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  1. Tuberculosis (TB) continues to cause a high toll of disease and death among children worldwide. The diagnosis of childhood TB is challenged by the paucibacillary nature of the disease and the difficulties in o...

    Authors: Lilly M Verhagen, Aldert Zomer, Mailis Maes, Julian A Villalba, Berenice del Nogal, Marc Eleveld, Sacha AFT van Hijum, Jacobus H de Waard and Peter WM Hermans
    Citation: BMC Genomics 2013 14:74
    Content type: Research article Published on:

  2. Buchnera aphidicola is an obligate symbiotic bacterium, associated with most of the aphididae, whose genome has drastically shrunk during intracellular evolution. Gene regulation in Buchnera has been a matter of ...

    Authors: Lilia Brinza, Federica Calevro and Hubert Charles
    Citation: BMC Genomics 2013 14:73
    Content type: Research article Published on:

  3. Polyploidy is an important evolutionary mechanism in flowering plants that often induces immediate extensive changes in gene expression through genomic merging and doubling. Brassica napus L. is one of the most e...

    Authors: Jinjin Jiang, Yanlin Shao, Kun Du, Liping Ran, Xiaoping Fang and Youping Wang
    Citation: BMC Genomics 2013 14:72
    Content type: Research article Published on:

  4. Class 2 transposable elements (TEs) are the predominant elements in and around plant genes where they generate significant allelic diversity. Using the complete sequences of four grasses, we have performed a n...

    Authors: Yujun Han, Shanshan Qin and Susan R Wessler
    Citation: BMC Genomics 2013 14:71
    Content type: Research article Published on:

  5. An emerging Hi-C protocol has the ability to probe three-dimensional (3D) architecture and capture chromatin interactions in a genome-wide scale. It provides informative results to address how chromatin organi...

    Authors: Junbai Wang, Xun Lan, Pei-Yin Hsu, Hang-Kai Hsu, Kun Huang, Jeffrey Parvin, Tim H-M Huang and Victor X Jin
    Citation: BMC Genomics 2013 14:70
    Content type: Research article Published on:

  6. Comparative genomics is a formidable tool to identify functional elements throughout a genome. In the past ten years, studies in the budding yeast Saccharomyces cerevisiae and a set of closely related species hav...

    Authors: Gianni Liti, Alex N Nguyen Ba, Martin Blythe, Carolin A Müller, Anders Bergström, Francisco A Cubillos, Felix Dafhnis-Calas, Shima Khoshraftar, Sunir Malla, Neel Mehta, Cheuk C Siow, Jonas Warringer, Alan M Moses, Edward J Louis and Conrad A Nieduszynski
    Citation: BMC Genomics 2013 14:69
    Content type: Research article Published on:

  7. Alzheimer’s disease (AD) is intimately tied to amyloid-β (Aβ) peptide. Extraneuronal brain plaques consisting primarily of Aβ aggregates are a hallmark of AD. Intraneuronal Aβ subunits are strongly implicated ...

    Authors: Debomoy K Lahiri, Bryan Maloney, Jack T Rogers and Yuan-Wen Ge
    Citation: BMC Genomics 2013 14:68
    Content type: Research article Published on:

  8. Meiotic recombination events are not randomly located, but rather cluster at hotspot regions. Recently, the fine-scale mapping of genome-wide human recombination hotspots was performed. Here, we systematically...

    Authors: Tao Zhou, Zhibin Hu, Zuomin Zhou, Xuejiang Guo and Jiahao Sha
    Citation: BMC Genomics 2013 14:67
    Content type: Research article Published on:

  9. Phosphorus (P) plays important roles in plant growth and development. MicroRNAs involved in P signaling have been identified in Arabidopsis and rice, but P-responsive microRNAs and their targets in soybean lea...

    Authors: Feng Xu, Qian Liu, Luying Chen, Jiebin Kuang, Thomas Walk, Jinxiang Wang and Hong Liao
    Citation: BMC Genomics 2013 14:66
    Content type: Research article Published on:

  10. The genomic basis of teleost phenotypic complexity remains obscure, despite increasing availability of genome and transcriptome sequence data. Fish-specific genome duplication cannot provide sufficient explana...

    Authors: Liandong Yang, Ming Zou, Beide Fu and Shunping He
    Citation: BMC Genomics 2013 14:65
    Content type: Research article Published on:

  11. Marek’s disease (MD) is a commercially important neoplastic disease of chickens caused by the Marek’s disease virus (MDV), a naturally occurring oncogenic alphaherpesvirus. Enhancing MD genetic resistance is d...

    Authors: Sudeep Perumbakkam, William M Muir, Alexis Black-Pyrkosz, Ron Okimoto and Hans H Cheng
    Citation: BMC Genomics 2013 14:64
    Content type: Research article Published on:

  12. Introduction of a transgene that transcribes RNA homologous to an endogenous gene in the plant genome can induce silencing of both genes, a phenomenon termed cosuppression. Cosuppression was first discovered i...

    Authors: Megumi Kasai, Hideo Matsumura, Kentaro Yoshida, Ryohei Terauchi, Akito Taneda and Akira Kanazawa
    Citation: BMC Genomics 2013 14:63
    Content type: Research article Published on:

  13. The molecular bases of mammalian pancreatic α cells higher resistance than β to proinflammatory cytokines are very poorly defined. MicroRNAs are master regulators of cell networks, but only scanty data are ava...

    Authors: Davide Barbagallo, Salvatore Piro, Angelo G Condorelli, Loriana G Mascali, Francesca Urbano, Nunziatina Parrinello, Adelina Monello, Luisa Statello, Marco Ragusa, Agata M Rabuazzo, Cinzia Di Pietro, Francesco Purrello and Michele Purrello
    Citation: BMC Genomics 2013 14:62
    Content type: Research article Published on:

  14. Despite the crucial role that heterosis has played in crop improvement, its genetic and molecular bases are still elusive. Several types of structured populations were used to discover the genetic architecture...

    Authors: Giorgio Pea, Htay Htay Aung, Elisabetta Frascaroli, Pierangelo Landi and Mario Enrico Pè
    Citation: BMC Genomics 2013 14:61
    Content type: Research article Published on:

  15. Wheat leaf rust (Puccinia triticina Eriks; Pt) and stem rust fungi (P. graminis f.sp. tritici; Pgt) are significant economic pathogens having similar host ranges and life cycles, but different alternate hosts. Th...

    Authors: John P Fellers, Bahram M Soltani, Myron Bruce, Rob Linning, Christina A Cuomo, Les J Szabo and Guus Bakkeren
    Citation: BMC Genomics 2013 14:60
    Content type: Research article Published on:

  16. High density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high r...

    Authors: Andreas Kranis, Almas A Gheyas, Clarissa Boschiero, Frances Turner, Le Yu, Sarah Smith, Richard Talbot, Ali Pirani, Fiona Brew, Pete Kaiser, Paul M Hocking, Mark Fife, Nigel Salmon, Janet Fulton, Tim M Strom, Georg Haberer…
    Citation: BMC Genomics 2013 14:59
    Content type: Research article Published on:

  17. Tilapia is the common name for a group of cichlid fishes and is one of the most important aquacultured freshwater food fish. Mozambique tilapia and its hybrids, including red tilapia are main representatives o...

    Authors: Feng Liu, Fei Sun, Jian Li, Jun Hong Xia, Grace Lin, Rong Jian Tu and Gen Hua Yue
    Citation: BMC Genomics 2013 14:58
    Content type: Research article Published on:

  18. Histone post-translational modifications (HPTMs) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. Although Solanum lyc...

    Authors: Riccardo Aiese Cigliano, Walter Sanseverino, Gaetana Cremona, Maria R Ercolano, Clara Conicella and Federica M Consiglio
    Citation: BMC Genomics 2013 14:57
    Content type: Research article Published on:

  19. Evidence has been assembled to suggest synonymous codon usage bias (SCUB) has close relationship with intron. However, the relationship (if any) between SCUB and intron number as well as exon position is at pr...

    Authors: Zhen Qin, Zhengqiu Cai, Guangmin Xia and Mengcheng Wang
    Citation: BMC Genomics 2013 14:56
    Content type: Research article Published on:

  20. Colorectal cancer (CRC) is a disease of complex aetiology, with much of the expected inherited risk being due to several common low risk variants. Genome-Wide Association Studies (GWAS) have identified 20 CRC ...

    Authors: Ceres Fernandez-Rozadilla, Jean-Baptiste Cazier, Ian P Tomlinson, Luis G Carvajal-Carmona, Claire Palles, María J Lamas, Montserrat Baiget, Luis A López-Fernández, Alejandro Brea-Fernández, Anna Abulí, Luis Bujanda, Juan Clofent, Dolors Gonzalez, Rosa Xicola, Montserrat Andreu, Xavier Bessa…
    Citation: BMC Genomics 2013 14:55
    Content type: Research article Published on:

  21. Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar-beet rhizosphere. This bacterium has been extensively studied as a model strain for genetic regulation of sec...

    Authors: Miguel Redondo-Nieto, Matthieu Barret, John Morrissey, Kieran Germaine, Francisco Martínez-Granero, Emma Barahona, Ana Navazo, María Sánchez-Contreras, Jennifer A Moynihan, Candela Muriel, David Dowling, Fergal O’Gara, Marta Martín and Rafael Rivilla
    Citation: BMC Genomics 2013 14:54
    Content type: Research article Published on:

  22. Small RNA mediated gene silencing is a well-conserved regulatory pathway. In the parasite Entamoeba histolytica an endogenous RNAi pathway exists, however, the depth and diversity of the small RNA population rema...

    Authors: Hanbang Zhang, Gretchen M Ehrenkaufer, Neil Hall and Upinder Singh
    Citation: BMC Genomics 2013 14:53
    Content type: Research article Published on:

  23. Transcriptomes are powerful resources, providing a window on the expressed portion of the genome that can be generated rapidly and at low cost for virtually any organism. However, because many genes have tissu...

    Authors: Joseph I Hoffman, Michael AS Thorne, Philip N Trathan and Jaume Forcada
    Citation: BMC Genomics 2013 14:52
    Content type: Research article Published on:

  24. Genomic deletions are known to be widespread in many species. Variant sequencing-based approaches for identifying deletions have been developed, but their powers to detect those deletions that affect medium-si...

    Authors: Qiang Gong, Yong Tao, Jian-Rong Yang, Jun Cai, Yunfei Yuan, Jue Ruan, Jin Yang, Hailiang Liu, Wanghua Li, Xuemei Lu, Shi-Mei Zhuang, San Ming Wang and Chung-I Wu
    Citation: BMC Genomics 2013 14:51
    Content type: Methodology article Published on:

  26. The green anole lizard, Anolis carolinensis, is a key species for both laboratory and field-based studies of evolutionary genetics, development, neurobiology, physiology, behavior, and ecology. As the first non-a...

    Authors: Walter L Eckalbar, Elizabeth D Hutchins, Glenn J Markov, April N Allen, Jason J Corneveaux, Kerstin Lindblad-Toh, Federica Di Palma, Jessica Alföldi, Matthew J Huentelman and Kenro Kusumi
    Citation: BMC Genomics 2013 14:49
    Content type: Research article Published on:

  27. Select retrotransposons in the long terminal repeat (LTR) class exhibit interindividual variation in DNA methylation that is altered by developmental environmental exposures. Yet, neither the full extent of va...

    Authors: Christopher Faulk, Amanda Barks and Dana C Dolinoy
    Citation: BMC Genomics 2013 14:48
    Content type: Research article Published on:

  28. Listeria monocytogenes is an important food-borne pathogen and model organism for host-pathogen interaction, thus representing an invaluable target considering research on the forces governing the evolution of su...

    Authors: Carsten Kuenne, André Billion, Mobarak Abu Mraheil, Axel Strittmatter, Rolf Daniel, Alexander Goesmann, Sukhadeo Barbuddhe, Torsten Hain and Trinad Chakraborty
    Citation: BMC Genomics 2013 14:47
    Content type: Research article Published on:

  29. Network biology (systems biology) approaches are useful tools for elucidating the host infection processes that often accompany complex immune networks. Although many studies have recently focused on Haemophilus ...

    Authors: Ming Zhao, Xiang-dong Liu, Xin-yun Li, Hong-bo Chen, Hui Jin, Rui Zhou, Meng-jin Zhu and Shu-hong Zhao
    Citation: BMC Genomics 2013 14:46
    Content type: Research article Published on:

  30. Erhualian pigs, one of Chinese Taihu pig breeds, are known to have the largest recorded litter size in the world. A lower prenatal death rate is the major contributing factor to the prolificacy of Taihu pigs. ...

    Authors: Hao Zhang, Shouqi Wang, Manqing Liu, Ailing Zhang, Zhenfang Wu, Zhe Zhang and Jiaqi Li
    Citation: BMC Genomics 2013 14:45
    Content type: Research article Published on:

  31. ADA2 proteins, together with ADA3, SGF29 and GCN5 form the acetyltransferase module of GNAT-type histone acetyltransferase complexes. ADA2b is present in the SAGA complex, which plays roles in various chromati...

    Authors: Tibor Pankotai, Nóra Zsindely, Edith E Vamos, Orbán Komonyi, László Bodai and Imre M Boros
    Citation: BMC Genomics 2013 14:44
    Content type: Research article Published on:

  32. Gene duplication, followed by functional evolution of duplicate genes, is a primary engine of evolutionary innovation. In turn, gene expression evolution is a critical component of overall functional evolution...

    Authors: Jia Zeng and Sridhar Hannenhalli
    Citation: BMC Genomics 2013 14(Suppl 1):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  33. One challenge in applying bioinformatic tools to clinical or biological data is high number of features that might be provided to the learning algorithm without any prior knowledge on which ones should be used...

    Authors: Habil Zare, Gholamreza Haffari, Arvind Gupta and Ryan R Brinkman
    Citation: BMC Genomics 2013 14(Suppl 1):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  34. With the introduction of next-generation sequencing (NGS) technologies, we are facing an exponential increase in the amount of genomic sequence data. The success of all medical and genetic applications of next...

    Authors: Hongyi Xin, Donghyuk Lee, Farhad Hormozdiari, Samihan Yedkar, Onur Mutlu and Can Alkan
    Citation: BMC Genomics 2013 14(Suppl 1):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  35. Structural variations in human genomes, such as deletions, play an important role in cancer development. Next-Generation Sequencing technologies have been central in providing ways to detect such variations. M...

    Authors: Roland Wittler
    Citation: BMC Genomics 2013 14(Suppl 1):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

    The Erratum to this article has been published in BMC Genomics 2013 14:S16

  36. Identifying the genetic variants that contribute to disease susceptibilities is important both for developing methodologies and for studying complex diseases in molecular biology. It has been demonstrated that...

    Authors: Jiayin Wang, Zhongmeng Zhao, Zhi Cao, Aiyuan Yang and Jin Zhang
    Citation: BMC Genomics 2013 14(Suppl 1):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  37. Reconstructability of population history, from genetic information of extant individuals, is studied under a simulation setting. We do not address the issue of accuracy of the reconstruction algorithms: we ass...

    Authors: Filippo Utro, Marc Pybus and Laxmi Parida
    Citation: BMC Genomics 2013 14(Suppl 1):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  38. The cost of RNA-Seq has been decreasing over the last few years. Despite this, experiments with four or less biological replicates are still quite common. Estimating the variances of gene expression estimates ...

    Authors: Ellis Patrick, Michael Buckley, David Ming Lin and Yee Hwa Yang
    Citation: BMC Genomics 2013 14(Suppl 1):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  39. Recent studies in genomics have highlighted the significance of structural variation in determining individual variation. Current methods for identifying structural variation, however, are predominantly focuse...

    Authors: Nathaniel Parrish, Benjamin Sudakov and Eleazar Eskin
    Citation: BMC Genomics 2013 14(Suppl 1):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  40. Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (mul...

    Authors: Sergey I Nikolenko, Anton I Korobeynikov and Max A Alekseyev
    Citation: BMC Genomics 2013 14(Suppl 1):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  41. Yeast deletion-mutant collections have been successfully used to infer the mode-of-action of drugs especially by profiling chemical-genetic and genetic-genetic interactions on a genome-wide scale. Although ten...

    Authors: Minho Lee, Sangjo Han, Hyeshik Chang, Youn-Sig Kwak, David M Weller and Dongsup Kim
    Citation: BMC Genomics 2013 14(Suppl 1):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  42. Glycine max is an economically important crop and many different varieties of soybean exist around the world. The first draft sequences and gene models of G. max (domesticated soybean) as well as G. soja (wild so...

    Authors: Trupti Joshi, Babu Valliyodan, Jeng-Hung Wu, Suk-Ha Lee, Dong Xu and Henry T Nguyen
    Citation: BMC Genomics 2013 14(Suppl 1):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  43. Deciphering cis-regulatory networks has become an attractive yet challenging task. This paper presents a simple method for cis-regulatory network discovery which aims to avoid some of the common problems of previ...

    Authors: Zhen Gao, Ruizhe Zhao and Jianhua Ruan
    Citation: BMC Genomics 2013 14(Suppl 1):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  44. Pairwise comparison of time series data for both local and time-lagged relationships is a computationally challenging problem relevant to many fields of inquiry. The Local Similarity Analysis (LSA) statistic i...

    Authors: W Evan Durno, Niels W Hanson, Kishori M Konwar and Steven J Hallam
    Citation: BMC Genomics 2013 14(Suppl 1):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  45. MicroRNAs (miRNAs) play a critical role in down-regulating gene expression. By coupling with Argonaute family proteins, miRNAs bind to target sites on mRNAs and employ translational repression. A large amount ...

    Authors: Chih-Hung Chou, Feng-Mao Lin, Min-Te Chou, Sheng-Da Hsu, Tzu-Hao Chang, Shun-Long Weng, Sirjana Shrestha, Chiung-Chih Hsiao, Jui-Hung Hung and Hsien-Da Huang
    Citation: BMC Genomics 2013 14(Suppl 1):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  46. Genome-wide association studies (GWAS) have identified many common polymorphisms associated with complex traits. However, these associated common variants explain only a small fraction of the phenotypic varian...

    Authors: Quan Chen and Fengzhu Sun
    Citation: BMC Genomics 2013 14(Suppl 1):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  47. Though India has sequenced water buffalo genome but its draft assembly is based on cattle genome BTau 4.0, thus de novo chromosome wise assembly is a major pending issue for global community. The existing radiati...

    Authors: Sarika, Vasu Arora, Mir Asif Iquebal, Anil Rai and Dinesh Kumar
    Citation: BMC Genomics 2013 14:43
    Content type: Database Published on:

  48. Plants such as grapevine (Vitis spp.) display significant inter-cultivar genetic and phenotypic variation. The genetic components underlying phenotypic diversity in grapevine must be understood in order to dis...

    Authors: Luca Venturini, Alberto Ferrarini, Sara Zenoni, Giovanni Battista Tornielli, Marianna Fasoli, Silvia Dal Santo, Andrea Minio, Genny Buson, Paola Tononi, Elisa Debora Zago, Gianpiero Zamperin, Diana Bellin, Mario Pezzotti and Massimo Delledonne
    Citation: BMC Genomics 2013 14:41
    Content type: Research article Published on:

  49. The outer cell wall of the pollen grain (exine) is an extremely resistant structure containing sporopollenin, a mixed polymer made up of fatty acids and phenolic compounds. The synthesis of sporopollenin in th...

    Authors: Gabino Ríos, Francisco R Tadeo, Carmen Leida and María L Badenes
    Citation: BMC Genomics 2013 14:40
    Content type: Research article Published on:

  50. The C. elegans cell fate map, in which the lineage of its approximately 1000 cells is visibly charted beginning from the zygote, represents a developmental biology milestone. Nematode development is invariant fro...

    Authors: Wenyu Zhou, Yunbing Tan, Donovan J Anderson, Eva M Crist, Hannele Ruohola-Baker, Stephen J Salipante and Marshall S Horwitz
    Citation: BMC Genomics 2013 14:39
    Content type: Research article Published on:

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BMC Genomics

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