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  1. 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:

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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:

  15. 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:

  16. 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:

  18. 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:

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. Spore germination of the yeast Saccharomyces cerevisiae is a multi-step developmental path on which dormant spores re-enter the mitotic cell cycle and resume vegetative growth. Upon addition of a fermentable carb...

    Authors: Cecilia Geijer, Ivan Pirkov, Wanwipa Vongsangnak, Abraham Ericsson, Jens Nielsen, Marcus Krantz and Stefan Hohmann
    Citation: BMC Genomics 2012 13:554
    Content type: Research article Published on:

  31. The MHC, which is regarded as the most polymorphic region in the genomes of jawed vertebrates, plays a central role in the immune system by encoding various proteins involved in the immune response. The chicke...

    Authors: Biao Wang, Robert Ekblom, Tanja M Strand, Silvia Portela-Bens and Jacob Höglund
    Citation: BMC Genomics 2012 13:553
    Content type: Research article Published on:

  32. 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:

  33. As for other non-model species, genetic analyses in quail will benefit greatly from a higher marker density, now attainable thanks to the evolution of sequencing and genotyping technologies. Our objective was ...

    Authors: Laure Frésard, Sophie Leroux, Patrice Dehais, Bertrand Servin, Hélène Gilbert, Olivier Bouchez, Christophe Klopp, Cédric Cabau, Florence Vignoles, Katia Feve, Amélie Ricros, David Gourichon, Christian Diot, Sabine Richard, Christine Leterrier, Catherine Beaumont…
    Citation: BMC Genomics 2012 13:551
    Content type: Research article Published on:

  34. Small non-coding RNAs (sRNAs) have attracted attention as a new class of gene regulators in both eukaryotes and bacteria. Genome-wide screening methods have been successfully applied in Gram-negative bacteria ...

    Authors: Nadja Patenge, André Billion, Peter Raasch, Jana Normann, Aleksandra Wisniewska-Kucper, Julia Retey, Valesca Boisguérin, Thomas Hartsch, Torsten Hain and Bernd Kreikemeyer
    Citation: BMC Genomics 2012 13:550
    Content type: Research article Published on:

  35. Studies of temperature-induced adaptation on the basis of genomic sequence data were mainly done in extremophiles. Although the general hypothesis of an increased molecular flexibility in the cold is widely ac...

    Authors: Heidrun Sigrid Windisch, Magnus Lucassen and Stephan Frickenhaus
    Citation: BMC Genomics 2012 13:549
    Content type: Research article Published on:

  36. Epinotia aporema (Lepidoptera: Tortricidae) is an important pest of legume crops in South America. Epinotia aporema granulovirus (EpapGV) is a baculovirus that causes a polyorganotropic infection in the host larv...

    Authors: María Leticia Ferrelli, Ricardo Salvador, Marina Elizabeth Biedma, Marcelo Facundo Berretta, Santiago Haase, Alicia Sciocco-Cap, Pablo Daniel Ghiringhelli and Víctor Romanowski
    Citation: BMC Genomics 2012 13:548
    Content type: Research article Published on:

  37. New advances in high-throughput technologies have allowed for the massive analysis of genomic data, providing new opportunities for the characterization of the transcriptome architectures. Recent studies in pi...

    Authors: Yuliaxis Ramayo-Caldas, Nuria Mach, Anna Esteve-Codina, Jordi Corominas, Anna Castelló, Maria Ballester, Jordi Estellé, Noelia Ibáñez-Escriche, Ana I Fernández, Miguel Pérez-Enciso and Josep M Folch
    Citation: BMC Genomics 2012 13:547
    Content type: Research article Published on:

  38. Coordinated cell growth and development requires that cells regulate the expression of large sets of genes in an appropriate manner, and one of the most complex and metabolically demanding pathways that cells ...

    Authors: James T Arnone, Adam Robbins-Pianka, Jeffrey R Arace, Sara Kass-Gergi and Michael A McAlear
    Citation: BMC Genomics 2012 13:546
    Content type: Research article Published on:

  39. The classical Bordetella subspecies are phylogenetically closely related, yet differ in some of the most interesting and important characteristics of pathogens, such as host range, virulence and persistence. The ...

    Authors: Jihye Park, Ying Zhang, Anne M Buboltz, Xuqing Zhang, Stephan C Schuster, Umesh Ahuja, Minghsun Liu, Jeff F Miller, Mohammed Sebaihia, Stephen D Bentley, Julian Parkhill and Eric T Harvill
    Citation: BMC Genomics 2012 13:545
    Content type: Research article Published on:

  40. The MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four...

    Authors: Amit Katiyar, Shuchi Smita, Sangram Keshari Lenka, Ravi Rajwanshi, Viswanathan Chinnusamy and Kailash Chander Bansal
    Citation: BMC Genomics 2012 13:544
    Content type: Research article Published on:

  41. The accuracy of genomic prediction is highly dependent on the size of the reference population. For small populations, including information from other populations could improve this accuracy. The usual strate...

    Authors: Rasmus Froberg Brøndum, Guosheng Su, Mogens Sandø Lund, Philip J Bowman, Michael E Goddard and Benjamin J Hayes
    Citation: BMC Genomics 2012 13:543
    Content type: Methodology article Published on:

  42. The bacterium Caulobacter crescentus is a popular model for the study of cell cycle regulation and senescence. The large prolate siphophage phiCbK has been an important tool in C. crescentus biology, and has been...

    Authors: Jason J Gill, Joel D Berry, William K Russell, Lauren Lessor, Diego A Escobar-Garcia, Daniel Hernandez, Ashley Kane, Jennifer Keene, Matthew Maddox, Rebecca Martin, Sheba Mohan, Ashlyn M Thorn, David H Russell and Ry Young
    Citation: BMC Genomics 2012 13:542
    Content type: Research article Published on:

  43. Myostatin, a member of the TGFβ superfamily, is well known as a potent and specific negative regulator of muscle growth. Targeting the myostatin signalling pathway may offer promising therapeutic strategies fo...

    Authors: Olivier Monestier, Caroline Brun, Katy Heu, Bruno Passet, Mélanie Malhouroux, Laetitia Magnol, Jean-Luc Vilotte and Véronique Blanquet
    Citation: BMC Genomics 2012 13:541
    Content type: Research article Published on:

  44. S. aureus is one of the main pathogens responsible for the intra-mammary infection in dairy ruminants. Although much work has been carried out to understand the complex physiological and cellular events that occu...

    Authors: Paola Cremonesi, Rossana Capoferri, Giuliano Pisoni, Marcello Del Corvo, Francesco Strozzi, Rachel Rupp, Hugues Caillat, Paola Modesto, Paolo Moroni, John L Williams, Bianca Castiglioni and Alessandra Stella
    Citation: BMC Genomics 2012 13:540
    Content type: Research article Published on:

  45. Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. ...

    Authors: Liang Zhao, Lv Yuanda, Cai Caiping, Tong Xiangchao, Chen Xiangdong, Zhang Wei, Du Hao, Guo Xiuhua and Guo Wangzhen
    Citation: BMC Genomics 2012 13:539
    Content type: Research article Published on:

  47. Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To fac...

    Authors: Qiong Zhang, Baiquan Ma, Hui Li, Yuansheng Chang, Yuanyuan Han, Jing Li, Guochao Wei, Shuang Zhao, Muhammad Awais Khan, Ying Zhou, Chao Gu, Xingzhong Zhang, Zhenhai Han, Schuyler S Korban, Shaohua Li and Yuepeng Han
    Citation: BMC Genomics 2012 13:537
    Content type: Research article Published on:

  48. Artificial insemination and genetic selection are major factors contributing to population stratification in dairy cattle. In this study, we analyzed the effect of sample stratification and the effect of strat...

    Authors: Li Ma, George R Wiggans, Shengwen Wang, Tad S Sonstegard, Jing Yang, Brian A Crooker, John B Cole, Curtis P Van Tassell, Thomas J Lawlor and Yang Da
    Citation: BMC Genomics 2012 13:536
    Content type: Research article Published on:

  49. Although many diseases have been well characterized at the molecular level, the underlying mechanisms are often unknown. Nearly half of all human genes remain poorly studied, yet these genes may contribute to ...

    Authors: Sipko van Dam, Rui Cordeiro, Thomas Craig, Jesse van Dam, Shona H Wood and João Pedro de Magalhães
    Citation: BMC Genomics 2012 13:535
    Content type: Research article Published on:

  50. Bacteria of the genus Arthrobacter are ubiquitous in soil environments and can be considered as true survivalists. Arthrobacter sp. strain Rue61a is an isolate from sewage sludge able to utilize quinaldine (2-met...

    Authors: Heiko Niewerth, Jörg Schuldes, Katja Parschat, Patrick Kiefer, Julia A Vorholt, Rolf Daniel and Susanne Fetzner
    Citation: BMC Genomics 2012 13:534
    Content type: Research article Published on:

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BMC Genomics

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