Aibar, Jose Manuel Sanchez-Santos and Javier De Las Rivas
    Citation: BMC Genomics 2012 13(Suppl 5):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 5

  41. The shotgun strategy (liquid chromatography coupled with tandem mass spectrometry) is widely applied for identification of proteins in complex mixtures. This method gives rise to thousands of spectra in a sing...

    Authors: Fabio R Cerqueira, Ricardo S Ferreira, Alcione P Oliveira, Andreia P Gomes, Humberto JO Ramos, Armin Graber and Christian Baumgartner
    Citation: BMC Genomics 2012 13(Suppl 5):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 5

  42. Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical On...

    Authors: Gabriela DA Guardia, Ricardo ZN Vêncio and Cléver RG de Farias
    Citation: BMC Genomics 2012 13(Suppl 5):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 5

  43. Inference of biological networks has become an important tool in Systems Biology. Nowadays it is becoming clearer that the complexity of organisms is more related with the organization of its components in net...

    Authors: Adriano V Werhli
    Citation: BMC Genomics 2012 13(Suppl 5):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 5

  44. An essential step of a metagenomic study is the taxonomic classification, that is, the identification of the taxonomic lineage of the organisms in a given sample. The taxonomic classification process involves ...

    Authors: Susan Higashi, André da Motta Salles Barreto, Maurício Egidio Cantão and Ana Tereza Ribeiro de Vasconcelos
    Citation: BMC Genomics 2012 13(Suppl 5):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 5

  45. Small RNAs have proven to be essential regulatory molecules encoded within eukaryotic genomes. These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamic...

    Authors: James Lindsay, Dawn M Carone, Judy Brown, Laura Hall, Sohaib Qureshi, Sarah E Mitchell, Nicholas Jannetty, Greg Hannon, Marilyn Renfree, Andrew Pask, Michael O’Neill and Rachel O’Neill
    Citation: BMC Genomics 2012 13:559
    Content type: Research article Published on:

  46. Social insects, such as honey bees, use molecular, physiological and behavioral responses to combat pathogens and parasites. The honey bee genome contains all of the canonical insect immune response pathways, ...

    Authors: Freddie-Jeanne Richard, Holly L Holt and Christina M Grozinger
    Citation: BMC Genomics 2012 13:558
    Content type: Research article Published on:

  47. Marek’s disease (MD) is a neoplastic disease in chickens caused by the MD virus (MDV). Successful vaccine development against MD has resulted in increased virulence of MDV and the understanding of genetic resi...

    Authors: Apratim Mitra, Juan Luo, Huanming Zhang, Kairong Cui, Keji Zhao and Jiuzhou Song
    Citation: BMC Genomics 2012 13:557
    Content type: Research article Published on:

  48. Trypanosoma brucei is the causative agent of human African sleeping sickness and Nagana in cattle. In addition to being an important pathogen T. brucei has developed into a model system in cell biology.

    Authors: Kapila Gunasekera, Daniel Wüthrich, Sophie Braga-Lagache, Manfred Heller and Torsten Ochsenreiter
    Citation: BMC Genomics 2012 13:556
    Content type: Research article Published on:

  49. MicroRNAs (miRNAs) are small, non-coding 21–25 nt RNA molecules that play an important role in regulating gene expression. Little is known about the expression profiles and functions of miRNAs in skin and thei...

    Authors: Xue Tian, Junbing Jiang, Ruiwen Fan, Haidong Wang, Xiaolin Meng, Xiaoyan He, Junping He, Hongquan Li, Jianjun Geng, Xiuju Yu, Yunfei Song, Danli Zhang, Jianbo Yao, George W Smith and Changsheng Dong
    Citation: BMC Genomics 2012 13:555
    Content type: Research article Published on:

  50. Cardiac sarco(endo)plasmic reticulum calcium ATPase-2 (SERCA2) plays one of the central roles in myocardial contractility. Both, SERCA2 mRNA and protein are reduced in myocardial infarction (MI), but the corre...

    Authors: Emanuela Boštjančič, Nina Zidar and Damjan Glavač
    Citation: BMC Genomics 2012 13:552
    Content type: Research article Published on:

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BMC Genomics

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